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opencc-zeroDec 2011View details →

Data from: Comparative population genetic analysis of bocaccio rockfish Sebastes paucispinis using anonymous and gene-associated simple sequence repeat loci

Comparative population genetic analyses of traditional and emergent molecular markers aid in determining appropriate use of new technologies. The bocaccio rockfish Sebastes paucispinis is a high-gene-flow marine species off the west coast of North America that experienced strong population decline over the past three decades. We used 18 anonymous and 13 gene associated simple sequence repeat loci (EST-SSRs) to characterize range-wide population structure with temporal replicates. No FST-outliers were detected using the LOSITAN program, suggesting that neither balancing nor divergent selection affected the loci surveyed. Consistent hierarchical structuring of populations by geography or year class was not detected regardless of marker class. The EST-SSRs were less variable than the anonymous SSRs, but no correlation between FST and variation or marker class was observed. General Linear Model analysis showed that low EST-SSR variation was attributable to low mean repeat number. Comparative genomic analysis with Gasterosteus aculeatus, Takifugu rubripes, and Oryzias latipes showed consistently lower repeat number in EST-SSRs than SSR loci that were not in ESTs. Purifying selection likely imposed functional constraints on EST-SSRs resulting in low repeat numbers that affected diversity estimates, but did not affect the observed pattern of population structure.

opencc-zeroDec 2011View details →

Data from: Influence of parameter settings in automated scoring of AFLPs on population genetic analysis

The use of procedures for the automated scoring of AFLP fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package RAWGENO to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations (Fst). Steps were implemented in R to automatically run the scoring process in RAWGENO for a set of different parameter combinations. While we found the scoring parameters minimum bin width and minimum number of samples per bin to have only weak influence on pairwise Fst values, maximum bin width and bin reproducibility had much stronger effects. The minimum average bin fluorescence scoring parameter affected Fst values in an only moderate way. At a range of scoring parameters around the default settings of RAWGENO, the number of polymorphic bins as well as pairwise Fst values stayed rather constant. This study thus shows the particularities of AFLP scoring, be it either manual or automatical, can have profound effects on subsequent population genetic analysis.

opennotspecifiedOct 2001View details →

FIGURE 5 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure

FIGURE 5. Unrooted phylogenetic tree constructed with Freqpars (Swofford & Berlocher 1987) on the basis of allele frequencies.

opennotspecifiedOct 2001View details →

FIGURE 4 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure

FIGURE 4. UPGMA dendrogram showing evolutionary relationships between populations based on genetic identity values (Nei 1978).

opennotspecifiedOct 2001View details →

FIGURE 3 in Taxonomic diagnosis of Dicyrtomina ornata and D. saundersi (Collembola: Dicyrtomidae) and analysis of their population genetic structure

FIGURE 3. Map of collecting sites. See Table 1 for abbreviations. Solid boxes are sites where only D. ornata was found; solid circles are sites where only D. saundersi was found; asterisks are sites where both species live sympatrically.

opennotspecifiedDec 2022View details →

Fig. 7. Bayesian Skyline Plot analysis showing population size over time. The x in Echinoderes galadrielae Grzelak & Sørensen 2022, sp. nov.

Fig. 7. Bayesian Skyline Plot analysis showing population size over time. The x-axis is the time to the present in years, while the y-axis is the product between the effective population size (Ne) and the generation length (t) in a log scale. The mean estimate (black solid line) and 95% highest probability density limits (grey area) are shown.

Fig. 5 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India

Fig. 5. Variation in percentage distribution of CRA (a) in different parts of L. speciosa (b) in all 12 populations of L. speciosa collected across a north–south geographical gradient in the Southern Western Ghats region of peninsular India.

Fig. 3 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India

Fig. 3. Principal Component Analysis performed on (a) SSR data obtained from 12 natural populations of L. speciosa (b) estimate of corosolic acid content across these populations. The percentage of variance explained by each axis is indicated in parenthesis.

Fig. 2 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India

Fig. 2. UPGMA cluster analysis of SSR data for 12 wild populations of L. speciosa across the Southern Western Ghats depicting pattern of grouping among populations.

Fig. 6 in Corosolic acid content and SSR markers in Lagerstroemia speciosa (L.) Pers.: A comparative analysis among populations across the Southern Western Ghats of India

Fig. 6. Map showing geographical location of collection sites of all 12 populations of L. speciosa in the Southern Western Ghats.

opencc-by-4.0Jun 2024View details →

PixelPop: Nonparametric analysis of correlations in the binary black hole population with LIGO–Virgo–KAGRA data

Data release accompanying the PixelPop papers, analyzing gravitational wave populations. The first dataset (in gwtc3_result_files) is the posterior samples for the runs presented in analysis of LIGO--Virgo--KAGRA data, following the third gravitational wave catalog, see https://arxiv.org/abs/2406.16844. We include a python notebook (example_plot.ipynb) showing how to create the plots presented in this paper. In v2, we also include samples from the predictive distributions. Due to the large uncertainties, marginalizing over the hyperposterior may be a poor representation of the inferred distribution, and so instead we provide samples from the median predictive distribution. That is, samples from the distribution shown in the central panels of the figures.  The second dataset (in o4inj_result_files) is the posterior samples accompanying the runs presented in the technical background paper, see https://arxiv.org/abs/2406.16813.

opennotspecifiedDec 2020View details →

Figure 3. Four dendrograms depicting the hierarchical relationship between the nine Chthamalus populations. A in Molecular analysis reveals a cryptic species of Chthamalus (Crustacea: Cirripedia) in the Cape Verde Islands

Figure 3. Four dendrograms depicting the hierarchical relationship between the nine Chthamalus populations. A, Pearson's correlation coefficient with UPGMA amalgamation. B, modified Morisita's similarity coefficient with farthest neighbour amalgamation. C, squared Euclidean distance with minimum variance amalgamation. D, Manhattan distance with nearest neighbour amalgamation.

opencc-zeroJan 2022View details →

Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number

The release of captive-bred plants and animals has increased worldwide to augment declining species. However, insufficient attention has been given to understanding how neutral and adaptive genetic variation are partitioned within and among proximal natural populations, and the patterns and drivers of gene flow over small spatial scales, which can be important for restoration success. A seascape genomics approach was used to investigate population structure, local adaptation, and the extent to which environmental gradients influence genetic variation among natural and restored populations of Chesapeake Bay eastern oysters Crassostrea virginica. We also investigated the impact of hatchery practices on neutral genetic diversity of restored reefs and quantified the broader genetic impacts of large-scale hatchery-based bivalve restoration. Restored reefs showed similar levels of diversity as natural reefs, and striking relationships were found between planting frequency and broodstock numbers and genetic diversity metrics (effective population size and relatedness), suggesting that hatchery practices can have a major impact on diversity. Despite long-term restoration activities, haphazard historical translocations, and high dispersal potential of larvae that could homogenize allele frequencies among populations, moderate neutral population genetic structure was uncovered. Moreover, environmental factors, namely salinity, pH, and temperature, play a major role in the distribution of neutral and adaptive genetic variation. For marine invertebrates in heterogeneous seascapes, collecting broodstock from large populations experiencing similar environments to candidate sites may provide the most appropriate sources for restoration and ensure population resilience in the face of rapid environmental change. This is one of a few studies to demonstrate empirically that hatchery practices have a major impact on the retention of genetic diversity. Overall, these results contribute to the growing body of evidence for fine-scale genetic structure and local adaptation in broadcast-spawning marine species and provide novel information for the management of an important fisheries resource.

opencc-zeroDec 2010View details →

Data from: Genetic analysis of life-history constraint and evolution in a wild ungulate population

Trade-offs among life-history traits are central to evolutionary theory. In quantitative genetic terms, trade-offs may be manifested as negative genetic covariances relative to the direction of selection on phenotypic traits. Although the expression and selection of ecologically important phenotypic variation are fundamentally multivariate phenomena, the in situ quantification of genetic covariances is challenging. Even for life-history traits, where well-developed theory exists with which to relate phenotypic variation to fitness variation, little evidence exists from in situ studies that negative genetic covariances are an important aspect of the genetic architecture of life-history traits. In fact, the majority of reported estimates of genetic covariances among life-history traits are positive. Here we apply theory of the genetics and selection of life histories in organisms with complex life cycles to provide a framework for quantifying the contribution of multivariate genetically based relationships among traits to evolutionary constraint. We use a Bayesian framework to link pedigree-based inference of the genetic basis of variation in life-history traits to evolutionary demography theory regarding how life histories are selected. Our results suggest that genetic covariances may be acting to constrain the evolution of female life-history traits in a wild population of red deer Cervus elaphus: genetic covariances are estimated to reduce the rate of adaptation by about 40%, relative to predicted evolutionary change in the absence of genetic covariances. Furthermore, multivariate phenotypic (rather than genetic) relationships among female life-history traits do not reveal this constraint.

opencc-zeroJul 2022View details →

Genetic admixture and population structure analysis of Indian water buffaloes (Bubalus bubalis) using STR markers

We generated genetic diversity data for 10 different buffalo populations of India using 20 highly polymorphic microsatellite markers. The buffalo populations of Odisha were the primary focus, viz. Chilika, Paralakhemundi, Kalahandi, Sambhalpuri, and Manda. The total observed number of alleles ranged between 143 (Manda) and 301 (Paralakhemundi) with an average of 204 alleles per breed. The minimal spanning network based on Bruvo's distance, PCA based on the Fst values, and genetic admixture analysis using both the STRUCTURE and 'snapclust' could identify the Manda population distinct from other Odisha buffalo breeds as well as Chhattisgarhi buffalo breed. The Sambhalpuri buffalo population also clustered into two separate subpopulations, half of the unique sub-population located geographically south-wards displayed no admixture with any of the adjacent buffalo populations. The Sambhalpuri population requires elaborate analysis to confirm the existence of two distinct sub-populations and if they could be recognized as separate breeds. The limited number of sires in the Manda population has resulted in excess of heterozygosity. Furthermore, the Manda population is left with very little allelic richness and this poses a huge threat to the population's existence. In another way, the study has led to the identification of the Manda buffalo as a distinct population, and the germplasm has been registered based on the study.

opencc-zeroAug 2022View details →

Favoring recruitment as a conservation strategy to improve the resilience of long-lived reptile populations: insights from a population viability analysis

In long-lived species, although adult survival typically has the highest elasticity, temporal variations in less canalized demographic parameters are the main drivers of population dynamics. Targeting recruitment rates may thus be the most effective strategy to manage these species. We analyzed 1136 capture–recapture histories collected over 9 years in an isolated population of the critically endangered Lesser Antillean iguana, using a robust-design Pradel model to estimate adult survival and recruitment rates. From an adult population size estimated at 928 in 2013, we found a yearly decline of 4% over the 8-year period. As expected under the canalization hypothesis for a long-lived species, adult survival was high and constant, with little possibility for improvement, whereas the recruitment rate varied over time and likely drove the observed population decline. We then used a prospective perturbation analysis to explore whether managing the species' immature cohorts would at least slow the population decline. The prospective perturbation analysis suggested that a significant and sustained conservation effort would be needed to achieve a recruitment rate high enough to slow the population decline. We posit that the high recruitment rate achieved in 2014 – likely due to the maintenance in 2012 of the main nesting sites used by this population – would be sufficient to slow this population's decline if it was sustained each year. Based on the results of diverse pilot studies we conducted, we identified the most likely threats targeting the eggs and immature cohorts, stressing the need to improve reproductive success and survival of immature iguanas. The threats we identified are also involved in the decline of several reptile species, and species from other taxa such as ground-nesting birds. These findings on a little-studied taxon provide further evidence that focusing on the immature life stages of long-lived species can be key to their conservation.

opennotspecifiedSep 2022View details →

FIGURE. Map of specimens collected for the phylogenetic analysis in this study, excluding Tulipa iliensis and T. altaica, which both lacked GPS information. Populations of the new species T. toktogulica are labelled in order of discovery. in Tulipa toktogulica (Liliaceae), a cryptic, endangered new species from the western Tien-Shan, Kyrgyzstan

FIGURE. Map of specimens collected for the phylogenetic analysis in this study, excluding Tulipa iliensis and T. altaica, which both lacked GPS information. Populations of the new species T. toktogulica are labelled in order of discovery.

opencc-zeroOct 2022View details →

Insights into Mus musculus population structure across Eurasia revealed by whole-genome analysis

For more than 100 years, house mice (Mus musculus) have been used as a key animal model in biomedical research. House mice are genetically diverse, yet their genetic background at the global level has not been fully understood. Previous studies suggested that they originated in South Asia and diverged into three major subspecies almost simultaneously, approximately 350,000–500,000 years ago; however, they have spread across the world with the migration of modern humans in prehistoric and historic times (∼10,000 years ago to present), and undergone secondary contact, which have complicated the genetic landscape of wild house mice. In this study, we sequenced the whole genomes of 98 wild house mice collected from Eurasia, particularly East Asia, Southeast Asia, and South Asia. We found that although wild house mice consist of three major genetic groups corresponding to the three major subspecies, individuals representing admixture between subspecies are much more ubiquitous than previously recognized. Furthermore, several samples showed an incongruent pattern of genealogies between mitochondrial and autosomal genomes. Using samples likely retaining the original genetic components of subspecies with least admixture, we estimated the pattern and timing of divergence among the subspecies. The results are important for understanding the genetic diversity of wild mice on a global level and the information will be particularly useful in future biomedical and evolutionary studies using laboratory mice established from these wild mice.

opencc-by-4.0May 2024View details →

Data used for analysis in "Calibrating tropical forest coexistence in ecosystem demography models using multi-objective optimization through population-based parallel surrogate search"

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