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opencc-zeroMay 2023View details →

Genetic diversity varies with species traits and latitude in predatory soil arthropods (Myriapoda: Chilopoda)

Aim To investigate the drivers of intra-specific genetic diversity in centipedes, a group of ancient predatory soil arthropods. Location Asia, Australasia and Europe Time period Present Major taxa studied Centipedes (Class: Chilopoda) Methods We assembled a database of 1245 mitochondrial cytochrome c oxidase subunit I sequences representing 128 centipede species from all five orders of Chilopoda. This sequence dataset was used to estimate genetic diversity for centipede species and compare its distribution with estimates from other arthropod groups. We studied the variation in centipede genetic diversity with species traits and biogeography using a beta regression framework, controlling for the effect of shared evolutionary history within a family. Results A wide variation in genetic diversity across centipede species (0 to 0.1713) falls towards the higher end of values among arthropods. Overall, 27.57% of the variation in mitochondrial COI genetic diversity in centipedes was explained by a combination of predictors related to life history and biogeography. Genetic diversity decreased with body size and latitudinal position of sampled localities, was greater in species showing maternal care and increased with geographic distance among conspecifics. Main conclusions Centipedes fall towards the higher end of genetic diversity among arthropods, which may be related to their long evolutionary history and low dispersal ability. In centipedes, the negative association of body size with genetic diversity may be mediated by its influence on local abundance or the influence of ecological strategy on long-term population history. Species with maternal care had higher genetic diversity, which goes against expectations and needs further scrutiny. Hemispheric differences in genetic diversity can be due to historic climatic stability and lower seasonality in the southern hemisphere. Overall, we find that despite the differences in mean genetic diversity among animals, similar processes related to life history strategy and biogeography are associated with the variation within them.

opencc-by-4.0Mar 2023View details →

Figure 1 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil

Figure 1 Adult specimen of O. impluviata - Dorsal view.

opencc-zeroJul 2023View details →

Data for: Surrounding landscape, habitat and hybridization dynamics drive population structure and genetic diversity in the Saltmarsh Sparrow (Ammospiza caudacuta)

Determining factors that shape a species' population genetic structure is beneficial for identifying effective conservation practices. We assessed population structure and genetic diversity for Saltmarsh Sparrow (Ammospiza caudacuta), an imperiled tidal marsh specialist, using 13 microsatellite markers and 964 individuals sampled from 24 marshes across the breeding range. We show that Saltmarsh Sparrow populations are structured regionally by isolation-by-distance, with gene flow occurring among marshes within ~110-135 km of one another. Isolation-by-resistance and isolation-by-environment also shape genetic variation; several habitat and landscape features are associated with genetic diversity and genetic divergence among populations. Human development in the surrounding landscape isolates breeding marshes, reducing genetic diversity and increasing population genetic divergence, while surrounding marshland and patch habitat quality (proportion high marsh and sea-level-rise trend) have the opposite effect. The distance of the breeding marsh to the Atlantic Ocean also influences genetic variation, with marshes farther inland being more divergent than coastal marshes. In northern marshes, hybridization with Nelson's Sparrow (A. nelsoni) strongly influences Saltmarsh Sparrow genetic variation, by increasing genetic diversity in the population; this has a concomitant effect of increasing genetic differentiation of marshes with high levels of introgression. From a conservation perspective, we found that the majority of population clusters have low effective population sizes, suggesting a lack of resiliency. To conserve the representative breadth of genetic and ecological diversity and to ensure redundancy of populations, it will be important to protect a diversity of marsh types across the latitudinal gradient of the species range, including multiple inland, coastal and urban populations, which we have shown to exhibit signals of genetic differentiation. It will also require maintaining connectivity at a regional level, by promoting high marsh habitat at the scale of gene flow (~130 km), while also ensuring "stepping stone" populations across the range.

opencc-by-4.0Mar 2023View details →

Figure 3 in Genetic diversity, phylogenetic and phylogeographic analyses of Oncideres impluviata (Germar, 1823) (Coleoptera: Cerambycidae) in Rio Grande do Sul state, Brazil

Figure 3 Physiographic regions of Rio Grande do Sul state, Brazil.

opencc-zeroJul 2023View details →

Low genetic diversity and shallow population structure in the broom hare, Lepus castroviejoi (Lagomorpha:Leporidae)

Microsatellite dataset of 322 hare samples from five species: 76 samples from the broom hare (Lepus castroviejoi); 81 for the European hare (L. europaeus); 68 for the Iberian hare (L. granatensis); 77 for the mountain hare (L. timidus); and 20 for the Italian hare (L. corsicanus).

opencc-by-4.0Jul 2023View details →

Additional Files for "Assessing the potential of germplasm collections for the management of genetic diversity: the case of the French National Cryobank"

Additional files for the article entitled "Assessing the potential of germplasm collections for managing genetic diversity: the case of the French National Cryobank". Additional file 1: Table S1 Title: Report on the output of material since the creation of the French National Cryobank Additional file 2: Figure S1 Title: Summary of material outputs from the French National Cryobank since 1999 Additional file 3: Table S2 Title: Descriptors from the French National Cryobank data for six species Additional file 4: Figure S2 Title: Distribution of data and definition of intervals regarding breed diffusion (A), donor birth-year classes (B), and classes of donor’s age at 1st collection (C) Additional file 5: Table S3 Title: Statistics of the number of effective donors (De) according to species Additional file 6: Table S4 Title: Distribution of donors and doses across breeds Description: In green, the breeds for which the FNC collections meet FAO conditions for reconstitution of an extinct breed. In blue, the breeds for which the collections of the FNC do not yet meet FAO conditions for reconstitution of an extinct breed. In gray, FAO recommendations not available. Based on the 2012 FAO report, with 100 founder females for ruminants and horses, or 30 founder females for pigs (with a pregnancy rate of 0.6). Additional file 7: Figure S3 Title: Evolution of genetic contributions of sires and their production of direct descendants in the French National Cryobank over the period 2011–2020 for three livestock species Description: Two breeds of pigs are represented in pink (a, b), three breeds of sheep are represented in blue (c, d, e), and five breeds of cattle are represented in ochre (f, g, h, i, j). Additional file 8: Figure S4 Title: Distribution of individual IDIs of cryopreserved sires for the 17 breeds analyzed Description: Pig breeds are represented in pink, sheep breeds are represented in blue, and cattle breeds are represented in ochre. Additional file 9: Figure S5 Title: Correlation between IDI values and the year of birth of donors Additional file 10: Figure S6 Title: Prediction of IDI values based on donor’s year of birth and the motivation for entry into collection Description: Type I (for endangered breeds) is represented in purple and type III (for representative individuals of a breed over a period) is represented in orange.

opencc-zeroAug 2023View details →

Preservation of genetic diversity in a highly fragmented population of the gray-sided vole Myodes rufocanus in an intensive farming region

Individual dispersal plays an important role in preserving genetic diversity in density-fluctuating populations of arvicoline rodents. When habitats are fragmented and dispersal between habitats is severely constrained, genetic diversity can be lost. Here, I investigated whether genetic diversity in the gray-sided vole Myodes rufocanus was preserved in an intensive farming region in Japan, where voles inhabited isolated windbreak forests along the borders of plowed lands. Genetic structure was examined in 673 vole samples (330 in spring and 343 in fall) collected at 34 windbreak forests located 0.35–20 km apart. A part of the control region (425 bp) of mitochondrial DNA (mtDNA) was sequenced in 673 voles, yielding 76 haplotypes. Genetic differentiation of maternally inherited mtDNA among trapping sites was markedly lower in males than in females in both seasons, indicating strong male-biased dispersal. Genotypes at six microsatellite DNA loci were determined in 494 voles (245 in spring and 249 in fall) from 18 trapping sites, and loci harbored 16–24 alleles. The mean number of alleles per locus (allelic diversity) at trapping sites was positively correlated with the number of examined individuals (density) in both seasons, and the relationship was very similar to that of a previous study performed in much less fragmented populations. Genetic differentiation of microsatellite DNA among trapping sites decreased considerably from spring to fall. In a STRUCTURE analysis with a most probable cluster number of two, closer trapping sites showed more similar mean values of cluster admixture proportions. The present findings indicate that gene flow among isolated windbreak forests, which occurred mainly by dispersal of males, was not restrained in this intensive farming region. Furthermore, the results suggest that genetic diversity in the study population was preserved as well as in less fragmented populations.

opencc-zeroAug 2023View details →

Multiplexing PCR allows the identification of within-species genetic diversity in ancient eDNA

Sedimentary ancient DNA (sedaDNA) has rarely been used to obtain population-level data due to either a lack of taxonomic resolution for the molecular method used, limitations in the reference material or inefficient methods. Here, we present the potential of multiplexing different PCR primers to retrieve population-level genetic data from sedaDNA samples. Vaccinium uliginosum (Ericaceae) is a widespread species with a circumpolar distribution and three lineages for present-day populations. We searched 18 plastid genomes for intraspecific variable regions and developed 61 primers to target these. Initial multiplex PCR testing resulted in a final set of 38 primers. These primers were used to analyse 20 lake sedaDNA samples (11,200 cal. yr BP to present) from five different localities in northern Norway, the Alps and the Polar Urals. All known V. uliginosum lineages in these regions and all primers could be recovered from the sedaDNA data, where for each sample 28.1 primers containing 34.15 variant sequences were obtained on average. All sediment samples were dominated by a single lineage, except three alpine samples which had co-occurrence of two different lineages. Furthermore, lineage turnover was observed in the Alps and northern Norway, suggesting that present-day phylogeographical studies may overlook past genetic patterns. Multiplexing primers is a promising tool for generating population-level genetic information from sedaDNA. The relatively simple method, combined with high sensitivity, provides a scalable method that will allow researchers to track populations through time and space using environmental DNA.

Data for: Assessment of genetic diversity and protein content of Scandinavian peas (Pisum sativum)

We produced homogeneous lines of 227 pea accessions from the Nordic Genetic Resource Center by single seed descent. The genetic diversity among these, mostly Scandinavian accessions, was investigated using three microsatellite markers, A9, AC58 and AA5. The microsatellites were highly informative and separated 153 of 194 accessions on a Neighbor Joining topology. The high polymorphism information content (PIC) values between 0.87 and 0.91 indicated that the gene bank material contains a large number of pea accessions with different breeding. The peas were grown in the field for two years and seed protein content showed variation between 9.3% and 34.1% over years and accessions. Mean thousand seed weight was 152.05 g. More than 10 accessions had protein content above 28% showing that the collection has potential as a breeding nursery for high-protein pea.

Data and Code for: Reproductive strategies and their consequences for divergence, gene flow, and genetic diversity in three taxa of Clarkia

Differences in reproductive strategies can have important implications for macro- and micro-evolutionary processes. We used a comparative approach through a population genetics lens to evaluate how three distinct reproductive strategies shape patterns of divergence among as well as gene flow and genetic diversity within three closely related taxa in the genus Clarkia. One taxon is a predominantly autonomous self-fertilizer and the other two taxa are predominantly outcrossing but vary in the primary pollinator they attract. In genotyping populations using genotyping-by-sequencing and comparing loci shared across taxa, our results suggest that differences in reproductive strategies in part promote evolutionary divergence among these closely related taxa. Contrary to expectations, we found that the selfing taxon had the highest levels of heterozygosity but a low rate of polymorphism. The high levels of fixed heterozygosity for a subset of loci suggests this pattern is driven by the presence of structural rearrangements in chromosomes common in other Clarkia taxa. In evaluating patterns within taxa, we found a complex interplay between reproductive strategy and geographic distribution. Differences in the mobility of primary pollinators did not translate to a difference in rates of genetic diversity and gene flow within taxa – a pattern likely due to one taxon having a patchier distribution and a less temporally and spatially reliable pollinator. Taken together, this work advances our understanding of the factors that shape gene flow and the distribution of genetic diversity within and among closely related taxa.

Phenotypic and genetic diversity data recorded in island and mainland populations worldwide

We used this dataset to assess the strength of isolation due to geographic and macroclimatic distance across island and mainland systems, comparing published measurements of phenotypic traits and neutral genetic diversity for populations of plants and animals worldwide. The dataset includes 112 studies of 108 species (72 animals and 36 plants) in 868 island populations and 760 mainland populations, with population-level taxonomic and biogeographic information, totalling 7438 records.

Data from: the Siam chicken bioresource project: genetic diversity and origin of Thai chicken breeds

Three separate studies have delved into the genetic characteristics, origins, and unique attributes of various chicken breeds in Thailand, providing crucial insights for future breeding programs. The first study focused on Chee Fah and Fah Luang, black-boned chicken breeds in Chiang Rai, Thailand. Despite their economic and cultural significance, little was known about their genetics. Mitochondrial DNA D-loop sequencing and microsatellite genotyping revealed shared genetic heritage with Chinese black-boned chickens, suggesting their origin. Distinct genetic patterns were identified compared to Thai domestic chickens and red junglefowl, indicating crossbreeding and introgression during domestication. Interestingly, the Chee Fah and Fah Luang chickens from different localities exhibited different gene pool structures, possibly influenced by environmental factors like elevation. The second study centered on the Mae Hong Son chicken, a local breed in Northern Thailand. Genetic analyses, including microsatellite markers and mitochondrial D-loop sequencing, unveiled high genetic diversity and unique allelic gene pool patterns. This breed likely originated as a crossbreed between red junglefowl and Thai indigenous village chickens, adapting to local environmental, social, and cultural conditions. The third study examined Lao Pa Koi (LPK) chickens, a popular fighting breed in Thailand. Genetic diversity assessments using microsatellite markers and mitochondrial DNA (mtDNA) D-loop sequences confirmed high variability and genetic admixture between red junglefowl and Thai domestic chickens. Spatial suitability analysis highlighted the importance of elevation in shaping LPK chicken distribution. In conclusion, these studies collectively enhance our understanding of the genetic foundations, origins, and adaptation of diverse chicken breeds in Thailand. This knowledge is crucial for developing effective breeding programs and preserving these valuable genetic resources.

opencc-by-4.0Dec 2018View details →

Fig. S3 in High Genetic Diversity of Amoebae Belonging to the Genus Mayorella (Amoebozoa, Discosea, Dermamoebida) in Natural Habitats

Fig. S3

opencc-by-4.0Dec 2018View details →

Fig. S1 in High Genetic Diversity of Amoebae Belonging to the Genus Mayorella (Amoebozoa, Discosea, Dermamoebida) in Natural Habitats

Fig. S1

opencc-zeroOct 2023View details →

Reference genome resources associated with the project: Functional genetic diversity is correlated with intensity of genetic drift in populations of an endangered rattlesnake

Theory predicts that genetic erosion in small, isolated populations of endangered species can be assessed using estimates of neutral genetic variation reflecting long-term impacts of genetic drift, yet this widely used approach has been questioned in the genomics era. Here we leverage a chromosome-level assembly and whole genome resequencing data (N=110 individuals) from an endangered rattlesnake (Sistrurus catenatus) to evaluate the relationship between genome-wide neutral and functional diversity over long- and short-term timescales. As predicted for populations at long-term equilibrium, we found a positive correlation between population-level estimates of neutral genetic diversity (π) and the mean number of highly detrimental loss-of-function mutations, and a negative relationship between neutral genetic diversity and an estimate of genetic load. In contrast, we found only a weak, non-significant positive correlation between levels of neutral and adaptive variation. Additional analyses using estimates of drift at more recent time scales (> 100 generations) show expected correlations between both measures of genetic load, but a lack of a significant correlation with levels of adaptive variation. Individual-based demographic metrics that capture drift impacts over recent time scales confirm these results. Broadly, our results confirm that estimates of diversity and demography based on neutral genetic variation provide an accurate measure of a key component of genetic erosion – genetic load – in populations of a threatened vertebrate. Our findings also provide nuance to the neutral-functional diversity controversy by demonstrating that neutral genetic diversity is useful in predicting some, but not all, components of functional genetic diversity.

opencc-zeroOct 2023View details →

Data from: Revealing biogeographic patterns in genetic diversity of native and invasive plants and their association with soil community diversity in the Chinese coast

Within-species genetic diversity is shaped by multiple evolutionary forces within the confines of geography, and has cascading effects on the biodiversity of other taxa and levels. Invasive species are often initially limited in genetic diversity but still respond rapidly to their new range, possibly through 'pre-adapted' genotypes or multiple sources of genetic diversity, but little is known about how their genetic structure differs from that of native species and how it alters the genetic-species diversity relationship. Here, we selected a widespread native species (Phragmites australis) and its co-occurring invasive competitor (Spartina alterniflora) as our model plant species. We investigated the genetic structure of P. australis using two chloroplast fragments and ten nuclear microsatellites in 13 populations along the Chinese coastal wetlands. We discovered a distinct geographical differentiation, showing that the northern and southern populations harbored unique genotypes. We also found a significant increase in genetic diversity (allelic richness and expected heterozygosity) from south to north. Combined with previous studies of S. alterniflora, the Mantel tests revealed a significant correlation of genetic distances between P. australis and S. alterniflora even when controlling for geographic distance, suggesting that the invasive species S. alterniflora might exhibit a phylogeographic pattern similar to that of the native species to some extent. Furthermore, our results suggest that the S. alterniflora invasion has altered the relationship between the genetic diversity of the dominant native plant and the associated species richness of soil nematodes. The reason for the alteration of genetic-species diversity relationship might be that the biological invasion weakens the environmental impact on both levels of biodiversity. Our findings contribute to understanding the latitudinal patterns of intraspecific genetic diversity in widespread species. This work on the genetic diversity analysis of native species also provides significant implications for the invasion stage and ecological consequences of biological invasions.

opencc-zeroOct 2023View details →

Effects of disturbance on genetic diversity in the submersed aquatic plant Vallisneria americana

In summer 2011, Tropical storms Lee and Irene caused an estimated 90% decline of the submersed aquatic plant Vallisneria americana Michx. (Hydrocharitaceae) in the Hudson River, of New York (USA). To understand the genetic impact of such large-scale demographic losses, we compared diversity at 10 microsatellite loci in 135 samples collected from 5 sites just before the storms with 239 shoots collected from 9 sites four years after. Although 80% of beds sampled in 2011 lacked V. americana in 2015, we found similar genotypic and genetic diversity and effective population sizes in pre-storm versus post-storm sites. These similarities suggest that despite local extirpations concentrated at the upstream end of the sampling area, V. americana was regionally resistant to genetic losses. Similar geographically based structure among sites in both sampling periods suggested that cryptic local refugia at previously occupied sites facilitated re-expansion after the storms. However, this apparent resistance to disturbance may lead to a false sense of security. Low effective population sizes and high clonality in both time periods suggest that V. americana beds were already small and had high frequency of asexual reproduction before the storms. Dispersal was not sufficient to recolonize more isolated sites that had been extirpated. Chronic low diversity and reliance on asexual reproduction for persistence can be risky when more frequent and intense storms are paired with ongoing anthropogenic stressors. Monitoring genetic diversity along with extent and abundance of V. americana will give a more complete picture of long-term potential for resilience.

publicJan 2020View details →

Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?

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publicFeb 2025View details →

Data from: An established plant invader may still benefit from increasing genetic diversity – Insights from artificial populations in a common garden experiment

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