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opennotspecifiedMay 2022View details →

Figure 13 in The monophyly of Crenuchinae and description of two new species of Poecilocharax (Teleostei: Crenuchidae) based on phenotypic and genotypic evidence

Figure 13. Poecilocharax rhizophilus sp. nov., medial view of premaxilla, maxilla and dentary, right side, MZUSP 121651, paratype, 16.5 mm SL.

opencc-zeroMar 2023View details →

Data for: Immune genotypes, immune responses, and survival in a wild bird population

Individuals vary in their immune genotype, inbreeding coefficient f, immune responses, survival to adulthood, and adult longevity. However, whether immune genes predict survival or longevity, whether such relationships are mediated through immune responses, and how f affects immune genotype remain unclear. We use a wild song sparrow (Melospiza melodia) population in which survival to adulthood, adult longevity, and f were measured precisely, and in which immune responses have previously been assessed. We investigate four toll-like receptors (TLR) and the major histocompatibility complex (MHC) class IIB exon 2 genes. We test: a) whether immune genes predict fitness (survival to adulthood or adult longevity); b) whether immune genes predict immune response; c) whether immune response predicts fitness; and d) whether fitness, immune responses, or immune genotypes are correlated with f. We find that survival to adulthood is not associated with immune gene variation, but adult longevity is decreased by high MHC allele diversity (especially in birds that were relatively outbred), and by the presence of a specific MHC supertype. Immune responses were affected by specific immune genotypes. Survival to adulthood and adult longevity were not predicted by immune response, implying caution in the use of immune response as a predictor for fitness. We also found no relationship between f and immune genotype. This finding indicates that immune gene associations with longevity and immune response are not artefacts of f, and suggests that pathogen-mediated selection at functional loci can slow the loss of genetic variation arising from genetic drift and small population size.

opencc-zeroApr 2023View details →

Ontario black bear genotypes and locations (2017-2019)

Characterizing patterns and drivers of dispersal is fundamental to our understanding of animal ecology and ultimately informing species conservation and management strategies. In this study, we used microsatellite data from 3,941 individual black bears, Ursus americanus, occupying 73 spatially distinct sampling areas across a large heterogeneous landscape to characterize dispersal via gene flow directionality. We fit spatial models to quantified gene flow to test hypotheses regarding drivers of putative dispersal patterns. Specifically, we tested the relative influence of food productivity gradients, bear density, and bear harvest on dispersal. We also evaluated differences in gene flow patterns within and between sexes to assess sex-biased dispersal. We found evidence suggestive of positive density-dependent, male-biased dispersal. Our data show evidence of a relationship between dispersal and broad food productivity gradients. Specifically, male bears displayed preferential dispersal towards mixed deciduous forests with higher food productivity relative to less productive boreal forests. Given the dense sampling scheme across a continuous population, occupying a large heterogeneous landscape, these results provide key insight as to the likely drivers of dispersal patterns in a wide-ranging mammal.

opencc-by-4.0May 2023View details →

The genotype data accompanying the paper titled "Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights into their genetic interactions beyond Mainland Southeast Asia"

The newly generated genome-wide genotype data for 10 Lao individuals used in the paper "Reanalyzing the genetic history of Kra-Dai speakers from Thailand and new insights into their genetic interactions beyond Mainland Southeast Asia" ( https://www.nature.com/articles/s41598-023-35507-8 )

opencc-zeroMay 2023View details →

Genotyping-by-sequencing data of common quails from the Azores

In this study, we focused on common quails (Coturnix coturnix) from the Azores archipelago and used morphological, stable isotope, genetic and genomic data to characterise this lineage and to assess the divergence from neighbouring common quail populations. We detected the presence of a large chromosomal inversion that had been already described in other populations and we studied its role in this remote archipelago. The genotyping-by-sequencing data generated in this project were analysed together with those from Sanchez-Donoso et al. 2022 (<a href="https://doi.org/10.1016/j.cub.2021.11.019" rel="noopener" title="Persistent link using digital object identifier">https://doi.org/10.1016/j.cub.2021.11.019</a>).

opencc-zeroMay 2023View details →

Species, hybrid and genotype effects on leaf litter curling, and their extended consequences for spiders and soil moisture dynamics

This archive contains datasets from a group of studies testing the hypotheses that leaf litter curling is influenced by plant species, hybridization and genotype, and has extended consequences for associated organisms and soil processes. A novel litter curling index (LCI) was used to characterize the curling of newly senesced leaves. There are four distinct datasets represented here. 1) A dataset of LCI from 11 plant species (tall annual forb = Helianthus annuus L.; evergreen shrubs = Arctostaphylos pungens Kunth, Quercus turbinella Greene, Rhus ovata S. Watson; deciduous shrubs = Rhus trilobata Nutt., Ribes cereum Douglas, Acer glabrum Torr.; deciduous trees = Elaeagnus angustifolia L., Quercus gambelii Nutt., Populus tremuloides Michx., Populus fremontii S. Watson) mostly growing in natural habitats of Northern Arizona, USA. 2) A dataset containing LCI from two Populus species (P. fremontii James, P. angustifolia S. Watson) and their F1 hyrbids in a common garden in Ogden, UT, USA (including replicated genotypes of P. angustifolia but not the other tree types). 3) The third dataset examined the relationship between average LCI for a tree and the abundance of agilenid webs under Populus trees growing in a common garden; the LCI values are averages per tree from data collected for dataset 2, and previously published spider web data. 4) The last dataset contains litter and soil moisture values from a litter/soil drying experiment that tested the effect of litter curling on soil moisture dynamics. See the README file for more details on the different datasets.

opennotspecifiedMay 2023View details →

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 3. STRUCTURE plot for Leucotaraxis argenticollis genotyped with 15 microsatellite loci.The height of each bar represents the proportion of an individual′s genotype assigned to each of K = 4 clusters.The names of the clusters correspond to those in Fig. 1C. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.

opennotspecifiedMay 2023View details →

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 in Prey-associated genetic differentiation in two species of silver fly (Diptera: Chamaemyiidae), Leucotaraxis argenticollis and L. piniperda

Fig. 4. STRUCTURE plot for Leucotaraxis piniperda genotyped with 16 microsatellite loci. The height of each bar represents the proportion of an individual′s genotype assigned to: A) each of K = 2 clusters for analysis of all individuals, and B) each of K = 2 clusters for analysis of only western individuals.The names of the clusters correspond to those in Fig. 1D. Vertical black lines separate groups of individuals collected in different states or provinces and on different adelgid host plant genera.

opennotspecifiedJul 2022View details →

Fig. 3 in Classification of sugarcane genotypes susceptible and resistant to the initial attack of sugarcane borer Diatraea saccharalis using epicuticular wax composition

Fig. 3. Graph with the importance of each selected compound by OPSDA. A) Resistant class – before infestation; B) Susceptible class – before infestation; C) Resistant class – after infestation; and D) Susceptible class – after infestation.

opennotspecifiedJul 2022View details →

Fig. 2 in Classification of sugarcane genotypes susceptible and resistant to the initial attack of sugarcane borer Diatraea saccharalis using epicuticular wax composition

Fig. 2. Classification of GC-MS dataset before (A–D) and after (E–H) infestation for PLS-DA, LDA, OPSDA, and GA-LDA models. Filled red circles (●) and empty red circles (○) are samples of resistant class. Filled black squares (■) and empty black squares (□) are samples of susceptible class. Filled and empty shapes refer respectively to training and test sets. AI: after infestation; BI: before infestation; Res: resistant; Sus: susceptible. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

opennotspecifiedJul 2022View details →

Fig. 1 in Classification of sugarcane genotypes susceptible and resistant to the initial attack of sugarcane borer Diatraea saccharalis using epicuticular wax composition

Fig. 1. Chromatogram obtained from refined wax after derivatization of genotypes IM76-228 (resistant) and RB047016 (susceptible) highlights important peaks. AI: after infestation; BI: before infestation; Res: resistant; Sus: susceptible. Peak number identification was listed in Table 2.

opencc-zeroAug 2023View details →

Data for: Genotypes selected for early and late avian lay date differ in their phenotype, but not fitness, in the wild

Global warming has shifted phenological traits in many species, but whether species are able to track further increasing temperatures depends on the fitness consequences of additional shifts in phenological traits. To test this, we conducted a genomic selection experiment on wild great tits from the Hoge Veluwe study population (The Netherlands) to obtain great tits (Parus major) with genotypes for extremely early and late egg lay dates and measured phenology and fitness of selected great tit females under wild conditions. Females with early genotypes advanced lay dates relative to females with late genotypes, but not relative to non-selected females. Females with early and late genotypes did not differ in the number of fledglings produced, in line with the weak effect of lay date on the number of fledglings produced by non-selected females in the years of the experiment. Our study is the first application of genomic selection in the wild and led to an asymmetric phenotypic response that indicates the presence of constraints toward early, but not late, lay dates.

opencc-zeroAug 2023View details →

Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation and a systematic review

Purpose: Searched for novel bi-allelic CRB1 mutations, then analyzed the CRB1 literature at the genotypic and phenotypic levels from 439 patients worldwide. Approach: We screened various variables such as the CRB1 mutation types, domains, exons, and genotypes and their relation with specific ocular phenotypes. An emphasis was given for the bi-allelic missense and nonsense mutations because of their high prevalence compared to other mutation types. Finally, we quantified the effect of various non-modifiable factors over the BCVA OU using multivariate linear regression models and identified genetic interactions. Results: We first identified a novel bi-allelic missense in the exon 9 of CRB1; c.2936G>A; p.(Gly979Asp) associated with RCD. CRB1 mutation type, exons, domains, and genotype distribution vary significantly according to Fundus characteristics, such as peripheral pigmentation and condition, optic disc, vessels, macular, and pigmentation (P<0.05). Of the 154 articles retrieved from PubMed, 96 studies with 439 bi-allelic CRB1 patients were included. Missense mutations were significantly associated with an absence of macular pigments, pale optic disc, and periphery pigmentation, resulting in a higher risk of RCD (P<0.05). In contrast, homozygous nonsense mutations were associated with macular pigments, periphery pigments, and a high risk of LCA (P<0.05) and increased BCVA OU (best-corrected visual acuity) levels. We found that age, mutation types, and inherited retinal diseases were critical determinants of BCVA OU as they significantly increased it by 33%, 26%, and 38%, respectively (P<0.05). Loss of function alleles additively increased the risk of LCA, with nonsense having a more profound effect than indels. Finally, our analysis showed that p.(Cys948Tyr) and p.(Lys801Ter) and p.(Lys801Ter); p.(Cys896Ter) might interact to modify BCVA OU levels. Conclusion: This meta-analysis updated the literature and identified genotype-phenotype associations in bi-allelic CRB1 patients.

opencc-zeroSep 2023View details →

Perna perna metadata and genotypic data

Studies investigating gene flow in sessile or sedentary marine species typically draw conclusions about larval dispersal by investigating genetic structure of adults. Here, we generated microsatellite data from adults, recruits, settlers and planktonic larvae of the brown mussel, Perna perna, from the south-east coast of South Africa, and identified a consistent mismatch in genetic structure between the adults and all earlier life stages. While adults could be assigned to two major geographical groups (western and eastern), most of the early-stage mussels were strongly affiliated with the eastern group. This result suggests that few of the early-stage individuals present in the western portion of the sampling range will become part of the adult population. Our findings highlight the importance of post-settlement processes as key drivers of population structure and caution against the exclusive use of genetic data generated from adults to assess population connectivity facilitated by the dispersal of planktonic propagules.

opencc-by-4.0Oct 2023View details →

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Open the record for dataset details and reuse information.

Safety and Efficacy of Albumin Interferon Administered Every 4 Weeks in Genotype 2/3 Hepatitis C Patients

ClinicalTrials.gov study NCT00759200. IPD Sharing: Not stated. Countries: 12. Publications: 1.

Routine Fetal RhD Genotyping for RhD- Pregnant Women

ClinicalTrials.gov study NCT00832962. IPD Sharing: Not stated. Countries: 1. Publications: 21.

Natural History, Genetic Bases and Phenotype-genotype Correlations in Autosomal Dominant Spinocerebellar Degenerations

ClinicalTrials.gov study NCT00136630. IPD Sharing: Not stated. Countries: 1. Publications: 13.

Does Incorporation of EPA and DHA in Lipoproteins Differ According to Apolipoprotein E Genotype?

ClinicalTrials.gov study NCT01544855. IPD Sharing: Not stated. Countries: 1. Publications: 1.

Telaprevir With Peginterferon Alfa & Ribavirin in Ex-People Who INject Drugs Infected by Genotype 1 Chronic Hepatitis C

ClinicalTrials.gov study NCT01980290. IPD Sharing: Not stated. Countries: 6. Publications: 1.