Eunectes notaeus) are large, semiaquatic boid snakes found in wetland systems in South America. These snakes are commercially harvested under a sustainable management plan in Argentina, so information regarding population structuring can be helpful for determination of management units. We evaluated genetic structure and migration using partial sequences from the mitochondrial control region and mitochondrial genes cyt-b and ND4 for 183 samples collected within northern Argentina. A group of landscape features and environmental variables including several treatments of temperature and precipitation were explored as potential drivers of observed genetic patterns. We found significant population structure between most putative population comparisons and bidirectional but asymmetric migration in several cases. The configuration of rivers and wetlands was found to be significantly associated with yellow anaconda population structure (IBD), and important for gene flow, although genetic distances were not significantly correlated with the environmental variables used here. More in-depth analyses of environmental data may be needed to fully understand the importance of environmental conditions on population structure and migration. These analyses indicate that our putative populations are demographically distinct and should be treated as such in Argentina's management plan for the harvesting of yellow anacondas.Yellow anacondas ( Genetic data offer high resolution and power for evaluating population structure and dispersal patterns, which is especially useful in species that are difficult to find or observe such as yellow anacondas. Combined with landscape information, genetic approaches can increase our understanding of spatial, environmental and even ecological constraints to dispersal. Yellow anacondas in northern Argentina are good candidates for these types of landscape genetics studies as they are found in a heterogeneous environment, with presumably limited opportunities for dispersal between populations Several mechanisms have been proposed for the formation of spatial genetic structuring; these mechanisms may act individually as main drivers or act in concert. Gene flow between populations might simply be limited due to the physical distance between groups, creating a spatial genetic pattern known as isolation by distance (IBD) Eunectes notaeus is a commercially-important species that was heavily exploited for their valuable skins until the late 1990s -b), with a resulting low degree of resolution. The current study aims to carry out a more detailed evaluation of population structure and connectivity in relation to presumably relevant habitat features, as well as estimating effective migration rates between anaconda groups in northern Argentina. Understanding the connections and movement between these populations will increase our knowledge about the species'ecology and demography and some of the environmental or ecological drivers of population structuring. This, in turn, will be helpful for the sustainable harvesting and management of yellow anacondas in Argentina A previous study by Mendez et al. Eunectes notaeus, extending as far down as 30° S Yellow anacondas occur from the Pantanal region in Brazil and Bolivia, throughout Paraguay, to northeastern Argentina. Our study area encompasses the Argentinean portion of the species range, in the Formosa and Corrientes provinces . This reEunectes notaeus and continuous wetland systems as areas where gene flow is not prevented other than by geographical distance. We also considered the different habitat types and wetland systems as possible isolating factors, as described below. The defined putative populations are Formosa N, Formosa PR, Formosa SE, Corrientes E and Corrientes W  located 54 base pairs (bp) upstream of the control region within tRNA-proline, and the reverse primer (ENCR1R: AGGGGCTCCACCTTGACTA) 691 bp downstream within the control region. A single control region was then amplified using the following thermal profile: preliminary denaturation for 3 minutes at 94°C followed by 40 amplification cycles consisting of 30 seconds of denaturation at 94°C, 1 minute of annealing at 56°C, and one minute of elongation at 72°C, with a final extension period of 5 minutes at 72°C. Sequencing was carried out on an ABI 3730×l using Big Dye terminator .Blood samples were obtained from 183 yellow anacondas from 36 sampling sites within Formosa Province and Corrientes Province  and expoSequences were aligned using ClustalW in MEGA 5.03 with a gap opening penalty of 15, a gap extension penalty of 6.66, and a transition weight of 0.5 www.fluxusengineering.com).We first visualized the overall structure of the genetic data and potential spatial patterns of genetic diversity through the construction of haplotype networks. We used networks to visualize such relationships as they are more appropriate than trees at depicting data in which ancestral haplotypes are still present st (using pairwise differences between haplotypes) We evaluated genetic structuring between our putative populations by computing the pairwise fixation indices Fst (using haplotype frequencies) st/(1–Fst) and Φst/(1–Φst)) on geographic distance We were particularly interested in the potential mechanisms that may cause the observed genetic structure and gene flow. As a first approach to this question, we evaluated the importance of a suite of spatial and environmental variables to the observed genetic patterns. We evaluated the plausibility of a pattern of IBD for the arrangement of populations in our study using a regression of standardized fixation index (i.e. Fθ (2Neµ) where m is the immigration rate, µ the mutation rate, and Ne the effective population size. The product θ M results in the number of immigrants per generation 2Nem. We adopted a migration matrix model allowing for asymmetric migration rates between populations and variable subpopulation sizes. Our migration model prevented gene flow between populations Formosa N and Corrientes E or Corrientes W, since Formosa PR is a stepping-stone between them. We ran five replicates of a Markov chain scheme to produce initial values for our parameter estimation. Here, our data was tested with default starting values for the population size and M parameters, in 5 independent runs of the Markov chain scheme: 20 short chains , and 3 long chains . Using as initial parameters the consistent resulting values from these five initial runs, we launched three series of longer Markov chain schemes to estimate our parameters of interest. In the first series (s1), we launched in parallel 10 runs with 10 independent replicates each of the following Markov chain scheme: 15 short chains , and 5 long chains . The second series (s2) was a run consisting of 100 independent replicates of the same Markov chain scheme and starting parameter set. The third series (s3) was another run with 100 replicates of the same Markov chain scheme and increased starting M values , to ensure a wider exploration of the parameter space.To complement this approach, we evaluated the possibility of asymmetric gene flow in the study area, as this information may enhance our understanding of the relative roles of the rivers and associated areas in mediating gene flow for this species. We estimated asymmetric migration rates using the maximum likelihood procedures implemented in the software MIGRATE For the first series we report the average results of the 10 individual runs and the frequency of runs that resulted in non-zero M values, to illustrate the relative importance of individual runs. For the second and third series we simply report the resulting final matrices, each with the likelihood-weighted mean pairwise population size and bi-directional M values for each of their 100 replicates.b and 622 bp for ND4 were sequenced for 181 individuals. Control region sequences of 652 bp were obtained for 143 individuals. Full three-gene concatenated sequences of 1,901 bp were assembled for 141 individuals. These sequences are available in GenBank under accession numbers JN967113-JN967617. Within these 141 individuals, a total of 54 segregating sites were found for a nucleotide diversity (π) of 0.00477, with 34 sites being parsimony informative. A total of 36 haplotypes were present yielding a haplotype diversity of 0.853 (SD = 0.021).A total of 627 bp for cyt-b/ND4 network, and the three-gene concatenated network showing the clearest overall geographic structuring . The exact test of population differentiation Fixation indices showed significant differentiation (p<0.05) between most putative populations . Using tTests for IBD were significant (p<0.05) when measuring geographic distance between putative populations along rivers, and not significant (p>0.05) when measuring straight-line distance between putative populations, for both genetic distance measures . Our envθ; the remaining 2 runs showed some qualitative differences as well. The second and third series were almost identical qualitatively, with the third series displaying two additional non-zero pairwise M values as a result of the larger initial parameters. Specifically, all three series produced the following agreeing results: positive and relatively large values of gene flow from Formosa PR to Formosa N (with little gene flow in the opposite direction), from Formosa SE to Corrientes E, from Corrientes E to Formosa PR, and from Corrientes W to Formosa SE. The third series also produced positive gene flow to Corrientes W from Formosa PR and from Formosa SE, and smaller gene flow from Formosa SE to Formosa PR. Finally, the two non-identical runs in the first series produced five additional cases of very small gene flow , all of which were single occurrences (frequency of 1).All three series of MIGRATE runs produced consistent results that indicate asymmetric gene flow in the study area . Within Our analysis revealed clear evidence of spatial structure of yellow anacondas in the study area. Interestingly, as we detail below, such structure cannot be fully explained by simple spatial patterns but rather by a combination of spatial, environmental, and ecological factors.Boa constrictor occidentalisEunectes notaeus, the northern water snake (Nerodia sipedon sipedon) from Ontario, Canada has shown evidence of population structure between populations much closer together than those in our analysis (less than 2 km apart), and dry areas were found to greatly reduce capacity for dispersal for this aquatic snake Natrix natrix) over a 90 km2 area of habitat highly fragmented by agriculture. Dispersal capabilities are slightly better understood for large snakes, as there have been several ecological studies done. For instance, Rivas et. al discovered that large female green anacondas (Eunectes murinus) move very little, and large individuals typically move less than 20–30 m for several weeks after feeding or during pregnancy Most putative population comparisons showed very strong population structuring, which is likely a result of the relative autonomy of the different wetland systems in our study area and also the absence of suitable habitat between populations throughout the wide latitudinal gradient they occupy. Comparisons of genetic structuring with other large semiaquatic snakes are difficult due to lack of published genetic studies in large snakes. Lower levels of population structuring were found in studies of the closely-related Argentine boa constrictor, The reliability of our analysis and observed patterns stem from the power of the data we analyzed. It is often suggested that adding individuals or genetic markers results in increased resolution of performed analyses such as , though Eunectes murinus) Boa constrictorIn parallel to the evident power of our analyses and resolution in our data, it is important to highlight the inherent limitations of genetic analyses focusing on matrilineal markers. Yellow anacondas exhibit a high degree of sexual size dimorphism, with females attaining weights approximately twice that of males Eunectes notaeus requires habitat that is associated with rivers, like floodplains, and floating vegetation may influence their directionality of movement. Snakes move along the marshes abutting the rivers in both directions: upstream and downstream. As such, traditional methods of testing for IBD using straight-line distance between populations are inappropriate. By instead measuring linear distance along rivers we can better approximate the distance snakes must travel to reach other populations. Significant support for IBD using along-river distance, together with nonsignificant tests for IBD using Euclidean distance, indicates that rivers and their associated floodplains are important in the dispersal of this species. The environmental variables used in this study did not prove useful in predicting genetic distance between populations, as more complex and finer-scaled environmental variables are likely needed to accurately predict environmental isolation in this system. For instance, precipitation within the study area will be less important than presence or absence of riverine or flooded habitat. Variables and analyses that can give a better representation of suitable habitat will likely be more relevant in uncovering potential environmental isolation. Several options exist, such as predicting flooding with a digital elevation model and inundation simulation Eunectes notaeus would allow for additional approaches such as least-cost path Although anacondas appear to be using rivers to disperse, they do not use them as channels to swim with the current. However, Stegonotus cucullatus) from the riparian zone around the Adelaide River in the Northern Territory of Australia. Investigating more species exclusive to riverine habitat would help to reveal to what degree rivers drive asymmetric migration and gene flow.Confirming that riverine habitat is important to yellow anaconda dispersal allows us to focus on specific aspects of rivers that might be important to dispersal. Our gene flow analysis shows clear evidence of asymmetric gene flow, which indicates that the barriers to dispersal  are also asymmetric. Rivers are inherently directional in their flow, and this very likely contributes to the patterns of migration found here. Directional gene flow has previously been found in other snakes Putting our analyses in light of the historical geomorphology of our study area and the natural history of our species allows a better understanding of the issues we sought to evaluate. Our MIGRATE analysis shows that gene flow occurs from Formosa PR to Formosa N, but not in the opposite direction. The strong directional gene flow likely reflects the colonization events of Formosa N. Specifically, it could be the result of the highly dynamic hydrological processes that established the La Estrella marshes several decades ago Gene flow was detected from Formosa PR to Corrientes W, and not in the reverse direction. The directionality and strong flow of the Paraguay and Paraná rivers probably aids in the dispersal of vegetation and anacondas in a southerly direction, though only a small degree of gene flow was detected, and was only found in the MIGRATE analysis with extremely high starting M values. This may indicate that the strength of river flow is not as important for dispersal as other factors such as presence of suitable habitat in the areas surrounding rivers (i.e. floodplains). A low degree of gene flow between populations is supported by strong and highly significant values for fixation indices between Formosa PR and Corrientes W. The population at Formosa PR is situated on the Paraguay River downstream of wetlands in Paraguay and Brazil, where yellow anacondas are also found. Therefore there may be some unaccounted for migration of unsampled populations into our system, also known as a ghost population Migration from Corrientes E individuals to Formosa PR may also dilute the effect of Formosa PR to Corrientes W migration. Strong and consistent gene flow was discovered from Corrientes E to Formosa PR, but little to no migration was found in the opposite direction. Corrientes E swamps and marshlands are located along the ancient alluvial cone of the Paraná River, and its waters slowly flow from east to west. This combined with continuous favorable habitat supports the possibility of directional migration between these two populations.The patterns of gene flow between Formosa SE, Corrientes W, and Corrientes E are less intuitive. These three populations show that movement in this system is bidirectional but asymmetric. Migration was found from Formosa SE to Corrientes W and Corrientes E, and also from Corrientes W to Formosa SE. This appears to indicate strong upstream dispersal from Formosa SE to Corrientes E along the Paraná River and its ancient alluvial valley now covered with multiple swamp systems (with a much lower rate of gene flow in the opposite direction), and also upstream dispersal from Corrientes W to Formosa SE along the Paraná and Paraguay rivers and through the Paraguay River tributary streams. Since these populations are found relatively far away from their closest river, the observed patterns of gene flow could reflect a demographic history of connectivity by more extensive suitable habitat, rather than current gene flow. Small amounts of gene flow were also found from Formosa SE to Corrientes W, which follows the directionality of the Paraguay and Paraná rivers. Fixation indices support the presence of gene flow and lack of differentiation between these populations, as Fst values were nonsignificant for Formosa SE/Corrientes E and Formosa SE/Corrientes W.Eunectes notaeus is currently being harvested under a sustainable management plan in a single wetland located within Formosa N Genetic analysis helps us delineate management units and augments our understanding of demographic processes, which is particularly valuable in species such as aquatic organisms, which are notoriously difficult to observe.


Anseranas semipalmata  and wandering whistling-duck Dendrocygna arcuata . Microsatellite data were obtained from 237 magpie geese and 64 wandering whistling-duck. Samples were collected across northern Australia, and at one site each in New Guinea and Timor Leste. In the wandering whistling-duck, genetic diversity was significantly apportioned by region and sampling location. For this species, the best model of population structure was New Guinea as the source population for all other populations. One remarkable result for this species was genetic separation of two flocks sampled contemporaneously on Cape York Peninsula only a few kilometers apart. In contrast, evidence for population structure was much weaker in the magpie goose, and Cape York as the source population provided the best fit to the observed structure. The fine scale genetic structure observed in wandering whistling-duck and magpie goose is consistent with earlier suggestions that the west-coast of Cape York Peninsula is a flyway for Australo-Papuan anseriforms between Australia and New Guinea across Torres Strait.There are many large, easy-to-observe anseriform birds  in northern Australia and New Guinea and they often gather in large numbers. Yet, the structure of their populations and their regional movements are poorly understood. Lack of understanding of population structure limits our capacity to understand source-sink dynamics relevant to their conservation or assess risks associated with avian-borne pathogens, in particular, avian influenza for which waterfowl are the main reservoir species. We set out to assess present-day genetic connectivity between populations of two widely distributed waterfowl in the Australo-Papuan tropics, magpie goose  The evolution in isolation of Australo-Papua's distinctive avifauna is well known . Less wiAnas gracilis , of which eight species occur in both biomes see . Most ofgracilis , and somgracilis , but thegracilis . The latgracilis .Anseranas semipalmata) and wandering whistling-duck (Dendrocygna arcuata), both of which are known, at least anecdotally, to move between Australia and New Guinea  and D. arcuata pygmaea (New Britain)  . The movBritain) . The timBritain) .No prior population-level genetic data exist for the two species examined in this study. We used rapidly evolving microsatellite loci to examine contemporary genetic processes and spatial patterns see  by compaD. arcuata. The TIM population is recognized as part of the nominotypical subspecies D. a. arcuata. All other studied populations represent D. a. australis. Differences in wing length diagnose these two subspecies (Two hundred and thirty-seven magpie goose and 64 wandering whistling-duck specimens were predominantly collected afresh by the authors and others (Appendix S1). Apart from some cryo-frozen tissue samples, most samples were blood taken from live birds captured in mist nets over 2 years from mid 2007. On Cape York Peninsula, we also used a CODA Netlauncher  to target larger aggregations of anseriforms. Birds were sampled at multiple sites within the following regions : Northwebspecies . No prioBlood was collected from the brachial vein, centrifuged to form serum and red blood cell fractions, and stored in ethanol, although some samples were received as whole blood in ethanol or on FTA©  cards. Cryo-frozen tissues were subsampled and stored in ethanol for transport to the laboratory. Samples were transported and stored at room temperature. DNA extraction methods largely followed MGgagt19, Smo6, Caud24, Caud4, Bcau10, Aph13, Blm3. In magpie geese, the same protocol resulted in only Caud24 and Blm3 being suitable. Three further microsatellite loci, MGgagt14, MGgagt19, and MG11, were derived from a single library enriched for clones containing GA and GT repeats. These clones were constructed using DNA from one bird following Forty-seven primer pairs previously shown to amplify polymorphic microsatellites in one or more anseriform birds were first tested in wandering whistling-ducks with amplification protocols based on IS and thus test for HWE using a re-sampling procedure (9999 permutations were used). We present results calculated across all loci. Pairwise FST values were also calculated in GenoDive 2.0, which uses the ΦST value obtained from AMOVA ; model II is the same as Model I, but the locations Aurukun A and Aurukun B are pooled ; model III with PNG as the source population with direct migration routes to Aurukun A, Aurukun B, NWA, and TIM. The sink populations are not interconnected ; model IV is the same as model III, but the locations Aurukun A and Aurukun B are pooled ; In model V, all locations are part of a panmictic population (1 population parameter). For magpie goose, we evaluated the following seven models: model I with NWA, NT, CYP, FNQ, and PNG connected permitting gene flow among all locations. model II is the same as model I, but here, we pooled NWA and NT (NWA + NT) as biogeographic studies across northern Australia often find close relationships among populations in these two areas  were screened from PNG (28), CYP (21), NT (1), NWA (9), and Timor Leste (5). The number of alleles per locus across all regions ranged from 2 (Caud4) to 19 (Smo6), whereas the mean number of alleles per region ranged from 1.71 ± 0.18 (NT) to 8.9 ± 2.26 (PNG). Rarefaction analyses  showed that although numbers of alleles are increasing with sample size in each region, differences are non-significant. Notably, though, the PNG value is continuing to rise. Locus-specific heterozygosity ranged from 0.094 (Caud4) to 0.844 (Caud24).Specimens . The CYP samples of wandering whistling-duck, however, are not in HWE  and that of Aurukun approaches significance . Pairwise ΦST values are shown in SC = 0.064 ± 0.024, P = 0.002). Not surprisingly, AMOVA with the Aurukun samples splits into A and B slightly reinforced this result with the P value changing from 0.002 to 0.000 (full AMOVA not shown).When all samples of wandering whistling-duck were pooled, HWE was not rejected  were obtained from PNG (24), CYP (31), NT (51), NWA (20), and FNQ (111). Between seven and nine alleles were observed at each locus in magpie goose and heterozygosity per locus ranged from 0.35 (Blm3) to 0.75 (MGgagt14). Mean numbers of alleles per region ranged from 4.60 ± 0.51(NWA) to 6.80 ± 0.37 (FNQ). Observed heterozygosity ranged from 0.58 ± 0.07 (NT) to 0.61 ± 0.08 (CYP), 0.63 ± 0.05 (PNG), and 0.63 ± 0.07 (NWA). Rarefaction analyses suggest that the PNG sample has more private alleles than others, but standard errors overlap substantially (data not shown). Hardy–Weinberg equilibrium across all loci was not rejected in any sample.Specimens . The presence of private alleles in the PNG samples suggests caution here because the observed genetic variation is almost all within individuals, although a small, non-significant component was apportioned to regional differences. STRUCTURE suggests no subpopulation division: log-likelihoods of any estimate of the number of populations being greater than one were non-significant and no significant differences were detected among any samples at any level (model VII (panmixia) is clearly rejected and model IV is the best model tested. model IV uses the population on Cape York as a source and all other populations as sinks. The other models do represent the data better than the panmictic model, but do not explain the data well . The genetic divergence between the two Aurukun A and B further affirms the value of sampling at smaller scales.The observed genetic differentiation in wandering whistling-duck populations (or flocks) is remarkable in comparison to that observed in magpie goose populations that occupy the same habitats. The STRUCTURE result, in part, reflected the distinction between the two subspecies of WWD in our samples, inea see . We evalinea see  have higinea see . If we aWandering whistling-duck and magpie goose show considerable population structure and a model that assumes that the sampling locations are part of a large panmictic population can be excluded for both species. The best of the tested models, as estimated by Bayes factors, suggest a center of variability on Cape York Peninsula for the magpie goose and in Papua New Guinea for wandering whistling-ducks. One may assume that Cape York Peninsula represents a simple corridor. The presence there of differentiated populations in close geographic proximity to each other but differentiated genetically suggests that population structure is more complicated than can be explained by simple isolation-by-distance models, particularly in vagile species that flock.Anas clypeata), northern pintail (A. acuta), and garganey (A. querquedula) are regular  migrants to the vast floodplains and coastal swamps of southern New Guinea (D. a. australis of Australia and New Guinea and D. a. arcuata of Timor Leste, a distance of at least 550 km over water between adjacent populations. By contrast, the fine scale genetic structure observed in wandering whistling-duck and magpie goose is consistent with earlier suggestions that Cape York Peninsula, in particular the west-coast, is a flyway for Australo-Papuan anseriforms between Australia and New Guinea (Our findings also moderate any sense of isolation from avian-borne pathogens circulating in waterfowl populations in the archipelagos of Southeast Asia . The Ausw Guinea . In nearw Guinea , suggestw Guinea , thus po


Myrmica rubra over most of its Palearctic area, using mitochondrial DNA (mtDNA). The western and eastern populations of M. rubra belonged predominantly to separate haplogroups, which formed a broad secondary contact zone in Central Europe. The distribution of genetic diversity and haplogroups implied that M. rubra survived the last glaciation in multiple refugia located over an extensive area from Iberia in the west to Siberia in the east, and colonized its present areas of distribution along several routes. The matrilineal genetic structure of M. rubra was probably formed during the last glaciation and subsequent postglacial expansion. Additionally, because M. rubra has two queen morphs, the obligately socially parasitic microgyne and its macrogyne host, we tested the suggested speciation of the parasite. Locally, the parasite and host usually belonged to the same haplogroup but differed in haplotype frequencies. This indicates that genetic differentiation between the morphs is a universal pattern and thus incipient, sympatric speciation of the parasite from its host is possible. If speciation is taking place, however, it is not yet visible as lineage sorting of the mtDNA between the morphs.Widely distributed Palearctic insects are ideal to study phylogeographic patterns owing to their high potential to survive in many Pleistocene refugia and—after the glaciation—to recolonize vast, continuous areas. Nevertheless, such species have received little phylogeographic attention. Here, we investigated the Pleistocene refugia and subsequent postglacial colonization of the common, abundant, and widely distributed ant  The genetic constitution of species living today is partly a result of demographic processes during the Pleistocene climatic cycles . In the Traditionally, the main refugia of the European temperate fauna and flora have been placed in southern Europe—in the Iberian, Apennine, and Balkan peninsulas . IndicatLately, several researchers have pointed out that—to understand better phylogeographic patterns in Europe—studies on many additional taxa are needed . We sharTo expand the comprehension of the phylogeography of the western Palaearctic fauna and flora, we suggest that suitable study organisms should: (1) be common and abundant, (2) have extensive, continuous temperate–boreal Palaearctic distributions, and (3) be relatively cold-tolerant. Taxa such as these have had a high potential to survive in many refugia and, after the glaciation, to recolonize vast areas in the continuous zone suitable for the species. Consequently, the potential to survive in many refugia is likely to decrease the extinction risk of the species during the glaciation, and to increase the genetic differences among the populations during the long glacial isolation—both factors that will increase the genetic diversity of the present-day species . Thus, aFormica have been studied in the context of Palearctic refugia (Species that meet the above criteria (1–3) include many Palearctic insect taxa, but these have received phylogeographically little attention . For exa refugia , b, 2007Myrmica rubra (Linnaeus), is a perennial, cold-tolerant species  differentiation of the peculiar life forms of crogynes . The miccrogynes . The twocrogynes . Based ocrorubra . It was,y denied . Neverthetically , which setically . Such a Myrmica rubra from 60 localities in the Palearctic, including many sites within the putative refugia or their adjacent areas. We selected nests located at least 3 m apart and collected from each nest all castes of the host and parasite (if available), and preserved them in absolute ethanol. We also obtained through our colleagues 103 nest samples from 28 additional localities in the Palearctic, and four nest samples from two localities in Maine and Massachusetts, where M. rubra is an invasive species (M. rubra samples of We collected 241 nest samples of  species . In addin = 202) for which we extracted DNA from, we measured the mesosoma length using a Leica MZ95 stereomicroscope with 10× oculars and a Planapo 1.6× objective , to identify them as host and parasite morphs as specified by From each nest, we used one host and one parasite queen, if available, for sequencing. We extracted DNA from legs with the salt extraction method , and seqh) and nucleotide diversity (π) for each host and parasite population with the program Arlequin 3.11  to genetic distance. We used the Delaunay triangulation-based connectivity network to connect neighboring sampling locations to each other. Between each neighboring pair of locations, the program calculates genetic distance that results in a certain height in the topography. The peaks indicate large genetic distances between neighboring locations and, thus, high areal genetic diversity. To avoid possible effect of isolation by distance on the results, we used the residual genetic distances. For the total area covered (2204 km2), we specified an 89 × 24 grid and 0.5 as a distance-weighting parameter.To survey the genetic diversity geographically, we applied two approaches to the Eurasian host populations. First, using the Mantel test  and 1000M. rubra hosts, (2) within M. rubra parasites, and (3) between M. rubra hosts and their parasites with Φ -statistics  within atistics . In Arlee AMOVA,  to partiTo compare genetic connections of geographic areas and to infer locations of glacial refugia and postglacial recolonization routes, we reconstructed a haplotype network using statistical parsimony . HaplotySF test of selective neutrality, which is based on the infinite-site model  can be estimated applying the equation t = τ/2u, where u is the mutation rate of the sequences calculated from u = tmµ, where tm is the length of sequence (1428 bp) and µ the mutation rate per nucleotide year.We used Fu's te model , and a mte model  to assesFS value . The misFS value . The disFS value ; Fu 1997FS value  and usedt) of haplogroups as follows. The climate began to warm approximately 15 ka BP  values of three haplogroups that showed the strongest signs of recent expansion and included many tip haplotypes that were sampled only in the areas previously covered by glacial ice: 3-1 , 3-2 and 3-7, to estimate minimum and maximum mutation rates. If the expansion (t) of these haplogroups occurred 10–15 ka BP, then according to the equation t = τ/2u, the mutation rate would be 4–5% Ma−1.We estimated the time since divergence (t) from equation d = 2rt, where d is the number of substitutions and r the nucleotide substitution rate per site per year. Substitution rates of insect mitochondrial genes vary substantially  was 0.95 and nucleotide diversity (π) 0.0041.The COI gene fragment (565 bp) had 34 polymorphic sites and 40 haplotypes, and the Cyt b gene fragment (863 bp) had 77 polymorphic sites and 70 haplotypes. Neither fragment included stop codons or ambiguous regions. The combined gene fragments (1428 bp) included 101 haplotypes . The seqST = 0.54 ± 0.34, mean ± SD) and genetically diverse, though genetic diversity varied considerably among populations (h = 0.52 ± 0.38 and π = 0.0015 ± 0.0017 (mean ± SD), respectively. Genetic and geographic distances correlated weakly , indicating weak isolation by distance. In the genetic landscape, genetic diversity was highest in Central Europe, the Balkan–Southern Carpathian region and Siberia, and lowest in the north  and that of the microgynes (the inquiline) 1.65 ± 0.055 mm .The queens formed two size groups without medium-sized individuals. The mean (± SD) mesosoma length of the macrogynes (the host) was 2.12 ± 0.064 mm . The parasite populations were genetically less diverse than those of the host (Table S3).All haplogroups except 3–5 and 3–6 were encountered in parasitic individuals . Local hP = 0.00000) of the genetic variation was explained by queen morph within populations  occurred throughout western and Central Europe. Within potential refugia, we collected h1 in Spain A,  and sout species —occurred species  as the m species , though  species .M. rubra and favored regional differentiation of haplogroup 3–1, though without successful colonization beyond the Alps. The Alps have, indeed, been an effective dispersal barrier of many taxa  all differentiated from the central starlike set of the other 17 haplotypes in the same haplogroup ; Table 6any taxa , for exarallelus  and the oravicum .M. rubra is cold-tolerant and its distribution extends north, close to the forest-tundra zone  occurred in two potential refugia: southern Siberia H,  and the egion C,  to Italyegion C, —our sampegion C,  as a refFormica ants  occurred from southern Siberia H,  and Middica ants —the soutica ants .M. rubra. The area has been climatically stable through the Quaternary  and several local haplotypes (including some of the other haplogroups) occurred in the Balkan–Southern Carpathian region C, ; Table 6aternary , and it aternary . In the oravicum , the Foroup ants , and theratensis . We cannratensis , Middle ratensis , or soutratensis  as refugHaplogroup 3–4 is the most eastern in our samples, with most of its central, common haplotype (h13)—and notable differentiation, typical of refugia—found in Siberia H, ; Table 6M. rubra survived the ice age in several refugia, scattered over an extensive area from Iberia in the west to Siberia in the east. As also suggested by the multiple-refugia hypothesis, postglacial recolonization of the species to the present areas of distribution occurred along several routes. These postglacial colonization routes, headed northward from Iberia and the Balkan–Carpathian region, formed a wide secondary contact zone of high genetic diversity in Central Europe (seen also in Temnothorax ants (T. moravicum (Messor cf. structor (Our results on the distribution of the haplotypes thus support the hypothesis that rax ants . The souoravicum  and diffstructor .Myrmica rubra has been introduced from Europe to North America ( America , where i America . Since t America . In thisSF values. Such negative values may, however, also result from genetic hitchhiking and selection (After each Pleistocene glaciation, populations often experienced demographic and spatial expansions that left genetic imprints on their population structure . Haplogrelection .−1 based on this assumption holds, then most third-level haplogroups diverged during and possibly after the last glaciation, in the Holocene–Late Pleistocene (−1 (M. rubra has occurred during the last glaciation and the subsequent postglacial expansion.If the assumption that the haplogroups expanded after the LGM is correct and the mutation-rate estimate of 4–5% Maistocene . Even wicene (−1 , the thi


Amaranthus retroflexus, Carduus acanthoides, Pastinaca sativa. In four populations of each species we analysed the extent to which allele and genotype frequencies vary in consecutive life history stages including the summer seed bank, which has been overlooked up to now. We compared the winter seed bank , seedlings, rosettes, the summer seed bank  and fruiting plants. We found that: (1) All three species partitioned most of their genetic diversity within life history stages and less among stages within populations and among populations. (2) All genetic diversity parameters, except for allele frequencies, were similar among all life history stages across all populations in different species. (3) There were differences in allele frequencies among life history stages at all localities in Amaranthus retroflexus and at three localities in both Carduus acanthoides and Pastinaca sativa. (4) Allele frequencies did not differ between the winter and summer seed bank in most Carduus acanthoides and Pastinaca sativa populations, but there was a marked difference in Amaranthus retroflexus. In conclusion, we have shown that the summer seed bank is not genetically depleted by spring germination and that a majority of genetic diversity remains in the soil through summer. We suggest that seed banks in the species investigated play an important role by maintaining genetic diversity sufficient for recovery rather than by accumulating new genetic diversity at each locality.We attempted to confirm that seed banks can be viewed as an important genetic reservoir by testing the hypothesis that standing (aboveground) plants represent a nonrandom sample of the seed bank. We sampled multilocus allozyme genotypes from three species with different life history strategies:  The term “seed bank” refers to dormant seeds that are present in the soil. Buried seeds of many species can retain their viability for long periods Besides the ecological role of seed banks, several authors have studied their importance from an evolutionary perspective. This idea was first formulated by Templeton and Levin Many authors have tried to confirm that seed banks represent important genetic reservoirs by testing the hypothesis that standing (aboveground) plants represent a nonrandom sample of their species’ seed bank et al. et al. et al. Three mechanisms have been proposed to explain the commonly observed pattern of higher homozygosity and inbreeding in seed banks et al. Lesquerella fendleri. By contrast, Lundemo et al. et al. Arabidopsis thaliana and Arabidopsis lyrata subsp. petraea, respectively. Such large-scale, multipopulation studies are necessary to test whether there are any broad genetic differences between soil seeds and surface plants rather than mere idiosyncratic differences between these life-history stages in particular populations. These studies will also allow to test the hypothesis that seed banks reduce the rate of population differentiation by retaining alleles preserved from different generations Only a few empirical studies have investigated the genetic relationship between above- and belowground populations on large data sets . Moreover, few studies e.g.,  have invIn this study, we have introduced the term “summer seed bank”. It refers to seeds that persist in the soil after the spring germination peak and before new seeds are added to the soil by fruiting plants. It represents the actual seed bank for the next year(s) even if the aboveground population is completely destroyed. The summer seed bank thus holds very important information concerning the real amount of genetic diversity persisting in the seed bank through summer. If we compare only genetic diversity in the soil seed bank with the diversity of standing plants, we completely miss any information concerning genetic diversity that is actually present in the seed bank through summer. Despite this, the role of the summer seed bank has been overlooked until now, and studies that deal with the genetic relationship among various life history stages, including the summer seed bank on larger spatial scales, are missing. Such studies may answer the question: “What factors are responsible for nonrandom patterns of genetic variability commonly found in natural populations?” In this study, we sampled multilocus allozyme genotypes from three species with different life history strategies to test whether there are any broad genetic differences between soil seeds and surface plants. We analysed four populations of each species to ascertain the extent to which allele and genotype frequencies vary among life history stages including the summer seed bank. Specifically, we sought answers to the following questions: (1) Are there any differences in population genetic characteristics among species with different life history strategies? (2) Is the pattern of genetic variability consistent over several localities within each species? (3) Does the winter and summer seed bank differ from other life history stages and do seed banks in general thus serve as a genetic reservoir of the population? (4) Do seed banks reduce the rate of among-population differentiation?Amaranthus retroflexus, Carduus acanthoides and Pastinaca sativa revealed that most of the genetic diversity was partitioned within life history stages; the analysis accounted for 71.19, 93.44 and 95.55% of the overall variance, respectively  computed separately for ectively . In Cardulations .RS), observed heterozygosity (HO), gene diversity (HS), inbreeding coefficient f(FIS) and levels of differentiation among populations θ(FST) – among life history stages across all populations of individual species, we did not reveal any statistically significant differences (f(FIS) in Amaranthus retroflexus and Carduus acanthoides, and fixation indices θ(FST) in all species and life history stages were significantly different from zero  in Carduus acanthoides at one locality   and inbreeding coefficient f(FIS) were significantly different among life history stages only at locality Psov.When we tested differences among life history stages separately for individual populations of the three species, we obtained inconsistent results concerning individual parameters, populations and species , 2, 3. Wy Orech)  and onlylocality . Statistulations . SignifiAmaranthus retroflexus, the results for both Carduus acanthoides and Pastinaca sativa were not consistent . As pointed out by Morris et al. Amaranthus retroflexus has the potential to build large, persistent seed banks. This species, however, did not accumulate higher genetic diversity in its seed bank either. The winter seed bank did not accumulate genetic diversity and was not significantly different from other stages in other species such as Calluna vulgarisAtriplex tataricaCardamine amaraArabidopsis lyrata subsp. petraeaet al. et al. et al. Amaranthus . In the annual and invasive Amaranthus retroflexus, the number of seeds in the seed bank must decrease dramatically due to massive spring germination. The process of self-thinning can later remove a significant portion of individuals, which might be the reason why changes in allele frequencies were observed among nearly all life history stages. In the perennial, outcrossing species, this question seems less relevant. However, the analysis of Honnay et al. The potential role of soil seed banks in evolutionary dynamics of plant populations has evoked many theoretical  species . The annaranthus , 5, 6. Waranthus , 5, 6. Tobserved . These raccumulating local genetic diversity. Instead, our results suggest that seed banks in the species investigated play an important role by merely maintaining genetic diversity sufficient for recovery of population genetic diversity at localities.Even though the presence of a seed bank acting as a long-term reservoir of genetic diversity has been first pondered by Templeton & Levin maintaining genetic diversity sufficient for recovery rather than by accumulating new genetic diversity at each locality. Finally, we have shown that seed banks in the species under study did not have the effect of slowing population differentiation by retaining alleles preserved over multiple generations.We have demonstrated for the first time the extent to which the summer soil seed bank differs from other life history stages. Knowing this difference is crucial for answering the question that concerns the soil seed bank as a genetic reservoir of a population. We have clearly shown that the summer seed bank is not completely depleted by spring germination and that most of the genetic diversity can survive through summer. Our results support the assumption that seed banks may protect plant populations from detrimental consequences of size fluctuations. We suggest that seed banks in the species investigated play an important role by Amaranthus retroflexus L., Carduus acanthoides L. and Pastinaca sativa L. subsp. sativa. The principal criteria for species selection were diploid ploidy level and production of persistent seed banks. Furthermore, we selected species with different life history strategies and habitat preferences in order to test whether there are any broad genetic differences. The species characteristics were mostly taken from Amaranthus, Pastinaca and Carduus and can be summarized as follows: Amaranthus retroflexus is an annual species of highly disturbed habitats. It is a neophyte to the Czech flora, with its first record of occurrence from 1818 Amaranthus retroflexus is a self-compatible and probably primarily self-pollinated species, able to produce huge numbers of seeds, depending on the growing conditions. Seed production varies between tens and hundreds of thousands and occasionally reaches millions of seeds per plant. Seeds with impermeable and both mechanically and chemically resistant coats form persistent seed banks. Buried seeds can remain viable for at least 6 to 10 years. This period, however, may vary depending on the depth of burial, soil temperature and moisture, frequency of soil disturbance, and dormancy. Dormancy is regulated primarily by seasonal variation in temperature. Small seeds and a structured seed coat facilitate dispersal by water, animals (mainly humans) and, to a lesser extent, by wind.We chose the following species for our study: Carduus acanthoides is an annual, winter annual or biennial species of moderately disturbed habitats. It is an archaeophyte in the Czech flora Carduus acanthoides survives winter either as seeds or rosettes. The species forms dense stands at disturbed sites where competition is low.Pastinaca sativa is a biennial or short-lived, monocarpic, perennial species of habitats with a low level of disturbance P. sativa are protandrous, promoting outcrossing between different plants. The species is insect-pollinated and able to produce up to 2000 fruits per plant. Its seeds are efficiently dispersed by wind to a distance of several meters from the maternal plant as well as by humans along roadways and highways. The seeds of P. sativa possess morphological dormancy due to an underdeveloped embryo. Most seeds therefore germinate in the following spring Amaranthus retroflexus and Carduus acanthoides has been published by Mandák et al.  was same as in Mandák et al. Amaranthus retroflexus for which high inbreeding and among population differentiation was indicated  value is obviously the result of the high dispersal capacity of Carduus acanthoidesPastinaca sativa, which lacks any apparatus that would enable dispersal over long distances. In the present study, we therefore compared individual life history stages of species that differ not only in their life history strategies but also in levels and patterns of genetic diversity in order to test whether there are any broad genetic differences between soil seeds and surface plants.Population genetic diversity of the three species, regardless of their different life history stages, has been investigated earlier. A summary of population genetic diversity across 20 populations of ndicated . Howevernthoides . The lowWe tested the relationship among plants derived from seeds extracted from the soil seed bank, seedlings, rosettes and mature plants over a range of localities and species. We took samples at four different localities of our species’ ranges. Populations were selected on the basis of known genetic variability (see above), i.e. the most genetically variable populations were selected . These dAmaranthus retroflexus, we did not sample the rosette life history stage. In the perennial Carduus acanthoides, we sampled only the rosette life history stage instead of the seedling stage because we were unable to differentiate between large seedlings and small rosettes in the field. In Pastinaca sativa, we were able to sample all stages because they strongly differed among each other. We did not succeed in obtaining the summer seed banks from four populations: Pocedelice (Amaranthus), Orech (Carduus), and Ostopovice and Sedlec (Pastinaca).In four natural populations of our three species, we took 40 samples of each life history stage from regularly distributed permanent plots. To ensure sampling consistency, we used the same sampling strategy for all three species. To obtain samples from different phases of the life history cycle for our genetic analysis, we sampled several consecutive life history stages: (1) the winter soil seed bank (i.e. seed bank before the spring germination peak), (2) seedlings, (3) rosettes, (4) the summer soil seed bank (i.e. seed bank after the spring germination peak) and (5) fruiting plants . Each soil block was slightly disturbed to increase the probability of seed germination and placed on a layer of sterilized soil in a 25×25×25 cm garden pot. Emerging seedlings were harvested and transplanted into small pots. After 14 days, the soil was disturbed once again and sprayed with a gibberellic acid solution to break dormancy and speed up as well as synchronise germination of ungerminated seeds. From each population, forty seedlings were randomly harvested, grown to maturity and subjected to allozyme electrophoresis. We believe that we were able to establish plants from most seeds stored in the seed banks. Using a gibberellic acid solution, we broke dormancy of a majority of ungerminated dormant seeds because only a minimal portion of the seeds remained in the soil. We have to admit, however, that our results could be influenced by a bias in the differential establishment rates of seeds from different seed banks collected from different populations and different species. The same problem was encountered by Mandák et al. for Atriplex tataricaAtriplex tatarica.Soil samples of the winter seed bank were collected in February, of the summer seed bank in July. We then collected subsequent life history stages within the grid established during the winter seed bank soil sample collection. We randomly collected 4 seedlings, 4 rosettes and 4 fruiting plants around each of ten intersections of the gridlines but no further than 5 m away. Seedlings and rosettes were transported to the Experimental garden where they were grown to maturity and subjected to allozyme electrophoresis. From each fruiting plant, a single young expanded leaf was collected in the field, kept in a cool box and transported to the laboratory for subsequent analysis. Soil samples of summer seed banks were taken and processed in the same way as in the winter seed bank.Carduus acanthoides, 561 in Amaranthus retroflexus and 666 in Pastinaca sativa. All samples were analysed by gel electrophoresis using selected enzymes , observed heterozygosity (HO) and gene diversity (HS) were estimated using the software FSTAT F statistics F statistics f(FIS), which represents the inbreeding index due to non-random mating within populations, and θ(FST), which represents the fixation index due to population subdivision. This method allowed us to test whether these F statistics were significantly different from zero (determined by 5000 bootstrap replicates). Probability values for differences between various life history stages are given for two-sided t-tests after 10 000 permutations. All analyses were performed using FSTAT.To estimate genetic diversity and genetic structure, a locus was considered polymorphic if the frequency of the most common allele did not exceed 0.95. Genetic diversity parameters, i.e. allelic richness .(PDF)Click here for additional data file.Table S2Allele frequencies of Carduus acanthoides. Allele frequencies at eight loci in four populations and life history stages of Carduus acanthoides are given (.pdf).(PDF)Click here for additional data file.Table S3Allele frequencies of Pastinaca sativa. Allele frequencies at eight loci in four populations and five life history stages of Pastinaca sativa are given (.pdf).(PDF)Click here for additional data file.


Oligoryzomys nigripes and Euryoryzomys russatus) was examined for mitochondrial DNA (mtDNA) sequence haplotypes of the control region. Samples were taken from three localities in the Atlantic Rain Forest in southern Brazil, along an altitudinal gradient with different types of habitat. In both species there was no genetic structure throughout their distribution, although levels of genetic variability and gene flow were high.The population genetic structure of two sympatric species of sigmodontine rodents ( The rodent subfamily Sigmodontinae comprises about 371 species, grouped into eight tribes  is a small mouse (averaging 25 g in body mass) that occurs in grasslands and forests in Brazil  is a terrestrial rodent, typically found in forest areas, with a medium-sized body (averaging 60 g in body mass)  were captured with live traps. DNA was extracted from frozen liver samples according to a protocol described by et al. 2006). PCR conditions were the same as those described by FST (dy mass) . Both spdy mass) . The pred by FST  using thOligoryzomys nigripes and E. russatus were similar  when using RAPD markers in populations of six species of Oligoryzomys, including O. nigripes. An enzyme-electrophoretic study by Oligoryzomysflavescens from Argentina, and found a lack of isolation-by-distance pattern among these populations. The haplotype network topologies of O. nigripes and E. russatus are shown in Overall gene-flow estimates yielded a low and nonsignificant value for O. nigripes was more abundant in dense and mixed ombrophilous forest, whereas O. russatus was more so in lowland swamp forest (Delomys dorsalis (Akodon reigi (Both sigmodontine species exhibited no population genetic structuring, although they showed similar patterns of shared haplotypes within the different types of habitat and altitudes of the rainforest. According to p forest . However


Ascaridia galli has reappeared in hens kept for egg production in Sweden after having been almost absent a decade ago. Today this is a frequent intestinal nematode parasite in non-caged laying hens. The aim of this study was to investigate the genetic diversity (Fst) in A. galli collected from different poultry production sites in southern Sweden, to identify possible common routes of colonization.The poultry roundworm Adult parasites (n = 153) from 10 farms, including both broiler breeder parents and laying hens, were investigated by amplified restriction fragment length polymorphism analysis (AFLP). Worms from a Danish laying hen farm were also included for comparison. Most of the farms were represented by worms from a single host, but on two farms multiple samples from different hosts were assessed in order to study flock variation.A. galli genetic variation within the same flock (Fst = 0.01 and 0.03 for two farms). Between-farm analysis showed a moderate population genetic structure (Fst = 0.13), along with a low mutational rate but high gene flow between different farms, and absence of strong genetic selection. Network analysis showed repeated genetic patterns among the farms, with most worms on each farm clustering together as supported by high re-allocation rates.A total of 97 fragments (loci) were amplified among which 81% were variable alleles. The average genetic diversity was 0.13 (range = 0.09-0.38), which is comparable to other AFLP studies on nematodes of human and veterinary importance. Within-farm variation showed that worms harboured by a single hen in a flock covered most of the A. galli populations were not strongly differentiated, indicating that they have undergone a genetic bottlenecking and subsequent drift. This supports the view that the investigated farms have been recently colonized, and that new flocks are reinfected upon arrival with a stationary infection.The investigated  Organisms vary genetically as a reflection of their evolutionary history and, thus information about the population genetic structure is basic to the understanding of biodiversity. Quantifiable components of this structure include: genetic diversity, population hierarchical structure, population mutation rate, rate of gene flow, and selective neutrality . ParasitDictyocaulus viviparus, a trichstrongylid lungworm of ungulates [Ascaris suum, an Ascarid intestinal parasite of pigs [Haemonchus contortus, a trichostrongylid abomasal parasite of ruminants [Necator americanus, a strongylid intestinal nematode of humans [However, unlike most free-living organisms, genomic variation of parasites is not only influenced by their own reproductive and transmission patterns but also by host genetics and behavior (e.g. migration) . In the ngulates , Ascaris of pigs , and Haeuminants ; as wellf humans .Ascaridia galli[A. galli within and between flocks on different farms using AFLP. The overall aim was to quantify the A. galli population diversity and structure, and to compare the results with what is known about the recent reapperance of A. galli in the Swedish egg industry.By the end of 2004 the housing system for almost all Swedish commercial laying hens had been changed from conventional battery cages to furnished cages, indoor litter-based housing systems or free-range production, in order to improve bird welfare. In non-caged hens, this change was accompanied by a rapid increase of roundworm infections, especially dia galli. The soudia galli,14. To eA. galli from laying hens and in one population from broiler breeder parents  and the T4 DNA ligase, which were from New England Biolabs. The restriction enzymes were used together with two classes of selective primers with three additional nucleotides at their 3′-end. PCR amplifications were performed in a PTC-200 Peltier Thermal Cycler (MJ Research) with fluorescent labeled EcoRI primers (5′-end), followed by fragment detection on a Genetic Analyzer (ABI 3100). Data were analysed using GeneMapper software (version 3.7), in which the obtained peaks were sized and converted to binary characters . The AFLP procedure requires a decision to be made about the cut-off level for when to score an AFLP peak from a given locus as present or absent: a low threshold will produce too much ‘noise’ while a high level will reject too much real genetic variation. There are few established criteria for this [From most farms, 10 roundworms were collected from an individual hen  is also assumed, as is the absence of sequence recombination. Conversion of data formats used AFLPdat (version 20.10.2010) [There are many methods available for quantifying various aspects of population genetics . Here, w10.2010) . In all j), genetic diversity (Hs and Ht) and population structure (Fst) from these estimates followed the procedures of Lynch and Milligan [Following Bonin et al. , the estMilligan , with 10Milligan .μ) was estimated using the iterative procedure described by Chakraborty and Weiss [j. Gene flow between the field isolates (Nm) was estimated using the Fst method described by Slatkin and Barton [The rarity index, which is a measure of the number of rare markers in each population corresponding to the frequency down-weighed marker value proposed by Schönswetter and Tribsch , was calnd Weiss  based ond Barton . The Ewed Barton , with 10d Barton . Pairwisd Barton  as modifd Barton , using td Barton , these dd Barton .The genetic similarity of each nematode to the other members of the same population was formally tested using the maximum-likelihood jackknife re-allocation technique described by Campbell et al. , based oPairwise genetic distances between the populations were calculated following Reynolds et al. , using AWe evaluated cut-off levels for recognizing presence or absence of each gene fragment of 50–100 Units (U) for each sample Table . A cut-oA. galli were analysed from the 6 chickens from Jönköping, and a total of 68 AFLP markers were generated, of which 46 were variable among the worms , which averaged across all loci excluding the non-variable ones, was in the range of 0.18–0.23 for all of the individual hens from Jönköping  was very weak for both the Jönköping and Denmark samples  and a total of 97 informative AFLP markers were generated, of which 79 were variable among the worms  of A. galli, was (0.09–0.15) for all of the farms, as would be predicted from the within-hen results, indicating an equivalent amount of genetic diversity among the nematodes irrespective of whether they had been obtained from a single or from multiple host animals  was moderate  was only 0.11, indicating that drift dominates mutation in determining the amount of genetic variation. Furthermore, the gene flow among isolates  was relatively high . This pattern of variation is most appropriately investigated and can be visualized by a phylogenetic network . The only notable exception to this pattern was the sample from Denmark, where the 10 worms were scattered in 3 equal clusters, each cluster associated with a different Swedish farm  of the worms to their farm of origin , and relatively little total genetic diversity (Ht = 0.15). However, this structure was greater than that previously reported for Haemonchus contortus in northern Europe  was very similar . Thus, the lungworm D. viviparus shows much greater genetic differentiation between farms than do the two gastrointestinal parasites, although the levels of genetic diversity are similar. Because AFLP markers are sampled throughout the genome they are appropriate for fine scale-studies, and there is a negligible risk that the results are biased due to directional selection of a single or few gene(s) that may not be representative of the whole genome per se [When the parasites from different flocks on separate farms were compared, we found evidence of a relatively moderate population genetic structure F = 0.07; ) but sma;  but sme per se . Thus, wst values, there were distinct patterns of genetic differentiation among farms. The worm re-allocation success was high (87%) and the phylogenetic network showed evident clusters. Thus, most of the worms on each farm were genetically more closely related to each other, and distinct from the worms on other farms. However, each farm contained a few individuals that were more closely related genetically to worms on other farms suggesting new immigrants or retention of polymorphism from the original founders. This may indicate that the investigated farms were colonized by a common genotype in the past and that genetic bottlenecking and subsequent drift have occurred on each farm. This supports the idea that worm eggs deposited by the previous flock infected most laying hens [In spite of the moderate Fing hens . The altIt is unclear how the biological characteristics of a particular parasitic nematode affect the outcome of the genetic variation, especially when studied with a molecular technique targeting dominant multilocus markers, such as with the AFLP. So, our results need to be interpreted with caution. Still, it is interesting to note that the exception to the above pattern is the sample from the Danish farm, where the worms were scattered in three clusters (in the network) associated with different Swedish farms. This suggests the intriguing possibility that the Danish Ascarids may be the historical source of some of the genetic variation among the Swedish Ascarids, which may have occurred in the past. This is a hypothesis that could be tested by collecting similar data from a wider sample of Danish farms.μ = 0.11) and migration rate (Nm = 1.7) indicate that the low genetic diversity might be a result of either a low mutation rate  or of movement of worms among farms (facilitating gene exchange). Most of the genetic diversity appeared to be under neutral evolution (75% of the fragments), suggesting a lack of strong selection in these nematodes. Geography, parental type and housing conditions apparently did not influence the genetic structure of the worms, suggesting that similar transmission patterns occur irrespective of production system. Unfortunately, no quantitative data are available for direct comparison.The estimates of population mutation rate (4NA. galli, which has been recently introduced to the investigated laying hen farms, has undergone a small amount of differentiation due to genetic drift or founder effects, and thus formed genetically distinct but still closely related A. galli isolates on the different farms. This conclusion accords with epidemiological data from Jansson et al. [A. galli eggs that have survived the cleaning procedures of the empty chicken houses between consecutive flocks, and are thus present before the replacement pullets arrive at the farms.Our analysis suggests that n et al.  and Högln et al. , who sugThe authors declare that they have no competing interests.JH conceived and coordinated the study, analysed the results and wrote the first draft together with DJ. DM carried out the molecular genetic analyses. AE contributed to the laboratory work and generation of the molecular data. PN critically revised the manuscript and contributed with interpretation of the data. All authors read and approved and contributed to the final version of the manuscript.


Macaca fascicularis, was introduced onto the island of Mauritius in the early 17th century. The species experienced explosive population growth, and currently exists at high population densities. Anecdotes collected from nonhuman primate trappers on the island of Mauritius allege that animals from the northern portion of the island are larger in body size than and superior in condition to their conspecifics in the south. Although previous genetic studies have reported Mauritian cynomolgus macaques to be panmictic, the individuals included in these studies were either from the southern/central or an unknown portion of the island. In this study, we sampled individuals broadly throughout the entire island of Mauritius and used spatial principle component analysis to measure the fine-scale correlation between geographic and genetic distance in this population. A stronger correlation between geographic and genetic distance was found among animals in the north than in those in the southern and central portions of the island. We found no difference in body weight between the two groups, despite anecdotal evidence to the contrary. We hypothesize that the increased genetic structure among populations in the north is related to a reduction in dispersal distance brought about by human habitation and tourist infrastructure, but too recent to have produced true genetic differentiation.The cynomolgus macaque,  Macaca fascicularis, are distributed widely throughout mainland Indochina and insular Southeast Asia Cynomolgus macaques, The island of Mauritius encompasses a total area of only 1860 square kilometers and population estimates of cynomolgus macaques have ranged from as high as 35,000 to 40,000 animals in the 1980's Macaca mulatta) is still the most commonly used non-human primate research model, the number of cynomolgus macaques imported into the United States for research purposes is increasing rapidly, with 126,000 cynomolgus macaques imported into the United states between the years of 2000 and 2005 Although the rhesus macaque  at Amboseli National Park in Kenya that fed from a lodge garbage dump were just as well nourished as, but spent half as much time feeding and had a much smaller home range than, other animals Anecdotal reports of trappers employed by breeding farms and biomedical research companies on Mauritius allege that animals from the northern half of the island can be easily distinguished from those in the south, with the northern animals exhibiting both larger body size and better condition than those in the south. While neither such a difference, nor its causes , has been quantitatively documented, the larger animals may be gaining a nutritional advantage from human presence. Muruthi et al. We collected 233 wild cynomolgus macaques from 14 different sites on the island of Mauritius  differentiation with regard to geography. However, a spatial principle component (sPCA) analysis found that the correlation between genetic differentiation and geographic distance was greater among populations on the northern coast of the island than elsewhere. Given the rapid population expansion and high population density of cynomolgus macaques on Mauritius, we discuss these results in relation to topography, land use and human population density.Estimates of heterozygosity and allele numbers for each sampling site can be found in The results of the spatial principle component analysis (sPCA) are illustrated in The pairwise Fst The results of the phenotypic analysis are shown in M. fascicularis across Mauritius must have been “explosive”, as no monkeys were mentioned in a list of animals found on Mauritius just eight years before the first description of monkeys on the island in 1606. Such a rapid expansion in the relatively recent past naturally fosters minimal geographic structure. Kondo et al. ST = 0.0892, with Nei's pairwise genetic distance between sampling sites not exceeding 0.0127; the authors concluded that there was no remarkable genetic differentiation between the sampling sites in south and south central Mauritius. These results are comparable to our comparison of the northern and south/central clusters; (Fst = 0.011), and our PCA could not significantly differentiate any of the sampling sites. In combination with the low mtDNA diversity and MHC homogeneity Sussman and Tattersall Despite the lack of true genetic differentiation, the sites on the northern coast of the island exhibited a greater correlation between geographic and genetic distance than the sampling sites in the south and south central portions of the island, suggesting that the dispersal among animals on the north coast is restricted compared to animals elsewhere. Mauritius is ringed by a low-lying coast that rapidly rises to a central plateau, the highest point of which roughly corresponds to the positions of sampling sites 1, 6, 7, and 10 M. fascicularis across the entire species' range, comparable to the values observed for the seven- to ten-year-old age group for both the northern  and southern/central  populations. Although both populations are slightly larger than the species average, they are nearly indistinguishable from each other. We conclude that differences in body size are not a factor in the genetic differentiation of M. fascicularis on Mauritius – body size differences neither drive nor result from genetic differences.Despite anecdotal reports that cynomolgus macaques on the northern end of Mauritius are larger than that elsewhere on the island, our analysis did not support this observation. No statistically significant difference in weight at capture was found between animals through 10 years of age sampled from the northern sites and the southern/central sites. The age at first reproduction in this species is approximately four years Founder effect and subsequent rapid expansion have resulted in a paucity of mtDNA, MHC and microsatellite variability in Mauritian, compared to other populations of cynomolgus macaques2), Mauritius has one of the greatest population densities of any sovereign territory in the world. Between 1965 and 1986 urban land use increased by over two-fold The resolution of this paradox may lie in the history of urbanization and development on the island of Mauritius. With a population of 1.1 million people  is dedicated to sugar cane plantations 2, slightly larger than that reported for other groups of Macaca fascicularis throughout Asia. Rodman 2 and 0.2 km2, respectively, for groups of cynomolgus macaques in the Kutai reserve, Indonesia that participated in crop raiding, although not specifically of sugar cane. Clinical and physiological examinations of animals in southern While making no direct comparison of home range sizes of northern groups versus those elsewhere on the island, Sussmann and Tattersall Despite broader sampling, the results of this study were concordant with previous genetic investigations of cynomolgus macaques on Mauritus. While significant genetic differentiation among the 14 sampling sites was not found, individuals formed two clusters in the PCA that roughly corresponded to the northern and southern/central portions of the island, albeit with substantial overlap. The Fst between the two groups was low, and calculations of Fis were comparable, suggesting a consistent excess of homozygosity across the island.A higher correlation between genetic and geographic distance was found in sites on the northern portion of the island compared to the southern/central portion. This divide may be moderately affected by changes in topography, but topography alone does not adequately explain the differentiation between neighboring sites along the uniformly low-lying northern shore. Similarly, no significant difference in body weight at capture was found between animals in the northern and southern/central parts of Mauritius. We hypothesize that the increase in human habitation and tourist infrastructure in northern Mauritius since the 1980s has contributed to, if not created, this effect, as animals supplement their diets with food from anthropogenic sources, reducing both the travel distance required to secure adequate nutrition and contact with neighboring groups.This study was carried out in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health and the Weatherall report, “The use of non-human primates in research”. The Institutional Animal Care and Use Committee of the University of California-Davis approved the protocol (#16549). The research described herein is part of larger study in which blood samples for DNA analysis were collected from multiple cynomolgus macaque breeding facilities and analyzed for purposes of genetic management, identification of country of origin, kinship, and phenotype association studies. Only blood samples were used as a DNA source in this study. Blood was collected from anesthetized animals following the standard blood collection procedure at the facility in question, not exceeding 2 ml per kg of body weight.Whole blood was collected from 233 cynomolgus macaques from 14 different locations on the island of Mauritius, as shown in 4)2SO4, 0.01% Tween-20, 0.05 mM each dNTP, 0.2 µm each primer, 1.7 mM MgSO4, 0.025 units/ml; Invitrogen Platinum Taq. The annealing temperatures and final hold times were independently optimized for each primer pair, but included an initial hold of 94°C for 3 minutes followed by 60 cycles of denaturing at 94°C for 30 seconds, annealing at 56–60°C for 30 seconds, extension at 72°C for 45 seconds and finally a hold at 72°C for 5–60 minutes. All samples were analyzed on an ABI 3130×l genetic analyzer following the manufacturer's protocol and using the GeneScan™ LIZ size standard to assign genotypes. No individual had more than 5% missing data.All samples were genotyped at 28 autosomal microsatellite loci, listed in Allele number per locus as well as observed and expected heterozygosity were calculated with the adegenet package 1.3–1 for R Upon capture, each animal was weighed and age was estimated from dentition and body condition. Individuals were categorized by age at capture into the following groups: three years old or less, four to six years, seven to ten years, eleven to thirteen years, and fourteen to seventeen years. Age could not be accurately determined for 110 of the individuals. To avoid biasing the comparison of body weight, ten males were removed from the analysis. One of the males was from the northern population (site 13) while the remaining eight males were from the southern/central population . Of the remaining 113 females, 11 were sampled from the northern population and 101 were sampled from the southern/central population. The distribution of weight at capture for each age group was tested for normality using the Shapiro-Wilk test Table S1Observed and expected heterozygosity values for each of the sampling sites.(XLSX)Click here for additional data file.


Hemidactylus mabouia, a nocturnal African gecko recently introduced to Florida, USA. Twelve highly variable microsatellite loci were used to screen 418 individuals collected from 43 locations from four sampling sites across Florida, representing a gradient from earlier (∼1990s) to very recent colonization. We found earlier colonized locations had little detectable genetic structure and higher allelic richness than more recently colonized locations. Genetic structuring was pronounced among locations at spatial scales of tens to hundreds of meters near the leading edge of range expansion. Despite the rapid pace of range expansion in this introduced gecko, dispersal is limited among many suitable habitat patches. Fine-scale genetic structure is likely the result of founder effects during colonization of suitable habitat patches. It may be obscured over time and by scale-dependent modes of dispersal. Further studies are needed to determine if such genetic structure affects adaptation and trait evolution in range expansions and range shifts.Processes of range expansion are increasingly important in light of current concerns about invasive species and range shifts due to climate change. Theoretical studies suggest that genetic structuring may occur during range expansion. Ephemeral genetic structure can have important evolutionary implications, such as propagating genetic changes along the wave front of expansion, yet few studies have shown evidence of such structure. We tested the hypothesis that genetic structure arises during range expansion in  Genetic structure often arises as the result of restricted gene flow and genetic drift among populations over relatively long periods of time Despite the potential importance of genetic structure at the leading edge of range expansions, very few empirical studies have investigated it Invasive species are ideal systems for investigating dynamics of range expansion Hemidactylus mabouia as a model system to investigate the fine-scale genetic patterns that arise during range expansion. Hemidactylus mabouia is native to Africa st/θF = 0.06) We used the ongoing invasion of the tropical house gecko H. mabouia. The likely cause of increased structure at these brief time scales is the subsampling of genetic diversity during colonization and founding events, so we also tested for the predicted loss of genetic diversity in recently colonized locations. While limited gene flow should generate population structure initially, even low levels of subsequent gene flow among locations will erode the signature of colonization. Therefore, we also tested the hypothesis that genetic structure will be most pronounced at the leading edge of invasion by comparing the genetic structure of recently colonized sites with that in Miami, the source of the Florida invasion. These tests were conducted in 43 locations in four sample sites across Florida using genetic variation at twelve highly variable microsatellite loci.We tested the hypothesis that fine-scale genetic structure arises during the colonization of new locations in Florida by All tissue collection for this study was approved by the Institutional Animal Care and Use Committee at the University of Cincinnati under protocol 06-06-01-01, and all efforts were made to minimize animal suffering.Hemidactylus mabouia is a nocturnal, sexually reproducing, insectivore that can be found commonly on human structures. Buildings represent patches because the habitat between buildings  is generally unsuitable and likely limits dispersal. We collected 418 gecko tissue samples (tail tips) from 43 locations (buildings) in Florida , Fort De Soto Park  and Florida Institute of Technology .As H. mabouia using multiplex PCR with four loci in each reaction Geckos were captured by hand from March–September 2009 and the location of each individual was noted with a handheld GPS (Garmin). Tail tissue samples were collected and stored in 70% ethanol. We amplified 12 microsatellite loci developed for stF by calculating θ, which accounts for small and unequal sample sizes, in gda v.1.1 θ were calculated by bootstrapping across loci in gda and used to assess overall levels of structure within sites. We tested for differences in pairwise θ values among locations using exact tests in genepopfstatθ accounts for small and unequal sample sizes, we further explored the effect of sample size differences on θ with resampling down to a size of 3 individuals. We used analysis of molecular variance (amova) to partition genetic variance among hierarchical levels To determine the degree of population differentiation, we estimated structure v.2.3.1 structure analyses produced no qualitative change in the results, so sample size differences among sites can be ruled out as a factor that accounts for clustering differences. To incorporate geographic information into our analyses of population structure, we also used spatial Bayesian inference in genelandWe used the Bayesian clustering program We used MCMC simulations to assess the relative likelihoods of a migration-drift equilibrium (gene flow) model versus a nonequilibrium drift model. We used 2MOD microchecker v. 2.2.3 genepop on the Web genepop on the Web.Tests for null alleles were conducted in fstat v.2.9.3.2 fstat. To test for differences in allelic richness among sites (pooling locations within sites), we used a Wilcoxon sign-rank test. Significance tests were conducted in JMP 7.0, with alpha of 0.05.Allelic richness was calculated using rarefaction to account for differences in sample size among locations in bottleneck v.1.2.02 We tested for bottlenecks on individual buildings with We sampled 124 individuals from 12 locations at the University of Miami , 140 individuals from 12 locations in the Everglades National Park , 90 individuals from 9 locations at Fort De Soto , and 64 individuals from 10 locations at F.I.T. , it was only marginally significantly different from zero (lower CI = 0.000), and 10.6% of all pairwise comparisons were significant . Comparisons among sites showed that Miami was significantly less differentiated compared to F.I.T. (P = 0.002) and marginally so from Fort De Soto (P = 0.053), while the Everglades was also marginally less differentiated than F.I.T. (P = 0.063). Resampling simulations confirmed that slightly lower sample sizes at Fort De Soto and F.I.T. did not explain their higher θ values (results not shown).Near the origin of invasion at the University of Miami there was little genetic differentiation among locations , most likely because populations are not at equilibrium. At Fort De Soto, there appeared to be substantial differentiation between the campground locations and the other locations, but within each group of locations there was no evidence for isolation by distance. There was a positive spatial autocorrelation at all sites except Miami. In the Everglades, there was positive autocorrelation (P<0.05) over distances of 70 meters . At Fort De Soto, there was positive autocorrelation over distances of 80 meters . At F.I.T., there was positive autocorrelation over distances of 70 meters .Results of the AMOVA suggested that the percentages of total genetic variation among locations (as opposed to within locations) were as follows: University of Miami (earliest colonized), 3%; Everglades, 9%; Fort De Soto, 13%; and F.I.T. (most recently colonized), 17%. These results reflect a relative lack of differentiation among locations at Miami and highest differentiation at F.I.T., the most recently colonized site. There was no evidence for isolation by distance (IBD) at any of the four sites according to Mantel tests , the Everglades , and Fort De Soto . However, F.I.T., showed evidence for the drift model, which suggests locations within this site have been more recently colonized .In our tests for migration-drift equilibrium, there was support for the gene flow model in the three sites occupied for the longest period of time, which suggests locations within these sites are nearer to equilibrium: Miami (bottleneck program. One location in the Everglades (E11) had heterozygosity deficit according to the program, and this could be due to recent admixture occurring at this location.Pronounced genetic structure that arises rapidly is likely the product of genetic drift, which predicts that recently colonized sites should be less genetically diverse. Locations at the two most recently colonized sites, Fort De Soto and F.I.T., had significantly lower allelic richness than those at the other two sites, the University of Miami and Everglades National Park ; Fig. 3.H. mabouia surveyed from small habitat patches, those closer to the leading edge of range expansion showed pronounced genetic structure at surprisingly small spatial scales (<100 m), while other populations colonized earlier near the point of introduction showed little evidence of genetic structure Click here for additional data file.


Survival can be greatly facilitated by phenotypic plasticity, and heritable variation in plasticity can further speed up genetic evolution. Multivariate selection and genetic correlations are frequently assumed to constrain adaptation, but this is not necessarily the case and depends on the geometric relationship between the fitness landscape and the structure of genetic variation. Similar conclusions hold for adaptation to shifting spatial gradients. Recent models of adaptation in multispecies communities indicate that the potential for rapid evolution is strongly influenced by interspecific competition.An increasing number of studies demonstrate phenotypic and genetic changes in natural populations that are subject to climate change, and there is hope that some of these changes will contribute to avoiding species extinctions (‘evolutionary rescue’). Here, we review theoretical models of rapid evolution in quantitative traits that can shed light on the potential for adaptation to a changing climate. Our focus is on quantitative-genetic models with selection for a moving phenotypic optimum. We point out that there is no one-to-one relationship between the rate of adaptation and population survival, because the former depends on relative fitness and the latter on absolute fitness. Nevertheless, previous estimates that sustainable rates of genetically based change usually do not exceed 0.1  Over the past two decades, it has become clear that evolutionary change can be fast enough to be observed in present-day populations . In particular, we will not treat evolutionary rescue via the fixation of single large mutations , but this favored phenotype changes over time. The most important scenarios are the following:A single, sudden change in the optimum: this is a classic scenario studied in population genetics and also in recent models about the genetic basis of adaptation Orr  and evolGradual  movement of the optimum: this scenario seems best suited to investigate the effects of continued climate change Fig. .Random fluctuations of the optimum, either around a constant value or around a linear trend: these fluctuations may or may not show autocorrelation. Such models are useful to study the effects of environmental stochasticity that overlay all climate-driven trends.The majority of models reviewed here are based on quantitative genetics theory. Evolving traits are assumed to have a polygenic basis and follow a normal distribution with phenotypic variance t, that is, the derivative of log mean fitness haldanes can be obtained by standardizing with σp, yieldingwhere that eqn  is analoβσ,t = cov/σp is the variance-standardized selection gradient  genetic covariance matrix and E the matrix of environmental variances and covariances. The multivariate version of Lande's equation isFor multiple traits, the structure of phenotypic variation is summarized by the matrix n traits, G-matrix. In particular, genetic correlations can cause the response to selection to show a bias toward trait combinations with high genetic variation . The eigenvectors  can be viewed as composite traits  that are genetically uncorrelated  and whose genetic variances are given by the corresponding eigenvalues. Graphically, if the distribution of breeding values  is multivariate Gaussian, isoclines of this distribution can be represented by ellipses , with axes given by the eigenvectors and their lengths proportional to the roots of the eigenvalues  represents the trait combination with a maximum of genetic variation. Is has been called gmax or the genetic line of least resistance  Lande . The keyk. This model has been analyzed by Lynch et al.  have low fitness.Thus, in contrast to the sudden-change scenario, evolutionary rescue in a gradually changing environment requires that the population maintain a positive growth rate at all times. This is a consequence of the ‘relentless’ movement of the optimum, which means that a population that has fallen behind in the race will get no chance to catch up. It also is noteworthy that extinction in this model usually is not due to a lack of genetic variance , nor due the classical ‘cost of selection’  induces a high standing load, which reduces the realized growth rate and diminishes the ability of the population to tolerate environmental change. On the other hand, sufficiently weak selection in combination with a moving optimum increases lag load, because the population will follow the optimum at a greater distance. This somewhat counter-intuitive result is due to the fact that, on a flatter fitness landscape, reaching a given selection gradient requires a larger decrease in mean population fitness  when kcrit  that are under pure stabilizing selection . As illustrated in Fig. G-matrix is roughly constant over the timescale of interest. Evolution of the G-matrix has been studied in a recent series of papers by Jones, Arnold and Bürger  that is sensitive to measurement error when real rates of change are small , whereas the effect in small populations is negligible . In summary, κcrit is, indeed, likely to often be around or below 0.1 haldanes. Faster observed rates may be a sign that the population is under stress κcrit of t-test with α = 0.05). On the other hand, differences of this magnitude can easily be created by sampling effects . The variance of the mean phenotype due to genetic drift is Ne being the effective population size  to the mean rate of phenotypic change is N being the census population size). Together, these two sources of variation may dominate the generation-to-generation changes in the mean phenotype of small populations , it seems impossible to make general statements about the range and scope of plasticity. Here, we will instead focus on reviewing models that investigate the interaction between plasticity, population dynamics, and genetic evolution. Because several important aspects have already been reviewed elsewhere .For a single population, Reed et al.  studied Gienapp et al.  recentlyIn the following, we briefly review models in which plasticity can itself evolve. Conditions for the evolution of plasticity are fairly well understood. Plasticity is adaptive if individuals encounter different environmental conditions that favor different phenotypes and that can be assessed by a reliable cue . However, relative constraints arise in the same way, whenever an eigenvalue is positive but small. Using their concept of demographic constraints, Gomulkiewicz and Houle  to the smallest (λn). If genetic variation is uniformly distributed among the eigenvectors, nd takes it maximal value of n, whereas it is minimal  when genetic variation is only present along a single axis. A review of empirical estimates of nd suggests that it is often (much) smaller than the number of traits considered  modified G-matrix in which all off-diagonal entries  have been set to zero. Using data from empirical estimates of G- (or P)-matrices and selection gradients, they found that removing genetic correlations sometimes increases and sometimes decreases the rate of adaptation and that often, the effect is minor. In this context, it is worth pointing out that genetic correlations do not necessarily decrease the variance in a particular direction. For example, adding arbitrary covariances to a diagonal G-matrix can only increase genetic variation in the direction of the leading eigenvector . For a gradual-change model, this was confirmed via simulation by Bürger  see als. In partSeveral theoretical studies have compared adaptation in  haploid and diploid populations, but the results are complex. Haploid populations can be expected to evolve faster than diploid populations, because selection is more efficient in haploids , which has been pretested by selection in past environments Masel , differeDrosophila; Kellermann et al. On the other hand, species that have evolved under highly stable conditions are expected to be the most sensitive to environmental change . These effects are particularly pronounced if other factors acting on G, such as the input of mutational variance and mutational or selective correlations, are weak.The effect of gene flow on the Whitlock . Using aThe effect of phenotypic plasticity on local adaptation and the colonization of new habitats has been studied by Chevin and Lande  and ThibReal populations do not evolve in isolation but are embedded in a network of ecological interactions, and so predictions of responses to climate change should be made in a community context. Several studies have investigated the effects of interspecific competition on the rate of adaptation and the likelihood of evolutionary rescue. Both positive and negative effects are possible. The presence of competitors can reduce the rate of adaptation in a focal species by reducing its population size  and by ‘blocking’ the access to new ecological niches , community evolution depends on the interaction of local adaptation and dispersal  features, whereas the latter two are about external  factors. Further integrating these various models promises to significantly advance our understanding of species adaptations to climate change.