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opennotspecifiedMay 2013View details →

Figure 3 in Effects of islanding on the genetics of Niviventer confucianus (Mamalia: Rodentia: Muridae) populations in the Thousand Island Lake region

Figure 3. Relationship between values of FST and geographic distance, n = 78.

opencc-zeroDec 2021View details →

STR data from: Temporal analysis shows relaxed genetic erosion following improved stocking practices in a subarctic transnational brown trout population

Maintaining standing genetic variation is a challenge in human-dominated landscapes. We used genetic (i.e., 16 short tandem repeats) and morphological (i.e., length and weight) measurements of 593 contemporary and historical brown trout (Salmo trutta) samples to study fine-scale and short-term impacts of different management practices. These had changed from traditional breeding practices, using the same broodstock for several years, to modern breeding practices, including annual broodstock replacement, in the transnational subarctic Pasvik River. Using population genetic structure analyses (i.e., Bayesian assignment tests, DAPCs, and PCAs), four historical genetic clusters (E2001A-D), likely representing family lineages resulting from different crosses, were found in zone E. These groups were characterized by consistently lower genetic diversity, higher within-group relatedness, lower effective population size, and significantly smaller body size than contemporary stocked (E2001E) and wild fish (E2001F). However, even current breeding practices are insufficient to prevent genetic diversity loss and morphological changes as demonstrated by on average smaller body sizes and recent genetic bottleneck signatures in the modern breeding stock compared to wild fish. Conservation management must evaluate breeding protocols for stocking programs and assess if these can preserve remaining natural genetic diversity and morphology in brown trout for long-term preservation of freshwater fauna.

opencc-zeroJan 2022View details →

Genetic diversity of Horsfieldia tetratepala (Myristicaceae), an endangered plant species with extremely small populations to China: implications for its conservation

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. Horsfieldia tetratepala 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 H. tetratepala are required urgently, but limited information about its genome is available. Accordingly, restriction site-associated DNA sequencing (RAD_seq) was used to sequence sixty-three H. tetratepala 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 H. tetratepala 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 H. tetratepala that will significantly advance the formulation of effective conservation strategies.

opencc-zeroFeb 2022View details →

Microsatellite data from: Multiple colonizations and genetic differentiation from the mainland populations in insular populations of the perennial herb Solidago virgaurea complex (Asteraceae) on recently formed nearshore oceanic islands

Aim: Although the evolution of island endemic plants has long been investigated, the majority of such studies have focused on species with remarkable levels of morphological variation and on islands substantially far from the mainland. Except for a few examples such as the Canary Islands, endemic plants on nearshore oceanic islands have received less attention. In this study, we examined the Solidago virgaurea complex on the Japanese mainland Honshu and the adjacent Izu Islands to investigate the population genetic structure and dynamics in plants endemic to nearshore and recently formed oceanic islands. Location: Japanese mainland Honshu and the adjacent Izu Islands Taxon: Solidago virgaurea (Asteraceae) Methods: Sixteen and nine populations of S. virgaurea complex were sampled from the mainland and islands, respectively; phylogeographic and population genetics analyses were performed using plastid DNA and nuclear microsatellite DNA variations. Results: Phylogenetically close plastid DNA haplotypes were shared between the mainland and islands, although the populations of S. virgaurea from different islands tended to exhibit phylogenetically distinct haplotypes. Admixture analyses based on nuclear DNA variations revealed distinct genetic structures between the mainland and island populations. Gene flow among islands is restricted but may partially offset genetic drift on each island. Main conclusions: The genetic structure observed in this study may not have originated from a single dispersal event and successive expansion but rather from at least three colonization events and subsequent gene flow among island populations. Based on the nuclear DNA variations, the Izu Island populations of S. virgaurea are genetically distinct from the mainland ones. Repeated colonization events may have provided sufficient genetic diversity, which would generally be susceptible to founder effects and exert a driving force for evolutionary adaptation, to these oceanic island populations.

opencc-zeroFeb 2022View details →

Data from: A longitudinal analysis of the growth rate and mass of tail feathers in a great tit population: ontogeny, genetic effects and relationship between traits

Feathers have a diversity of functions in birds and are costly to produce, so their growth rate and mass can be reliable indicators of nutritional condition at the time of production. Despite the potential for feather metrics to advance our understanding of foraging, they are underused in avian ecology. One reason for this is the difficulty of interpreting whether individual variation is driven by ontogenetic, genetic, or environmental effects, which is exacerbated by the fact that most analyses have been done on cross-sectional data. We addressed this deficit using a longitudinal dataset of tail feathers collected from Great tits Parus major to test for ontogenetic and genetic effects on growth rate, mass and length, while controlling for body/feather size differences and other confounding factors. First, we found that the type of moult episode and experimentally-induced replacement differentially affected the length, mass and growth of feathers, providing evidence of an ontogenetic effect that should be considered when comparing these feather traits across individuals as a measure of condition. Second, we detected moderate to high repeatability and heritability values from parent-offspring regression for these three feather traits, which are suggestive of an underlying genetic component of variation. Third, we used a mean centring within-individual approach to test whether feather growth rate and feather mass (length-corrected) are indeed positively correlated with each other as overlapping indicators of body condition in birds, and found that this association, although positive, is weak and only significant between individuals. This suggests that both metrics are not so intimately linked as originally thought, and probably have different sensitivities to variation in foraging performance and ecological conditions. Together with the higher plasticity of feather growth rate compared to feather mass, our results support the idea that feather growth rate is better suited for examining short-term responses to environmental variation.

opencc-zeroMar 2022View details →

Data from: Amphibious mudskipper populations are genetically connected along coastlines, but differentiated across water

Aim: Many mudskippers in the family Gobiidae are obligately amphibious, requiring both aquatic and terrestrial portions of their life cycle. The terrestrial phase involves restrictions to mudflat habitats during breeding, when adults build burrows in the mud to lay eggs. The effects of this restricted out-of-water phase might be reflected in the population structure of the species. However, dispersal during the aquatic larval phase could connect distant populations. We examine one such mudskipper, Periophthalmus modestus, to test whether populations separated by water are more differentiated than those connected along a coastline. Location: South and East China Sea Taxon: Periophthalmus modestus (family: Gobiidae, subfamily: Oxudercinae) (Cantor 1842) Methods: We collected 236 individuals from ten locations around the East and South China Seas. We used a targeted capture sequencing method, RADcap, to call SNPs from 365 loci. We used multiple spatial and population genetics analyses and coalescent models to address the contemporary and historic biogeography of the species. Results: Based on observed levels of genetic variation and population structure, populations of Ps. modestus are connected across large distances of continuous coastline and small spans of water. Restricted long-distance dispersal across deep water has resulted in fragmentation of populations. We recovered no signal of isolation by distance, but instead, found genetic differentiation associated with regional groupings separated by large expanses of water. Main conclusions: These results are consistent with the hypothesis that a limited dispersal phase significantly affects population structure in fishes. The restrictive amphibious life history may be a key factor in the present-day distribution and population structure of Ps. modestus. Interactions between organismal life history and geography are critical for explaining the population genetic structure of a species.

opencc-by-4.0Mar 2022View details →

Figure 5 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860

Figure 5 Bayesian Skyline Plots based on the mtDNA partial control region sequences of Odontamblyopus lacepedii.

opencc-by-4.0Mar 2022View details →

Figure 2 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860

Figure 2 Maximum Likelihood tree is shown based on the control region haplotypes of Odontamblyopus lacepedii. The species of O. rebecca was used as the outgroup.

opencc-by-4.0Mar 2022View details →

Figure 4 from: Zhao L, Wang S, Qu F, Liu Z, Gao T (2022) A genetic assessment of the population structure and demographic history of Odontamblyopus lacepedii (Perciformes, Amblyopinae) from the northwestern Pacific. ZooKeys 1088: 1-15. https://doi.org/10.3897/zookeys.1088.70860

Figure 4 Mismatch distribution for demographic expansion based on mtDNA partial control region sequences of Odontamblyopus lacepedii.

opencc-zeroMar 2022View details →

Micro-endemic species of snails and amphipods show population genetic structure across very small geographic ranges

Understanding variation in population genetic structure, even across small distances and for species with extremely limited ranges, is critical for conservation planning and the development of effective management strategies for imperiled species. Organisms that occupy the same geographic extent can maintain different population structures, ranging from highly diverged to panmictic. Such differences can result from differences in biological characteristics such as dispersal ability or demographic history. We used microsatellite loci to evaluate population genetic structure and variation of four desert spring invertebrates having high to low dispersal ability: the lung snail Physa acuta, two species of gilled snails (Juturnia kosteri and Pyrgulopsis roswellensis; family Hydrobiidae) and the amphipod Gammarus desperatus. The study location represents entire species ranges for the micro-endemic hydrobiids and G. desperatus, while P. acuta is ubiquitous throughout much of North America. We found little evidence of significant population genetic structure for P. acuta and J. kosteri, but much more for P. roswellensis and G. desperatus. Our results demonstrate differences in habitat preference and/or dispersal ability between the species. While significant isolation-by-distance was detected in the two hydrobiids, dispersal is likely more limited in P. roswellensis than J. kosteri. This information provides insight into how gene flow shapes varying population genetic structure between species across small spatial scales (<100 km2). Most importantly, our results suggest that conservation agencies should not consider these microendemic species to be composed of single populations, but rather, that management plans for such species should account for population genetic variation across the species' ranges.

opencc-zeroDec 2014View details →

Data from: Genetic diversity and population structure of wild/weedy eggplant (Solanum insanum L., Solanaceae) in southern India: implications for conservation

[No abstract entered]

opencc-zeroDec 2015View details →

Data from: Genetic divergence and isolation by thermal environment in geothermal populations of an aquatic invertebrate

[No abstract entered]

opencc-zeroJul 2022View details →

Microsatellite genotyping data for habitat-linked genetic structure for white-crowned sparrow (Zonotrichia leucophrys): local factors shape population genetic structure

Ecological, environmental, and geographic factors all influence genetic structure. Species with broad distributions are ideal systems because they cover a range of ecological and environmental conditions allowing us to test which components predict genetic structure. This study presents a novel, broad geographic approach using molecular markers, morphology, and habitat modelling to investigate rangewide and local barriers causing contemporary genetic differentiation within the geographical range of three white-crowned sparrow (Zonotrichia leucophrys) subspecies: Z. l. gambelii, Z. l. oriantha, and Z. l. pugetensis. Three types of genetic markers showed geographic distance between sampling sites, elevation, and ecosystem type are key factors contributing to population genetic structure. Microsatellite markers revealed white-crowned sparrows do not group by subspecies, but instead indicated four groupings at a rangewide scale and two groupings based on coniferous and deciduous ecosystems at a local scale. Our analyses of morphological variation also revealed habitat differences; sparrows from deciduous ecosystems are larger than individuals from coniferous ecosystems based on principal component analyses. Habitat modeling showed isolation by distance was prevalent in describing genetic structure, but isolation by resistance also had a small but significant influence. Not only do these findings have implications concerning the accuracy of subspecies delineations, they also highlight the critical role of local factors such as habitat in shaping contemporary population genetic structure of species with high dispersal ability.

opencc-zeroAug 2022View details →

Susceptibility to a sexually transmitted disease in a wild koala population shows heritable genetic variance but no inbreeding depression

The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g., habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and to date we know little about the determinants of individual susceptibility to disease. Here we investigated the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combined data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 5007 SNPs to investigate the role of genetic variation in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.11 (95%CI = 0.05 – 0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management, as it suggests adaptive potential for the population.

opencc-zeroOct 2022View details →

SNP data: Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high-transmission

Genetic diversity and population structure of Plasmodium falciparum are assessed here using three established methods (i) SNP barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in 82.3% (median 3; range 1–18) and 57.8% (median 2; range 1–12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose 200 low-complexity infections for analysis. Each genotyping method presented a different pattern of change in population diversity and structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (<a>SNPs < microsatellites < var</a>). In terms of neutral variation, the 24-SNP barcode was the least informative, largely due to the bi-allelic nature of SNPs leading to a high proportion of double-allele calls (<a>DACs</a>), whereas multiallelic microsatellites showed high haplotype diversity with ten markers but no measurable change in population structure after IRS. Varcoding provided the most informative and nuanced description of changes in population structure, showing high diversity with a subtle but measurable change to less related var repertoires as a result of the IRS intervention. Relative performance, suitability, and cost-effectiveness of the methods relevant to local malaria elimination in high-transmission endemic areas are discussed.

Supplementary material 7 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618

STRUCTURE sequential assignments:

Supplementary material 5 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618

Estimated null allele proportions:

Supplementary material 6 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618

Linkage disequilibrium:

Supplementary material 4 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618

Observed and expected heterozygosity:

Supplementary material 3 from: Virgilio M, Delatte H, Nzogela YB, Simiand C, Quilici S, De Meyer M, Mwatawala M (2015) Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae). In: De Meyer M, Clarke AR, Vera MT, Hendrichs J (Eds) Resolution of Cryptic Species Complexes of Tephritid Pests to Enhance SIT Application and Facilitate International Trade. ZooKeys 540: 525-538. https://doi.org/10.3897/zookeys.540.9618

Pearson's Chi-squared test for Hardy-Weinberg equilibrium: