Male-specifically inherited Y-STRs, harboring the features of haploidy and lack of crossing over, have gained considerable attention in population genetics and forensic investigations. Goldeneye® Y-PLUS kit was a recently developed amplification system focused on the genetic diversity of 36 Y-chromosomal short tandem repeats (Y-STRs) in East Asians. However, no population data and corresponding forensic features were reported in China. Here, 36 Y-STRs were first genotyped in 400 unrelated healthy Tai-Kadai-speaking Bouyei male individuals. A total of 371 alleles and 396 haplotypes could be detected, and the allelic frequencies ranged from 0.0025 to 0.9875. The haplotype diversity, random match probability and discrimination capacity values were 0.9999, 0.0026 and 0.9900, respectively. The gene diversity (GD) of 36 Y-STR loci in the studied group ranged from 0.0248 (DYS645) to 0.9601 (DYS385a/b). Population comparisons between the Guizhou Bouyei and 80 reference groups were performed via the AMOVA, MDS, and phylogenetic relationship reconstruction. The results showed that the population stratification was almost consistent with the geographic distribution and language-family, both among Chinese and worldwide ethnic groups. Our newly genotyped Bouyei samples show a close affinity with other Tai-Kadai-speaking groups in China and Southeast Asia. Our data may provide useful information for paternal lineage in the forensic application and population genetics, as well as evidence for archaeological and historical research. Since the Y-chromosomal short tandem repeats (Y-STRs) were discovered in 1992, they have been regarded as valuable markers in forensic analysis, population genetics, and evolutionary studies . In receChina is a multi-ethnic country with 55 minorities. The Bouyei, which has a population of approximately 2.87 million in the 2010 census, is one of the most widely distributed ethnic groups in southwestern China. Many Bouyei people live in Guizhou province, accounting for 97% of the total Bouyei population[Many published population genetic data Guizhou Bouyei were focused on autosomal-STRs, X-ChromPeripheral blood samples were collected from a total of 400 unrelated healthy Bouyei people residing in Guiyang, Guizhou province (Southwest China). The geographic distribution of the studied populations is shown in Thirty-six Y-STR loci were co-amplified in one multiplex PCR reaction on a GeneAmp PCR System 9700  from the FTA card, using Goldeneye® Y-PLUS kit  based on the manufacturer’s instructions. DNA was amplified using 10μL reaction volume, which contained 2ul reaction mix, 2μL primers, 1μL A-Taq DNA polymerase and 6μL sdH2O. PCR conditions were 95°C for 2 min, followed by 30 cycles of 94°Cfor 1 min, 60°Cfor 45s, and 72°Cfor 45s, and a final extension at 60°C for 45min. PCR products were separated on the ABI 3730 Genetic Analyzer  with the POP-7 polymer. The electrophoretic sampling mixture included 1 μL amplified product 10 μL Hi-Di formamide and 1 μL ORG500 size standard. Standard DNA templet 9947A was analyzed for positive control, and sdH2O for negative control as well. Allele nomenclature was conducted using the GeneMapper ID-X v.1.4 software.2), where n was the total number of samples and Pi was the frequency of the ith haplotype; GD = (n/n − 1) (1 − ∑ Pi2), where n was the total number of samples and Pi was the frequency of the ith allele. Haplotype match probability (HMP) was calculated according to HMP = ∑ Pi2, where Pi was the frequency of the haplotype. Discrimination capacity (DC) was calculated based on the formula: DC = k/Σ(Pi×n), where k was the number of haplotypes, Pi was the frequency of its haplotype, n was the total number of individuals.Allele frequencies of 36 Y-STR loci and haplotype frequencies were calculated using the direct counting method. Forensic statistical parameters of gene diversity (GD) and haplotype diversity (HD) were calculated using the Nei’s formula: HD =  between Guizhou Bouyei and reference populations extracted from the Y Chromosome Haplotype Reference database YHRD, includiThis study strictly followed ISFG recommendations on the analysis of the DNA polymorphisms and nomenclature and guidWe genotyped 36 Y-STRs in a total of 400 Guizhou Bouyei individuals successfully , and a tTo reveal the partial population substructure between large-scale geographic divisions, Rst values between our studied subject and 36 populations with 8623 haplotypes from Asia, Europe and Africa were calculated based on 27 Y-STRs. As shown in Subsequently, to further explore the partial population substructure between large-scale geographic divisions, we calculated pairwise Rst values between our subject and 17 meta-populations  with 9838 haplotypes from Asia, Europe, Africa and America, as showed in 9303 Y-STR haplotypes from 9 Han Chinese populations were used to investigate the degree of differentiation between our studied subject and 9 Han Chinese populations via analysis of molecular variance (AMOVA), 8010 Y-STR haplotypes from 18 populations were employed to calculate the pairwise Rst values as showed in ® Y, AmpFlSTR® Yfiler, PowerPlex® Y23 and AmpFlSTR® Yfiler Plus), and other two RM Y-STRs (DYF404S1 and DYS449) and one multi-copy loci (DYS527). Thus, the DC value of our system (0.9900) was higher than the 27 Y-STRs (Yfiler Plus) (0.9825), demonstrating that it was highly informative and polymorphic, and exhibited great efficiency in Guiyang Bouyei populations investigated in this study. However, there were still five loci with a low level of polymorphism, including DYS645 (0.0248), DYS438 (0.3935), DYS391 (0.4089), DYS596 (0.4885), DYS437 (0.4890), which seemed not to be suitable for forensic purpose in this population.In our study, we used the Goldeneye® Y-Plus kit including 36 loci to investigate the Guiyang Bouyei  population, which contained all markers of previous commercial kits  and have a high power of discrimination (DC: 0.9900). Additionally, the genetic relationships between Guizhou Bouyei and 61 ethnic populations and 17 meta-groups based on 27 Y-STRs showed that the population stratification was almost consistent with geographic distribution and language-family, both among Chinese and worldwide ethnic groups.S1 Table(XLSX)Click here for additional data file.S2 Table(XLSX)Click here for additional data file.S3 Table(XLSX)Click here for additional data file.S4 Table(XLSX)Click here for additional data file.S5 Table(XLSX)Click here for additional data file.S6 Table(XLSX)Click here for additional data file.S7 Table(XLSX)Click here for additional data file.


Acyrthosiphon svalbardicum in Spitsbergen, the main island of the Svalbard archipelago, and compared its genetic structure with that of its close relative Acyrthosiphon brevicorne, sampled in the top of Scandinavian mainland. We found that A. svalbardicum is common but heterogeneously distributed along the west coast of Spitsbergen. We recorded this species up to 79°12’, which constitutes the northernmost location for any aphid. Genetic structure examined using microsatellite markers showed more pronounced spatial differentiation in A. svalbardicum than in A. brevicorne populations, presumably due to reduced dispersal capacities in the former species. Although populations of A. brevicorne and A. svalbardicum were well-delineated at nuclear loci, they shared similar cytoplasmic DNA haplotypes as revealed by sequence analysis of two DNA barcodes. These results raise questions about whether these two taxa are different species, and the colonization sources and history of the Svalbard archipelago by A. svalbardicum.Arctic ecosystems are subjected to strong environmental constraints that prevent both the colonization and development of many organisms. In Svalbard, few aphid species have established permanent populations. These high arctic aphid species have developed peculiar life-history traits such as shortened life cycles and reduced dispersal capacities. Here, we present data on the distribution and population genetics of  Species are all limited in their geographical distribution. In some cases, geographic ranges are restricted to small areas and are stable over long periods of time, while in others, they include large territories and shift very frequently . Many hySpitsbergen (70° to 80° North) is the main island of the Svalbard archipelago and is about 700 km from the top of the Scandinavian mainland. The climate of this archipelago is characterised by sub-zero temperatures for most of the year, and only a short summer season allows the growth and reproduction of arthropods . The harAcyrthosiphon svalbardicum, which feeds exclusively on Dryas octapetala (Rosaceae), Sitobion calvulum, which feeds primarily on Salix polaris , and a Pemphigus sp., which reportedly feeds on roots of Poa spp. (Poaceae)  and ΔK calculated on 10 iterations for K = 2 to K = 30 indicated an optimal clustering into three distinct groups which correspond to well-defined geographic zones. At K = 3  comprised most A. svalbardicum individuals from the Isfjorden zone, and the third cluster included most A. svalbardicum individuals from the Ny Ålesund zone. At K = 4 , another (C4) formed with A. svalbardicum individuals from the north side of Kongsfjorden (including islands scattered in the fjord). At K = 5 : mean expected heterozygosity and allele richness were 0.515 and 3.87, respectively for A. brevicorne populations from Lapland vs. 0.430 and 3.04 for A. svalbardicum populations from Spitsbergen. The combination of the eight microsatellite loci allowed the discrimination of a large number of multilocus genotypes (MLGs). Most populations had G/N ratios near or equal to 1, meaning that each individual bore a unique MLG  was the only exception with a G/N of 0.30. This population also had the lowest expected heterozygosity and allele richness . Populations showed no heterozygote excess, while about a third of them showed a heterozygote deficit. As expected, populations in heterozygote deficit also had positive FIS values, with the two A. brevicorne populations from Abisko (Sweden) showing the highest values (above 0.3). Again, A. svalbardicum population from Camp Zoé 2004 was special in that it displayed a very high negative FIS value (−0.281). Overall, FIS values did not vary between the two aphid species . Linkage disequilibria were frequent among pairs of loci, ranging from 5% to 43% of the tests, and the extent of linkage disequilibrium did not differ according to aphid species .Populations of  Lapland . Mean exique MLG . The A. A. brevicorne and A. svalbardicum. However, the divergence between these haplotypes was very small and not associated with geographic origin. As a result, samples from A. brevicorne and A. svalbardicum grouped in the same clade, very distinct from the outgroups such as A. pisum. For gnd sequences, all samples from A. brevicorne and A. svalbardicum shared the same haplotype. Again, this haplotype was very divergent from closely related outgroups. Not surprisingly, when sequences from both COI and gdn were concatenated, samples from A. brevicorne and A. svalbardicum grouped into the same clade and were well differentiated from the related species A. pisum, as seen in The sequence analysis of COI fragment revealed 11 haplotypes among the samples from A. svalbardicum in the summer, we were able to show that this aphid was rather common but heterogeneously distributed along the west coast of Spitsbergen. At a large scale, some zones were free of aphids such as beyond certain latitudes, in isolated places such as some islands or for other reasons we could not test here, e.g., snow cover depth [Dryas unoccupied by aphids usually coexisted with occupied patches without obvious reasons. This heterogeneous distribution of the A. svalbardicum populations confirmed previous studies but does not allow us to substantiate the hypothesis that site occupancy increased with geographical distance from the fjord mouth [A. svalbardicum could not establish populations beyond 79°12′, which constitutes its northernmost limit and the most north location for any aphid. It is likely that beyond this latitude, prevailing climatic conditions prevent aphid populations from persisting and growing due to physiological constraints.From our field surveys in Svalbard, during which time we extensively sampled er depth . At a smrd mouth . From ouDryas octopetala, the exclusive host plant for A. svalbardicum and A. brevicorne, colonised Svalbard from Russian after the last glaciation [A. svalbardicum originated from postglacial dispersal either from North American or European refugia. The genetic analysis as here assessed using microsatellite markers, showed no marked increase in divergence between populations from A. brevicorne and from A. svalbardicum: the populations from Lapland were differentiated from those from Svalbard but differentiation coefficients (FST) were not higher than between some distant Spitsbergen populations. In addition, analysis using two barcodes, which generally differentiate aphid taxa with good confidence [A. brevicorne and A. svalbardicum. Given the fact that the two species share Dryas as their exclusive host plant and differ only slightly in terms of their morphology [A. svalbardicum from mainland Scandinavian populations, although this hypothesis needs further supports.The Svalbard archipelago was completely covered by ice during the last glacial maximum, which occurred 15,000 years ago, except for some small mountain areas in the northwest . Althougaciation . We may nfidence ,38, did rphology ,16, it iA. brevicorne and A. svalbardicum generally showed as many multilocus genotypes as sampled individuals . This means that the set of markers used had sufficient power to resolve most of the genotypic diversity present locally. In the rare cases where several individuals shared the same multilocus genotype, we may have sampled individuals belonging to the same genetic clone. This is possible for A. brevicorne populations because this species produces several clonal generations during its annual life-cycle [A. svalbardicum, which generally produces only two clonal generations a year, the probability of sampling two individuals from the same clone in the same patch is not zero. However, this could hardly explain the situation of Camp Zoé in 2004, where many individuals with the same MLGs have been found  and may also prevail in A. brevicorne (despite the possibility of this species producing winged forms in response to crowding). Whether A. brevicorne and A. svalbardicum populations suffer from inbreeding depression has yet to be investigated.Heterozygote deficit and linkage disequilibrium were frequent in populations of both A. brevicorne, A. svalbardicum populations showed much stronger spatial differentiation (more than twice as great), while temporal variation, when assessed, was generally modest in both aphid species. We found that populations of A. svalbardicum were highly differentiated even at distances around 100 metres. This marked spatial genetic structure is not surprising in such a species with limited dispersal capabilities and high extinction probabilities. From our genetic structure analysis, it appears that geographic distances as well as physical barriers such as fjords and glaciers contribute to the observed spatial pattern of genetic variation in A. svalbardicum populations. Isfjorden populations formed a single genetic cluster, suggesting they derived from the same colonization event and still maintain some connectivity. By way of contrast, populations from the Ny Ålesund zone split into three distinct genetic clusters, which seem primarily isolated by physical barriers rather than by geographic distances. Populations from the small islands of Kongsfjorden were genetically related to each other and with other samples from the north part of the fjord. It is therefore, possible that island colonization may have been achieved by the rare winged forms of A. svalbardicum that have been only found so far in the north side of Kongsfjorden [A. svalbardicum from Krossfjorden, sampled at the northern limit of the species range, were strongly differentiated from the remaining A. svalbardicum populations, including the geographically closest ones . This differentiation likely results from a founder effect  followed by substantial inbreeding, as suggested above from within-population structure analysis.In comparison with sfjorden ,12. Biolsfjorden . The genA. svalbardicum, in comparison with its close related species A. brevicorne living in a relatively less harsh environment. Physiological constraints prevent aphid colonization beyond the range limit we detected for A. svalbardicum, although the temperature increase recorded in Svalbard in the last few decades might well favour population establishment further north [A. svalbardicum to extreme environment. Low dispersal apparently accounts for the overall strong genetic differentiation among populations, but again this could change if warming induces a sudden increase of wing morph production recently reported in Svalbard [A. svalbardicum requires further in-depth studies involving phylogeographic analyses of arctic and alpine populations of Acyrthosiphon sp. feeding on D. octopetala. This would allow for better inference of the source origins of A. svalbardicum populations that have colonised Svalbard. Finally, more work is needed to elucidate the mechanisms underlying the adaptation to the artic environment in both A. svalbardicum and A. brevicorne, which has led to such peculiar life cycles and traits.Very few genetic studies have so far been performed on terrestrial animals inhabiting the arctic environment. In the present work, we were able to assess the influence of the high arctic conditions on the population’s genetic structure of er north . At thisSvalbard ,12. The


Crop wild relatives (CWRs) contain genetic diversity, representing an invaluable resource for crop improvement. Many of their traits have the potential to help crops to adapt to changing conditions that they experience due to climate change. An impressive global effort for the conservation of various CWR will facilitate their use in crop breeding for food security.Brassica is listed in Annex I of the International Treaty on Plant Genetic Resources for Food and Agriculture. Brassica oleracea (or wild cabbage), a species native to southern and western Europe, has become established as an important human food crop plant because of its large reserves stored over the winter in its leaves.The genus Brassica cretica Lam. (Bc) is a CWR in the brassica group and B. cretica subsp. nivea (Bcn) has been suggested as a separate subspecies. The species Bc has been proposed as a potential gene donor to brassica crops, including broccoli, cabbage, cauliflower, oilseed rape, etc.Bc individuals, including two Bcn and two Bc. Demographic analysis based on our whole-genome sequence data suggests that populations of Bc are not isolated. Classification of the Bc into distinct subspecies is not supported by the data. Using only the non-coding part of the data , we find the gene flow between different Bc population is recent and its genomic diversity is high.We sequenced genomes of four Despite predictions on the disruptive effect of gene flow in adaptation, when selection is not strong enough to prevent the loss of locally adapted alleles, studies show that gene flow can promote adaptation, that local adaptations can be maintained despite high gene flow, and that genetic architecture plays a fundamental role in the origin and maintenance of local adaptation with gene flow. Thus, in the genomic era it is important to link the selected demographic models with the underlying processes of genomic variation because, if this variation is largely selectively neutral, we cannot assume that a diverse population of crop wild relatives will necessarily exhibit the wide-ranging adaptive diversity required for further crop improvement. Although many plant species are used in food and agriculture, only 30 crops account for the 95% of food production worldwide . DomestiAs wild ‘progenitors’ of crops continue to evolve under abiotic and biotic stresses, it is very important to conserve this resulting genetic biodiversity, which can be useful for agriculture (in situ conservation). Seed banks or germplasm collections are also important to preserve as another resource for agriculture (ex situ conservation). The total genome sequencing of CWRs may be used first to characterize wild populations and inform strategy for their conservation. On the other hand, analysis of the sequence can reveal genetic variation and important genetic characters that have been lost during domestication, and that could be transferred into crop species to support food security, climate adaptation and nutritional improvement . The reaPhytophthora infestans) from the wild potato Solanum demissum Lindl [Oryza rufipogon, a wild species of rice, to Oryza sativa [Hordeum spontaneum (wild barley) [Recent decades have seen some remarkable examples of introducing favored traits from CWRs into their respective domesticated crop plants. In most cases, these traits concern resistance to biotic stresses, such as resistance to late blight  .Brassica oleracea L. belongs to the family Brassicacea and is a very important domesticated plant species, comprised of many vegetable crops as different cultivars, such as cauliflower, broccoli, cabbages, kale, Brussels sprouts, savoy, kohlrabi and gai lan. Brassica oleracea includes wild cabbage, which is found in coastal southern and western Europe. The species has become very popular because of its high content of nutrients, such as vitamin C, its anticancer properties [operties  and the Brassica oleracea constitutes one of the three diploid Brassica species in the classical triangle of U (Nagaharu U. 1935) [B. rapa (L.) (genome: AA) with 10 chromosomes and B. nigra (L.) W. D. J. Koch (the black mustard) (genome: BB) with 8 chromosomes.U. 1935)  (genome:B. juncea (genome: AABB), B. napus L. (genome: AACC) and B. carinata (genome: BBCC). There is evidence for each of the Brassica genomes having undergone a whole-genome duplication [Brassicaceae-lineage-specific whole-genome triplication, which followed the divergence from the Arabidopsis lineage [These three closely related species gave rise to new allotetraploid species that are very important oilseed crops: lication , 12 and  lineage , 14.B. oleracea var. capitata and a genomic comparison with its very close sister species B. rapa. A total of 45,758 protein-coding genes were predicted, with mean transcript length of 1761 bp and 3756 non-coding RNAs . It is observed that there is a greater number of transposable elements (TEs) in B. oleracea than in B. rapa as a consequence of continuous amplification over the last 4 million years (MY), the time that the two species diverged from a common ancestor, whereas in B. rapa the amplification occurred mostly in the last 0.2 MY [In 2014, Liu et al.  reportedt 0.2 MY . MoreoveBrassica cretica Lam. , Brassica cretica [B. cretica is outcrossing (little deviation from Hardy-Weinberg equilibrium) and that populations on Crete have undergone extensive divergence at allozyme loci [B. cretica populations for several morphological traits [B. cretica populations have not been properly quantified, making it unclear whether the low gene flow alone could explain the population divergence, or whether local adaptation (divergent selection) must be invoked. Widén and colleagues [B. cretica populations, were consistent with non-adaptive differentiation combined with limited gene flow. However, allozymes may not provide accurate assessments of population structure and gene flow, since, at least one allozyme locus is under diversifying selection in a variety of species [B. cretica and concluded that current patterns of diversification in B. cretica mainly result from genetic drift.Among the Aegean islands, Crete is the largest and the most floristically diverse. It has experienced a much longer history of isolation compared to the smaller Aegean islands. Over two-thirds of all Greek plant species are found in Crete and it has the greatest proportion of endemic species in the Aegean area –18. Cret cretica  is hermayme loci . The geol traits , 24. Furl traits . However species , 26–28.  species  using nuBrassica cretica Lam. is a wild relative of many crops in the genus Brassica, proposed to be one of the ancestors of broccoli, Brussel sprouts, cabbage, cauliflower, kale, swede, turnip and oilseed rape. Since this species is thought to be a gene donor of many crops in the Brassica oleracea group, it might contain genes that are not present in the domesticated crops, as well as, a different set of resistance genes (R genes) that code for the intracellular immunity NLRs receptors (NOD-Like Receptors). Analysis of the NLRsome of wild species would potentially help us find which genes or loci are responsible for the recognition of effectors from important phytopathogens and thus create resistant plants in the field via transfer of these favored genes/loci [nes/loci .B. cretica to investigate mechanisms of diversification of four isolated B. cretica populations taking into consideration their genomic and subspecies variation. That analysis is based on alignment of sequence data against the reference genome of B. oleracea and is not dependent on de novo assembly of the B. cretica genome. Nevertheless, we also assembled the sequence data to generate draft assemblies of the four B. cretica genomes, which may serve as a useful resource for bioprospecting of traits for introgression into brassicaceous crops.Here, we perform genome-wide resequencing of four individuals of B. oleracea reference genome resulted in 54.8, 62.6, 63.6 and 39.5-fold average depths of coverage respectively. The alignments of resequencing reads versus reference genome were used for variant calling on which the demographic analysis is based (see below). The distribution of variants across the reference genome is summarized as a Circos plot in Fig. Sequencing of genomic DNA yielded 73.3 M, 83.3 M, 82.4 M and 53.1 M pairs of 300-bp reads respectively from individuals PFS-1207/04, PFS-001/15, PFS-109/04 and PFS-102/07. Aligning these reads against the B. cretica genomes, by examining coverage of annotated genes in the B. oleracea reference genome . This compares with levels of up to 82% (1752 / 2121) completeness in previously published related genomes , we find the gene flow between different B. cretica population is recent and its genomic diversity is high.Demographic analysis based on genome-wide analysis of genetic variation suggests that populations of B. cretica data. The two approaches are related to the separation of the individual plants into distinct groups . According to the first, the subspecies approach, we separate the individuals into two groups specified by their subspecies definition. Plants A and B are characterized as B. cretica subsp. nivea SFP1207/94 and Brassica cretica subsp. nivea SFP0001/15 (Cretan isolate), respectively, and they constitute group 1, whereas plants C and D are B. cretica SFP109/07 and B. cretica SFP102/07, respectively, and they define group 2. The second approach is based on the principal component analysis (PCA) plot of the data, which depends on the differences at the DNA level. We call the second approach the genetic approach. We applied logistic principal component analysis (http://arxiv.org/abs/1510.06112v1) (logPCA) since the polymorphisms at each site define a binary state. The results of the logPCA are shown in Fig. We followed two approaches to infer the neutral demographic model for the Following the subspecies definition of the two groups of plants, the model “Vicariance with late discrete admixture” is the most likely among the 30 different models with two populations. Such a model suggests that the two subspecies were discrete for a long period of time. However, recently, introgression took place from group 1 (plants A and B) to group 2. Such a massive gene flow suggests that the two groups of plants may not define distinct subspecies, therefore they can be considered as different population of the same species Fig. .Fig. 5DBased on the logPCA results, we identified two populations, the first comprising three individuals  and the second containing one (A). This result is based on the first principal component axis (PC1). It is important to note that although the A, B, and C plants were sampled from Central Greece and D from Crete, logPCA shows that the Cretan individual is genetically closer to B and C than to A. The distances of A and D to the B-C clusters are similar and as a result, we generated an additional population schema grouping together A, B, C and D as another subpopulation, in accordance to the data variability presented along PC2 axis.For the first grouping, the “Founder event and discrete admixture, two epoch” model, was selected as the most possible demography model Fig. . The secBrassica cretica plants may be, in fact, not supported by the modelling outputs. The parameter values for all inferred demographic models as well as the AIC scores of the competing models are presented in the Additional file In all grouping definitions, it is apparent that populations are not isolated. There is considerable gene flow between all possible groupings of the populations. Especially, in the subspecies-based grouping, the inferred model proposes introgression between the two groups, i.e., massive, directional gene flow. Furthermore, a simulation examination suggests that dadi is able to distinguish a model with gene flow from a model without gene flow in about 79% of the cases indicating a rather robust inference outcome (see Methods). Thus, the subspecies classification scheme of the studied B. cretica and their effects in adaptive traits in both in situ and ex situ conservation strategies, as well as in cases of genetic improvement especially with newly introduced genes [The above finding poses the need for further studies concerning the potential gene flow between populations of ed genes .B. cretica populations, taking into consideration their genomic and subspecies variation. There is already evidence of gene flow between wild and crop types of Brassica [This study used genome-wide resequencing to investigate mechanisms of diversification of four isolated Brassica . SimilarBrassica , 41, whiBrassica , 42, sinBrassica , 44 is hBrassicaceae have already revealed a significant signal indicating local adaptation [In the case of taxonomic segregation, the “vicariance-driven divergence with no migration in the early stages” model indicates that the two taxa typically formed as the result of novel and/or emerging geographical barriers, possibly in combination with genetic drift and/or with the contribution of local adaptation for some traits. Concerning whether non-ecological versus ecological process of genetic isolation took place , we cannaptation . Smykal aptation  also proPodarcis gaigeae subsp. weigandi) into another (Podarcis gaigeae subsp. gaigeae) but not in the other direction, recorded by Runemark et al. [B. cretica subsp. nivaea into the B. cretica. Flower colour might be an explanatory factor of the unidirectional admixture event, as in B. cretica subsp. nivea it is white, while in B. cretica it may vary from white to bright yellow; however, this explanation contradicts Edh et al. [B. cretica populations. Nevertheless, in the view of Edh et al. [Unidirectional gene flow has also been reported in other organisms, such as in the case of two lizard subspecies, where gene flow from one subspecies , whichB. cretica subsp. aegaea , B. cretica subsp. cretica and B. cretica subsp. subsp. laconica (Gust. & Snogerup), while B. cretica subsp. nivea  and B. nivea (Boiss & Spruner) are considered as synonyms and misapplied to B. cretica Lam. subsp. cretica, which has been reported for the mainland of Greece and for the floristic region of Crete and Karpathos [According to the Vascular Flora of Greece  there ararpathos .B. cretica from Greece have been studied. Two B. cretica subsp. nivea (Boiss & Spruner) M. A. Gust. & Snogerup individuals from the first two mainland populations respectively  and two B. cretica Lam. individuals, one from the third mainland population (C) and the other from Crete, the island population (D), have been used for the genome assemblies  extraction protocol for total plant DNA isolation, as it has been described before .The yield and quality of DNA were assessed by agarose gel electrophoresis and by a NanoDrop spectrophotometer  and quantified by Qubit broad range assay (Thermo Fisher Scientific). Illumina sequencing libraries were prepared, after fragmenting 500 ng of DNA to an average size of 500 bp, using NEXTflex 8-barcode Rapid DNAseq kit for Illumina sequencing (Perkin Elmer) with adapters containing indexes and 5–8 cycles polymerase chain reaction (PCR) . LibrarySequencing was performed on the Illumina HiSeq 2500 at the University of Exeter, using a Rapid-Run flowcell, yielding pairs of 300-bp reads.Prior to assembly and alignment, Illumina HiSeq sequence reads were filtered on quality scores and trimmed to remove adapter sequences using Trim Galore  with q =After trimming and filtering with TrimGalore, sequence reads were aligned against the reference sequence using Burrows-Wheeler Aligner (BWA)  mem versBrassica oleracea as reference to map the contigs from the four plants using the Burrows-Wheeler Aligner [samtools mpileup -u -f genome.fasta alignment.bam 4 alignment.bcf and  Aligner . The pro Aligner . Using t Aligner  output sArabidopsis. Configuration files for the MAKER annotation can be found on FigShare under DOI 10.6084/m9.figshare.7583672. The GFF file generated by MAKER was converted into NCBI’s Feature Table (.tbl) format using Genome Annotation Generator [Genome annotation was performed using the MAKER pipeline , 68 versenerator  version i: number of sites with derived allele counts being i} is a useful summary of the data especially for demography inference. To calculate the AFS, we mapped the reads of B. cretica to the B. oleracea reference genome. This allowed us to use all specimens and also to use the B. oleracea as an outgroup that denotes the ancestral state. Following the GATK best practices pipeline [The AFS defined as ξ = {ξpipeline , this maBrassica oleracea has been examined thoroughly in the past and there is a gene list of the organism organized into chromosomes. We used this list to exclude SNPs with a distance less than 10 kb from those coding regions. This process of removing SNPs is necessary when the SNPs are used to infer the demographic model. Due to linkage disequilibrium SNPs within or in the proximity of genic regions are affected by selection forces, especially negative selection. Negative selection effectively increases the low frequency derived variants and therefore it introduces biases in the demographic inference. For this reason, we excluded SNPs located within or in the proximity of genic regions.Reconstructing the demographic history of a population is a process based on statistical inference. The amount of available information is therefore critical for the robust inference of the demographic model. Analyzing a small number of non-recombining loci, even with large sample size  results in poor inference because the power fades rapidly upon moving back in time and only a few independent lineages remain . A better approach is to use genome-wide data even with a small number of individuals. Thus, in contrast to the many-individuals approach, a few genomes (even a single diploid genome) contains hundreds of thousands of independent loci (due to recombination), each of which provides information about the demographic history of the population. It has been shown that it is possible to infer the demographic history of a whole population even by using a single diploid individual .Inferring a demographic model consistent with a particular data set requires random walks into a large parameter space by simulating the model using Monte Carlo coalescent-theory based approaches. The most well-known approach based on Monte Carlo coalescent simulations is the Approximate Bayesian Computation (ABC) inference . The maiIn spite of the existence of efficient algorithms for the simulation of a single population AFS –80, the dadi python package [dadi_pipeline described in [dadi_pipeline consists of three optimization rounds and a final plotting step. We used 30 demography models ranging from simple (populations never diverge) to complex (ancient divergence with asymmetric migrations between the two populations) to find the best fitting model. These demographic models comprise a thorough list of two population possible models and they were first examined by Portik et al. [The  package  implemenribed in  allows fk et al. .B. cretica population a simple comparison between the respective AIC scores from each model is not valid because AIC is not comparable between non-nested models. We compared the models using Akaike weights [i of each model i and by dividing each Li with the sum of Li we can normalize the weights and compare the models, and therefore we can find the model that better fits the data [The initial two rounds of optimizations search the parameter space for the parameter set that best describes the data under each of the thirty models. For every model we sampled 50 different parameter sets and 50 repetitions of the each set to get the actual global maximum for each model while avoiding local maxima. We based our selections of the best parameter values on the AIC score for each model. To assess which demographic model better reflects the true demographic history of the  weights , by calcthe data .The dadi_pipeline was successfully used in the past for identifying the demography model of populations with more than 8 samples . To estiWe run the three optimization rounds of the pipeline for each dataset, using our proposed model and a model that specifies no gene flow between the populations.We used the Akaike Information Criterion (AIC) to compare the fit of a model with gene flow and a model without gene flow.. We subtracted the AIC of the gene flow model from the AIC of the no gene flow model. A positive result indicates that dadi correctly identifies our proposed model with gene flow as the better fit for the simulated data. The dadi_pipeline is successful in this task in 79% of the cases  model.Additional file 2: Table S1A. Top 3 AIC relative weights models with BCD-A cluster. Table S1B. Parameters of optimal model on BCD-A cluster. Table S2A. Top 3 AIC relative weights models with ABC-D clusters. Table S2B. Parameters of optimal model on ABC-D cluster. Table S3A. Top 3 AIC relative weights models with the AB-CD clusters. Table S3B. Parameters of optimal model on AB-CD clusters.Additional file 3: Table S5. The full list of coverages for each gene.


Aedes albopictus has emerged as a species of major medical concern following its global expansion and involvement in many arbovirus outbreaks. On Réunion Island, Ae. albopictus was responsible for a large chikungunya outbreak in 2005–2006 and more recently an epidemic of dengue which began at the end of 2017 and is still ongoing at the time of writing. This dengue epidemic has seen a high number of human cases in south and west coastal regions, while few cases have been reported in the north and east of the island. To better understand the role of mosquito populations in such spatial patterns of dengue virus transmission in Réunion Island, we examined the genetic diversity and population structure of Ae. albopictus sampled across the island.In recent years, the Asian tiger mosquito FIS values were significantly positive and correlated to individual relatedness within populations using a hierarchical clustering approach based on principal components analyses (HCPC). However, the largest part of genetic variance was among individuals within populations (97%) while only 3% of genetic variance was observed among populations within regions. Therefore, no distinguishable population structure or isolation by distance was evidenced, suggesting high rates of gene flow at the island scale.Between November 2016 and March 2017, a total of 564 mosquitoes were collected from 19 locations in three main climatic regions  of Réunion Island and were genotyped using 16 microsatellite loci. A high genetic diversity was observed with 2–15 alleles per locus and the average number of alleles per population varying between 4.70–5.90. Almost all Ae. albopictus populations in Réunion Island thus reflecting frequent movements of mosquitoes between populations probably due to human activity. These data should help in the understanding of Ae. albopictus vector capacity and the design of effective mosquito control strategies.Our results show high genetic diversity but no genetic structure of  Aedes (Stegomyia) albopictus ) FST and the geographical distance by road. Sequential Bonferroni corrections were applied for all multiple comparisons [Isolation by distance was analyzed using R software , computiparisons .Ae. albopictus populations, mosquitoes from 19 sites across Réunion Island were genotyped  were genotyped using 16 microsatellite loci , 34. ForNa) varying from 4.70 (in W-P3B) to 5.90  to 15  and the average number of alleles per population (Ne) was lower than the observed average number of alleles (Na) thus reflecting imbalanced allelic frequencies in populations. Indeed, for most of the loci, one to three alleles were overrepresented within populations  varied from 0.47–0.62 while the expected heterozygosity (HE) varied from 0.55–0.66. In all populations, HE was higher than HO and the inbreeding coefficients (FIS) were significantly positive, indicating a deficit in heterozygotes except for E-PNDL and C-PHY for which it was not significantly different from zero . However, no deviation from HWE and no evidence of linkage disequilibrium were observed after sequential Bonferroni correction for multiple testing.In each population, the average number of effective alleles  that grouped individuals according to their genetic proximity  that allows relatedness among individuals to be taken into account when estimating the allelic frequencies. Both methods showed similar results  was lower than that measured among populations of the East coast or Center . A linear regression model between matrices of FST and geographical distances was not significant  revealed that 97% of the variance was found among individuals within populations (P = 0.001), while only 3% was found between populations (P = 0.001) and 0% between regions  where mosquitoes were collected.We assessed the genetic diversity and the genetic structure of 19 Ae. albopictus populations was high: on average more than five alleles were observed per population and 530 MLGs were identified among the 532 mosquitoes examined. Using microsatellite loci, Manni et al. [Ae. albopictus populations from Réunion Island compared to populations from Asia (e.g. from Japan and China), Europe  and America . A recent study based on 1561 genome-wide SNPs also described a higher genetic diversity in Ae. albopictus populations from Réunion Island compared to European populations [Ae. albopictus populations from Réunion Island. The first hypothesis is that Ae. albopictus populations in Réunion Island result from an admixture of several populations from different geographical origins. According to Manni et al. [Ae. albopictus populations from Réunion Island might result from admixture between populations from Thailand and Japan. By comparing mtDNA polymorphism between ancient (collected in 1956) and more recent samples (collected in 2007), Delatte et al. [Ae. albopictus invasion may have occurred in Réunion Island, the first one several centuries ago and the second one in the 1990s, leading to a replacement of populations. The assumption of population replacement from 1990s seems an unlikely explanation for our results because the genetic diversity in Réunion Island is higher than observed in Albania [Ae. albopictus has been recorded since 1979 [Ae. albopictus individuals from different geographical origins might have occurred in Réunion Island. The second hypothesis is that long-term established mosquito populations would have favored the accumulation of genetic variability within populations, countering the effects of any initial demographic bottleneck. This would be supported by the fact that Ae. albopictus was first recorded in Réunion Island in 1913 [The genetic diversity observed in the 19 i et al.  observedulations . Two maii et al.  investige et al.  suggeste Albania , 35 whernce 1979  or in ItFIS in almost all populations reflecting a deficit in heterozygotes. Ignoring closely related individuals can lead to bias in the estimation of allelic frequencies and thus in the resulting population genetics analyses such as tests of HWE and linkage disequilibrium [FIS values were also observed in several studies based on microsatellites  [Ae. albopictus) or eggs sampled at different times to increase the number of sampled progenies. Anyway, we recommend testing for relatedness between individuals when significantly positive FIS are detected in populations. This is all the more relevant given the rapid spread of Ae. albopictus and its involvement in arbovirus outbreaks that leads to an increasing number of studies to understand its genetics and adaptation.The analysis of the 19 mosquito populations with the 10 genotyped microsatellite loci revealed significant linkage disequilibrium between all pairs of loci. This could be explained by the imbalanced allelic frequencies observed in all populations and for all loci: the most frequent alleles are more often associated, regardless of their position on chromosomes. The over-representation of some alleles may be due to a founder effect  but may also reflect the fact that each of the sampled populations was probably represented by the progenies from few females. Indeed, we measured significant positive ilibrium . In thisilibrium , 58–62. 10–0.20; , 34) and Island; ) in popu methods . Indeed,n 500 m) , 65 and n 500 m) . Hence, Ae. aegypti [Ae. albopictus populations from the east and west coasts related to ecological factors [Both the Bayesian clustering algorithm implemented in STRUCTURE and the analysis of molecular variance (AMOVA) revealed an absence of population structure despite a high genetic diversity and a great variability of bioclimatic conditions . This suggests frequent exchange between individuals from different locations across the island. The absence of isolation by distance strongly suggested that human-assisted long-distance gene flows are frequent and play a key role in the dispersal of the Asian tiger mosquito in Réunion Island as has already been shown elsewhere at both large , 68 and  aegypti ) highlig factors , 30. Apa factors , 30.Ae. albopictus populations from Réunion Island, probably due to their long-term establishment. We also observed a lack of genetic structure reflecting a strong connectivity among populations. The absence of population structure and isolation by distance represent key information for the management of vector control strategies against Ae. albopictus in Réunion Island. Vector control strategies could be applied at the island scale by taking into account environmental characteristics and mosquito population densities through time because gene flow between mosquito populations may have a limited impact in their effectiveness. Additionally, these results increase our understanding of the evolutionary history of the Asian tiger mosquito in Réunion Island and will allow deciphering its vector capacity. Further studies on vector competence using the epidemic DENV-2 strain and Ae. albopictus populations sampled across Réunion Island should help understanding the transmission patterns of dengue virus currently causing an outbreak in the island. As vector capacity can also be affected by extrinsic or abiotic factors such as temperature, rainfall, vector density, vector survival and the probability a vector feeds on a host [In this study, we observed a high genetic diversity in n a host , these fAdditional file 1: Table S1. Environmental characteristics of the 19 sampling sites of Aedes albopictus in Réunion Island.Additional file 2: Table S2. Information on the microsatellite loci used for the genotyping of Aedes albopictus populations. Abbreviations: F, forward; R, reverse.Additional file 3: Table S3. Presence/absence of null alleles for each microsatellite locus in the 19 mosquito populations.Additional file 4: Table S4. Microsatellite variation in the 19 Aedes albopictus populations. Abbreviations: n, number of individuals analyzed; Na, number of alleles; Ne, effective number of alleles; Np, number of private alleles; HO, observed heterozygosities; HE, expected heterozygosities; FIS, inbreeding coefficient ; SE, standard error.Additional file 5: Figure S1. Hierarchical clustering of Aedes albopictus individuals from the same population. Example showing the case of the population C-PSA . a Dendrogram generated by the hierarchical clustering. b Principal component analysis. Abbreviation: Ind, individual.Additional file 6: Figure S2. Distribution of linkage disequilibrium Chi-square statistic estimated for each couple of loci. In grey: over the 100 subsampled datasets; in black: for the full dataset.Additional file 7: Figure S3. Relationship between FST values for Aedes albopictus pairs of populations. a Comparisons of FST estimated using R (x-axis) and GenAlEx v.6.5 [FST estimated using R without taking relatives into account (x-axis) and by taking relatives into account (y-axis). Full line: regression line; dotted line: y = x.Ex v.6.5  (y-axis)Additional file 8: Figure S4. Relationship between the FST and the distances by road calculated between pairs of mosquito populations. y = − 3.58 × 10−6 x + 2.61 × 10−2 .


Pterocarya stenoptera, a widespread tree species in China, to test the roles of these factors. Four noncoding spacers, eight microsatellite (simple sequence repeat) markers, and species distribution modeling were used to examine the phylogeographical pattern of P. stenoptera. Based on chloroplast DNA data, populations of P. stenoptera were clearly clustered into three groups. The divergence time of these groups fell into the stage of the Qinghai–Tibet Movement, 1.7–2.6 Ma. For simple sequence repeat data, only one western marginal population YNYB could be separated from other populations, whereas other populations were mixed together. Our results indicated that the environmental heterogeneity resulting from the Qinghai–Tibet movement might be response for this genetic divergence. The climatic fluctuations in the Pleistocene did not cause the substantial range shift of P. stenoptera, while the fluctuations affected its population size. Moreover, we also confirmed the river systems did not act as channels or barrier of dispersal for P. stenoptera.The geological events, past climatic fluctuations, and river systems played key roles in the spatial distribution, population dynamics, and genetic differentiation of species. In this work, we selected  The uplift of the Qinghai–Tibet Plateau (QTP) has not only changed the topography of the area and its surroundings but also played a remarkable role in the climate change of Asia . The comin situ in the form of local adaptation during multiple glacial–interglacial cycles  is a dominant deciduous broad-leaved tree growing in forests below 1,500 m above sea level. The species is widely distributed in the warm-temperate and subtropical regions in China. P. stenoptera is intolerant of cold and drought, and it is likely to grow in warm and humid environments  What is the genetic structure of P. stenoptera populations in China as revealed by cpDNA data and SSR markers? (ii) How do geological events, climate change, and river systems affect the genetic differentiation and population dynamics of P. stenoptera?Here, we employed chloroplast DNA (cpDNA) noncoding spacers, microsatellite [simple sequence repeat (SSR)] markers, and species distribution modeling (SDM) to investigate the phylogeographical pattern of P. stenoptera distributed in 22 localities were collected covering its entire distribution area in China during May to November 2017 -rpL32-F (trnV(UAC)x2-ndhC  and eight microsatellite markers  . Four noncoding cpDNA spacers of -rpL32-F , and trnnd Ps83)  were ampnd Ps83) Table 1.nd Ps83) . For SSRh) and nucleotide diversity (π) were estimated using dnasp version 6.12 (NPh) was counted by manual statistics. The networks of cpDNA haplotypes were constructed using TCS version 1.21  was selected in MEGA version 10.0  chain to 10 million generations at the sampling frequency of 1,000 generations each time. Tracer version 1.7.1 was used to visualize and check for convergence to a stationary distribution and ensure effective sampling size values (ESSs > 200). We discarded the first 10% as burn-in and constructed the maximum clade credibility tree by using TreeAnnotator version 2.5.1 (P. stenoptera were constructed the basis of their pairwise genetic distances in cpDNA and determined from the net average between populations of sequences (DA) by using the unweighted pair-group method with arithmetic module of MEGA version 10.0  in BEAST version 2.5.0 to further infer potential relatively complex changes given an effective population size  were calculated by FSTAT version 2.9.3 (NPA) was manually counted according to the allele frequencies in FSTAT. The role of rivers in the transmission of P. stenoptera was explored by performing correlation analyses between the level of genetic diversity based on SSR and cpDNA and longitude using the Mantel test in vegan package (K) in the SSR dataset. The program was run with K values from 1 to 10 in 10 replicates for each K, 20,000 burn-in periods and 100,000 MCMC iterations. An admixture model with correlated allele frequencies was chosen for this analysis. The optimal K value was determined by computing the ∆K values according to the method of K value was further estimated according to the value of the TI posterior probability by using RmavericK  and the ecological distance via the Mantel permutation procedure in vegan package . Nei’s gene diversity HE; , allele on 2.9.3 . The num package . Similar package  to infermavericK . The avemavericK . The barmavericK . A princmavericK . For bot package . The val package , and envFST) were calculated by nonhierarchical analyses of molecular variance (AMOVAs) in ARLEQUIN version 3.5.1 (Nm) among populations for the cpDNA and SSR data was estimated as 1/4(1/FST − 1) (r) was estimated using a modified equation of r = mp/ms = [(1/FST(n) − 1) − 2(1/FST(c) − 1)]/(1/FST(c) − 1). Here, mp and ms is the pollen migration rate and seed migration ratio, FST(n) and FST(c) is the nuclear (SSR) FST and cytoplasmic (cpDNA) FST.Genetic differentiations of cpDNA data and SSR data among populations and for populations within each group (on 3.5.1 . The amoST − 1) . Pollen/P. stenoptera was determined by SDM in Maxent version 3.4.1 -rpL32-F, and 11 trnV(UAC)x2-ndhC haplotype sequences were deposited in GenBank with accession numbers MK002380 to MK002387, MK002389 to MK002393, MK002395 to MK002403, and MK002405 to MK002415, respectively. These sequences, when combined, were aligned with a consensus length of 2,214 bp, and they contained 17 nucleotide substitutions and 15 indels. On the basis of these polymorphisms, 28 haplotypes (H1 to H28) were identified among all the surveyed samples  of each population ranged from 0.194 (JXLH) to 0.397 (HBJG). The level of allelic richness (AR) of each population ranged from 1.931 (SDTM) to 2.842 (YNYB). Among these populations, six populations were observed with private alleles, and the population of SDMM showed the highest number of private alleles. Mantel test showed that the genetic diversity of SSR  was detected by the analyses of molecular variance (AMOVA) (Nm = 0.053) among populations resulted in significant genetic differentiation. No significant isolations by geographical distance  and ecological distance  for cpDNA were detected at the species-range scale. Nonsignificant isolation by ecological distance for SSR was also detected along PC1, PC3, and PC4 , but a significant IBE existed along PC2 . However, significant isolation by geographical distance  for SSR was detected. AMOVA showed that 54.93% of the total cpDNA genetic differentiation existed among the three groups (FCT = 0.549), and 31.50% among populations within groups (FSC = 0.699), and 13.58% within populations (FST = 0.864) (FCT = 0.029), 6.34% among populations within groups (FSC = 0.065), and 90.78% within populations (FST = 0.092) (r) = 52.0 suggests that the high gene flow was mostly transmitted by pollen.Populations of c groups 3. TheseDivergence time in the time-calibrated tree Figure 3D and Fu’s Fs statistics showed negative values at the total level  At present and lgm were both continuous in china, and no habitat fragmentations were isolated by intervening unsuitable habitats (2) was not compressed compared with that at the present time . Similarly, no obvious difference existed between the area of high climatically suitability (logistic probabilities > 0.50) At the lgm  and that at the present time . The significant difference of the environmental variables . Moreover, bio12 and bio19 between the South group and the Southwest group were significantly different (p < 0.05).The values of the areas under the receiver operating characteristic curve based on both training and test presence data at the present and lgm periods were 0.994 And 0.990 (Present) 0.994 And 0.992 (Lgm), respectively. The results of areas under the receiver operating characteristic curve values demonstrated good model performance. The results of the predicted distribution of habitats Figure 7P. stenoptera across its distribution area in China to provide insights into the complex interplay among multiple factors. Our survey showed that the 22 populations of P. stenoptera were divided into three groups, i.e., North group, South group, and Southwest group.The spatial genetic structure of species is widely known to be linked to multiple factors . In thisP. stenoptera was caused by geographical barriers among groups, then the premise of this hypothesis was that geographical barriers existed among these groups. For the distribution area of P. stenoptera, no large mountains isolated the groups, but three major rivers, i.e., the Yellow River, Huaihe River, and Yangtze River, may have divided them. According to the literature, the Yellow River and Yangtze River, as phylogeographical boundaries, have promoted the genetic divergence of plant species that distributed across these rivers  also do not support the assumption that divergence is caused by ecological isolation. Moreover, the Pleistocene glacial epoch occurred after the Kunlun–Yellow River movement , which is mainly derived from pollen transmission with the high pollen/seed migration ratio (r = 52.0). Efficient gene flow (Nm > 1) will break the isolation between populations  of P. stenoptera have their own private genes. The results indicate the microrefugia hypothesis are likely suitable for P. stenoptera. Although our results did not support the range shift of P. stenoptera during the climatic fluctuations, its population size was affected. Tajima’s D and Fu’s Fs statistics and the mismatch distribution analysis all supported P. stenoptera experienced a population expansion. The results of EBSP indicate that this expansion occurred at approximately 0.40 Ma whose timeline is highly, consistent with the interglacial of MIS 11  and Henan Agricultural University Science & Technology Innovation Fund (KJCX2016A2) for population sampling, the Natural Science Foundation of Henan Province (182300410039) for sequencing and genotyping of this study, the Funding Scheme of Young Backbone Teachers of Higher Education Institutions in Henan Province (2015GGJS-081) for all experimental materials of this study.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Spartina alterniflora, 2n = 6x = 62) is a notorious invasive species that causes heavily negative effects on native ecosystems worldwide. Here we addressed the evolutionary mechanisms underlying the invasion and dispersal history of this species along the China coast in the past decades. We employed nine microsatellites and three chloroplast fragments to investigate phylogeographic structure and genetic diversity of 11 native US and 11 invasive Chinese S. alterniflora populations. Demographic history simulation was also performed for both the native and invasive populations, respectively. Comparative genetic analyses of these natural populations revealed that although all the Chinese populations were introduced only once, high level of genetic diversity with weak geographic structure was observed. In particular, both the genetic features and mathematical simulation illustrated very recent population expansion in the Chinese populations. We found that genetic variants identified in native US populations were mixed in the Chinese populations, suggesting the recombination of these original variants during the invasion process. These genetic attributes indicate that Chinese populations might not have experienced a genetic bottleneck during the invasion process. High genetic diversity and genetic admixture might have contributed to the success of invasion of S. alterniflora in China. Our study provides a framework of how the smooth cordgrass spreads along the China coast as well as its potential genetic mechanisms underlying the invasion.Biological invasion represents a global issue of concern due to its large negative impacts on native ecosystems and society. Elucidating the evolutionary history and genetic basis underpinning invasiveness is critical to understanding how alien species invade and adapt to novel environments. Smooth cordgrass ( Invasive alien species (IAS) represent one of the greatest threats to global biodiversity due to their negative impacts on the functioning of native ecosystems . CurrentSpartina (Poaceae) includes 13–15 species that all are perennial herbs and native to the Atlantic and northeastern Pacific coasts  is originally distributed in the Atlantic and Gulf coasts of North America but have become one of the most aggressive invaders in global coastal ecosystems  gave rise to a sterile hexaploid hybrid S. x townsendii. Thereafter, chromosome doubling of the F1 hybrid of the two hexaploid species resulted in the formation of a fertile and high aggressive dodecaploid species Spartina anglica   (The genus c coasts . Cytolog ability . Among tosystems . In the  century . Homoplo or 124) . In the eyrautii . These reyrautii . Similar6x = 62) . The res6x = 62) .Spartina species were introduced for the purpose of wetland restoration, tidal land reclamation, and saline soil mitigation , and Spartina cynosuroides (2n = 4x = 40), were introduced from North American Atlantic coast in 1979  revealed that all Chinese S. alterniflora populations were primarily originated from North Carolina, Georgia, and Florida of the US  and asexual reproductive strategies , 0.8 µl of dNTPs, 0.3 µl of each primer (10 µM), 1 µl of 10× PCR buffer (Mg2+ included), and 7.3 µl ddH2O. The forward primer for each primer pair was fluorescently labeled with FAM, HEX, or ROX  of 207 representative samples, of which 92 and 115 accessions were selected from the USA and Chinese populations, respectively (trnT-trnL and 56°C for the trnT2-rps4 and rbcL-psaI) for 1 min, 72°C for 2 min, and a final extension at 72°C for 5 min. All PCR amplicons were then purified and sequenced using an ABI 3730 automated sequencer .Previous studies have characterized a series of polymorphic microsatellites from rniflora . We testS. alterniflora can spread rapidly through its rhizomes. We therefore eliminated the data bias caused by the asexual reproduction based on the clonal diversity (the number of genotypes/sample size). A total of 173 accessions with genotype occurring more than once were excluded from the data matrix. To further minimize the effects of sample size on genetic indices, these populations with relatively large sample size (>43 samples) were recollected. To further explore the tendency that genetic diversity of native populations might vary with sample size, we performed a simulation of sampling, of which individuals from US populations were randomly sampled along a gradient of sample sizes: 2, 5, 25, 50, 100, 200, and 400. Ten replicates were conducted for each simulation for a given sample size. We also calculated Shannon’s information index (I) for each sampling and determined the proportion of I (I for the sampled population/I for US populations as a whole). The fitted curve was then added after a simulation of nonlinear model in the software R v.3.0.2 . To this end, we defined the 22 Chinese and US populations as three groups: (1) the source group containing the 3 USA populations  that were supposed to be the ancestors of all Chinese populations; (2) the non-source group including all the other 8 native USA populations; and (3) the introduced group that consisted of all the 11 Chinese populations (Ae), Shannon’s information index (I), individual inbreeding coefficient (Fi), and private allele (Pa). To further assess the genetic variation pattern within and between populations, analysis of molecular variation (AMOVA) and principal coordinate analysis (PCoA) were performed for all 22 populations using Arlequin v.3.5.1.2  iterations, and the delta K was used to determine the best genetic assignment.The corrected microsatellite data set was subjected to subsequent analyses of genetic diversity and population structure. Hardy–Weinberg equilibrium was tested for each microsatellite using Genepop v.4 . It has ulations  was empl.3.5.1.2 . We also.3.5.1.2 . The K vhttp://www.fluxus-engineering.com;Chloroplast sequences were checked against the original graphic files and aligned using MEGA v.5  with corr=ln(Nt/N0)/t, where r represents the population growth rate per year, N0 is the initial population size, and t is the time since growth began. To further estimate the genetic contribution rate from the native populations to the introduced populations, we used a, b, (1 – a − b) to respectively represent the relative genetic contributions of the 3 source populations  to all the 11 Chinese populations. The probability obtained from observed alleles and their frequencies in Chinese populations was calculated as follows:Theoretically, invasive species are expected to show relatively low genetic diversity due to the bottleneck effect during the invasion process. To experimentally test whether the invasive populations found in China have undergone a genetic bottleneck, we used the microsatellite data set to simulate the effective population size for both the native and introduced populations using Bottleneck v.1.2.02 , with thi ranges from the first microsatellite locus SP02 to the ninth locus SP27; j ranges from the first allele to the last allele for each locus; fij,MC, fij,SI, and fij,TB represent the frequencies of allele j at locus i in populations U-MC, U-SI, and U-TB, respectively; and nij,China represents the number of allele j at locus i in Chinese populations. With the feasibility of calculation considered, we applied the logarithmic transformation to equation (1). We then obtained:where a, b, and (1 – a − b) ranging from 0 to 1. To further simulate population genetic mixing, we explored the effect of admixture on amount of genetic variation with the assumption that the three native source populations were mixed evenly. Thus, N was taken as the original sample size for each native source population. We then conducted a simulation of genetic mixing to produce observed alleles frequencies (where expected = admixture from three source populations and observed = Chinese) and then generated the optimal value of N. Based on allele frequency data of native source populations estimated above, we next calculated the expected distribution of alleles at the nine microsatellite loci for Chinese populations based on the formulas a×2N for U-MC, b×2N for U-SI, and (1 – a − b)×2N for U-TB, respectively. All these simulations were performed using the approximate Bayesian computation (ABC), with the times of repetition for each N being set to 1 billion. The computer codes for simulation are given in the A grid search was then conducted to find the optimal solution to equation (2), with S. alterniflora is an allohexaploid species, we examined whether or not the null alleles existed in the microsatellite matrix. At the population level, all the 22 populations showed different degrees of null alleles in the nine microsatellites, with the Chinese population C-NF only possessing null alleles in the locus SP27 but the source US population U-SI having null alleles across all microsatellite markers , the 11 US populations (Ae = 6.614) harbored relatively higher genetic diversity, and this trend was more pronounced in the 3 US source populations (Ae = 7.005). Similar phenomena were also observed in the other three genetic diversity parameters  where the population C-TJ and U-MC harbored the lowest and highest genetic diversity among the 22 populations, respectively; and the US group showed relatively high genetic diversity compared to the Chinese group (Fi), all these samples were found to show significant deviation from Hardy–Weinberg equilibrium at both the population and group levels. For the three chloroplast fragments, a total of nine sequence polymorphisms corresponding to 10 haplotypes were identified across the 207 individuals (Hd and π) varied among the 22 populations, with 6 populations  showing no sequence polymorphisms and the populations U-GV (Hd = 0.867) and U-SI (π = 0.978 × 10 −3) harboring higher Hd and π values (−3) exhibited relatively higher genetic diversity compared to all the 11 Chinese populations   that is different from the four Caribbean populations (mostly in red color), and the remaining four populations exhibited a mixed genetic structure Table 2.p > 0.05). However, the haplotype network showed that seven minor haplotypes (H4-H10) were specific to the US populations, whereas the three major haplotypes were shared between the US and Chinese groups (ST = 0.400–0.439) compared to the microsatellite data set (FST = 0.070 – 0.170) , all of which confer it exceptionally high adaptability to salinity and tidal submersion   is possibly an independent refugee during the last glacial maximum, we propose that distinct recolonization routes of the two geographic groups might be partially responsible for the observed genetic divergence. In addition, environmental differences between the local habitats as well as migration barriers are also potential factors that might have contributed to the observed geographic patterns (bmersion . Therefobmersion . In casen China) . In thisch other . This phpatterns .S. alterniflora in China. This demographic attribute is different from that observed in S. alterniflora of the US west coast as well as some other invasive species, in which founder effect and genetic bottleneck are common features during the colonization and range expansion process  and the southern Chinese populations harboring the unique haplotype identified in the U-TB population. Of significance, the two southern invasive populations, C-NH and C-NF, are geographically very close to the primary transplanting location. These findings suggest independent dispersal routes of the northern and southern Chinese populations during the invasion process.The three source US populations  showed mixed genetic structure, and most of the genetic variability was identified in the Chinese populations. This observation is further confirmed by the demographic simulation that no significant genetic bottleneck was found in the Chinese populations. Instead, obvious recent population expansion with high growth rate was detected in these invasive populations, which is consistent with the rapid invasion history of  process . High ge process . In our  process . To thisS. alterniflora and native congeneric species not only reunites diverged genomes within the same nucleus but also confers aggressive traits that allow the alien species to adapt to local environments (Alliaria periolata) is thought to result from multiple introductions . In this study, our results illustrate that all the Chinese populations harbor high genetic diversity and show no significant genetic differentiation from the source US populations. In particular, mathematical simulation indicates that sampling size of the three source US populations is enough to represent the genetic constitution of the S. alterniflora in China. In addition, an opposite example is the congeneric invasive species S. anglica in which low genetic diversity is thought to be a potential factor that has resulted in its rapid decrease in its range in China  have been introduced in China and co-occur in natural habitats. It remains a worthwhile issue to examine whether interspecific hybridizations have conferred adaptability to the S. alterniflora.While above analyses demonstrate the importance of intraspecific genetic admixture, the contribution of high genetic diversity harbored in the source US populations cannot be ignored. It has been well documented that high level of genetic diversity shows positive effects on the adaptability of species in responses to varying environments and colonization . As demoin China . Taken tAll data sets generated in this study are included in the article/LS, L-FL, and BL designed the study. LS, S-YQ, and J-XH performed the experiment. Genetic data analysis was done by LS, with the help of Z-PS and C-CW, and the mathematical simulation was done by YW. The paper was written by LS and L-FL, and revised by Z-PS, LW, JY, C-CW, MN, and BL.This project was financially supported by the National Key Research and Development Program of China (grant no. 2017YFC1200100), National Science Foundation of China (grant no. 41630528 and 31670491), and Shanghai Pujiang Scholar Program (grant no. 19PJ1401500 and 16PJ1400900).The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.


Dyscolus and Dercylus.Páramo is a tropical alpine ecosystem present in the northern Andes. Its patchy distribution imposes limits and barriers to specialist inhabitants. We aim to assess the effects of this habitat distribution on divergence across two independently flightless ground beetle lineages, in the genera One nuclear and one mitochondrial gene from 110 individuals from 10 sites across the two lineages were sequenced and analyzed using a combination of phylogenetics, population genetic analyses, and niche modeling methods.Dyscolus alpinus, where one dominant haplotype is found in four out of the six populations analyzed for both molecular markers. However, complete population isolation was revealed in species of the genus Dercylus, where high levels of differentiation exist at species and population level for both genes. Maximum entropy models of species in the Dercylus lineage show overlapping distributions. Still, species distributions appear to be restricted to small areas across the Andes.The two lineages show different degrees of population subdivision. Low levels of gene flow were found in Dyscolus alpinus appears to be a better disperser than species in the genus Dercylus.Even though both beetle lineages are flightless, the dispersal ability of each beetle lineage appears to influence the genetic diversity across fragmented páramo populations, where  The distribution of a species is determined by environmental conditions, ecological interactions of species, and dispersal dynamics. In particular, the dispersal ability of species plays an important role in determining species ranges and biogeographical patterns . The evoFlightlessness has been recorded in insect faunas in stable habitats such as oceanic islands and caves , as wellFlightlessness in carabid beetles has been the focus of several studies, some of which support the idea that wing loss promoted genetic isolation across populations . HoweverThe higher elevations of the northern Andes host a unique plant community known as páramo. Limited to elevations above 3,000 m, páramo is patchily distributed among the many higher peaks and volcanos in the range. Páramo contains a high number of endemic species, which are mostly are restricted to small elevational ranges , is a micropterous species present in the northern and central portion of the Ecuadorian Andes, between 2,750 and 4,200 m, in páramo, subpáramo, and montane forest . The second beetle lineage assessed comprises multiple species in the genus DercylusDercylus is a new world genus with 35 species (LinodercylusDercylus orbiculatusDercylus praepilatusDercylus cordicollis (In this study we focused on two flightless ground beetle (Coleoptera: Carabidae) lineages from páramo. Most of the ground beetles present in páramo are micropterous (76% of species), with only few macropterous and brachypterous species reported . To exame forest . MembersDyscolus. Of 320  species , includi species . All Ecudicollis , and twoThe aim of this study is to analyze the effects of montane isolation in these two flightless beetle lineages from páramo, and to ask how their phylogenetic structure and population connectivity have been affected by potential geographical barriers, their dispersal abilities, and their ages of divergence. We analyzed two molecular markers, cytochrome c oxidase subunit I (COI) and carbamoyl phosphate synthetase 2 (CAD), alone and combined, to determine phylogenetic relationships among individuals for each lineage, population genetic diversity and structure, and approximate ages of each clade with the use of molecular clocks. In addition to the analyses of the molecular data, geographic information was used to generate models of species distribution as a way of assessing habitat continuity.The study area encompassed the Ecuadorian Andes, where all the sampling took place above 3,100 m in the páramo ecosystem. The selection of sites was based on previous records of occurrence of the target taxa, and potential geographical barriers. Some of these potential barriers include: dry valleys, rivers, faults, and the east/west split of the Andes mountain range . In partDyscolus alpinus was found in six out of the eight sites sampled (Dercylus specimens were collected in five sites (Dercylus cordicollis (SIMT265) from Cotacachi, this sample was included for the analysis of Dercylus cordicollis populations. Outgroup taxa were chosen based on availability of fresh material and taxa considered closely related carabid lineage within the Harpalinae. Outgroup taxon sampling included 12 taxa: two were collected in the Ecuadorian páramo; six taxa were collected in the southeastern United States; and four additional samples were retrieved from GenBank  using GeneJet’s Genomic DNA Purification Kit  following the manufacturer’s instructions. A fragment of the mitochondrial cytochrome c oxidase subunit I (COI) gene was amplified using the primers TL2–N–3014  and aligned in MAFFT v.7  togetherDyscolus alpinus; (2) Dercylus orbiculatus; and (3) Dercylus species together  in order to contrast inter– and intrapopulation variability. Parameters estimated included: estimated haplotype diversity (h), nucleotide diversity (π), number of polymorphic sites (S), number of migrants per generation (Nm), and Tajima’s D neutrality test statistic (D). ɸST values were calculated to assess the population structure, while an analysis of the molecular variance (AMOVA) was performed to test the influence of geographical barriers, including the rivers, dry valleys discussed above, and the division between populations of eastern and western cordilleras. A Mantel test of correlation between genetic and geographic distances was performed using 1,000 randomizations . Lastly, Structure 2.3.4. (K), using no admixture for the mtDNA and admixture for the nuclear gene. A total of 10 iterations were run per potential K, and the presence of one to eight populations were tested for both beetle lineages.The levels of genetic diversity were calculated using Arlequin 3.5.2.2  and DnaSe 2.3.4.  was usedPhylogenetic analyses were performed to determine relationships among individuals for each lineage and among lineages. To explore marker-specific effects, mitochondrial and nuclear data sets were initially analyzed separately, but combined data were used to generate the most robust hypotheses for each beetle lineage using MrBayes 3.2  and RAxMDyscolus alpinus, one point of fossil calibration was used to designate minimum node ages, using a log-normal distribution and enforced monophyly. This fossil represents the same tribe as Dyscolus (Platynini): a fossil of Limodromus from the late Eocene (37.2–33.9 Mya), of Baltic origin  from the Middle Eocene (44.1 Mya), of Baltic origin  from the Eocene (37.2–33.9 Mya) of Teller County, Colorado (http://tree.bio.ed.ac.uk/software/tracer/) to ensure effective samples sizes. Trees were visualized in TreeAnnotator 2.0.02 (http://beast.bio.ed.ac.uk), using maximum clade credibility after a 10% burn–in.To understand the timing and rate of diversification for each ground beetle lineage, divergence times were estimated using an uncorrelated relaxed clock in BEAST 2.0  using thc origin . The divc origin , and PteColorado . In addiDercylus was modeled to determine if species distribution overlapped, using present bioclimatic variables at 2.5’ spatial resolution ), BIO5 = Max Temperature of Warmest Month, BIO6 = Min Temperature of Coldest Month, BIO12 = Annual Precipitation, BIO13 = Precipitation of Wettest Month and BIO14 = Precipitation of Driest Month. The analyses ran for 10 replicates of 500 iterations and using a 10% training presence, using the default settings for the convergence threshold (10−5). For each species, the output from the average run was reclassified using ArcMap 10.4.1  with a 10% threshold. Model performance was evaluated using the area under the curve (AUC) calculated by MAXENT, where values between 0.7 and 0.9 indicated a good discrimination . Haplotype 1 is the most widespread across populations, found in four of six sites (h) is shown in h = 0.71). The overall nucleotide diversity of COI was low (π = 0.00–0.01). Structure analyses tended to overestimate the number of populations; results from multiple simulations show that the number of populations using this data set is one (K = 1). Results from the neutrality test for the overall values , as well as on most populations are not significant  between genetic (ɸST) and geographical distances.The portion of the COI gene analyzed for ix sites . Unique ix sites . Haplotynificant . Cayambenificant . AdditioDyscolus alpinus spanned 744 bp, with 64 parsimony informative sites. These represented five haplotypes (GenBank accessions MK440260–MK440264), with no heterozygote individuals observed. Haplotype 1 is found in four of the six populations. Unique haplotypes were recorded from Atillo (H4) and Cayambe (H5). Haplotype networks for both genes show that most haplotypes are present at multiple sites (h) and nucleotide diversity was low for CAD data set (h = 0.91). Structure analyses of the nuclear data set showed three populations (K = 3). Similar to the results from the mitochondrial data, most neutrality tests using CAD  were not significant, with Cayambe and Pichincha as exceptions. Again, however, these apparent exceptions exhibit few haplotypes, inconsistent with a population expansion scenario. Results from the Mantel test show there was no correlation between genetic and geographic distances .The CAD data set for le sites . The ovedata set . Among aDyscolus alpinus shows that most of the variation occurs within populations , which suggest moderate levels of population subdivision among populations. When ɸST values were compared on a population–by–population basis, some genetic differentiation was found among populations : ɸST = –0.10. The CAD data set shows lower genetic differentiation among all populations of Dyscolus alpinus . The overall number of migrants between Dyscolus populations (Nm = 0.31) indicates that there is population subdivision across sites. Higher levels of genetic connectivity were observed between Mojanda and Cayambe (Nm = 1.79), results that are also supported by the low ɸST values between these two sites . No haplotypes were shared among sites  among Dercylus species and populations. Structure analyses of Dercylus orbiculatus individuals all resolved as one population, even though the two sites do not share haplotypes. These analyses were also performed for the entire clade, and one population was found (K = 1). Neutrality test values were not significant , with the exception of the population of Dercylus orbiculatus from Culebrillas, for which significantly positive D and Fs were found  between genetic and geographical distances.In the case of ng sites , and oveng sites . Eight hre found . Lastly,Dercylus species was 669 bp with 24 parsimony informative sites (GenBank accessions MK440236–MK440251). A total of 13 alleles were identified across the Dercylus lineage and the overall nucleotide diversity was low (π = 0.00–0.02). Four alleles were recovered from Dercylus orbiculatus populations, and three alleles from Dercylus cordicollis, with one shared with Dercylus from Cotacachi , whereas results from the analyses of the whole clade show five distinct populations (K = 5), corresponding to each species. Neutrality tests supported significantly positive Fs for Dercylus cordicollis from Pichincha  between genetic (ɸST) and geographical distances.The portion of the CAD gene amplified for achi H5; . Four aldicollis . Structuichincha . ResultsDercylus orbiculatus, occurring across the southern Ecuadorian Andes . A high level of genetic differentiation was also observed when ɸST values were compared between populations and species in COI data set .The AMOVA showed that most of the genetic variation was found among groups when testing the effect of geographical barriers . The higan Andes . The higdata set . In thisST (ɸST = 0.93) shows high levels of population differentiation. When each population was compared against each other, we found moderate to complete population subdivision between some sites , as well as between Pichincha and Cotacachi (ɸST = 0.00), Pichincha and Salinas (ɸST = 0.00), Salinas and Atillo (ɸST = 0.03), and Salinas and Cotacachi (ɸST = 0.00). The number of migrants per generation was calculated for two populations of Dercylus orbiculatus (Cajas and Culebrillas), which revealed low gene flow (Nm = 0.39).In the case of the nuclear coding gene CAD, the overall value of ɸDyscolus alpinus yields similar resolution  as sister to the Dyscolus alpinus clade . The timing of splitting–events for the Dyscolus alpinus clade , and between Dercylus cordicollis and Dercylus sp. from Cotacachi , Dercylus from Cotacachi  and Dercylus sp. from Atillo  during the Miocene (16.4–6.04 Mya). Dercylus cordicollis, on the other hand, originated in the Pliocene , and Dercylus praepilatus  in the Pleistocene. Only these last two diversifications were contemporary with the diversification of most páramo plants , shows a low haplotypic diversity across sampled populations. In Dercylus (entirely micropterous), however, high levels of differentiation were found at the species and population levels. The reasons for these differences are not entirely clear.The effect of dispersal ability on population genetic structure and diversification represents a rich focus of study . InsectsDyscolus alpinus, a dominant haplotype for each marker is found in four out of the six populations analyzed, with one site (Mojanda) exhibiting unusually high diversity. The diversity at this site could be associated with multiple colonization events due to dynamic habitat shifts from volcanic activity dated prior to the Last Glacial Maximum  to other sites. Some population pairs on opposite sides of the cordillera also present high population structure , but this is not the case for most sites, so simple E–W and N–S groupings show minimal explanatory power. High ɸST values found among sites on the same side of the cordillera could have resulted from habitat discontinuity reinforced by the presence of major geographical barriers such as major rivers and dry valleys , whereas the higher population structure in the COI data set probably results from both higher mutation rates and shorter coalescence times of mitochondrial DNA  species, high levels of differentiation are reported at the species and population levels for both genes. The mitochondrial marker showed no shared haplotypes among sites and species, whereas CAD showed three shared haplotypes, generally shared by proximate populations . Species in the genus Dercylus show smaller distributions , sharing no haplotypes in either marker. It is, however, intriguing that the three CAD haplotypes at Culebrillas appear to be derived from the single common one at Cajas. This may be the basis for Structure only recovering one population (K = 1) with COI and CAD sequences, suggesting that in the past these populations had higher connectivity levels. Based on AMOVA results, the Chimbo and Chanchan river valleys, which overlap with the Pallatanga fault  also seem to have contributed toward the genetic heterogeneity seen in Dercylus in the eastern cordillera, considering the high ɸST values (Dercylus cordicollis (Pichincha) and Dercylus sp. (from Cotacachi). Divergence time estimates show that the species in the Dercylus clade originated during the Miocene, Pliocene and Pleistocene  and Dercylus praepilatus .For the genus ibutions . Howeverga fault , appear T values  and the T values . Lastly,Dercylus largely support species distinctions, the status of Dercylus orbiculatus (sampled from both Cajas and Culebrillas) is less clear. It is resolved as a paraphyletic grade by COI, as well as in the combined data tree, but monophyletic by CAD, with strong support. While this difference may be a result of the difference in rate of nucleotide change between genes , perhaps facilitated by Quaternary glaciations, when páramo moved to lower elevation areas such as the inter–Andean valleys . How, then, Dyscolus alpinus has achieved its broad distribution, while Dercylus species have largely remained confined to restricted areas, remains an open question.When results from these two flightless lineages were compared to the patterns observed in n páramo , a commo valleys . Still, Understanding the history of movements and diversification of organisms in alpine tropical ecosystems has considerable importance, given the effects that climate warming is having on high elevation faunas . Beetle Pelmatellus columbianus exhibit broad elevational ranges  and sustain higher levels of gene flow among populations (Dyscolus alpinus, to high levels of differentiation among species and populations within the Dercylus lineage. Although species in the genus Dercylus show similar predicted distributional ranges, less genetic cohesiveness was found among populations, possibly as a result of division of the ecosystem by abrupt topographic features. Species with smaller elevation ranges are probably more susceptible to climate change, and elevational shifts toward higher elevations have been already been reported among ground beetle species from páramo (The effects of mountain isolation vary among páramo species. The genetic diversity found in both ground beetle lineages analyzed to date appears to be influenced by the range size and dispersal capability for each beetle lineage. While macropterous species such as ulations , flightlm páramo . The pat10.7717/peerj.7226/supp-1Supplemental Information 1Outgroups used in this study as also listed in this table. Accession numbers are recorded under each gene column.Click here for additional data file.10.7717/peerj.7226/supp-2Supplemental Information 2Click here for additional data file.10.7717/peerj.7226/supp-3Supplemental Information 3Click here for additional data file.