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31 results for “Population structure and phylogeography”
Fig. 3. The genetic distances among populations. A in Phylogeography and Genetic Structure of the Bush Cricket (Orthoptera, Tettigoniidae) in Southern China.
Fig. 3. The genetic distances among populations. A: based on Kimura's 2-parameter; B: based on Tamura 3-parameter.
Data from: Phylogeography, population structure, and species delimitation in rockhopper penguins (Eudyptes chrysocome and Eudyptes moseleyi)
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Data from: Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)
<p>The spruce budworm, <i>Choristoneura fumiferana</i>, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border) and Eastern (Manitoba-Ontario border and Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce, <i>Picea glauca</i>, providing evidence that spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations. </p>
Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
The cheetah (Acinonyx jubatus) has been described as a species with low levels of genetic variation. This has been suggested to be the consequence of a demographic bottleneck 10 000–12 000 years ago (ya) and also led to the assumption that only small genetic differences exist between the described subspecies. However, analysing mitochondrial DNA and microsatellites in cheetah samples from most of the historic range of the species we found relatively deep phylogeographic breaks between some of the investigated populations, and most of the methods assessed divergence time estimates predating the postulated bottleneck. Mitochondrial DNA monophyly and overall levels of genetic differentiation support the distinctiveness of Northern-East African cheetahs (Acinonyx jubatus soemmeringii). Moreover, combining archaeozoological and contemporary samples, we show that Asiatic cheetahs (Acinonyx jubatus venaticus) are unambiguously separated from African subspecies. Divergence time estimates from mitochondrial and nuclear data place the split between Asiatic and Southern African cheetahs (Acinonyx jubatus jubatus) at 32 000–67 000 ya using an average mammalian microsatellite mutation rate and at 4700–44 000 ya employing human microsatellite mutation rates. Cheetahs are vulnerable to extinction globally and critically endangered in their Asiatic range, where the last 70–110 individuals survive only in Iran. We demonstrate that these extant Iranian cheetahs are an autochthonous monophyletic population and the last representatives of the Asiatic subspecies A. j. venaticus. We advocate that conservation strategies should consider the uncovered independent evolutionary histories of Asiatic and African cheetahs, as well as among some African subspecies. This would facilitate the dual conservation priorities of maintaining locally adapted ecotypes and genetic diversity.
Data from: Population structure and comparative phylogeography of jack species (Caranx ignobilis and C. melampygus) in the high Hawaiian Islands
Members of the family Carangidae are top-level predators and highly prized food and sport fishes. Although ecologically and economically important, little is known about the biology of numerous species in the family. This is particularly true of the jacks Caranx ignobilis and C. melampygus, which have experienced recent population reductions around the high Hawaiian Islands due to overfishing. Previous studies have documented territorial tendencies as well as cases of long-distance excursions in both species, suggesting populations may exhibit a range of structure at the genetic level. To explore this possibility, mitochondrial (mtDNA) ATPase6 and ATPase8 gene sequence variation was assessed from 91 individuals (33 C. ignobilis and 58 C. melampygus) spanning the islands of Kauai, Oahu, Molokai, Maui and Hawai'i. While a total of 20 distinct haplotypes (eight for C. ignobilis; 12 for C. melampygus) were recovered, no evidence of population structure was found for either species across the examined geographic range. However, distinct demographic patterns were identified, implying differing evolutionary histories and/or population dynamics. Additionally, ~6% of the examined C. ignobilis were C. ignobilis x C. melampygus hybrids since they harbored mitochondrial haplotypes typical of C. melampygus. These hybrids contribute to measurable gene flow between the species and may play a significant role in the evolution of the genus.
Data from: Genetic diversity, population structure and phylogeography of Myanmar goats
The diversity of goats in Myanmar is represented by three indigenous breeds, Jade Ni, Nyaung Oo and Waithar Li. This study aimed at characterizing the genetic diversity and relationship of Myanmar goat breeds using microsatellite and mitochondrial DNA variations. A total of 147 goats from all three indigenous breeds were genotyped at 27 microsatellite loci. Genetic diversity in terms of allelic polymorphisms, observed and expected heterozygosities were moderately high. The mean observed heterozygosity within breeds varied between 0.566 ± 0.183 (Nyaung Oo) and 0.595 ± 0.182 (Waithar Li) while the expected heterozygosity varied from 0.605 ± 0.181 (Jade Ni) to 0.647 ± 0.176 (Waithar Li). Considerable heterozygosity deficit ranging from 5.5% to 8.2% was observed in Myanmar goat breeds. Wright's F statistics revealed most of the variations within breeds and only 1.9% of the total observed variation was explained by between breed differences. Principal components and Bayesian clustering analyses showed complete admixture of Nyaung Oo and Waithar Li goats indicating high rate of gene flow among these populations. Population stratification was observed in Jade Ni with a subset of individuals clustering distinctly. Variations in mitochondrial DNA control region revealed 22 distinct haplotypes belonging to two major haplogroups A and B. Haplogroup A was found to predominate Myanmar goats similar to other goat populations in Asia. Comparative analysis of mtDNA variations indicated possible Chinese origin of the maternal haplotypic lineages of Myanmar goats.
The genetic diversity, phylogeography, and population structure of Pacific harbor seals reveal isolation at the southern end of their distribution
<p>The Pacific harbor seal (<em>Phoca vitulina richardii</em>) occurs in the Mexican Pacific region at the southernmost edge of the subspecies' distribution, along 700 km of coastline and on nine islands west of the Baja California peninsula. Its abundance corresponds to 3% of its total abundance in the north Pacific Ocean. The species is considered relatively sedentary and highly philopatric, which make it vulnerable to stochastic processes; thus, reproductive and genetic isolation of the Mexican Pacific colonies is expected. This study aimed to genetically characterize the harbor seal in the Mexican Pacific to inform conservation efforts. We estimated the levels of genetic diversity for five colonies, using a 572-base pair mitochondrial DNA control region fragment and nine microsatellite loci. We examined the population genetic structure and its phylogeographic patterns. We found 15 variable sites that defined 18 mitochondrial DNA haplotypes. Results show one of the lowest levels of diversity reported for the species (overall haplotype diversity <em>h</em> = 0.626 ± SD 0.041; overall nucleotide diversity π = 0.0018 ± SD 0.0013; mean expected heterozygosity H<sub>E</sub> = 0.537). We found a stronger genetic structure with both markers than in the larger regions of the north Pacific, from Alaska to California. The Pacific harbor seal colonies found in Mexico may have their origins in northern colonies, via a founder event. We found only four haplotypes in common with those observed (451) along the rest of the Pacific colonies, while nine of the 14 haplotypes exclusive to the Mexican Pacific are private.</p>
Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)
<p><span>Human assisted movement has allowed the Asian longhorned beetle (ALB, <em>Anoplophora glabripennis</em> (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within its native range of China and the Korean peninsula, human-mediated dispersal has also caused cryptic translocation of insects, resulting in population structure complexity. Previous studies used genetic methods to detangle this complexity but were unable to clearly delimit native populations which is needed to develop downstream biosurveillance tools. We used genome-wide markers to define historical population structure in native ALB populations and contemporary movement between regions. We used genotyping-by-sequencing to generate 6,102 single nucleotide polymorphisms (SNPs) and amplicon sequencing to genotype 53 microsatellites. In total, we genotyped</span> <span>712 individuals from</span> <span>ALB's native distribution. We observed six distinct population clusters among native ALB populations, with a clear delineation between northern and southern groups. Most of the individuals from South Korea were distinct from populations in China. Our results also indicate historical divergence among populations and suggest limited large-scale admixture, but we did identify a restricted number of cases of contemporary movement between regions. We identified SNPs under selection and describe a clinal allele frequency pattern in a missense variant associated with glycerol kinase, an important enzyme in the utilization of an insect cryoprotectant. We further demonstrate that small numbers of SNPs can assign individuals to geographic regions with high probability, paving the way for novel ALB biosurveillance tools.</span></p>
Data from: Phylogeography of African locust bean (Parkia biglobosa) reveals genetic divergence and spatially structured populations in West and Central Africa
The evolutionary history of African savannah tree species is crucial for the management of their genetic resources. In this study, we investigated the phylogeography of Parkia biglobosa and its modelled distribution under past and present climate conditions. This tree species is very valued and widespread in West Africa, providing edible and medicinal products. A large sample of 1 610 individuals from 84 populations, distributed across 12 countries in Western and Central Africa, were genotyped using eight nuclear microsatellites. Individual-based assignments clearly distinguished three genetic clusters, extreme West Africa (EWA), centre of West Africa CWA), and Central Africa (CA). Overall, estimates of genetic diversity were moderate to high, with lower values for populations in EWA (AR=6.4, HE=0.78 and HO=0.7) and CA (AR=5.9, HE=0.67 and HO=0.61) compared to populations in CWA (AR=7.3, HE=0.79 and HO=0.75). The overall population differentiation was found to be moderate (FST=0.09). A highly significant isolation-by-distance pattern was detected, with a marked phylogeographic signature suggesting possible effects of past climate and geographic barriers to migration. Modelling the potential distribution of the species showed a contraction during the last glaciations followed by expansion events. The exploratory Approximate Bayesian Computation conducted suggests a best-supported scenario in which the cluster CWA traced back to the ancestral populations and a first split between EWA and CWA took place about 160 000 years BP, then a second split divided CA and CWA, about 100 000 years BP. However, our genetic data do not enable to conclusively distinguish among a few alternative possible scenarios.
Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification
<p class="MsoNormal"><span class="Fuentedeprrafopredeter1"><span>The Neotropics contain one of the most diverse assemblages of freshwater fishes worldwide. Part of this diversity is shared between the Orinoco and Amazon basins. These basins have been separated for a long time due to the Vaupes Arch, rising between 10 - 11 Ma. T</span></span><span class="Fuentedeprrafopredeter1"><span>oday, there is only one permanent connection between the Orinoco and Negro </span></span><span class="Fuentedeprrafopredeter1"><span>(Amazon) </span></span><span class="Fuentedeprrafopredeter1"><span>basins, known as the Casiquiare Canal</span></span><span class="Fuentedeprrafopredeter1"><span>. </span></span><span class="Fuentedeprrafopredeter1"><span>However, alternative corridors allowing fish dispersion between both basins have been proposed. The cardinal tetra (<em>Paracheirodon axelrodi),</em> the most important fish in the ornamental world market, is distributed in both basins. Here we investigated </span></span><span class="Fuentedeprrafopredeter1"><em><span>P. axelrodi </span></em></span><span class="Fuentedeprrafopredeter1"><span>phylogeography, population structure, and potential routes of migration and connectivity between the two basins. A total of 468 bp of the mitochondrial gene (COI), 555 bp of the nuclear gene fragment (MYH6), and 8 microsatellite loci were analyzed. </span></span><span class="Fuentedeprrafopredeter1"><span>As a result, we found two major genetic clusters as the most likely scenario (K=2), but they were not discreetly distributed between basins. A gradient of genetic admixture was observed in Cucui and </span></span><span class="Fuentedeprrafopredeter1"><span>São</span></span><span class="Fuentedeprrafopredeter1"><span> Gabriel da Cachoeira, between the upper Negro River and the upper Orinoco. Samples from the middle-lower Negro River were highly structured. </span></span><span class="Fuentedeprrafopredeter1"><span>Cucui (Negro basin) was more similar to the Orinoco than to the rest of the Negro basin populations. </span></span><span class="Fuentedeprrafopredeter1"><span>However, substructure was also observed by the discriminant analysis, fixation indices and other hierarchichal structure analyses (K=3-6), showing three major geographic clusters: Orinoco, Cucui, and the remaining of the Negro basin. </span></span><span class="Fuentedeprrafopredeter1"><span>Unidirectional migration patterns were detected between basins: via Cucui toward Orinoco and via the remaining of the Negro basin toward Orinoco. Results from the Relaxed Random Walk analysis support a very recent origin of this species in the headwater Orinoco basin (Western Guiana Shield, at late Pleistocene) with a later rapid colonization of the remaining Orinoco basin and almost simultaneously the Negro River via Cucui, between 0.115 until about 0.001 Ma. Historical biogeography and population genetic patterns observed here for Cardinal tetra, seem to be better explained by river capture, physical, or ecological barriers than due to the geographic distance.</span></span></p>
Data from: Continent-wide population genomic structure and phylogeography of North America’s most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)
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Data from: Phylogeography of African locust bean (Parkia biglobosa) reveals genetic divergence and spatially structured populations in West and Central Africa
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Data from: Population structure and comparative phylogeography of jack species (Caranx ignobilis and C. melampygus) in the high Hawaiian Islands
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Data from: Phylogeography of the catfish Hatcheria macraei reveals a negligible role of drainage divides in structuring populations
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Data from: Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc
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Genome-scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)
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Phylogeography and population genetic structure of the cardinal tetra (Paracheirodon axelrodi) in the Orinoco basin and Negro River (Amazon basin): evaluating connectivity and historical patterns of diversification
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Data from: Genetic structure and post-glacial expansion of Cornus florida L. (Cornaceae): integrative evidence from phylogeography, population demographic history, and species distribution modeling
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Data from: Genetic diversity, population structure and phylogeography of Myanmar goats
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Data from: Phylogeography, genetic structure and population divergence time of cheetahs in Africa and Asia: evidence for long-term geographic isolates
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Allen Brain Atlas
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