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2,445 results for “Genetics: population”
Data from: Challenges in analysis and interpretation of microsatellite data for population genetic studies
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (FST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.
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: Predicting local adaptation in fragmented plant populations: implications for restoration genetics
Understanding patterns and correlates of local adaptation in heterogeneous landscapes can provide important information in the selection of appropriate seed sources for restoration. We assessed the extent of local adaptation of fitness components in 12 population pairs of the perennial herb Rutidosis leptorrhynchoides (Asteraceae) and examined if spatial scale (0.7 – 600km), environmental distance, quantitative Q_ST and neutral genetic differentiation F_ST, and size of the local and foreign populations could predict patterns of adaptive differentiation. Local adaptation varied among populations and fitness components. Including all population pairs, local adaptation was observed for seedling survival, but not for biomass, while foreign genotype advantage was observed for reproduction (number of inflorescences). Among population pairs, local adaptation increased with Q_ST and local population size for biomass. Q_ST was associated with environmental distance, suggesting ecological selection for phenotypic divergence. However, low F_ST and variation in population structure in small populations demonstrates the interaction of gene flow and drift in constraining local adaptation in R. leptorrhynchoides. Our study indicates that for species in heterogeneous landscapes, collecting seed from large populations from similar environments to candidate sites is likely to provide the most appropriate seed sources for restoration.
Data from: Strong population genetic structure in a broadcast-spawning Antarctic marine invertebrate
Although studies of population genetic structure are commonplace, a strong bias exists towards species from low latitudes and with relatively poor dispersal capabilities. Consequently, we used 280 Amplified Fragment Length Polymorphism (AFLP) bands to explore patterns of genetic differentiation among eight populations of a high latitude broadcast-spawning marine mollusc, the Antarctic limpet Nacella concinna. Over three hundred individuals were sampled along a latitudinal gradient spanning the Antarctic Peninsula from Adelaide Island to King George Island (67º–62º S), then to Signy Island (60ºS) and South Georgia (54ºS). Populations from the Antarctic Peninsula exhibited little genetic structure, but were themselves strongly differentiated from both Signy and South Georgia. This finding was analytically highly robust and implies the presence of significant oceanographic barriers to gene flow in a species long regarded as a classic example of a widely-dispersing broadcast-spawner.
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.
FIGURES 1-2. 1 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure
FIGURES 1-2. 1, Dicyrtomina ornata, habitus; 2, Dicyrtomina saundersi, habitus.
FIGURE 7 in Morphological and genetic evolution in eastern populations of the Macrhybopsis aestivalis complex (Cypriniformes: Cyprinidae), with the descriptions of four new species
FIGURE 7. Proposed phylogenetic relationships among various species/lineages recognized in the Macrhybopsis aestivalis complex of eastern North America. Not all species in the complex were evaluated. One study is based on morphological characters (Eisenhour 2004 [A]), whereas the other two studies are based on allozyme variation. Underwood et al. (2003 [B]) focused on western diversity (SB = Sabine, BZ = Brazos, PC = Pecos River, SM = San Marcos River); and Mayden & Powers (2004 [C-G]) mostly involved eastern lineages, excluding Colorado River (CR) and Guadalupe River (GR). In Mayden & Powers (2004) different distances were examined, as well as parsimony: C = Edwards and Cavalli-Sforza Edwards Chord distances; D = Prevosti and Rogers distances; E = Cavalli-Sforza Edwards Arc and Modified Rogers distances; F = Fitch Generalized Parsimony with coded characters.
Abundant genetic variation is retained in many laboratory schistosome populations - Code and data
<p>Code and data used for the generation of figures in manuscript.</p>
Figure 6 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 6 Species tree Hipposideridae based on StarBEAST analysis of four introns. Posterior probabilities appear at all nodes.
Figure 5 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 5 Phylogeny of Hipposideridae based on Bayesian analysis of 103 concatenated nuclear intron sequences. Numbers denote posterior probabilities (BI) and bootstrap percentages (ML); red circles at more terminal nodes indicate BS ≥ 70%, PP ≥ 0.95.
Figure 4 from: Patterson BD, Webala PW, Lavery TH, Agwanda BR, Goodman SM, Kerbis Peterhans JC, Demos TC (2020) Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae). ZooKeys 929: 117-161. https://doi.org/10.3897/zookeys.929.50240
Figure 4 Substitution network plots for Afrotropical hipposiderids AHipposideros caffer clades 1–4 BHipposideros caffer clades 5–8 CH. ruber clades.
Figure 4 in Morphogeometric and genetic variations among North African populations of the Mediterranean killifish Aphanius fasciatus (Valenciennes, 1821) from different habitats
Figure 4. – Neighbour-joining tree on genetic distances D (Reynolds et al., 1983) between A. fasciatus samples from four North African habitats.
Data from: Population genetics of a broadcast-spawning coral across a tropical-temperate transition zone reveals regional differentiation and isolation of high-latitude reefs
<p>Aim: Genetic connectivity is a key component of species resilience to climate change in terms of recovery capacity following disturbance and capacity to disperse to novel locations as the climate warms and isotherms shift poleward. We aimed to strengthen our understanding of resilience in this context by characterizing patterns of connectivity and genetic diversity in a broadcast spawning coral across a tropical-temperate transition zone. We hypothesize genetic differentiation between tropical and temperate populations and decreasing genetic diversity with higher latitudes.</p> <p>Location: Western Australia (WA).</p> <p>Taxon: <i>Turbinaria </i>species complex. <i>Turbinaria reniformis </i>Oken, 1815 (Dendrophylliidae).</p> <p>Methods: Samples from 930 target corals were collected from ten locations between 13 - 32<sup> o</sup> latitude spanning a 9° C mean temperature range. <i>In-situ</i> species identification of <i>T. reniformis </i>is hindered by morphological plasticity and homoplasy with sister species. We<i> </i>combined Sanger sequencing of two mitochondrial DNA markers and high-throughput genotyping by sequencing (GBS) to isolate a single genetic <i>Turbinaria</i> lineage from our dataset through which patterns of genetic flow and diversity along the WA coastline could be explored using population- and individual-based analyses.</p> <p>Results: Mitochondrial DNA sequence variation was low among <i>Turbinaria</i> samples and could not resolve individual species. Using GBS, we identified three genetically distinct lineages. Subsequent analyses within one of these lineages revealed strong spatial subdivision with 2-3 genetic clusters. While temperate populations were genetically diverged from more tropical sites, we did not observe declines in genetic diversity with latitude.</p> <p>Main Conclusions: Temperate coral populations in Western Australia are genetically isolated from their tropical counterparts. Tropical populations of <i>T. 'reniformis' </i>exhibit adequate connectivity.<i> </i>Shark Bay represents the current southern limit of the tropical population of <i>T. 'reniformis'</i>. Interestingly, temperate <i>T. 'reniformis'</i> in this study exhibit some genetic resilience due to their relatively high genetic diversity, yet the strong patterns of genetic subdivision for this widely dispersing coral species potentially limit their resilience to future climate scenarios.</p>
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.
Figure 4 in Effects of islanding on the genetics of Niviventer confucianus (Mamalia: Rodentia: Muridae) populations in the Thousand Island Lake region
Figure 4. Relationship between polymorphic information content (PIC) and island area.
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