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opennotspecifiedFeb 2008View details →

Figure 3 in Genetic diversity of Atherina hepsetus (Osteichthyes: Atherinidae) populations as determined by RFLP analysis of three mtDNA regions

Figure 3. Dollo parsimony (Farris 1977) dendrogram showing the relationships between the 15 mtDNA haplotypes detected. Numbers indicate the bootstrap support (10,000 replicates) of each node of the majority-rule consensus tree.

opencc-zeroAug 2021View details →

Oxytenanthera abyssinica (A. Rich.) Munro; lowland bamboo (Poaceae, Bambusinea) in Ethiopia: Genetic diversity, population structure and gene flow analysis

As one of the most important non-timber forest resources, a potential alternative to wood and wood product and fastest-growing plant in the world (91 cm (35 in) per day), bamboo is a member of the grass family (Poaceae) and constitutes a single subfamily Bambusoideae. 67% of total area of bamboo in Africa and 7% of world total is contributed by Ethiopia giving more than 1.44 million hectares. Silica gel dried young fresh leaves from 130 individuals of O. abyssinica were collected for DNA extraction and PCR amplification. Each of the PCR amplified ISSR fragments using 19 ISSR primers were used to study band pattern and heterozigosity, level of polymorphism, calculating marker efficiency, Nei`s (H) and Shannon (I) genetic diversity, analysis of molecular variance (AMOVA), analysis for cluster, principal coordinates (PCoA) and admixture results. High genetic variation at species level was observed with the percentage of the polymorphic loci (PPL) = 84.48%. The H, I, observed number of alleles (Na) and effective number of alleles (Ne) at species level was 0.2702, 0.4061, 1.8448, and 1.4744, respectively, showing a relatively high level of genetic diversity. However, the genetic differentiation at the population level was relatively low. AMOVA using grouped populations revealed that, most of the diversity was distributed within the populations (61.05%) with FST = 0.38949, FSC = 0.10486 and FCT = 0.31797. Cluster analysis grouped the populations into sharply distinct clusters, which could be attributed to cross pollination nature of the plant and long lived to the area. STRUCTURE analyses for all population and excluding Gambella population gives different result K = 2 and K = 11. Using these markers, we find strong evidence linking geographic origin of diversity and samples from Gambella Region found different from others and might tell the availability of additional bamboo species in the country.

opencc-zeroAug 2021View details →

Sexual selection and the population genetics of a selfish gene

The segregation distorter allele (SD) found in Drosophila melanogaster distorts Medelian inheritance in heterozygous males by causing developmental failure of non-SD spermatids, such that >90% of the surviving sperm carry SD. This within-individual advantage should cause SD to rapidly fix, and yet SD is typically rare in wild populations. Here, we explore whether this paradox can be resolved by sexual selection, by testing if males carrying three different variants of SD suffer reduced pre or postcopulatory reproductive success. We find that males carrying the SD allele are just as successful at securing matings as control males, but that one SD variant (SD-5) reduces sperm competitive ability and increases the likelihood of female remating. We then used these results to inform a theoretical model; we found that sexual selection could limit SD to the frequencies observed in nature when sperm competitive ability and female remating rate equalled the values observed for SD-5. However, sexual selection was unable to explain natural frequencies of the SD allele when the model was parameterized with the values found for two other SD variants, indicating that sexual selection alone is unlikely to explain the rarity of SD.

opennotspecifiedApr 2012View details →

FIGURE 4 in Genetic and shell-shape analyses of Orlitia borneensis (Testudines: Geoemydidae) reveal limited divergence among founders of the European zoo population

FIGURE 4. PCA for plastron shape. Specimens are marked according to haplotype group. A—haplotype group 1, B—group 2, C—group 3, D—haplotype 61, U—unknown. The first axis PC1 explains 29.79% and second axis PC2 explains 14.14% of the total variance in the shapes.

opennotspecifiedApr 2012View details →

FIGURE 3 in Genetic and shell-shape analyses of Orlitia borneensis (Testudines: Geoemydidae) reveal limited divergence among founders of the European zoo population

FIGURE 3. Bayesian skyline plot demonstrating changes in effective population size in Orlitia borneensis based on mitochondrial data. Thick solid line represents median of the estimate, borders of grey area delineate the highest 95% posterior density interval.

opennotspecifiedApr 2012View details →

FIGURE 2 in Genetic and shell-shape analyses of Orlitia borneensis (Testudines: Geoemydidae) reveal limited divergence among founders of the European zoo population

FIGURE 2. Median-joining network indicating relationships among haplotypes of Orlitia borneensis based on cytochrome b sequences. Haplotypes are denoted as circles, their size is proportional to number of individuals carrying respective haplotype. Numbers at branches represent numbers of mutational steps (displayed for n> 1). Three main haplogroups are marked by ovals.

opencc-zeroDec 2020View details →

Genetic diversity and population structure of two endangered neotropical parrots inform In Situ and Ex Situ conservation strategies

A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.

opencc-zeroAug 2021View details →

Nonrandom missing data can bias PCA inference of population genetic structure

Population genetic studies in non-model systems increasingly use next-generation sequencing to obtain more loci, but such methods also generate more missing data that may affect downstream analyses. Here we focus on the Principal Component Analysis (PCA) which has been widely used to explore and visualize population structure with mean-imputed missing data. We simulated data of different population models with various total missingness (1%, 10%, 20%) introduced either randomly or biased among individuals or populations. We found that individuals biased with missing data would be dragged away from their real population clusters to the origin of PCA plots, making them indistinguishable from true admixed individuals and potentially leading to misinterpreted population structure. We also generated empirical data of the big brown bat (Eptesicus fuscus) using restriction site-associated DNA sequencing (RADseq). We filtered three data sets with 19.12%, 9.87%, and 1.35% total missingness, all showing nonrandom missing data with biased individuals dragged towards the PCA origin, consistent with results from simulations. We highlight the importance of considering missing data effects on PCA in non-model systems where nonrandom missing data are common due to varying sample quality. To help detect missing data effects, we suggest to 1) plot PCA with a color gradient showing per sample missingness, 2) interpret samples close to the PCA origin with extra caution, 3) explore filtering parameters with and without the missingness-biased samples, and 4) use complementary analyses (e.g., model-based methods) to cross-validate PCA results and help interpret population structure.

opennotspecifiedSep 2009View details →

FIGURE 1 in Experimental population genetics in insects: inheritance of ISSR-PCR bands in an artificial population

FIGURE 1. The NJ trees of the 0/1 matrices of the ISSR-PCR fingerprints. Numbers at internal branches indicate bootstrap support for the five families, if>50%.

Fig. 6. Maximum entropy models for A in Weak Genetic Differentiation among Populations of the Andean Ground Beetle Pelmatellus columbianus (Reiche, 1843) (Coleoptera: Carabidae)

Fig. 6. Maximum entropy models for A) the past (21,000 years) and B) present distribution of Pelmatellus columbianus, using five bioclimatic variables. Maps show the limit of the montane forest (above 2,450 m) in green and páramo (above 3,000 m) in light brown.

Fig. 5 in Weak Genetic Differentiation among Populations of the Andean Ground Beetle Pelmatellus columbianus (Reiche, 1843) (Coleoptera: Carabidae)

Fig. 5. Timing of the Pelmatellus columbianus clade lineage based on an uncorrelated relaxed molecular clock for a combined gene dataset.

Fig. 4. Fifty percent majority rule trees using Maximum Likelihood. A in Weak Genetic Differentiation among Populations of the Andean Ground Beetle Pelmatellus columbianus (Reiche, 1843) (Coleoptera: Carabidae)

Fig. 4. Fifty percent majority rule trees using Maximum Likelihood. A) COI, B) CAD. Bootstrap support shown above the branches.

Fig. 1 in Weak Genetic Differentiation among Populations of the Andean Ground Beetle Pelmatellus columbianus (Reiche, 1843) (Coleoptera: Carabidae)

Fig. 1. Habitat of Pelmatellus columbianus: A) Shrub páramo at Cashca Totoras, Province of Bol´ıvar; B) Grass

opencc-zeroSep 2021View details →

Population genetics informs the management of a controversial Australian waterbird

Widespread degradation across Australia's inland wetland network has contributed to severe declines for many waterbird species. In contrast, breeding colonies of the Australian white ibis (Threskiornis molucca) have increased in urbanised areas along the coast, but the level of dispersal and gene flow between inland and coastal areas remain unknown. This study uses single nucleotide polymorphisms (SNPs) to ascertain the variables influencing genetic connectivity among several inland and urban colonies of white ibis across south-eastern Australia between 2015 and 2018. The contemporary effective population size was estimated, and this value was used in simulations to evaluate the impact of various management scenarios on future genetic diversity. We found no significant differences in allele frequencies between localities, or robust evidence of site fidelity, therefore suggesting widespread dispersal and gene flow between inland and urban colonies. Furthermore, effective sizes were large enough to maintain genetic diversity into the future under various realistic management scenarios. However, the lack of genetic partitioning found suggests that urban management of the ibis should not be undertaken in isolation of the conservation requirements of inland colonies.

opencc-zeroOct 2021View details →

Microsatellites data set: Correlated population genetic structure in a three-tiered host-parasite system: the potential for coevolution and adaptive divergence

Three subspecies of Northern Bahamian Rock Iguanas, Cyclura cychlura, are currently recognized: C. c. cychlura,restricted to Andros Island, and C. c. figginsi and C. c. inornata, native to the Exuma Island chain. Populations on Andros are genetically distinct from Exuma Island populations, yet genetic divergence among populations in the Exumas is inconsistent with the two currently recognized subspecies from those islands. The potential consequences of this discrepancy might include the recognition of a single subspecies throughout the Exumas rather than two. That inference also ignores evidence that populations of C. cychlura are potentially adaptively divergent. We compared patterns of population relatedness in a three-tiered host-parasite system: C. cychlura iguanas, their ticks (genus Amblyomma, preferentially parasitizing these reptiles), and Rickettsia spp. endosymbionts (within tick ectoparasites). Our results indicate that while C. c. cychlura on Andros is consistently supported as a separate clade, patterns of relatedness among populations of C. c. figginsi and C. c. inornata within the Exuma Island chain are more complex. The distribution of the hosts, different tick species, and Rickettsia spp., supports the evolutionary independence of C. c. inornata. Further, these patterns are also consistent with two independent evolutionarily significant units within C. c. figginsi. Our findings suggest coevolutionary relationships between the reptile hosts, their ectoparasites, and rickettsial organisms, suggesting local adaptation. This work also speaks to the limitations of using neutral molecular markers from a single focal taxon as the sole currency for recognizing evolutionary novelty in populations of endangered species.

opencc-by-4.0Oct 2022View details →

Population structure and genetic variation of fragmented mountain birch forests in Iceland

Data avilability for the manuscript JOH-2022-096.R2 accepted for application

Data from: Increasing temperature weakens the positive effect of genetic diversity on population growth

Genetic diversity and temperature increases associated with global climate change are known to independently influence population growth and extinction risk. Whether increasing temperature may influence the effect of genetic diversity on population growth, however, is not known. We address this issue in the model protist system Tetrahymena thermophila. We test the hypothesis that at temperatures closer to the species' thermal optimum (i.e., the temperature at which population growth is maximal, or Topt), genetic diversity should have a weaker effect on population growth compared to temperatures away from the thermal optimum. To do so, we grew populations of T. thermophila with varying levels of genetic diversity at increasingly warmer temperatures and quantified their intrinsic population growth rate, r. We found that genetic diversity increases population growth at cooler temperatures, but that as temperature increases, this effect weakens. We also show that a combination of changes in the amount of expressed genetic diversity (G), plastic changes in population growth across temperatures (E), and strong GxE interactions, underlie this temperature effect. Our results uncover important but largely overlooked temperature effects that have implications for the management of small populations with depauperate genetic stocks in an increasingly warming world. --

Genetic loci associated with winter survivorship in diverse lowland switchgrass populations: SNP read count data

High winter mortality is the most important factor limiting biomass yield of lowland switchgrass planted in the northern latitudes of North America. Due to the perennial growth habit and strong dependence on weather conditions to generate sufficient selection pressure to identify winter-hardy individuals, breeding of cold tolerant switchgrass cultivars requires many years. Identification of causal genetic variants for winter survivorship would accelerate the improvement of switchgrass biomass production. The objective of this study was to identify allelic variation associated with winter survivorship in lowland switchgrass populations using bulk segregant analysis (BSA). Twenty-nine lowland switchgrass populations were evaluated for winter survival at two locations in southern Wisconsin and 21 population with differential winter survivorship was used for BSA. A maximum of 10% of the individuals per population (8-20) was bulked to create survivor and non-survivor DNA pools. The DNA pools were evaluated using exome capture sequencing and allele frequencies were used to conduct statistical tests. The BSA tests revealed nine QTL from tetraploid populations and seven QTL from octoploid populations. Some markers were identified in multiple populations that originated across a broad geographic landscape, while other markers were site-specific. QTL at positions 88 Mb on chromosome 2N, 115 Mb on chromosome 5K, and 1 and 100 Mb on chromosome 9N were potentially the most useful QTL. Markers associated with winter survivorship in this study can be used to accelerate breeding cycles of lowland switchgrass populations and should lead to improvements in adaptation within USDA hardiness zones 4 and 5.

Supplementary material 14 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986

Population structure on Aedes albopictus samples from all Connecticut samples (no temporal series) based on 15 microsatellite markers

Supplementary material 12 from: Gloria-Soria A, Shragai T, Ciota AT, Duval TB, Alto BW, Martins AJ, Westby KM, Medley KA, Unlu I, Campbell SR, Kawalkowski M, Tsuda Y, Higa Y, Indelicato N, Leisnham PT, Caccone A, Armstrong PM (2022) Population genetics of an invasive mosquito vector, Aedes albopictus in the Northeastern USA. NeoBiota 78: 99-127. https://doi.org/10.3897/neobiota.78.84986

Population structure of Aedes albopictus at the United States northeastern invasion front (New York, Connecticut, Massachusetts) based on 15 microsatellite markers