Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of  The study of adaptive radiation, the evolution of ecological diversity in rapidly multiplying lineages Schluter , is impoet al. et al. et al. et al. et al.  sequencing  and Magadi (Kenya)  Fig. . Based o2 varying from 81 to 804 km2 , terminal/prognathous snout (A. grahami), inferior thick‐lipped (A. latilabris) and subterminal thin‐lipped  , and did not differ in response to food type, indicating a genetic component rather than a plastic response to environment  include the following: ureotelism . Unique physiological adaptations to alkaline/saline and hypoxic conditions  are thought to be of an Oreochromis species exhibiting considerably larger body size than present‐day Alcolapia  or microsatellite nuclear markers. These studies found shared haplotypes between the lakes and species , and lake‐perimeter distances between sites were estimated using the GPS coordinates plotted in ArcGIS version 10 and summing over distances from intermediate sites.Samples were collected in 2012 using hand, cast or seine nets . Fish were euthanized using tricaine methanesulfonate (MS222) and preserved as voucher specimens in 80% ethanol, with genetic samples (fin clips) stored in 95% ethanol. Specimens were identified to species level according to the current taxonomic key  selected as the outgroup . Libraries were initially sequenced across two lanes, but due to poor initial sequencing quality, each lane was resequenced once. One library showed a highly variable number of reads across samples and was therefore prepared again before sequencing in one‐third of a lane. Reads from all lanes were combined to maximize coverage.RAD library preparation, sequencing and preliminary bioinformatic processing were undertaken by Edinburgh Genomics (University of Edinburgh). Library preparation followed the protocol of Davey et al. , using Set al. O. niloticus reference genome Orenil1.1  to mitigate the effect of biased PCR amplification during library construction. BAM files were realigned around indels using the Genome Analysis Toolkit (GATK) 2.7–2 . The filtered species vcf files were merged to form a single alignment file. Further filtering included imposition of maximum levels of missing data and a minimum allele frequency threshold; these parameters differed by analysis, so the specific values for each analysis are described below and in Table S2 (Supporting information).The resultant vcf files were filtered using custom perl scripts as used in Hoffman et al.  at the fde novo using IDBA‐UD  has not previously been investigated in g et al. , using tO. niloticus (for mapped reads) or O. amphimelas (for de novo‐assembled reads) specified as the outgroup for 100 bootstrap replicates. Most analyses were performed within the CIPRES Science Gateway V. 3.3  phylogenetic inference was conducted using RAxML , the northernmost Natron sampling site (site 19) and only Lake Magadi A. grahami sites (18 and 21). The data set comprised all biallelic SNPs across 44 Alcolapia samples (four samples for each of 11 populations) and four O. amphimelas samples, with a minimum distance between SNPs of 500 kb on each linkage group (to ensure SNPs were unlinked), and we removed any sites for which data were not available for all samples, leaving a total of 1266 SNPs. Backward and forward (u and v) mutation rates were estimated from the data using equation 8.4.1 from , and each analysis was run for 7 million generations, discarding the first 10% as burn‐in. Runs were checked for convergence using tracer v 1.5 software . For comparison, we also ran these analyses on the full data set without accounting for linkage disequilibrium. Given the very recent divergence of Alcolapia species, we also ran the analysis using the LOCPRIOR model  was estimated using an initial run of K = 1 with 50 000 burn‐in and 100 000 further iterations, giving a value of λ = 0.5252. This value was set in subsequent runs of 5 iterations at each value K = 1–12 with no prior population information, and 50 000 burn‐in/100 000 further iterations. Analyses were run with all different model parameters independently ; admixture model/independent allele frequencies; no admixture/allele frequencies correlated; no admixture/allele frequencies independent). STRUCTURE output was compiled and averaged using Structure Harvester  are described in the Supplementary Information.The allele frequency parameter  using modified python scripts adapted from Martin et al. (10.5061/dryad.dk712). The FST and f4 statistics were calculated using only reads that aligned to assigned linkage groups within the reference genome. Following phylogenomic analysis and an unexpected placement within the resulting phylogeny  and absolute (DXY) sequence divergence between species in sliding‐window analyses conducted in EggLib  as the maximum sample number of A. grahami from Lake Magadi, or seven samples (O. amphimelas), as the maximum sample number from lakes Manyara and Eyasi. Where more than the predefined number of individuals were available, selection was made based on geographic sampling and sequence quality of the RAD data. Only individuals from southern populations (sites 05 and 11) were included for A. alcalica. Analyses were run on the entire set of Alcolapia filtered biallelic SNPs  with a window size of 1 Mb, a slide length of 100 kb, included only windows with a minimum of 10 000 sites, and excluded any unplaced scaffolds.To investigate differentiation across the genome, we calculated relative , using a window size of 100 kb, a slide length of 100 kb and a minimum of 1000 sites. We tested nonrandom distribution of outlier windows using 10 000 permutations, comparing the closest interpeak distances between observed and permuted data sets, and employing a nearest neighbour index (NNI) as an indicator of the level of clustering in the observed data . The final data sets used in different analyses for phylogenomic inference and population genomic analysis are detailed in Table S2 (Supporting information).A total of 83.6 Gb of sequence was produced, of which 89% successfully mapped to the r2 for pairs of SNPs on the same linkage group and plotted against distance between SNPs. LD decreased with distance  and reached background level (mean LD between SNPs on different linkage groups) at 100–500 kb. This distance was smaller in A. alcalica and A. grahami than in A. latilabris and A. ndalalani, suggesting larger population sizes in these species. For all downstream analyses that required unlinked SNPs, we imposed a minimum distance between SNPs of 500 kb.We calculated n = 25) provides maximum support of a clade composed of A. grahami individuals as sister to the clade comprising Lake Natron Alcolapia . Short branch lengths within the ingroup relative to the outgroup indicate very low genomic differentiation. In contrast, there is maximum support for the separation of O. amphimelas (outgroup) populations between Lake Eyasi and Lake Manyara, and branch lengths between these populations are considerably longer than those across the entire Alcolapia radiation.The ML phylogeny of the full mapped‐read alignment reduced‐taxa data set  that exhibited an intermediate form, and we thereafter designated them A. aff. ndalalani.Notably, most taxa from site 17 comprise a clade, rather than clustering by species, and are sister to the northern A. alcalica nodes, we also visualized this data set as a phylogenetic network based on the Alcolapia samples only  that cluster together within these clades. Given the uncertainty of some branch placements and low bootstrap support for de novo assembly data sets  did not resolve clades within Alcolapia, and individuals did not cluster by site or species. Given the lack of resolution for almost all nodes, we present these phylogenies as majority rule (50%) consensus trees, and almost the entire Alcolapia forms a polytomy , Supporting information). However, the 100% bootstrap support for O. amphimelas nodes was maintained – both for the node separating O. amphimelas from Alcolapia, and the node separating O. amphimelas specimens between lakes Manyara and Eyasi. When the de novo data sets were combined with the mapped‐read data set (data sets K and L), ML analysis exhibited similar topology to the alignment of mapped reads alone and grouped by species, but with lower bootstrap support .Maximum‐likelihood trees generated from the A. grahami as sister to a clade composed of all Lake Natron terminals, but reveals a deeper divergence between this taxon and those from Lake Natron. Furthermore, the species analysis demonstrated long branch lengths to the outgroup taxa, but very close relationships within Alcolapia species from southern Natron populations.Similar to ML analysis of the full alignment (data set B), the SNAPP species tree  also places Alcolapia unlinked SNPs (data set N) gave the highest likelihood scores for the admixture and correlated allele frequencies models. Using these models, lnP(K) gave an optimum of K = 4 and the Evanno method exhibited a modest peak at K = 3 . The cluster membership at K = 3 and K = 4 reflects the differentiation observed in the ML tree, with shared cluster membership between species in the sympatric southern Lake Natron populations, but with the allopatric northern populations of A. alcalica showing strong probability of membership to a single cluster. Furthermore, A. grahami is assigned to a distinctly separate cluster from all other individuals, with no mixing.STRUCTURE analysis of f4 population test comparisons were all significant, indicating admixture between all species pair combinations: A. alcalica–A. ndalalani, A. alcalica–A. latilabris and A. latilabris–A. ndalalani  in Arlequin, so we present only the latter set of results here, as Arlequin accounts for differences in sample size. Pairwise population FST values revealed higher levels of differentiation between more distant populations and between described species . As expected, A. grahami populations exhibited the highest FST values when compared to Lake Natron populations, indicating population structuring between the two lakes, with lower pairwise FST values between A. grahami and the most northern A. alcalica population (site 19). Individuals from site 17 in Lake Natron exhibited the lowest interpopulation and interspecific values, which correlates with relationships as indicated by the ML tree and suggests very recent or contemporary hybridization occurring at this site. The range of intraspecific FST values between populations was similar across Lake Natron species , but substantially lower in Lake Magadi (A. grahami: 0.000–0.014). However, after correcting for multiple tests (Bonferroni correction), none of these population comparisons was significant.Interpopulation FST indicated heterogeneous differentiation across the genome in the Alcolapia comparisons, with several peaks of divergence in each pairwise comparison against a background of low divergence  exhibited a right‐skewed pattern for within‐Alcolapia comparisons with a majority of windows showing low differentiation, but a small number showing comparatively high FST values. Conversely, the Alcolapia‐outgroup comparison showed a left‐skewed distribution, with most comparisons showing high levels of differentiation and only a few regions of low differentiation. We also calculated FST values for nonoverlapping windows, and plotting the top 1% and 5% FST windows in the genomewide analysis indicated heterogeneous distribution across the genome . The range of FST values covered by the top 5% of values was considerably larger within the Alcolapia comparisons (FST = 0.2–0.8) than in the Alcolapia‐outgroup comparison (FST = 0.98–1.00). The distribution of 1% outliers was significantly nonrandom only in the A. alcalica vs. A. latilabris comparison (significant by permutation testing and Z‐statistic of the NNI ratio); however, all comparisons exhibited NNI < 1, indicating tendency to clustering rather than dispersion.Sliding‐window analyses of nce Fig. . This is 23 Fig. , althougbayescan analysis identified several FST outliers in each of the Alcolapia comparisons . The details of all the loci identified as outliers for Alcolapia comparisons are given in Tables S4–S7 (Supporting information), and the corresponding gene annotations for loci identified in more than one species comparison in Table S8 (Supporting information). All of the outliers indicated diversifying selection  rather than balancing selection, and the majority of outliers had log10 Bayes factor scores >0.5 , indicating that genomic divergence between populations is not correlated with distance.To investigate whether each species exhibits panmixia within the respective lakes, we tested isolation by distance by comparing pairwise population Alcolapia of 0.020%, which was the same as for that within Lake Natron alone (0.019%), and mean interspecific distances only marginally larger: 0.020–0.026% . As we focused our analyses on reads aligned to the O. niloticus reference genome, we also de novo‐assembled reads that did not align to the genome in case these reads represented regions of the genome that had substantially diverged from O. niloticus. However, these reads did not appear any more divergent from the outgroup O. amphimelas species than aligned reads based on genetic distance .Across the whole data set, there was very low phylogenomic differentiation, with a mean interindividual uncorrected p‐distance for the Alcolapia radiation. Here, we present an extensive genomic data set containing dense sampling of the entire Alcolapia and address existing species hypotheses and phylogeny of the entire radiation.Despite clear morphological differences and unique physiological adaptations in soda lake cichlids, previous genetic work has been unable to resolve relationships within the A. grahami, as well as the geographically restricted clades comprising A. latilabris and A. ndalalani, excluding the anomalous sampling site 17 clade. However, we unexpectedly find the geographically widely distributed A. alcalica to be comprised of two clades – clustering by northern and southern localities. This finding is likely to result from geographic isolation of certain A. alcalica populations (particularly between the northern and southern lagoons) coupled with gene flow between the southern A. alcalica and the other sympatric species. The widespread occurrence of A. alcalica across Lake Natron , with higher levels of reticulation between site 17 individuals and the A. latilabris/A. ndalalani clusters than over the rest of the network. Alcolapia alcalica did not form a clade, but clustered by population from the centre of the network, while A. grahami appeared the most distinct taxon and had the least reticulation with other groups. The SNAPP analysis  produced a species tree topology largely congruent with ML analysis and confidently resolved A. grahami as sister to all the Lake Natron species, with less certainty of Lake Natron species relationships.Consistent with described species, the ML tree Fig. A achieveron Fig. D is congO. amphimelas) is comparatively distant to the ingroup that has diverged rapidly, it is difficult to place the root accurately, which in turn can influence the ingroup topology  showing higher levels of cluster membership with sympatric species  exhibited minimal admixture with other species , with pairwise population FST values revealing higher levels of differentiation between more distant populations, and A. grahami populations exhibiting the highest FST values when compared to Lake Natron populations. Despite these differences between sampling sites, there was no correlation between genomic and geographic distances based on Mantel tests .The clusters identified in STRUCTURE analyses at optima FST values are slightly higher than, but generally show similar patterns to, those found in a recent Lake Natron study using microsatellites . However, the interspecific FST values seen within the current study are within the range of differentiation observed in adaptive divergence in other fish radiations, such as three‐spine stickleback populations  along with energy input (radiation) has been shown to be linked with propensity to diversify in cichlids  negates the benthic–pelagic axis along which freshwater diversification is often seen  and inferior mouth morphology  along the major ecological axis of pelagic or surface feeding vs. benthic feeding  could explain A. latilabris and A. ndalalani divergence. However, further empirical work would be required to test the ecological and functional relevance of these different trophic morphologies.While the current shallow habitat depth for et al. A. latilabris found more abundantly in the upper courses , Lake Magadi also differs in having no perennial inflowing streams, while Lake Natron has two inflowing rivers, Peninj and Ewaso Ngiro, as well as several perennial streams  did not cluster by species  grouped with one of the putative parental species . However, we may have expected the individuals identified as possible hybrids by phenotype to group separately from parental species. It is possible that, if narrow regions of the genome control traits of coloration and mouth morphology (on which species descriptions are based), hybrid individuals could possess a species‐typical phenotype of one parental species while exhibiting a combination of both parental genotypes across the rest of the genome. However, we do not test this hypothesis in our current analysis. Furthermore, while previous studies have shown hybridization to be an important mechanism in the diversification of other cichlid lineages  can be tested , UCL Graduate Scholarship and Graduate School Research Project Fund Award (AGPF), and Genetics Society training grant (AGPF), and the Percy Sladen Memorial Fund (JJD).All authors designed the study. A.G.P.F., J.J.D. and L.R. conducted fieldwork and collected samples. A.G.P.F., K.K.D., T.C. and K.G. conducted laboratory work and data analysis. A.G.P.F., J.J.D., L.R. and K.K.D. wrote the manuscript. All authors reviewed and contributed to editing of the manuscript.ERP009428).The demultiplexed, unaligned Illumina sequence data in fastq format have been uploaded to ENA .Table S1. Collection coordinates and sequencing statistics per sample.Table S2. Data subsets and respective analyses conducted on RAD data.Table S3. Population pairwise FST.Table S4. bayescan outlier loci for A. alcalica vs. A. grahami comparison.Table S5. bayescan outlier loci for A. alcalica vs. A. latilabris comparison.Table S6. bayescan outlier loci for A. alcalica vs. A. ndalalani comparison.Table S7. bayescan outlier loci for A. latilabris vs. A. ndalalani comparison.Table S8. Gene annotations of loci identified as outliers in multiple species comparisons.Table S9. Mantel test results for FST vs. geographic distance between sampling sites.Click here for additional data file.Fig. S1. Catchment area of the Natron–Magadi basin.Fig. S2. Plots of linkage disequilibrium dropoff with distance by species.Fig. S3. ML phylogeny for variable sites using the ASC_model.Fig. S4. Majority consensus (50%) ML phylogenies generated from additional RAD data sets.Fig. S5. Species tree generated by SNAPP analysis for selected populations.Fig. S6. Visualization of K = 2–5 for Alcolapia STRUCTURE analysis.Fig. S7. Visualization of K = 2–5 for sympatric Alcolapia STRUCTURE analysis.Fig. S8. Visualization of K = 2–5 for A. alcalica STRUCTURE analysis.Fig. S9. Frequency histograms of sliding‐window FST values for pairwise comparisons.Fig. S10. Highest scoring windows in the nonoverlapping window FST analysis.Fig. S11. Mean interspecimen uncorrected p‐distance for filtered RAD data from aligned and de novo‐assembled reads.Click here for additional data file.


Samples were collected from eight locations in four Central-Eastern (CE) Mediterranean countries . A new primer, specific for the F mtDNA type, was designed for the sequencing procedure. In total 40 different haplotypes were recorded, 24 of which were unique. Aside from the two populations situated in Thermaikos gulf , relatively high levels of haplotype and nucleotide diversity were estimated for both Central and Eastern Mediterranean populations. Eight out of the 40 haplotypes were shared by at least three populations while two of them were found in all populations. ΦST and cluster analysis revealed lack of structuring among CE Mediterranean populations with the exception of those located at the Sea of Marmara and Croatian coast which were highly differentiated. Apart from the species’ inherit dispersal ability, anthropogenic activities, such as the repeated translocations of mussel spat, seem to have played an important role in shaping the current genetic population structure of CE M. galloprovincialis mussels.The variable domain 1 (VD1) domain of the control region and a small segment of the  Mytilus constitute an economically and ecologically important group of organisms in Europe where more than 50% of their annual worldwide harvest is produced [Mytilus populations using a variety of molecular markers and techniques. However, the results of these studies were often controversial reflecting probably the differential resolving power of the various markers used and the individual characteristics of the examined populations. For instance, while microsatellite analyses indicated extensive gene flow across Croatian coasts [Marine mussels of the genus produced . Knowledn coasts  and poten coasts , RAPD man coasts  revealedMytilus is the taxon in which DUI has been firstly described by Zouros et al. [Mitochondrial DNA markers have generally proven to be very informative when examining genetic structure and routes of colonization in marine invertebrates . Howevers et al. . Accordis et al. , classifs et al. , providis et al. . Furthers et al. . The aves et al.  to 30% [s et al. . Neverths et al. , showings et al. .M. galloprovincialis mussels from the Central-Eastern Mediterranean.In the present study, sequencing analysis of the VD1 domain of the F genome was applied in order to investigate the genetic relationships and population structure of rrnaL gene were aligned for the 174 specimens scored, revealing 83 variable sites that defined 40 different haplotypes, 24 of which were unique (Almost the entire VD1 region (c. 600 bp) and a small part (215 bp) of the e unique . The lenST = 0.12, p = 0.0001), this was mainly due to the samples from Canakkale and Zadar. Indeed, particularly high and significant differentiation was observed in all pairwise comparisons of Canakkale and in the most pairwise comparisons of Zadar populations  suggesting homogeneity among populations and absence of geographical structure. This result was also supported by the analysis of molecular variance (AMOVA) performed on the six populations which showed that the 95.86% of the variation was attributed within populations and only 4.14% was due to variance among populations. In the cluster analysis, the highest marginal likelihood (closer to zero) was observed when the value K was set as 7 (K = 7), identifying seven distinct groups of haplotypes in optimal partition (hereafter referred as Κ1 to Κ7). With the exception of K5 and K7 groups including 21 out of the 25 specimens from Canakkale and 15 of the 23 from Zadar, respectively, no internal structuring was observed within the rest of the groups as all of them included numerous individuals from any of the remaining six populations . The remaining central branches were composed by haplotypes from all the other populations  and the Siculo-Tunisian strait  have been described as transition areas that can cause population genetic differentiation between Aegean—Adriatic and Adriatic—Ligurian Seas, respectively, in numerous marine organisms [i.e., transplantations of spat for aquaculture purposes and transport of ships ballast water, may have also played an important role in overcoming the barriers that prevent mass gene flow between these basins and consequently may have contributed to the genetic homogeneity among CE Mediterranean populations. Transplantations have influenced the genetic composition of native mussel populations in several areas i.e., along Chilean [The high dispersal potential of marine mussels of the genus rganisms ,19,20,21 Chilean  and nort Chilean . In Gree Chilean . MoreoveM. galloprovincialis were analyzed. These were collected in the period 2009–2011 from eight sampling sites, located in four different countries from CE Mediterranean  of the mitochondrial genome was amplified in each tissue sample using the primers UNFOR1 and UNREV1 , locatedi et al. ) and in  [et al. . PCR pro [et al. ). In adds et al. ), that iM. galloprovincialis mitochondrial F genome (GENBANK accession number: AY497292.2) was designed. Purified samples were sent to VBC-Biotech  for sequencing. All sequences were aligned using the software BioEdit version 7.1.9 [The successfully amplified products  were purified with the NucleoSpin PCR Clean-up Kit  to remove excess nucleotides, primers, enzymes and other impurities, following the manufacturer’s protocol. For the sequencing reactions, a new primer, MGF (5'-GCA AAC ACT ATT TAA GTG TA-3'), specific for the female mtDNA molecule of the VD1 domain in on 7.1.9  and wereMytilus [f) segment that has been paternally inherited. Hence, two additional haplotypes, obtained from complete M and F mitochondrial M. galloprovincialis genomes in GenBank  were included in the data set and the step-down correction method for significance was applied using the default settings.Since recombination between paternal and maternal lineages, as well as among female mtDNA haplotypes is possible in Mytilus ,15, the Mytilus  was usedST analyses using Arlequin version 3.5 [Haplotype and nucleotide diversities were estimated for each population using the software DnaSP version 5.0 . Geneticsion 3.5 . Throughsion 3.5 . Furthersion 3.5  which grsion 3.5 . SequencMitochondrial DNA variation revealed genetic homogenization of mussel populations in the biggest part of central-eastern Mediterranean. Apart from the species’ high dispersal ability, anthropogenic activities may have played an important role in shaping the current structuring of Mediterranean mussels. On the other hand, there are still genetically differentiated populations such as those of the Croatian coasts and the Sea of Marmara. Therefore, future management actions should be carefully designed, especially in localities harboring distinct native populations.


The development of molecular genetic technology has led to the discovery of large number of polymorphic loci in the human genome. This has renewed the interest in investigating genomic diversity (and affinity) between human populations with much more depth and clarity than that was possible with the erstwhile traditional serological and biochemical genetic markers. DNA markers are presently widely used in gene mapping, forensic studies and information on population structure and population genetics of regional and global populations. The study attempts to understand the genetic structure and affinity among six different populations of Manipur.The diversity of the studied populations was examined by investigating the polymorphism for a STR locus (TPOX). Unrelated individuals belonging to Muslims with different caste viz. Sheikh, Syed, Pathan & Moghul; Hindu (Meitei) and tribal (Naga) were randomly selected. Blood samples were collected after obtaining an informed consent. The DNA was extracted using standard phenol – chloroform extraction method and then amplified with PCR using previously published primers. The amplified PCR products were electrophoreses followed by Silver staining.Different population containing allele with repeated number varying from 5 -11 were detected. Discriminating Power Analysis (PD) lie in the range from 0.444 to 0.889 and Matching Probability (MP) was observed to vary from 0.111 to 0.556. Based on genetic distance, dendrogram was constructed to depict the genetic affinities among the six populations. The tree shows that the ethnic background of six populations is different.


HLA-B and MAPK10) that are involved in defense against endemic pathogens such as malaria. Genes that encode functions related to skin pigmentation (SCL4A5) and cutaneous glands (EDAR) are also found in regions with anomalous ancestry patterns. These results suggest the possibility that ancestry-specific loci were differentially retained in the modern admixed Colombian population based on their utility in the New World environment.The human dimension of the Columbian Exchange entailed substantial genetic admixture between ancestral source populations from Africa, the Americas and Europe, which had evolved separately for many thousands of years. We sought to address the implications of the creation of admixed American genomes, containing novel allelic combinations, for human health and fitness via analysis of an admixed Colombian population from Medellin. Colombian genomes from Medellin show a wide range of three-way admixture contributions from ancestral source populations. The primary ancestry component for the population is European , followed by Native American  and African . Locus-specific patterns of ancestry were evaluated to search for genomic regions that are enriched across the population for particular ancestry contributions. Adaptive and innate immune system related genes and pathways are particularly over-represented among ancestry-enriched segments, including genes ( The arrival of Columbus in the New World precipitated a massive and sudden exchange of life forms between the American and Afro-Eurasian hemispheres. European colonization and trade in the Americas entailed a bidirectional exchange of numerous species of plants, animals and microbes, many of which until that time had been evolving separately for millions of years. The conquest and settlement of the Americas, along with the African slave trade, also included exchanges among a variety of human populations. These biological and cultural exchanges, which were often intentional although sometimes not so, had a tremendous impact on the trajectory of human history in the centuries that followed. Among other effects, the exchange of crops and livestock allowed for a major increase in the global population, whereas the introduction of microbes that cause infectious disease had devastating effects on the naïve populations to which they were introduced.Columbian Exchange in his seminal book of the same name1493: Uncovering the New World Columbus Created by Charles MannThe historian Alfred Crosby referred to this massive transfer of life as the The modern human species emerged out of Africa and spread throughout the world starting between 60–100,000 years ago4in situ within ancestral populations’ endemic geographic regions. Some of these alleles may have drifted to high frequency within the ancestral populations by chance, whereas others are likely to have been swept to fixation based on selection pressures that were distinct to the ancestral populations’ environments678678101112131415678978Admixture rapidly brings together population-specific (or enriched) alleles that have not previously co-existed in the same genetic background, and thereby can be considered to result in the creation of completely novel human genomes. Population-specific (enriched) alleles are sequence variants that evolved to population-characteristic frequencies i.e. their relationship to health and fitness in a particular environment. We posit that these pre-evolved ancestral population-specific alleles may have been selected in the modern admixed population based on their utility in the new environment. The new environment could be a new physical environment, for populations that were transported to new regions, and/or a new ecological environment based on the mixing of previously isolated human populations and their associated microbial fauna.In this study, we sought to address what it means when genomic variants that have been separated for tens-of-thousands of years are suddenly brought back together over the course of a few hundred years. In other words, is the process of modern admixture somehow related to human health and fitness? Our working hypothesis is based on the well-supported axiom that specific allelic variants (SNPs) have evolved separately in ancestral human populations based on their regional-specific utility, We evaluate these ideas here via a study of the relationship between ancestry, admixture and fitness in Colombian genomes. The Colombian population is a particularly interesting subject for study in this regard owing to its high levels of ethnic admixture192021222426Admixed Colombian genome sequences from Medellin were compared with a number of world-wide populations that are likely to be closely related to Colombian ancestral source populations . To do tThe close clustering of the East Asian with the Bolivian Native American populations  is consiP = 1.8 × 10−7). Similarly, the relative level of Native American female ancestry was significantly higher for the Colombian population compared with the country with the next highest level . The Colombian population also shows a smaller, but not insubstantial, excess of African ancestry along the male lineage .A number of previous studies have uncovered sexual asymmetry in the contributions of different ancestral populations to admixed Latino genomes20212223The three-way continental ancestry origins of individual chromosomal segments across the entire genome were determined for all 60 individuals in the Colombian population as described in the Materials and Methods. Chromosome paintings that show the locations of ancestry-specific segments across the chromosomes of two Colombian individuals are shown in i.e. anomalous) ancestry proportion combination values. Chromosomal segments that bear such anomalous ancestry proportion combinations are the ones that are identified by the ancestry-enrichment statistical test applied here . When the ancestry-enrichment analysis technique is applied to population-wide ancestry proportion combination data, numerous statistically significant ancestry-enriched chromosomal segments are revealed across the entire genome  were used for these analyses. There are numerous genes in these regions that were previously identified to show evidence of positive selection in populations from one of the three ancestral regions that contributed to the modern admixed Colombian population; there are also a number of genes in ancestry-enriched regions that show evidence for a role in various health-related phenotypes based on previous selection and association studies .Having identified genomic loci with anomalous ancestry contribution levels, we then interrogated the genes located in these regions for previously identified signatures of natural selection and for associations with health-related traits. Only ancestry-enriched chromosomal segments that were highly statistically significant ( studies . In partHLA-B gene located in the major histocompatibility complex (MHC) on chromosome 6 is found in an African ancestry-enriched chromosomal segment  to immune system cells. HLA-B is a highly diverse gene with numerous allelic variants; high sequence diversity of HLA genes is thought to facilitate the ability to counter a diverse repertoire of foreign antigens. Indeed, HLA gene diversity levels among global populations are positively correlated with regional-specific levels of pathogen richness, with African populations having the most diverse repertoire of HLA allelesHLA-B allelic diversity levels world-wide show a strong positive correlation with malaria selective pressureHLA-B locus may have helped the Colombian population to more effectively counter malaria and/or other pathogenic agents. The MAPK10 gene is another immune-related gene that is located in an Asian-enriched ancestry segment in the Colombian population, and alleles of this gene were recently shown to be selected for malaria resistance in MalaysiaThe  segment . HLA-B iSCL4A5 and EDAR. The SCL4A5 gene is located in a genomic region enriched for European ancestry in the Colombian population. Positive selection at this locus has previously been associated with the evolution of decreased melanin skin pigmentation as European and Asian populations radiated out of AfricaSome other interesting genes from ancestry-enriched regions include EDAR gene has received considerable attention recently owing to an interesting connection between the phenotype it encodes and evidence of population-specific positive selection9EDAR encodes a cell surface receptor that is involved in the development of hair follicles and cutaneous glands, and there is evidence for positive selection of EDAR alleles in Asian and Native American populations. The selected allele reduces evaporation from exposed facial structures and upper airways, which is thought to represent an adaptation to cold and dry environments in East Asia. In the admixed Colombian population, EDAR is found in a chromosomal segment that is depleted for Asian (Native American) ancestry P-values reported here should be taken with some caution.The significant over-representation of ancestry-enriched genes among components of the immune system includes genes that map to pathways involved in both the innate and adaptive immune response . The relResults from our analysis of 60 Colombian genome sequences from Medellin point to high levels of three-way continental admixture, with contributions from African, Native American and European ancestral source populations, consistent with previous genetic studies1920212223It should be noted that different regions of Colombia show very distinct demographic patterns. For example, whereas people from Medellin have primarily European ancestry, the Atlantic and Pacific coastal regions are home to much larger populations of Afro-Colombians. Thus, the admixture patterns reported here for Medellin can not be taken to represent country-wide patterns of Colombian genetic ancestry. Indeed, studies on the genetic ancestry of Colombians sampled from different regions of the country often yield very different results1920212223Interestingly, the genetic ancestry and admixture results obtained here for the population of Medellin can be considered to be at odds with the demographic data for the city. Medellin is considered to have a population that is almost entirely descended from Europeans. In the 2005 census, 93.4% of the population of Medellin was classified as Euro-descendent, whereas 6.5% of individuals identified as Afro-Colombian and only 0.1% identified as Native AmericanThe distinction between genetic ancestry and ethnic self-identification in Medellin may be related to two important cultural concepts rooted in many Latin American societies: Mestizaje and Blanqueamiento39The relationship between genetic ancestry and ethnic self-identification has recently been studied in depth for five Latin American countriesColombian genome sequences also show strikingly asymmetrical patterns of sex-specific admixture with the male lineages dominated by European ancestry and female lineages comprised of more Native American ancestry . These r20212223When regional-specific ancestry contribution patterns are compared across the entire population of Colombian genomes studied here, it becomes very clear that the patterns of admixture are non-random . There ain situ in their ancestral regions, based on local selective pressures, over many thousands of years. When the populations that bore these alleles arrived in the New World, the pre-existing adapted alleles were ready to be rapidly re-assorted into novel admixed genomes. In other words, the long, slow process of natural selection had already occurred in the ancestral source populations to generate a standing pool of genetic variation with a wide variety of adaptive utility. From this existing pool of genetic variation, numerous ancestry-specific segments containing adaptive alleles were readily accessible for re-assortment. In this way, the enrichment of ancestry-specific segments in the Colombian population, based on their utility in the New World environment, could have occurred much more rapidly, i.e. within the relatively short time span following Columbus’ arrival in the Americas. The ability to rapidly shape admixed genomes over such a time span, with anomalous combinations of ancestry-specific alleles, is supported by the highly asymmetrical patterns of sex-specific admixture observed for Latino populations.We envision that the particular ‘selection’ process that occurred for the admixed Colombian population, based on assortment among pre-existing ancestry-specific alleles, was somewhat distinct from the concept of natural selection as typically formulated. Adaptive, also referred to as positive or directional, natural selection is most often considered to occur via the fixation of novel mutations based on differential reproductive success. This process starts with the introduction of new alleles by mutation at very low population frequencies and thus is relatively slow; it typically takes place on the order of tens- or hundreds-of-thousands of yearsA similar approach to search for evidence of selection based on ancestry-enrichment has been conducted in two recent studies of admixed African American populations43Interrogation of the functional roles of genes located in the anomalously admixed genomic regions detected here suggests that the retention of ancestry-specific alleles in the Colombian population is most closely tied to immune system function . This prColombia is located in the tropics, traversed by the equator, and has a high burden of infectious disease caused by a variety of pathogenic agents. Compared with other countries in the region and around the world, Colombia has a very high level of pathogen richness as measured by the number of known pathogens in the country (n = 244)17Susceptibility to cholera, which is endemic to South East Asia, is known to be strongly influenced by host genetic factors4749MICB locus along with additional significant SNPs at the adjacent HLA-B and HLA-C lociHLA gene alleles and susceptibility to dengue in Asian populations5556There have also been numerous studies that have identified host genetic factors that appear to mitigate susceptibility to dengue fever52535556th century United States provides compelling statistical evidence for an association between genetic ancestry and susceptibility to yellow fevere.g. social and/or economic) factors that could explain this difference and concluded that their findings support the existence of host genetic factors that mitigate the severity of yellow fever infections among individuals with African ancestry.As of this time, there are no known host resistance alleles associated with susceptibility to yellow fever. However, it has long been thought that populations with different genetic ancestries had differing degrees of susceptibility to yellow fever, suggesting a genetic component to susceptibility to this pathogen. In particular, populations with African ancestry were thought to have reduced susceptibility to yellow fever5859HBB) that evolved independently and provide increased resistance to malaria6667Malaria poses a particularly grave and consistent threat to public health in Colombia with both endemic and epidemic transmission regimesThere is a clear connection between the infectious disease burden in Colombia, for a number of the most common pathogen agents found in the country as described above, and host genetic factors that mediate susceptibility and resistance. Many of these host genetic factors are likely to be population-specific (or enriched) alleles that initially evolved within ancestral source populations. The results obtained from our ancestry-enrichment analysis indicate that the modern admixed Colombian population may have had the opportunity to draw from a variety of these ancestry-specific resistance alleles to assemble a diverse repertoire of immune system related genes capable of countering threats from the wide variety of pathogens found in the New World environment. In addition to being of interest from an evolutionary perspective, these results may have implications for better understanding the genetic determinants of health in highly admixed Latin American populations.n = 264) and genotypes characterized using SNP microarrays (n = 257) from a number of sources2627i.e. SNP calls) characterized using complete genome sequences and microarrays from these different studies (and formats) were merged using the program PLINK v1.90A total of 581 whole genome sequences or genotypes, taken from a variety of sources, were analyzed here see . Whole g26rays n = 7 from a Allele sharing distances between pairs of genomes were computed as the fraction of differences between SNP calls. Principal components analysis of the resulting pairwise allele sharing distance matrix was performed using the prcomp program from the R package v3.1.2Normalized ratios of the difference between admixture fractions for the X chromosome versus the autosomes were used to infer sex-specific admixture contributions for each of the three ancestral source populations. The admixture difference ratio , Asian (CHB) and European (CEU) chromosomal segments, for the entire population at a specific genomic locus, given the population-average levels of African, Asian and European ancestry. This probability is expressed as:Chromosomal regions with anomalous patterns of ancestry, when considered as an ensemble across the entire population of 60 Colombian genomes (120 chromosomes), were identified via ancestry-enrichment probability values. These values were computed as the trinomial probability of observing a particular numerical combination of African  anomalous patterns of ancestry identified in this way were interrogated for their potential functional significance using several sources of information. Genes that lie within these regions were compared to sets of genes previously identified as being subject to positive (adaptive) selection in a number of studies678910Genomic regions with highly statistically significant .


Modiolus modiolus  (horse mussel reefs) are marine habitats which support high levels of species biodiversity and provide valuable ecosystem services. Currently, M. modiolus reefs are listed as a threatened and/or declining species and habitat in all OSPAR regions and thus are highlighted as a conservation priority under the EU Marine Strategy Framework Directive (MSFD). Determining patterns of larval dispersal and genetic connectivity of remaining horse mussel populations can inform management efforts and is a critical component of effective marine spatial planning (MSP). Larval dispersal patterns and genetic structure were determined for several M. modiolus bed populations in the Irish Sea including those in Wales (North Pen Llŷn), Isle of Man (Point of Ayre) and Northern Ireland (Ards Peninsula and Strangford Lough). Simulations of larval dispersal suggested extant connectivity between populations within the Irish Sea. Results from the genetic analysis carried out using newly developed microsatellite DNA markers were consistent with those of the biophysical model. Results indicated moderately significant differentiation between the Northern Ireland populations and those in the Isle of Man and Wales. Simulations of larval dispersal over a 30 day pelagic larval duration (PLD) suggest that connectivity over a spatial scale of 150km is possible between some source and sink populations. However, it appears unlikely that larvae from Northern Ireland will connect directly with sites on the Llŷn or Isle of Man. It also appears unlikely that larvae from the Llŷn connect directly to any of the other sites. Taken together the data establishes a baseline for underpinning management and conservation of these important and threatened marine habitats in the southern part of the known range.Biogenic reefs created by  Modiolus modiolus  (horse mussel) is an Arctic-Boreal species with a distribution that extends from the seas around Scandinavia and Iceland southward to the Bay of Biscay  values.stimator  along wiFinally, population structure was analysed using two statistical approaches. Firstly, the Bayesian clustering techniques implemented in the software STRUCTURE 2.3.1 , 40. STRFinally, a connectivity matrix was constructed to show linkages between genetic spatial structure and biophysical model outputs. Seasonally-averaged and cohort-averaged connectivities between populations  were overlaid with significant genetic differentiated populations. Criteria for settlement (connectivity/retention) were for larvae to be located within 10 km of the settlement site after 30 days simulation. Modelled larval release (source) sites are labelled on the y-axis, and settlement (sink) sites are located on the x-axis; genetic values do not identify source/sink sites.The Particle Tracking Model simulated a general southerly movement of particles from the Northern Ireland release sites Sites 1–2), over the 30-day PLD , due to , over thAlthough no connectivity was simulated between each release site, several simulations suggested that there could be some one-way connectivity. For example, particles released from the Point of Ayre (Isle of Man) during April were located within 15 km of Ards Peninsula after the 30-day PLD . HoweverWhen looking at cohort-averaged radial dispersal distances , summer o) was lowest (0.4373) in the North Llŷn population and highest (0.5958) at Strangford Lough. Overall, the expected heterozygosity (He) was higher than the observed heterozygosity indicating a possible heterozygote deficiency  per population ranged from 9.4 at Point of Ayre to 20.8 at Strangford Lough; and the number of private alleles was greatest at Strangford Lough (51) and least at Point of Ayre (31). The observed heterozygosity . Therefore it was concluded that all populations were not in Hardy-Weinberg Equilibrium.The presence of null alleles was detected for 4 of the 5 markers for the majority of the populations tested (r >0.05). Modimicro 20 locus showed no null alleles across all 4 populations and the Point of Ayre population reported very low (0.0001) null allele frequencies for loci Modimicro 11 and 30. Significant positive Fst). Given that all but one of the markers and populations contained null alleles, it was therefore not possible to exclude the null allele markers from the calculations. To allow for this, Estimation of Null Allele (ENA) correction was performed using FreeNA software and pairwise Fst was calculated before and after the correction procedure was applied [st values before ENA correction ranged from 0.0023 (Strangford Lough/Ards Peninsula) to 0.10 (Strangford Lough/Point of Ayre); and after correction ranged from 0.01 (Strangford Lough/Ards Peninsula) to 0.12 (Strangford Lough/Point of Ayre)  . FollowiM. modiolus populations from Irish Sea counterparts . The Strangford Lough/Ards Peninsula and North Llŷn/Point of Ayre populations were not significantly differentiated.The Fstat pairwise test for differentiation showed low but significant (p<0.05) differentiation of Northern Ireland Results from data analysis in the software STRUCTURE and STRUCTURE Harvester indicated a mean Log Likelihood of K = 2 and the ‘Evanno method’  K = 2 . The gloThe connectivity matrix  from modM. modiolus reefs, followed by the use of microsatellite markers to directly test connectivity and validate the model to understand whether the genetic data had congruence with the modelling data. This study shows the applicability of using such genetic analysis in the context of protected habitats and is the first study to develop microsatellite markers of M. modiolus.The combined approach of using genetic diversity markers with population dispersal modelling have, in the past, not been fully incorporated into the design and placement of Marine Protected Areas (MPAs) . In thise) was highest within the Strangford Lough population and lowest in the Point of Ayre population suggesting greater gene diversity within the Strangford Lough population. The inbreeding co-efficient Fis was positive and significant for all populations and FreeNA analysis, reported null alleles for all loci at all populations (and zero for Modimicro 20). Overall, low genetic differentiation (and therefore more gene flow [The expected heterozygosity (Hene flow ) was recis values may indicate high levels of inbreeding, however, this is considered unlikely in bivalves with large populations and pelagic larvae [is values reported are due to the observed heterozygote deficiency and potentially to the quality of the sample DNA (DNA extraction for 3 of the 4 samples was undertaken at least 20 months after tissue storage in ethanol), however DNA quality was assessed prior to screening, with no apparent degradation of samples.Heterozygosity is an important measurement for population diversity . A signic larvae . It is lThe results show that there is limited structure within the populations screened and that there is an overall weak differentiation of the Ards Peninsula/Strangford Lough and North Llŷn/Point of Ayre reefs. This would suggest that there is little restriction in gene flow between these two groups of populations.M. modiolus in the Irish Sea.Further development is required regarding the type of connectivity screening undertaken on priority marine organisms . For example, it would be beneficial to screen potentially isolated populations or geographically distinct populations  to confResults from the particle dispersal model show that larval settlement location is driven by oceanographic-atmospheric processes and larval duration. Simulations for passive larvae suggest that larval dispersal has the potential for dispersal to be wide reaching. This result corroborates the genetic analysis showing an inter-connected Irish Sea metapopulation. However, simulated populations on the east and west of the Irish Sea seem to be separate from one another, for several releases over a typical year due to variations in wind speeds and thermal heating . The simM. modiolus reef off the south of the Isle of Man (Little Ness) between Point of Ayre and North Llŷn, this site may contribute to the connectivity of these two populations if included in the larval dispersal model and could represent a stepping stone population.Combining the larval dispersal model and the genetic analysis results allows for the validation of the two methods and provides a more accurate depiction of the relationships between the populations. Discrepancies noted between the two methods in this study showed that, from a modelled perspective, the North Llŷn and Point of Ayre populations were not connected, whereas the genetic analysis showed no significant differentiation. Given the existence of a M. modiolus are poorly understood—research suggests vertical migration that is synchronised with flood-tidal currents promotes coastal retention of larvae but also promotes long-distance dispersal to distant populations [M. modiolus is vital before further biophysical modelling takes place. In addition, multi-year hydrodynamic modelling is required to quantify the natural intra-seasonal, inter-annual and climatic variability in physical controls on larval dispersal. Of particular influence will be periods with extreme events such as storms (producing both large waves and strong winds), which may increase dispersal in the upper water column, but may also break down residual pathways. Conversely, ‘heat waves’/droughts may strengthen residual pathways. Additionally, the influence of atypical conditions such as prolonged easterly winds should be quantified with regard to dispersal. Such information is crucial for improved model simulations of larval dispersal and connectivity.Larval migration has been shown to be equally as influential to dispersal and connectivity as oceanographic controls . Howeverulations , 56. On ulations , 57. TheM. modiolus reefs implicated in this study and their decline and scarcity in the Irish Sea, it seems likely that they exist as a network of “stepping stone” habitats, each with an important role in gene flow. It was not possible to analyse Isolation by Distance of the populations in this study due to the limited number of markers developed but it would be useful to do so in the future, to understand in more detail the specific connections between each reef and identify direction of genetic flow (source/sink) to complement modelling outputs. Other known reefs are also scattered more widely along the west of the UK, perhaps indicating similar "stepping stones" for genetic exchange over the wider sea area.Due to the connectivity of the Habitat connectivity (including genetics) of marine organisms has been cited as a major concern to the maintenance of marine biodiversity but despite the large number of published articles that assert the importance of using genetic data for management and conservation, very few use data applicable to real-life situations  as demonThe global literature on the connectivity of MPAs tends to be directed towards their benefits for commercial fish and the role of no-take reserves in increasing stocks in neighbouring areas and maintaining gene flow within populations –61. HoweThe connectivity of PMHs may be of importance to commercial fisheries as well as to the biodiversity of an MPA network. Loss or damage to one of the stepping-stone habitats could have a knock-on effect to other areas of the marine ecosystem as a whole, resulting in consequences for biodiversity conservation and livelihoods, but also, in the achievement of objectives under MSFD, as the policy link has been made between the maintenance of PMHs and the achievement of GES .M. modiolus reefs (and other benthic habitats) are particularly susceptible to damage from certain types of fishing gear [2 of M. modiolus reefs have been lost since the mid-1970s [M. modiolus reefs with recent considerations including the transfer of adult mussels to areas characterized as having high potential for successful translocation  and falling within a proposed non-disturbance zone [M. modiolus from outside the area, the issue of introducing genetically non-compatible animals has been raised [M. modiolus population may be a prospective source of M. modiolus for translocation to Strangford Lough [It is well understood that ing gear , 67, 68.id-1970s , 69 and id-1970s , 69. Curnce zone , 70. Hown raised . Geneticrd Lough , 70, 71.Overall, in the Irish Sea, the general decline in horse mussel beds, and the apparent connectivity of the remaining beds , implies that it would be wise to manage them as inter-dependent stepping-stones, especially on either side of the Irish Sea. Creating a coherent network of MPAs and the achievement of GES the MSFD by 2020, requires information on the connectivity of populations; research on which is currently lacking across Europe. Greater study resolution and research over a larger spatial area will improve the ability to design MPA networks and could further inform future management; therefore achieving long term protection of Europe’s marine environment.


Leptothorax acervorum, colonies from central and peripheral populations differ in social structure: colonies from Central and Northern Europe may contain several equally reproductive queens (facultative polygyny), while in colonies from peripheral populations in Spain only one the most dominant of several queens lays eggs . By reconstructing the specie’s evolutionary and demographic history in Southwestern Europe we examine whether variation in social organization is associated with restricted gene flow between the two social forms.The disjunct distribution of several Palearctic species has been widely shaped by the changes in climatic conditions during the Quaternary. The observed genetic differentiation or reproductive isolation between extant populations may be the outcome of their contemporary geographic separation or reproductive incompatibility due to differences in phenotypic traits which have evolved in isolated refugia. In the boreal ant L. acervorum are functionally monogynous, whereas multi-queen colonies from all Pyrenean populations are polygynous, like those from other previously studied areas in Europe. Our analyses revealed complex spatial-genetic structure, but no association between spatial-genetic structure and social organization in SW-Europe. The population in the western Pyrenees diverged most strongly from other Iberian populations. Moreover, microsatellite data suggest the occurrence of recent bottlenecks in Pyrenean and inner Iberian populations.We show that multi-queen colonies from all so far known inner Iberian populations of L. acervorum, suggesting the existence of multiple refugia in SW-Europe, including two extra-Mediterranean refugia in France. While gene flow among inner Iberian refugia may have been larger during the late glacial, extra-Mediterranean refugia in southern France may have contributed to the post-glacial recolonization of W-Europe.Our study shows a lack of reproductive isolation between the two social forms in SW-Europe. This in turn suggests that demographic and spatial patterns in genetic variation as well as the distribution of social phenotypes are better explained by co-variation with climatic, ecological, and historical factors. Moreover, we for the first time show the existence of substantial spatial-genetic structure in The online version of this article (doi:10.1186/s12862-016-0711-3) contains supplementary material, which is available to authorized users. Quaternary climate changes and their dramatic effects on demography and distributional ranges have left behind their footprints on the evolution of Palearctic biota. Temperate species escaped the last glacial maximum LGM 23-18 ka BP) by retreating southwards to suitable habitats in Iberia, Italy and Balkans and recolonized Northern and Central Europe from these refugia after the retreat of the ice sheet 8 ka BP b.Leptothorax acervorum  . Across its range, a large fraction of L. acervorum colonies contain several reproductive queens (the others are queenless or have a single queen). Interestingly, the partitioning of reproduction among nestmate queens in such multi-queen colonies (“reproductive skew”) varies among populations ).L. acervorum reaches as far north as the tundra-taiga ecotone at the North Cape and the Lena delta  in FSTAT whereas geographical distances among populations in kilometres were calculated in GENALEX  based upon multi-locus genotypic data. Cluster analysis was run in STRUCTURE 2.3.4  allowingribed by  and implribed by . DISTRUCribed by  was usedribed by  to evaluL. acervorum in “mountainous islands” in Central Spain, we tested for the occurrence of bottlenecks in each sampled population. First, we used Wilcoxon’s sign rank test, which tests for an excess of heterozygosity, implemented in BOTTLENECK 1.2.02 [M-ratio statistic [Because of the patchy distribution of K 1.2.02 . Second,tatistic  to test tatistic  for the The primers C1-J-2183 and A8-N-3914  were useChromatograms were assessed and edited using CHROMAS LITE 2.1.1 (Technelysium) and subsequently concatenated in BIOEDIT . SequencLeptothorax kutteri , number of private haplotypes (hP), number of segregating sites (S), haplotype diversity (H) and nucleotide diversity (π) for each locality, for each geographic region, and for the whole mtDNA dataset except the extremely divergent haplotypes using DNASP v5.10.01 [ΦST – values from mean pairwise differences (NST) and haplotype frequencies (GST) in ARLEQUIN. By comparing both statistics of genetic differentiation it is possible to test whether the mtDNA-sequence dataset contains a signal of phylogeographic structure (if NST > > GST) beyond that in haplotype frequencies alone (see [ΦSC) than between regions . When both measures are equal, their ratio is expected to be one. Consequently, if their ratio is larger than one, then genetic differentiation is larger within than between regions . Significance of AMOVA results was evaluated over 10,000 replicates.For the quantification of genetic polymorphism we used the following standard diversity indices: number of haplotypes  were calculated for each region and for the whole dataset to measure whether data deviate from expectations of neutral evolution or equilibrium population size. For further details on methods see Additional file Mismatch distributions and test statistics for selective neutrality (Tajima’s n = 5) or queenless (n = 6). Not a single of the multi-queen colonies collected from various parts of the Pyrenees was functionally monogynous. In contrast, six of 12 Pyrenean colonies had multiple reproductive queens , four were monogynous and two were queenless. In accordance with previous studies documenting facultative polygyny in the Pyrenees and other parts of Central and Northern Europe [e.g. [L. acervorum as facultatively polygynous . Further results from ovary dissections are summarized in Additional file Results from ovary dissections are summarized in Table pe [e.g. , 8) we tve skew, , 20). BeHO) and expected heterozygosity (HE) (Table k (range: 6.3 to 9.5), AP (range: 3 to 14) and AR (range: 6.0 to 9.0) than the Pyrenean populations . However, HE is generally higher than HO for all genotyped populations.Significant deviation from HWE after Bonferroni correction for multiple tests  Table . The innD: 0.934).Genetic diversity at the mtDNA fragment did not differ strongly between geographic regions Table . HaplotyAnalysis of genealogical relationships among populations (based upon microsatellite data) resulted in an unrooted neighbour-joining tree with nodes supported by bootstrap values between 10 and 96 % Fig. . The lonFST) was low (0.075) and remained moderate even after correction for multiple alleles . The population from the western Pyrenees (PY II) again showed a higher differentiation than all inner Iberian populations  within the remaining microsatellite dataset  and log-transformed Euclidean distance .STRUCTURE runs using all locations strongly supported The mtDNA-haplotype network has a decentralized structure and shows a short to intermediate expanded genealogy with only limited geographic segregation of haplotypes  was observed for the total dataset from Spain and France (extremely divergent haplotypes excluded) and for all pairwise combinations of geographic regions (Table P < 0.01). The global analysis without regional partitioning of data revealed moderate genetic structure within the whole dataset as well . The data did not reveal strong phylogeographic structure (i.e. NST is never larger than GST) in pairwise comparisons of regions or the whole dataset including all regions  showed that two inner Iberian populations have a significant excess of heterozygosity only, indicating a recent bottleneck , the net migration from Iberian populations to PY I was high . The highest mean migration rate was from SA to PY I (mean M = 36.3), approximately two fold higher than between SA and PY II. Differences between migration rates for the Pyrenean populations provide support for higher immigration from Iberian populations to PYI and the relatively isolated nature of PY II. For all sampled populations, Bayesian Skyline plots show a long-term decrease in population sizes starting from various TBOTTLENECK. Similar trends of an acute reduction in population sizes were observed for PY II, SNW I and SA  and Sierra de Gúdar (SG) [In this study, we provide data on the distribution of the two social forms  of the ant dar (SG) , 11, 20.dar (SG) . This sudar (SG) , 50 for L. acervorum . In contrast, during the last interglacial populations would have fragmented and declined.Patterns of genetic diversity and genetic structure in is”; see , 56 for  species , 17 and AP) and the occurrence of populations with high vs. low admixture  are in accordance with the existence of multiple refugia and varying connectivity among them throughout the late Pleistocene. In contrast, mtDNA data did not reveal a pronounced genetic differentiation among Iberian populations.Our molecular analysis supports such a scenario: on a local scale, microsatellites suggest no current gene flow between inner Iberian populations. In addition, the patchy distributions of private alleles , a bird characteristic of Eurasian coniferous forests [The westernmost Cantabrian population (SNW II) provides a notable exception to this pattern. It shows a distinct mtDNA haplotype and forms a distinct genetic cluster in the multi-locus microsatellite data, suggesting a longer period of evolution in isolation. This resembles the situation in the capercaillie  did not provide clear evidence for historical changes in effective population sizes. In contrast, M-ratios in microsatellites were far lower than the critical M value of 0.68  that are reasonably large for L. acervorum . In addition, MIGRATE-N analysis confirmed the occurrence of bottlenecks in all seven populations, while excess heterozygosity confirmed recent bottlenecks in only two populations from the Iberian system (SA and SG). The different results between tests can be explained by differences in test procedures and the low power of the heterozygosity excess test due to low sample size or deviations in mutation models  in all sion see  and refeL. acervorum across Europe [L. acervorum in southern and Central France  among Iberian populations showed here for the first time, mtDNA sequence data did not reveal any spatial-genetic structure. This matches former studies on s Europe , 20, 62.s Europe , 63–67. L. acervorum shifted its range towards more suitable habitats in the surrounding mountains and their foothills, while at the same time populations of the second refugium would have expanded their range at least towards Massif Central and western Alps. A closely related haplotype from England suggests a direct connection to the first French refugium  recolonization of the central and western Pyrenees and western Alps from refugial lowlands in between and (ii) of the eastern Pyrenees from the unglaciated foothills south-east and east of it [Subsequent to the late glacial (post-10 ka BP), the first French refugium may have started to fragment and st of it .L. acervorum still could maintain gene flow between unglaciated parts of the eastern Pyrenees (PY I) and mountains of the Iberian System (e.g. via a network of suitable habitat patches in the Ebro basin). Subsequently, gene flow gradually broke down in parallel with the increasing aridification and the decline of pinewoods in the Ebro basin during the second half of Holocene [Similar to the latter scenario, our analysis revealed a differential contribution of the first French refugium and the inner Iberian refugial system to the postglacial recolonization of Pyrenees not just in colonization routes but also in patterns of gene flow by both genetic markers. In contrast to the French refugium, inner Iberian populations share no haplotypes with the Pyrenees (in particular the eastern Pyrenees), while microsatellite data indicate historical gene flow between inner Iberia and eastern Pyrenees, but no or only very restricted gene flow between the western Pyrenees and inner Iberian populations. These patterns suggest that during the early Holocene Holocene –71. The Holocene , 72, 73.L. acervorum in the Iberian Peninsula, the genetic relationship among its two social phenotypes and the recolonization of its Western-Palearctic range from glacial refugia north of the Pyrenees. First, our analyses show a lack of reproductive isolation between both social forms, which indicates that behavioural flexibility rather than a hard-wired genetic basis is underlying variation in social phenotype. Second, we demonstrate the occurrence of substantial genetic structure, which is congruent with the complex Iberian topography and SW-European climate history. Moreover, our results highlight the vulnerability of L. acervorum in Iberian mid Mountain ranges to climate change and human induced climatic warming in particular, where the species inhabits suitable microhabitat patches over 1500 m a. s. l. only. A complete picture of the postglacial migration of this Holarctic ant with samples from across its whole range in Eurasia and Northern America as well as new marker sets might help to better understand the dynamics of centre-to-periphery pattern of genetic variability and the history of boreal insect species with high dispersal capacity.Our study gives important insight into the evolutionary and demographic history of


Drug response variability observed amongst patients is caused by the interaction of both genetic and non-genetic factors, and frequencies of functional genetic variants are known to vary amongst populations. Pharmacogenomic research has the potential to help with individualized treatments. We have not found any pharmacogenomics information regarding Uygur ethnic group in northwest China. In the present study, we genotyped 85 very important pharmacogenetic (VIP) variants (selected from the PharmGKB database) in the Uygur population and compared our data with other eleven populations from the HapMap data set.CYP3A5 rs776746, VKORC1 rs9934438, and VKORC1 rs7294 were most different in Uygur compared with most of the eleven populations from the HapMap data set. Compared with East Asia populations, allele A of rs776746 is less frequent and allele A of rs7294 is more frequent in the Uygur population. The analysis of F-statistics (Fst) and population structure shows that the genetic background of Uygur is relatively close to that of MEX.Through statistical analysis, we found that Our results show significant differences amongst Chinese populations that will help clinicians triage patients for better individualized treatments. Reactions to the same drug differ significantly among individuals. Thus, analyzing a drug’s safety and efficacy is complicated, causing difficulties in finding new treatments for major diseases. Inherited differences in individual drug-metabolizing enzymes are typically monogenic traits, and their influence on the pharmacokinetics and pharmacologic effects of medications are determined by the importance of the polymorphic enzymes for the activation or inactivation of drug substrates . Pharmachttp://www.pharmgkb.org). In total, there are 126 VIP variants that occur in 44 different genes and variously code for cytochrome P450 oxidases, drug targets, drug receptors, and drug transporters.Recent studies have shown that certain genes have close relationships with the outcomes of drug therapy and that different genotypes may determine how the patient responds to a drug. These gene variants are called very important pharmacogenetic (VIP) variants , and areIndividual responses to medications vary significantly among different populations, and great progress in understanding the molecular basis of drug actions has been made in the past 50 years. The field of pharmacogenomics seeks to elucidate inherited differences in drug disposition and effects. While we know that different populations and ethnic groups are genetically heterogeneous, we have not found any pharmacogenomics information regarding minority groups, such as the Uygur ethnic group in northwest China.The Uygur is an ethnic group primarily located in the Xinjiang Uygur Autonomous Region of China. The Uygur is one of China’s largest ethnic groups, with a long history in the region and distinct culture and traditions. They were originally a nomadic Turkish people in north and northwestern China. The Uygur language is a Turkic language very similar to Turkish.In this study, we aimed to identify the allele frequencies of VIP variants in the Uygur and to determine the difference in allele frequencies between the Uygur and 11 populations from the HapMap data set. The results of this study will extend our understanding of ethnic diversity and pharmacogenomics, and enable medical professionals to use genomic and molecular data to effectively implement personalized medicine in the future.We recruited a random sample of unrelated Uygur adults from the Xinjiang Region of China. The subjects selected were judged to be of good health and had exclusively Uygur ancestry for at least the last three generations. Thus, the subjects were thought to be representative samples of the Uygur population with regard to ancestry and environmental exposures. Blood samples were taken according to the study protocol, which was approved by the Clinical Research Ethics of Northwest University, Tibet University for Nationalities, Xinjiang Medical University, and the people’s hospital of Xinjiang Uygur Autonomous Region. Signed informed consent was also obtained from each participant enrolled in the study. Based on the abovementioned inclusion criteria, 96 randomly-selected, healthy, unrelated Uygur individuals were recruited from the Xinjiang Province.We selected genetic variants from published polymorphisms associated with VIP variants from the PharmGKB database. We designed assays for the 85 genetically-variant loci in 37 genes that formed the basis for our our analyses. We excluded loci if we could not design an assay. We extracted genomic DNA from peripheral blood obtained from the subjects using the GoldMag-Mini Whole Blood Genomic DNA Purification Kit  according to the manufacturer’s protocol. The DNA concentration was measured with a NanoDrop 2000C spectrophotometer . The Sequenom MassARRAY Assay Design 3.0 software  was used to design multiplexed single nucleotide polymorphism (SNP) MassEXTEND assays . SNP genhttp://hapmap.ncbi.nlm.nih.gov/biomart/martview/e4f42d4d0acde5ea6c35312381c1e461. The eleven populations included those of (1) African ancestry in Southwest USA (ASW); (2) Utah, USA residents with Northern and Western European ancestry from the CEPH collection (CEU); (3) Han Chinese in Beijing, China (CHB); (4) Chinese in metropolitan Denver, CO, USA (CHD); (5) Gujarati Indians in Houston, Texas, USA (GIH); (6) Japanese in Tokyo, Japan (JPT); (7) Luhya in Webuye, Kenya (LWK); (8) Mexican ancestry in Los Angeles, California, USA (MEX); (9) Maasai in Kinyawa, Kenya (MKK); (10) Toscani in Italy (TSI); and (11) Yoruba in Ibadan, Nigeria (YRI).The genotype data of individuals from eleven populations were downloaded from the International HapMap Project web site (HapMap_release127) at χ2 test. The validity of the frequency of each VIP variant in the Uygur data was tested by assessing the departure from HWE using an exact test. We calculated and compared the genotype frequencies of the variants in the Uygur data with those in the eleven populations separately using the χ2 test. All p values obtained in this study were two-sided, and Bonferroni’s adjustment for multiple tests was applied to the level of significance, which was set at p < 0.05/(85*11). The purpose of the χ2 test was to discover sites with significant differences. Afterwards, we obtained the SNP allele frequencies from the ALleleFREquency Database , and analyzed the global patterns of genetic variation at specific loci.We used Microsoft Excel and SPSS 17.0 statistical packages  to perform Hardy–Weinberg Equilibrium (HWE) analysis and the http://pritchardlab.stanford.edu/structure.html).Some studies point out that population genetic structure is central to the study of human origins, DNA forensics, and complex diseases . We beliWe used the Arlequin ver 3.1 software to calculate the value of Fst to infer the pairwise distance between populations. Pairwise Fst values were calculated on the primary, 84 SNP dataset in Arlequin3.5  using ReTo analyze the genetic structure, the Bayesian clustering algorithm-based program Structure ver. 2.3.1 was used to assign the samples within a hypothetical K number of populations as proposed by Pritchard et al. . AnalyseBasic information about the selected VIP loci in Uygur is listed in Table χ2 test with the Bonferroni correction for multiple hypotheses and multiple comparisons, we found 0, 1, 3, 5, 7, 9, 10, 13, 16, 17, and 25 different loci in the frequency distributions when the Uygur population was compared to the TSI, MEX, GIH, CHD, CEU, CHB, ASW, JPT, MKK, LWK, and YRI populations, respectively. Three loci  located in the CYP3A5 and VKORC1 genes were different in the Uygur population when compared with most of the populations  variants in the Uygur population are quite different from that in other ethnic groups. We also found that the genetic backgrounds of the Uygur and MEX populations are similar, via Fst calculations and analysis of population structure.The genotype frequencies of VIP variants differs among human populations. In this study, we genotyped the variants related to drug response in the Uygur ethnic group and compared the genotype frequencies with those in eleven populations. From the CYP3A5, localized on chromosome 7q21-q22.1, encodes one of the CYP3A subfamily of enzymes [CYP3A5 is designated as CYP3A5*3. CYP3A5*3 status is determined by the derived allele at rs776746, a change from A to G located in intron 3. This change creates a cryptic splice site that results in altered mRNA splicing, which may alter the reading frame and result in a premature termination codon and hence a nonfunctional protein [ enzymes . The mos protein , 15.Individuals with CYP3A5*1/*1 and *1/*3 expresser genotypes metabolize some CYP3A substrates more rapidly than CYP3A5*3/*3 nonexpressers. One such substrate is tacrolimus, which is used to prevent post-transplantation organ rejection. CYP3A5*1 carriers have a higher rate of tacrolimus clearance than those with the other genotypes, with *1/*1 individuals having a higher clearance than *1/*3 individuals, who have higher clearance than *3/*3 individuals . In ideaCYP3A5 expressers are more likely to require higher CBZ maintenance doses than nonexpressers (GA + AA vs. GG). The CYP3A5 genotype may also have dose-dependent effects on ABT-773 plasma levels. CYP3A5 expressers have a higher rate of ifosfamide N-demethylation in the liver and kidney and of cyclosporine A metabolism in the kidney [Carbamazepine (CBZ), a first-line antiepileptic drug, has been widely prescribed for the treatment of partial and generalized tonic-clonic seizures. It has been reported that CYP3A5*3 is associated with CBZ pharmacokinetics in Japanese , Korean e kidney .CYP3A5. Its frequency varies widely across human populations. In white populations, the estimated allele G frequency of CYP3A5*3 is 0.82–0.95, in African American is 0.33, in Japanese is 0.85, in Chinese is 0.65, in Mexicans is 0.75, in Pacific Islanders is 0.65, and in Southwest American Indians is 0.4 [CYP3A5*3 is the most frequent and well-studied variant allele of s is 0.4 . In our VKORC1  gene, which encodes vitamin K epoxide reductase complex subunit 1, located on chromosome 16, includes three exons [The ee exons . The 117ee exons .VKORC1 genotype. Reitsma et al. showed in 2005 that Dutch patients carrying one or two variant alleles for the 1173 polymorphism required a 28 % and 47 % lower dose, respectively, when compared with wild types [VKORC1 polymorphism on phenprocoumon dose requirements. Patients with a CT genotype at position 1173 had a 10 % lower dose and patients with a TT genotype a 52 % lower dose than wild types (CC) [VKORC1 allele was 19–31 % lower than in wild type users, and 43–51 % lower in users with two variant alleles [Several authors have shown that acenocoumarol dose is also influenced by ld types . In Greeld types . Similarld types , in a Seld types . Reitsmapes (CC) . This ef alleles .Warfarin is a commonly prescribed oral anticoagulant, used to prevent thromboembolic diseases in patients with deep vein thrombosis, atrial fibrillation, recurrent stroke, or heart valve prosthesis . Some stVKORC1 polymorphisms can significantly alter warfarin pharmacodynamics and maintenance dose requirements. Patients with the 1173T (rs9934438) allele require a lower warfarin dose compared with 35 mg/week for the wild-type carriers [In summary, carriers . Patientcarriers , 33. In The genotype frequencies of VIP variants affect a populations’ response to drugs to a great extent. Determination of the genotype distribution and frequencies of VIP variants in a population is necessary to provide a theoretical basis for safer drug administration and an improved curative effect. Our results complement the currently available data on the Uygur ethnic group in the pharmacogenomics database, and furthermore, provide a basis for safer and more effective drug administration in the Uygur. However, our sample size of Uygur is relatively small, and further investigation in a larger cohort of Uygur is necessary to ascertain the generalizability and extrapolation of our results to these and other conditions in the Uygur population.


Acrocephalus sechellensis). We found low and stable microsatellite and MHC diversity in the source population and evidence for only a limited loss of either type of diversity in the four new populations. However, we found evidence of significant, but low to moderate, genetic differentiation between populations, with those populations established with fewer founders clustering separately. Stochastic genetic capture (as opposed to subsequent drift) was the main determinant of translocated population diversity. Furthermore, a strong correlation between microsatellite and MHC differentiation suggested that neutral processes outweighed selection in shaping MHC diversity in the new populations. These data provide important insights into how to optimize the use of translocation as a conservation tool.Translocations are an increasingly common tool in conservation. The maintenance of genetic diversity through translocation is critical for both the short- and long-term persistence of populations and species. However, the relative spatio-temporal impacts of translocations on neutral and functional genetic diversity, and how this affects genetic structure among the conserved populations overall, have received little investigation. We compared the impact of translocating different numbers of founders on both microsatellite and major histocompatibility complex (MHC) class I diversity over a 23-year period in the Seychelles warbler ( The translocation of populations for species conservation and ecosystem restoration is an increasingly common conservation tool . HoweverMany biotic and abiotic factors can influence translocation success, including genetic diversity  and willMost studies on the genetic impacts of translocation investigate diversity at putatively neutral markers such as microsatellites e.g. . This keHow many individuals to translocate is a difficult question to answer, although it is a central concern for conservationists. Guidelines recommend that ‘adequate’ numbers of founders should be taken IUCN/, althougAcrocephalus sechellensis), an isolated island species. The objective was to compare the spatio-temporal impact of translocation on neutral and functional diversity within and across populations. First, we characterize neutral and functional genetic diversity in the source population and how that has changed over time. Second, we compare predicted vs. observed levels of genetic capture across different founder sizes. Third, we quantify genetic diversity in the four new translocated populations, including how that compares with variation in the source population and if it changes over time. Fourth, we quantify levels of genetic differentiation among all the Seychelles warbler populations now in existence. Fifth, we estimate the effective population size for each population. We discuss the implications of our findings for the use of translocation in the conservation of this and other endangered species.Here, we present data from a study spanning 23 years and involving four translocations of different founder sizes of the Seychelles warbler  existing on Cousin Island . This population has been under intense study since 1986 . Rare alleles (frequency <0.01) were verified by two or more independent PCRs from different samples. We tested for deviations from Hardy–Weinberg equilibrium and linkage disequilibrium between loci using genepop version 4.1 (cervus version 3.0 (E) using arlequin version 3.5  in arlequin by entering the nucleotide sequence and number of individuals carrying each allele as haplotype data, following Variation at exon 3 of MHC class I, which codes for the peptide-binding region involved in antigen recognition , was scrP value was calculated as the proportion of times the difference between the means of the resampled data sets were equal to or greater than the observed difference between earliest and latest years. Differences in microsatellite variation between years were also tested using a global differentiation exact test  with 1000 repetitions. As we did not have source population diversity data prior to every translocation and diversity did not change over time within islands (see Study populations), we used the 2011 sample as a proxy for pretranslocation diversity at all four genetic capture events. A proportionally greater loss of genetic diversity is expected from microsatellite loci of higher initial diversity (n = 30) and ‘diverse loci’ only (n = 7), defined as possessing ≥4 alleles, a threshold that separates out the ca. 25% most polymorphic loci in our data set. As mean MHC/ind varied over time (see Study populations), a second MHC curve was constructed using the 1993 Cousin sample (n = 52) to check the accuracy of capture estimates for the earlier translocations to Aride (1988) and Cousine (1990). The rarefaction curves were then used to estimate the expected allelic richness captured during the translocations by taking the mean of the 1000 rarefaction repetitions for each number of translocated birds . To test model accuracy, we compared the observed microsatellite allelic richness captured for Denis and Frégate (where we had complete founder samples) with the distribution of expected values generated by rarefaction. A one-tailed P value was obtained by calculating the percentile of simulated data in which the observed mean was located.To model the expected genetic capture at each translocation, we constructed rarefaction curves of observed allelic richness using the 2011 Cousin sample ; hence, only FST is reported. The relationship between pairwise microsatellite and MHC FST values was assessed using a Mantel test. A Bayesian algorithm was also implemented in structure version 2.3 (K). As all islands have recent common ancestry, limited differentiation was expected, so samples from the latest sampling period (2011) were used along with a model of no admixture, prior information on sampling location and correlated allele frequencies, features which are suited to detecting subtle structure  of each population were obtained using two different methods: (i) We used the approximate Bayesian computation approach implemented in ONeSAMP (e priors of 2–150 for each island. This method bases Ne on a single population sample (from 2011); (ii) We used a linkage disequilibrium approach in LDNE  ≥0.1 more than twice except for locus Ase3 . Excluding the Ase3 locus did not qualitatively alter the results (data not shown). All 30 loci were retained in the final analyses.Microsatellite genotypes were compiled for 658 individuals and MHC genotypes for 581 individuals across the five populations. All populations were in Hardy–Weinberg equilibrium at all microsatellite loci. Linkage disequilibrium was detected in nine different loci pairs across the five islands after sequential Bonferroni correction (26 of 4933 pairwise comparisons significant). However, inconsistency of patterns between and within populations suggests they are not truly linked. Null allele frequency estimates were also inconsistent across years within each island, with no locus frequency  and the global exact test found no overall differentiation across years (P > 0.99). Mean MHC/ind increased from 1993 (3.93 ± 0.19) to 2011 . Full diversity estimates are given in TableMicrosatellite diversity in the source population on Cousin had an overall mean (± SE) P = 0.36, diverse loci: P = 0.37, Fig.P = 0.35, diverse loci: P = 0.35), indicating a good fit of the genetic capture models. It is therefore reasonable to assume that the rarefaction curve estimates of genetic capture for 29 individuals  provide an accurate representation of genetic diversity initially captured from the source population during the translocations to Cousine and Aride. Across all 30 loci, we observed a loss of eight and ten alleles in the Denis and Frégate translocations, respectively. On Denis, all losses were of rare alleles (frequency < 0.01 in source population) from diverse loci, and on Frégate, two alleles were also lost from less diverse loci, including the biallelic Pte24-CEST locus, leading to fixation of a single allele in this population. The lack of founder genotypes or complete population sampling for Aride and Cousine means we could not directly determine the exact roles of genetic capture vs. subsequent drift in allele loss for these two translocations.Resampling from the source population, the genetic capture model estimated that 95% (3.07 ± 0.01) of the overall microsatellite allelic richness would be captured with the translocation of 59 individuals, but only 87% (4.86 ± 0.01) of allelic richness for diverse loci. Virtually identical values were observed for 58 individuals . There was no difference between expected and observed allelic richness translocated to Frégate  to ca. 25 (1993 sample) individuals would be required for complete sampling of known class I variation . There was no difference in mean MHC/ind  between islands (pooled samples). Similarly, there were no differences in MHC/ind across time within each translocated population .Diversity estimates for translocated populations are given in TableFST analyses revealed moderate differentiation between the populations on Aride and Cousine . Subtle differentiation was also detected between all other pairwise comparisons  except for between Cousin and Frégate (P = 0.73). The MHC FST analyses also revealed subtle differentiation between Cousine and: Aride , Denis  and Cousin . Pairwise FST are given in Table S2 (Supporting information). A positive correlation was found between microsatellite and MHC FST . When visualized, the islands of Cousin, Denis and Frégate contained a mixture of both clusters, but clear segregation of the clusters was observed in the Aride and Cousine populations  appeared to be the main determinant of translocated population diversity. A small number of rare alleles from neutral markers were lost during translocation, but no statistically significant loss of either neutral or functional diversity was detected in any of the four new populations. Further, diversity in these new populations remained stable over time. Importantly, however, the populations established with a lower number of founders (Aride and Cousine) were central to the low to moderate levels of genetic differentiation observed among populations, indicating that translocations produced subtle changes in allele frequencies, if not in levels of diversity ca. 95% of neutral diversity (87% for diverse loci), but the earlier translocations of 29 birds to Aride and Cousine only captured ca. 91% (85% for diverse loci). In line with this, we found a slight, albeit nonsignificant, decrease in both allelic richness and heterozygosity in the Aride and Cousine populations  involving even smaller numbers of founders (lowest n = 16), although the source population also had lower initial variation. Our result supports their suggestion that long-term population history (i.e. previous severe bottlenecks) may negate any contemporary bottleneck effects caused by small numbers of founders. This is simply because if all but the commonest alleles are already lost, there is little variation left to lose in subsequent bottlenecks. However, this will only be true for the most extreme cases of genetically depauperate populations (as in the saddlebacks). The Seychelles warbler is severely bottlenecked, and yet we still find some loss of variation during translocations, indicating that care – and suitably high numbers of founders – must be taken to avoid further genetic impoverishment of translocated populations. Furthermore, statistical and biological significance may not concur, as rare alleles can play important roles in evolution  in the source population, in line with theoretical expectations , Chatham Island black robins (Petroica traversi), cheetah (Acinonyx jubatus) and falcons , survive despite extremely low MHC variability  estimates between the methods means caution should be exercised with interpretations. Both the severity and duration of bottleneck events will affect estimates of Ne . Further, each population has experienced rapid growth over many generations , which would limit further reduction in Ne. The general scale and order of Ne estimates across populations therefore appear logical in relation to known history, as well as founder and census population sizes. Our results show that while the translocations have clearly been very successful in massively expanding the overall Seychelles warbler population and range without significant extra loss of diversity, most of the estimates of Ne for our populations fall below any recommended minimum viable sizes (50–5000, The variability in effective population size (Nes of Ne . Althoug50–5000, . This an50–5000, .The demographic history of the Seychelles warbler is typical of many endangered species  and requ