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464 results for “Population Genetic Diversity”
Data from: A single migrant enhances the genetic diversity of an inbred puma population
Migration is essential for maintaining genetic diversity among populations, and pumas (Puma concolor) provide an excellent model for studying the genetic impacts of migrants on populations isolated by increasing human development. In densely populated southern California, USA, puma populations on the east and west side of interstate highway 15 (I-15) have become fragmented into a small inbred population on the west side (Santa Ana Mountains) and a relatively larger, more diverse population on the east side (Eastern Peninsular Range). From 146 sampled pumas, genetic analyses indicate seven pumas crossed I-15 over the last 15 years, including four males from west to east, and three males from east to west. However, only a single migrant (named M86) was detected to have produced offspring and contribute to gene flow across the I-15 barrier. Prior to the M86 migration, the Santa Ana population exhibited inbreeding and had significantly lower genetic diversity than the Eastern Peninsular Range population. After M86 emigrated, he sired 11 offspring with Santa Ana females, decreasing inbreeding measures and raising heterozygosity to levels similar to pumas in the Eastern Peninsular Range. The emigration of M86 also introduced new alleles into the Santa Ana population, although allelic richness still remained significantly lower than the Eastern Peninsular population. Our results clearly show the benefit of a single migrant to the genetics of a small, isolated population. However, ongoing development and habitat loss on both sides of I-15 will increasingly strengthen the barrier to successful migration. Further monitoring, and potential human intervention, including minimizing development effects on connectivity, adding or improving freeway crossing structures, or animal translocation, may be needed to ensure adequate gene flow and long-term persistence of the Santa Ana puma population.
Data from: Genetic diversity and population structure of wild sunflower (Helianthus annuus L.) in Argentina: reconstructing its invasion history
Studying the levels and patterns of genetic diversity of invasive populations is important to understand the evolutionary and ecological factors promoting invasions and for better designing preventive and control strategies. Wild sunflower (Helianthus annuus L.) is native to North America and was introduced, and has become invasive, in several countries, including Argentina (ARG). Here, using classical population genetic analyses and Approximate Bayesian Computation (ABC) modelling, we studied the invasion history of wild sunflower in ARG. We analyzed 115 individuals belonging to 15 populations from ARG (invasive range) and United States (US, native range) at 14 nuclear and three chloroplast simple sequence repeat markers along with 23 phenotypic variables. Populations from ARG showed similar levels of nuclear genetic diversity to US populations and higher genetic diversity in the chloroplast genome, indicating no severe genetic bottlenecks during the invasion process. Bayesian clustering analysis, based on nuclear markers, suggests the presence of three genetic clusters, all present in both US and ARG. Discriminant analysis of principal components (DAPC) detected an overall low population structure between central US and ARG populations but separated two invasive populations from the rest. ABC modelling supports multiple introductions but also a southward dispersal within ARG. Genetic and phenotypic data support the central US as a source of introduction while the source of secondary introductions could not be resolved. Finally, using genetic markers from the chloroplast genome, we found lower population structure in ARG when compared to US populations, suggesting a role for seed-mediated gene flow in Argentina.
Genetic diversity and population structure in Chrysolepis chrysophylla (golden chinquapin; Fagaceae): SSRs vs SNPs
<p>Simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotypes on the same plant samples of <i>Chrysolepis chrysophylla</i> (Fagaceae; golden chinquapin) from 22 sites were used to determine genetic diversity and population structure. One site of <i>C. sempervirens</i> allowed <i>inter</i>specific vs.<i> intra</i>specific comparison. SSRs and SNPs yielded many similar results. Among-site variation contributed 13% to 17% of the genetic variation and Fst estimates of 0.14 to 0.17 were in the range expected among Fagaceae species rather than among populations within a species. The northern sites tended to group separately on the first two axes of multivariate scatterplots from southern sites. Sites in two geographically isolated areas were divergent: 1) the Hood Canal, Washington population was relatively more genetically distant from other golden chinquapin sites than was our <i>C. sempervirens</i> site; 2) three coastal southern California sites were moderately diverged. The Hood Canal site had a negative inbreeding coefficient, fewer alleles, lower heterozygosity, and differed from the Skamania County, Washington site as well as all other sites. Hood Canal trees are distinguished by disjunct geography and by these molecular results. This suggests that the golden chinquapin near Hood Canal be treated as a management unit, and potential conservation actions are discussed.</p>
Data from: Tracking the origins of fly invasions; using mitochondrial haplotype diversity to identify potential source populations in two genetically intertwined fruit fly species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])
Bactrocera carambolae Drew and Hancock and B. dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1601 individuals from 18 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.
Data from: Elevated genetic diversity of mitochondrial genes in asexual populations of bark lice ("Psocoptera": Echmepteryx hageni)
Asexual reproduction is commonly thought to be associated with low genetic diversity in animals. Echmepteryx hageni (Insecta: "Psocoptera") is one of several psocopteran species that are primarily parthenogenetic, but also exists in small, isolated sexual populations. We used mitochondrial DNA sequences to investigate the population history and genealogical relationships between the sexual and asexual forms of this species. The asexual population of E. hageni exhibits extremely high mitochondrial haplotype diversity (H = 0.98), whereas the sexual forms had significantly lower haplotypic diversity (H = 0.25, after correcting for sample size). This diversity in asexuals represents one the greatest genetic diversities reported for asexual animals in the literature. Nucleotide diversities were also higher in asexual compared to sexual populations (π = 0.0071 vs. 0.00027). Compared to other reported estimates of π in insects, asexual nucleotide diversity is high, but not remarkably elevated. Three hypotheses might explain the elevated genetic diversity of asexual populations: 1) larger effective population size, 2) greater mutation rate, or 3) possible recent origin of sexuals. In addition, phylogeographic analysis revealed little geographic structure among asexual E. hageni, although specimens from the upper Midwest form a single clade and are genetically differentiated. The mismatch distribution and neutrality tests indicate a historical population size increase, possibly associated with expansion from glacial refugia.
Data from: Population size and time since island isolation determine genetic diversity loss in insular frog populations
Understanding the factors that contribute to loss of genetic diversity in fragmented populations is crucial for conservation measurements. Land-bridge archipelagoes offer ideal model systems for identifying the long-term effects of these factors on genetic variations in wild populations. In this study, we used 9 microsatellite markers to quantify genetic diversity and differentiation of 810 pond frogs (Pelophylax nigromaculataus) from 24 islands of the Zhoushan Archipelago and 3 sites on nearby mainland China and estimated the effects of the island area, population size, time since island isolation, distance to the mainland and distance to the nearest larger island on reduced genetic diversity of insular populations. The mainland populations displayed higher genetic diversity than insular populations. Genetic differentiations and no obvious gene flow were detected among the frog populations on the islands. Hierarchical partitioning analysis showed that only time since island isolation (square root transformed) and population size (log transformed) significantly contributed to insular genetic diversity. These results suggest that decreased genetic diversity and genetic differentiations among insular populations may have been caused by random genetic drift following isolation by rising sea levels during the Holocene. The results provide strong evidence for a relationship between retained genetic diversity and population size and time since island isolation for pond frogs on the islands, consistent with the prediction of the neutral theory for finite populations. Our study highlights the importance of the size and estimated isolation time of populations in understanding the mechanisms of genetic diversity loss and differentiation in fragmented wild populations.
Data from: Genetic structure and diversity among historic and modern populations of the Sumatran rhinoceros (Dicerorhinus sumatrensis)
The Sumatran rhinoceros (Dicerorhinus sumatrensis), once widespread across Southeast Asia, now consists of as few as 30 individuals within Sumatra and Borneo. To aid in conservation planning, we sequenced 218 bp of control region mitochondrial (mt) DNA, identifying 17 distinct mitochondrial haplotypes across modern (N = 13) and museum (N = 26) samples. Museum specimens from Laos and Myanmar had divergent mtDNA, consistent with the placement of western mainland rhinos into the distinct subspecies D. s. lasiotis (presumed extinct). Haplotypes from Bornean rhinos were highly diverse, but dissimilar from those of other regions, supporting the distinctiveness of the subspecies D. s. harrissoni. Rhinos from Sumatra and Peninsular Malaysia shared mtDNA haplotypes, consistent with their traditional placement into a single subspecies D. s sumatrensis. Modern samples of D. s. sumatrensis were genotyped at 18 microsatellite loci. Rhinos within Sumatra formed two sub-populations, likely separated by the Barisan Mountains, though with only modest genetic differentiation between them. There are so few remaining Sumatran rhinoceros that separate management strategies for subspecies or subpopulations may not be viable, while each surviving rhino pedigree is likely to retain alleles found in no other individuals. Given the low population size and low reproductive potential of Sumatran rhinos, rapid genetic erosion is inevitable, while an under-appreciated concern is the potential for fixation of harmful genetic variants. Both concerns underscore two overriding priorities for the species: (1) translocation of wild rhinos to ex situ facilities, and (2) collection and storage of gametes and cell lines from every surviving captive and wild individual.
Data from: High genetic diversity in the offshore island populations of the tephritid fruit fly Bactrocera dorsalis
Background: Geographic isolation is an important factor that limit species dispersal and thereby affects genetic diversity. Because islands are often small and surrounded by a natural water barrier to dispersal, they generally form discrete isolated habitats. Therefore, islands may play a key role in the distribution of the genetic diversity of insects, including flies. Results: To characterize the genetic structure of island populations of Bactrocera dorsalis, we analyzed a dataset containing both microsatellite and mtDNA loci of B. dorsalis samples collected from six offshore islands in Southern China. The microsatellite data revealed a high level of genetic diversity among these six island populations based on observed heterozygosity (Ho), expected heterozygosity (HE), Nei's standard genetic distance (D), genetic identity (I) and the percentage of polymorphic loci (PIC). These island populations had low F ST values (F ST = 0.04161), and only 4.16 % of the total genetic variation in the species was found on these islands, as determined by an analysis of molecular variance. Based on the mtDNA COI data, high nucleotide diversity (0.9655) and haplotype diversity (0.00680) were observed in all six island populations. F-statistics showed that the six island populations exhibited low or medium levels of genetic differentiation among some island populations. To investigate the population differentiation between the sampled locations, a factorial correspondence analysis and both the unweighted pair-group method with arithmetic mean and Bayesian clustering methods were used to analyze the microsatellite data. The results showed that Hebao Island, Weizhou Island and Dong'ao Island were grouped together in one clade. Another clade consisted of Shangchuan Island and Naozhou Island, and a final, separate clade contained only the Wailingding Island population. Phylogenetic analysis of the mtDNA COI sequences revealed that the populations on each of these six islands were closely related to different populations on mainland China. Conclusions: Our study suggests that these island populations have high genetic diversity, experience frequent gene flow and exhibit low or medium levels of genetic differentiation among some island populations. Therefore, the geographic isolation of the six islands does not appear to be a major dispersal barrier to B. dorsalis. Such knowledge is helpful for a better understanding of evolutionary processes of the species of island populations.
Supplementary material 3 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure S1
Supplementary material 2 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Table S2
Figure 2 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure 2 Neighbor-Net of S. lapponum individuals based on Nei (1973) coefficient. Population abbreviations are the same as in Table 1.
Supplementary material 1 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Table S1
Figure 1 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure 1 Location of the studied populations of S. lapponum. Population abbreviations are the same as in Table 1.
Figure 3 from: Urbaniak J, Kwiatkowski P, Pawlikowski P (2021) Genetic diversity of Salix lapponum populations in Central Europe. PhytoKeys 184: 83-101. https://doi.org/10.3897/phytokeys.184.71641
Figure 3 Results of the Bayesian admixture analysis data for populations of S. lapponum using STRUCTURE software. Population abbreviations are the same as in Table 1.
Genetic diversity of Horsfieldia tetratepala (Myristicaceae), an endangered plant species with extremely small populations to China: implications for its conservation
<p>Genetic variation determines the evolutionary potential of a species and is vital for fully understanding the evolution of a species, as well as for developing optimal conservation strategies. <i>Horsfieldia tetratepala</i> is an economically important rainforest tree which has declined steadily, mainly though habitat destruction, and an endangered, narrow endemic in China where it is also classified as a Plant Species with Extremely Small Populations (PSESP). Effective conservation strategies for <i>H. tetratepala</i> are required urgently, but limited information about its<i> </i>genome is available. Accordingly, restriction site-associated DNA sequencing (RAD_seq) was used to sequence sixty-three <i>H. tetratepala</i> trees covering ten isolated populations to assess genome-level diversity and population structure, generating 8,103 high-quality SNPs. Low genetic diversity and moderate genetic differentiation was observed among populations, but Bayesian clustering divided the sampled <i>H. tetratepala</i> populations into two genetic clusters, though with some populations from Guangxi and Yunnan intermixed. Because of increasing of habitat fragmentation and human disturbance, conservation priority should be placed on populations with higher genetic variation (e.g., BB, TKH, DWS, and GLQ). Overall, our study provides valuable genomic resources for <i>H. tetratepala</i> that will significantly advance the formulation of effective conservation strategies.</p>
Data from: Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum L., Solanaceae) in southern India: implications for conservation
[No abstract entered]
Fig. 1 in Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis
Fig. 1. Geographic distribution of N. falcata populations. Abbreviations are shown in Table 1. Pie charts represent assignment probability of belonging to each K = 2 clusters identified by STRUCTURE based on microsatellite allele frequencies, with probability values normalized using CLUMPP.
High genetic diversity but no geographic structure of Aedes albopictus populations in Reunion Island _ Dataset
<p>Microsatellite dataset of <em>Aedes albopictus</em> individuals sampled in Reunion Island. </p>
Figure 2 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 2 Total number of shared haplotypes between populations of Usnea subfloridana in the south-eastern (SE), the western (W) and northern (N) regions of Estonia; the thickness of lines reflects the number of shared haplotypes between populations.
Figure 3 from: Degtjarenko P, Jüriado I, Mandel T, Tõrra T, Saag A, Scheidegger C, Randlane T (2019) Microsatellite based genetic diversity of the widespread epiphytic lichen Usnea subfloridana (Parmeliaceae, Ascomycota) in Estonia: comparison of populations from the mainland and an island. MycoKeys 58: 27-45. https://doi.org/10.3897/mycokeys.58.36557
Figure 3 Usnea subfloridana multilocus genotypes in the principal component analysis (PCA) ordination plot of the first and second axes. Samples are grouped according to the presence of lichen substance: samples containing thamnolic (square) or squamatic acid (circle).
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