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424 results for “population differentiation”
Data from: Population genomic evidence reveals subtle patterns of differentiation in the trophically polymorphic Cuatro Ciénegas cichlid, Herichthys minckleyi
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Population differentiation and intraspecific genetic admixture in two Eucryptorrhynchus weevils (Coleoptera: Curculionidae) across northern China
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Data from: Mild temperatures differentiate while extreme temperatures unify gene expression profiles among populations of Dicosmoecus gilvipes in California
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Population structure and genetic differentiation in extant alligator snapping turtles (genus Macrochelys) with implications for taxonomy and conservation
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Supplementary material 1 from: Ollivier M, Kazakou E, Corbin M, Sartori K, Gooden B, Lesieur V, Thomann T, Martin J-F, Tixier MS (2020) Trait differentiation between native and introduced populations of the invasive plant Sonchus oleraceus L. (Asteraceae). NeoBiota 55: 85-115. https://doi.org/10.3897/neobiota.55.49158
Table S1. Location and climatic data for the 14 Sonchus oleraceus populations used for offspring comparisons under standardised conditions
Supplementary material 2 from: Ollivier M, Kazakou E, Corbin M, Sartori K, Gooden B, Lesieur V, Thomann T, Martin J-F, Tixier MS (2020) Trait differentiation between native and introduced populations of the invasive plant Sonchus oleraceus L. (Asteraceae). NeoBiota 55: 85-115. https://doi.org/10.3897/neobiota.55.49158
Table S2. Mean (± standard error) values for 20 traits assessed for native (Europe and North Africa) and invasive (Australia and New Zealand) populations of Sonchus oleraceus under standardised conditions
Supplementary material 3 from: Ollivier M, Kazakou E, Corbin M, Sartori K, Gooden B, Lesieur V, Thomann T, Martin J-F, Tixier MS (2020) Trait differentiation between native and introduced populations of the invasive plant Sonchus oleraceus L. (Asteraceae). NeoBiota 55: 85-115. https://doi.org/10.3897/neobiota.55.49158
Table S3. Results of mixed models assessing the effect of range (native: Europe and North Africa, introduced: Australia and New Zealand), population within range being considered as a random factor, for 20 plants traits measured on Sonchus oleraceus under standardised conditions
Climate manipulations differentially affect plant population dynamics within versus beyond northern range limits
<ol> <li>Predicting species' range shifts under future climate is a central goal of conservation ecology. Studying populations within and beyond multiple species' current ranges can help identify whether demographic responses to climate change exhibit directionality, indicative of range shifts, and whether responses are uniform across a suite of species.</li> <li>We quantified the demographic responses of six native perennial prairie species planted within and, for two species, beyond their northern range limits to a three-year experimental manipulation of temperature and precipitation at three sites spanning a latitudinal climate gradient in the Pacific Northwest, USA. We estimated population growth rates <span>(</span><span>λ</span><span>) </span>using integral projection models and tested for opposing responses to climate in different demographic vital rates (demographic compensation).</li> <li>Where species successfully established reproductive populations, warming negatively affected <span>λ</span> at sites within species' current ranges. Contrarily, warming and drought positively affected <span>λ</span> for the two species planted beyond their northern range limits. Most species failed to establish a reproductive population at one or more sites within their current ranges, due to extremely low germination and seedling survival. We found little evidence of demographic compensation buffering populations to the climate treatments.</li> <li> <i>Synthesis: </i>These results support predictions across a suite of species that ranges will need to shift with climate change as populations within current ranges become increasingly vulnerable to decline. Species capable of dispersing beyond their leading edges may be more likely to persist, as our evidence suggests that projected changes in climate may benefit such populations. If species are unable to disperse to new habitat on their own, assisted migration may need to be considered to prevent the widespread loss of vulnerable species.</li> </ol>
Data from: Population genomic analyses reveal a highly differentiated and endangered genetic cluster of northern goshawks (Accipiter gentilis laingi) in Haida Gwaii
Accurate knowledge of geographic ranges and genetic relationships among populations is important when managing a species or population of conservation concern. Along the western coast of Canada, a subspecies of the northern goshawk (Accipiter gentilis laingi) is legally designated as Threatened. The range and distinctness of this form, in comparison to the broadly distributed North American subspecies (Accipiter gentilis atricapillus), is unclear. Given this morphological uncertainty, we analyzed genomic relationships in thousands of single nucleotide polymorphisms identified using genotyping-by-sequencing of high-quality genetic samples. Results revealed a genetically distinct population of northern goshawks on the archipelago of Haida Gwaii and subtle structuring among other North American sampling regions. We then developed genotyping assays for ten loci that are highly differentiated between the two main genetic clusters, allowing inclusion of hundreds of low-quality samples and confirming that the distinct genetic cluster is restricted to Haida Gwaii. As the laingi form was originally described as being based in Haida Gwaii (where the type specimen is from), further morphological analysis may result in this name being restricted to the Haida Gwaii genetic cluster. Regardless of taxonomic treatment, the distinct Haida Gwaii genetic cluster along with the small and declining population size of the Haida Gwaii population suggests a high risk of extinction of an ecologically and genetically distinct form of northern goshawk. Outside of Haida Gwaii, sampling regions along the coast of BC and southeast Alaska (often considered regions inhabited by laingi) show some subtle differentiation from other North American regions. These results will increase the effectiveness of conservation management of northern goshawks in northwestern North America. More broadly, other conservation-related studies of genetic variation may benefit from the two-step approach we employed that first surveys genomic variation using high-quality samples and then genotypes low-quality samples at particularly informative loci.
Data from: Development of genetic diversity, differentiation and structure over 500 years in four ponderosa pine populations
Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range-margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range-margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500-year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within-population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (FST and Jost's Dest) and diversity within populations (FIS) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.
Data from: Phylogeography and population differentiation in the Psittacanthus calyculatus (Loranthaceae) mistletoe: a complex scenario of climate-volcanism interaction along the Trans-Mexican Volcanic Belt
Aim The formation of the Trans-Mexican Volcanic Belt (TMVB) played an important role in driving inter- and intraspecific diversification at high elevations. However, Pleistocene climate changes and ecological factors might also contribute to plant genetic structuring along the volcanic belt. Here, we analysed phylogeographic patterns of the parrot-mistletoe Psittacanthus calyculatus to determine the relative contribution of these different factors. Location Trans-Mexican Volcanic Belt Methods Using nuclear and chloroplast DNA sequence data for 370 individuals, we investigate the genetic differentiation of 35 populations across the species range. We conducted phylogenetic, population and spatial genetic analyses of P. calyculatus sequences along with ecological niche modelling and Bayesian inference methods to gain insight into the structuring of genetic variation of these populations. Results Our analyses revealed population structure with three genetic groups corresponding to individuals from Oaxaca and those from the central-eastern and western TMVB regions. A significant genetic signal of demographic expansion, an east-to-west expansion predicted by species distribution modelling, and approximate Bayesian computation analyses strongly supported a scenario of habitat isolation and invasion of TMVB by P. calyculatus during the late-Pleistocene. Main conclusions The genetic differentiation of P. calyculatus may be explained by the combined effects of (i) geographical isolation linked to the effects of the glacial/interglacial cycles and environmental factors, driving genetic differentiation from congeners into more xeric vegetation and (ii) the invasion of TMVB from east to west, suggesting a role for both colonization and glacial/interglacial cycles models.
Data from: Rates of population differentiation and speciation are decoupled in sea snakes
Comparative phylogeography can inform many macroevolutionary questions, such as whether species diversification is limited by rates of geographic population differentiation. We examined the link between population genetic structure and species diversification in the fully aquatic sea snakes (Hydrophiinae) by comparing mitochondrial phylogeography in 16 species from two closely related clades that show contrasting diversification dynamics across northern Australia. Contrary to expectations from theory and several empirical studies, our results show that, at the geographic scale studied here, rates of population differentiation and speciation are not positively linked in sea snakes. The eight species sampled from the rapidly speciating Hydrophis clade have weak population differentiation that lacks geographic structure. In contrast, all eight sampled Aipysurus-Emydocephalus species show clear geographical patterns and many deep intraspecific splits, but have three-fold slower speciation rates. Alternative factors, such as ecological specialisation, species duration, and geographic range size, may underlie rapid speciation in sea snakes.
Data from: Regional environmental pressure influences population differentiation in turbot (Scophthalmus maximus)
Unravelling the factors shaping the genetic structure of mobile marine species is challenging due to the high potential for gene flow. However, genetic inference can be greatly enhanced by increasing the genomic, geographic or environmental resolution of population genetic studies. Here we investigated the population structure of turbot (Scophthalmus maximus) by screening 17 random and gene-linked markers in 999 individuals at 290 geographical locations throughout the Northeast Atlantic Ocean. A seascape genetics approach with the inclusion of high resolution oceanographic data was used to quantify the association of genetic variation with spatial, temporal and environmental parameters. Neutral loci identified three subgroups: an Atlantic group, a Baltic Sea group and one on the Irish Shelf. The inclusion of loci putatively under selection suggested an additional break in the North Sea, subdividing southern from northern Atlantic individuals. Environmental and spatial seascape variables correlated marginally with neutral genetic variation, but explained significant proportions (respectively 8.7 % and 10.3 %) of adaptive genetic variation. Environmental variables associated with outlier allele frequencies included salinity, temperature, bottom shear stress, dissolved oxygen concentration and depth of the pycnocline. Furthermore, levels of explained adaptive genetic variation differed markedly among basins (3% vs 12% in the North and Baltic Sea, respectively). We suggest that stable environmental selection pressure contributes to relatively strong local adaptation in the Baltic Sea. Our seascape genetic approach using a large number of sampling locations and associated oceanographic data proved useful for the identification of population units as the basis of management decisions.
Data from: Large-scale genetic panmixia in the blue shark (Prionace glauca): a single worldwide population, or a genetic lag-time effect of the "grey zone" of differentiation?
The blue shark Prionace glauca, among the most common and widely studied pelagic sharks, is a top predator, exhibiting the widest distribution range. However, little is known about its population structure and spatial dynamics. With an estimated removal of 10 to 20 million individuals per year by fisheries, the species is classified as "Near Threatened" by International Union for Conservation of Nature. We lack the knowledge to forecast the long-term consequences of such a huge removal on this top predator itself and on its trophic network. The genetic analysis of more than 200 samples collected at broad scale (from Mediterranean Sea, North Atlantic and Pacific Oceans) using mtDNA and nine microsatellite markers allowed to detect signatures of genetic bottlenecks but a nearly complete genetic homogeneity across the entire studied range. This apparent panmixia could be explained by a genetic lag-time effect illustrated by simulations of demographic changes that were not detectable through standard genetic analysis before a long transitional phase here introduced as the "population grey zone". The results presented here can thus encompass distinct explanatory scenarios spanning from a single demographic population to several independent populations. This limitation prevents the genetic-based delineation of stocks and thus the ability to anticipate the consequences of severe depletions at all scales. More information is required for the conservation of population(s) and managements of stocks, which may be provided by large scale sampling not only of individuals worldwide, but also of loci genome-wide.
Data from: Evidence for genetic differentiation in timing of maturation among nine-spined stickleback populations
Timing of maturation is an important life-history trait that is likely to be subjected to strong natural selection. Although population differences in timing of maturation have been frequently reported in studies of wild animal populations, little is known about the genetic basis of this differentiation. Here, we investigated population and sex differences in timing of maturation within and between two nine-spined stickleback (Pungitius pungitius) populations in a laboratory breeding experiment. We found that fish from the high-predation marine population matured earlier than fish from the low-predation pond population and males matured earlier than females. Timing of maturation in both reciprocal hybrid crosses between the two populations was similar to that in the marine population, suggesting that early timing of maturation is a dominant trait, whereas delayed timing of maturation in the pond is a recessive trait. Thus, the observed population divergence is suggestive of strong natural selection against early maturation in the piscine-predator-free pond population.
Data from: Historical population size change and differentiation of relict populations of the endangered giant kangaroo rat
From a conservation management perspective it is important to understand how genetic diversity is partitioned across a species' range, including (1) identification of evolutionarily distinct units versus those recently isolated through anthropogenic activities and (2) the relative genetic contributions among components of fragmented (meta)populations. To address these questions, we investigated the phylogeography and metapopulation structure among relict populations of the endangered giant kangaroo rat (Dipodomys ingens) in the highly altered San Joaquin Desert Ecosystem. This keystone species underwent a ~97% range reduction over the past century, resulting in a current range that is highly fragmented, with two dominant northern and southern populations occurring 150 km apart. We sequenced >800 bp of mitochondrial DNA and genotyped 17 nuclear microsatellites in >275 D. ingens to assess the evolutionary relationship of these populations as well as the genetic structure within the northern metapopulation. A Bayesian Skyline Plot indicated that the species experienced a demographic expansion toward the end of the Pleistocene, with a recent population decline. Northern and southern D. ingens split 1,857–13,443 years ago, prior to the massive conversion of the San Joaquin Valley to irrigated agriculture. We recommend that the northern and southern populations of D. ingens be re-classified as distinct population segments under the United States Endangered Species Act. We also observed population structure and asymmetrical migration within northern D. ingens where the Tumey Hills acted as a source contributing gene flow to all peripheral populations. This emphasized the importance of this location in the conservation of the metapopulation as a whole.
Data from: Population differentiation or species formation across the Indian and the Pacific Oceans? An example from the brooding marine hydrozoan Macrorhynchia phoenicea
Assessing population connectivity is necessary to construct effective marine protected areas. This connectivity depends, among other parameters, inherently on species dispersal capacities. Isolation by distance (IBD) is one of the main modes of differentiation in marine species, above all in species presenting low dispersal abilities. This study reports the genetic structuring in the tropical hydrozoan Macrorhynchia phoenicea α (sensu Postaire et al., 2016a), a brooding species, from 30 sampling sites in the Western Indian Ocean and the Tropical Southwestern Pacific, using 15 microsatellite loci. At the local scale, genet dispersal relied on asexual propagation at short distance, which was not found at larger scales. Considering one representative per clone, significant positive FIS values (from −0.327*** to 0.411***) were found within almost all sites. Gene flow was extremely low at all spatial scales, among sites within islands (<10 km distance) and among islands (100 to >11,000 km distance), with significant pairwise FST values (from 0.035*** to 0.645***). A general pattern of IBD was found at the Indo-Pacific scale, but also within ecoregions in the Western Indian Ocean province. Clustering and network analyses identified each island as a potential independent population, while analysis of molecular variance indicated that population genetic differentiation was significant at small (within island) and intermediate (among islands within province) spatial scales. As shown by this species, a brooding life cycle might be corollary of the high population differentiation found in some coastal marine species, thwarting regular dispersal at distances more than a few kilometers and probably leading to high cryptic diversity, each island housing independent evolutionary lineages.
Data from: How populations differentiate despite gene flow: sexual and natural selection drive phenotypic divergence within a land fish, the Pacific leaping blenny
Background: Divergence between populations in reproductively important features is often vital for speciation. Many studies attempt to identify the cause of population differentiation in phenotype through the study of a specific selection pressure. Holistic studies that consider the interaction of several contrasting forms of selection are more rare. Most studies also fail to consider the history of connectivity among populations and the potential for genetic drift or gene flow to facilitate or limit phenotypic divergence. We examined the interacting effects of natural selection, sexual selection and the history of connectivity on phenotypic differentiation among five populations of the Pacific leaping blenny (Alticus arnoldorum), a land fish endemic to the island of Guam. Results: We found key differences among populations in two male ornaments—the size of a prominent head crest and conspicuousness of a coloured dorsal fin—that reflected a trade-off between the intensity of sexual selection (male biased sex ratios) and natural selection (exposure to predators). This differentiation in ornamentation has occurred despite evidence suggesting extensive gene flow among populations, which implies that the change in ornament expression has been recent (and potentially plastic). Conclusions: Our study provides an early snapshot of divergence in reproductively important features that, regardless of whether it reflects genetic or plastic changes in phenotype, could ultimately form a reproductive barrier among populations.
Data from: Does local adaptation to resources explain genetic differentiation among Daphnia populations?
Substantial genetic differentiation is frequently observed among populations of cyclically parthenogenetic zooplankton despite their high dispersal capabilities and potential for gene flow. Local adaptation has been invoked to explain population genetic differentiation despite high dispersal, but several neutral models that account for basic life history features also predict high genetic differentiation. Here, we study genetic differentiation among four populations of Daphnia pulex in east central Illinois. As with other studies of Daphnia, we demonstrate substantial population genetic differentiation despite close geographic proximity (< 50 km; mean θ = 0.22). However, we explicitly tested, and failed to find evidence for, the hypothesis that local adaptation to food resources in these populations. Recognizing that local adaptation can occur in traits unrelated to resources, we estimated contemporary migration rates (m) and tested for admixture to evaluate the hypothesis that observed genetic differentiation is consistent with local adaptation to other untested ecological factors. Using Bayesian assignment methods, we detected migrants in three of the four study populations including substantial evidence for successful reproduction by immigrants in one pond, allowing us to reject the hypothesis that local adaptation limits gene flow for at least this population. Thus, we suggest that local adaptation does not explain genetic differentiation among these Daphnia populations, and that other factors related to extinction / colonization dynamics, a long approach to equilibrium FST, or substantial genetic drift due to a low number of individuals hatching from the egg bank each season may explain genetic differentiation.
Data from: Rapid, pervasive genetic differentiation of urban white-footed mouse (Peromyscus leucopus) populations in New York City
We investigated genetic diversity and structure of urban white-footed mouse, Peromyscus leucopus, populations in New York City (NYC) using variation at 18 microsatellite loci. White-footed mice are "urban adapters" that occur at higher population densities as habitat fragments are reduced in area, but have a limited ability to disperse through urbanized areas. We hypothesized that this combination of traits has produced substantial genetic structure but minimal loss of genetic variation over the last century in NYC. Allelic diversity and heterozygosity in fourteen NYC populations were high, and nearly all of our NYC study sites contained genetically distinct populations of white-footed mice as measured by pairwise FST, assignment tests, and Bayesian clustering analyses performed by Structure and BAPS. Analysis of molecular variance revealed that genetic differences between populations separated by a few km are more significant than differences between prehistorically isolated landmasses (i.e. Bronx, Queens, and Manhattan). Allele size permutation tests and lack of isolation-by-distance indicated that mutation and migration are less important than drift as explanations for structure in urban, fragmented P. leucopus populations. Peromyscus often exhibit little genetic structure over even regional scales, prompting us to conclude that urbanization is a particularly potent driver of genetic differentiation compared to natural fragmentation.
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Annotated Behaviour and Observability Dataset (ABODe)
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