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1,659 results for “structured population”

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dryad36/100

Data from: Phylogenetic, population structure, and population demographic analyses reveal that Vicia sepium in Japan is native and not introduced

Vicia sepium (bush vetch) is a perennial legume widely distributed throughout the Eurasian continent. However, its distribution in Japan is limited to Mt. Ibuki and small parts of central and southern Hokkaido. Therefore, each Japanese V. sepium lineage has been considered to have been introduced separately from Europe. Here, we examined whether the species was introduced or not on the basis of cpDNA sequences and genome-wide SNPs from Japanese and overseas samples. Both the cpDNA haplotype network and the nuclear DNA phylogenetic tree showed that Japanese V. sepium is monophyletic. Furthermore, although the nuclear DNA phylogenetic tree also showed that each lineage is clearly monophyletic, genetic admixture of the genetic cluster dominated in the Hokkaido lineage was also detected in the Mt. Ibuki lineage. Population divergence analysis showed that the two lineages diverged during the last glacial period. The Mt. Ibuki lineage showed a sudden population decline 300–400 years ago, indicating that some anthropogenic activity might be involved, while the Hokkaido lineage showed a gradual population decline from 5,000 years ago. Consequently, these two lineages show low current genetic diversity compared with overseas lineages. These results show that the Japanese V. sepium is not introduced but is native.

opencc-zeroAug 2023View details →

dryad36/100

Genomic diversity and population structure of teosintes (Zea spp.) and its conservation implications

The wild species of the genus Zea commonly named teosintes, comprise nine different taxa, distributed from northern Mexico to Costa Rica. Although this genus of plants has been extensively studied from a morphological, ecogeographical and genetic point of view, most contributions have been limited to the study of a few populations and taxa. To understand the great variability that exists between and within teosinte species, it is necessary to include the vast majority of known populations. In this context, the objective of this work was to evaluate the diversity and genomic structure of 276 teosinte populations. Molecular analyzes were performed with 3,604 plants and with data from 33,929 SNPs. The levels of genetic diversity by taxonomic group show a marked difference between species, races and sections, where the highest values of genomic diversity were found in ssp. parviglumis and ssp. mexicana. The lower values were obtained for the Luxuriantes section as well as ssp. huehuetenagensis of the section Zea. The results of the structure show that there is a great genetic differentiation in all the taxonomic groups considered. For ssp. parviglumis and mexicana, which are the taxa with the largest number of populations, a marked genomic differentiation was found that is consistent with their geographic distribution patterns. These results showed a loss of diversity in several teosinte populations, making a strong case for further collection, and ex situ and in situ conservation. Also, this study highlights the importance of integrating genomic diversity and structure for the applications of conservation and management.

opencc-zeroSep 2023View details →

zenodo36/100

Age Structure and Body Size of The Tibetan Toad (Bufo tibetanus) Populations from Two Different Altitudes in China

Knowledge about the altitudinal patterns in age and body size helps to highlight the evolution of life history parameters in animals. In this study, we investigated the demographic traits of the Tibetan toad (Bufo tibetanus) between populations from low and high altitude habitats (2650 vs 3930m) using skeletochronology. We found 1) the mean age and body size of females were significantly greater than those of males in either population; 2) both sexes of toads from the higher altitude tended to be significantly older in age and larger in body size; 3) a significant positive relationship between age and body size within each sex of the toad at both altitudes; 4) growth rates varied between the two populations, with the higher rate observed in the low-altitude population, and lower in the high-altitude population. Our results suggest that factors other than age can influence altitudinal patterns in body size, such as altitude-associated temperature. Future research should pay attention to these factors and evaluate their influences on the growth patterns of animals.Knowledge about the altitudinal patterns in age and body size helps to highlight the evolution of life history parameters in animals. In this study, we investigated the demographic traits of the Tibetan toad (Bufo tibetanus) between populations from low and high altitude habitats (2650 vs 3930m) using skeletochronology. We found 1) the mean age and body size of females were significantly greater than those of males in either population; 2) both sexes of toads from the higher altitude tended to be significantly older in age and larger in body size; 3) a significant positive relationship between age and body size within each sex of the toad at both altitudes; 4) growth rates varied between the two populations, with the higher rate observed in the low-altitude population, and lower in the high-altitude population. Our results suggest that factors other than age can influence altitudinal patterns in body size, such as altitude-associated temperature. Future research should pay attention to these factors and evaluate their influences on the growth patterns of animals.

opencc-by-4.0Sep 2023View details →

dryad36/100

Population genomic analyses reveal hybridization and marked differences in genetic structure and demographic history of Scurria limpet sister species with parapatric distributions across the southeastern pacific

The study of sister species that occur in parapatry around biogeographic transition zones can help understand the evolutionary processes that underlie the changes in species composition across biogeographic transition zones. The South Eastern Pacific (SEP) coast is a highly productive coastal system that exhibits a broad biogeographic transition zone around 30–35ºS. Here, we present a comparative genome-wide analysis of the sister species Scurria viridula and Scurria zebrina, that occur in parapatry and whose poleward and equatorward range edges intersect in the 30–35ºS SEP biogeographic transition zone. We sampled 118 specimens sourced from nine sites from Tocopilla (22ºS) to Chiloé (41ºS) including one site where both species overlap and analyzed over 8,000 biallelic single nucleotide polymorphisms. We found evidence of hybridization between these species in the contact zone and found significant but contrasting population structures for both species. Our results indicate that the genetic structure in S. viridula, which is currently expanding its range poleward, follows a simple isolation-by-distance model with no traces of natural selection (no evidence of outlier loci). In contrast, S. zebrina, which finds its equatorward range edge at the transition zone, displayed a pronounced genetic break approximately at 32-34ºS, along a region of marked environmental heterogeneity in association with a semi-permanent coastal upwelling regime. For S. zebrina, we also found 43 outlier loci associated with this genetic break, with a significant proportion of them clustering in a single linkage group. This marked difference in the presence of outlier loci between species suggests that they could be responding differently to local environmental challenges found at their overlapping geographic range edges, thus providing important new insights about genomic changes around biogeographic transition zones in sister species and the forces that shape genetic diversity in intertidal marine species.

opencc-zeroSep 2023View details →

dryad36/100

Data from: Divergence in the internal genital morphology of females is correlated with divergence in male intromittent structures among populations of a millipede

Our understanding of genital evolution comes largely from studies of male genitalia. Females have received far less attention because of the difficulties inherent in quantifying the shapes of their internal genital structures. Here we combine advances in micro-computed tomography with a new landmark free method of quantifying three-dimensional trait shape, to document patterns of divergence in female genital shape, and the correlated divergence of male genitalia among populations of the millipede Antichiropus variabilis. We used single nucleotide polymorphisms to estimate levels of neutral genetic divergence among seven populations of millipede. Genetic divergence was high and correlated with geographic distance. Comparing phenotypic divergence in genital shape to neutral genetic divergence, we found that genital shape for both females and males has diverged more than would be expected from random drift, consistent with a pattern of directional selection. While there was significant covariation between female and male genital shape across populations, the magnitude of divergence in genital shape between the sexes was not correlated. Our results demonstrate the utility of using three-dimensional scanning technologies to examine female genital traits and add to a small but growing number of studies showing that like male genitalia, female genitalia can be under strong directional selection.

opencc-zeroSep 2023View details →

dryad36/100

Data from: Genomic architecture drives population structuring in Amazonian birds

Geographic barriers are frequently invoked to explain genetic structuring across the landscape. However, inferences on the spatial and temporal origins of population variation have been largely limited to evolutionary neutral models, ignoring the potential role of natural selection and intrinsic genomic processes known as genomic architecture in producing heterogeneity in differentiation across the genome. To test how genomic architecture impacts our ability to reconstruct general patterns of diversification in species that co-occur across geographic barriers, we sequenced the whole genomes of multiple bird populations that are distributed across rivers in southeastern Amazonia. We found that phylogenetic relationships within species and demographic parameters varied across the genome in predictable ways. Genetic diversity was positively associated with recombination rate and negatively associated with species tree support. Gene flow was less pervasive in regions of low recombination, making these windows more likely to retain patterns of population structuring that matched the species tree. We further found that approximately a third of the genome showed evidence of selective sweeps and linked selection, skewing genome-wide estimates of effective population sizes and gene flow between populations towards lower values. In sum, we showed that the effects of intrinsic genomic characteristics and selection can be disentangled from neutral processes to elucidate how inferring spatial patterns of diversification are sensitive to genomic architecture.

opencc-zeroSep 2023View details →

zenodo36/100

Data From: Dynamic environments generate geographic fluctuations in population structure of an inland shorebird

Data From: Dynamic environments generate geographic fluctuations in population structure of an inland shorebird. Table S2: δ2H values in breast feathers sampled from 352 pre-fledged young mountain plovers from across the breeding range used for isoscape calibration. The table provides the latitude and longitude coordinates for each δ2H feather sample.

opencc-by-4.0May 2023View details →

zenodo36/100

Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds

Genotyping data in ped and map format (ped/map) for 72 goats and 53,347 genotypes.

opencc-by-4.0May 2019View details →

dryad36/100