Find research datasets worth reusing

Data and code for: Species-specific effects of production practices on genetic diversity in plant reintroduction programs

Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pre-treatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three Viola species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pre-treatments.

Original FASTQ files of: Global genetic diversity and historical demography of the Bull Shark

Aim Biogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (Ne) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high-trophic shark using population genomics and assessed our ability to detect recent bottlenecks events. Location Western and Central Indo-Pacific (IPA), Western Tropical Atlantic (WTA), Eastern Tropical Pacific (EPA) Taxon Carcharhinus leucas (Müller & Henle, 1839) Methods A <a>DArTcap</a>TM approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC-RF framework coupled with coalescent simulations, to investigate within-cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with fastsimcoal. Ne temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size. Results Three genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within-cluster structuring was detected. Ne increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion. Main conclusions This study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predator. Ne Historical increases of Ne are potentially linked to extended coastal habitat availability. The limited within-cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole genome sequencing.

opencc-by-4.0Dec 2023View details →

zenodo36/100

Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer's disease

Connectome, traits and behavior data for APOE234 mice. <ul> <li>1. connectome.zip: mouse brain structural connectivity matrices from diffusion MRI.</li> <li>2. FAGNN_Phenotype.csv: a sheet of trait information of mice used in the study.</li> </ul> columns: winding numbers, total distance, normalized NE time, normalized NE distance, normalized NW time, normalized NW distance, normalized SE time, normalized SE distance, normlaized SW time, normalized SW distance, island latency to first entry, island entries, normalized thigmataxis time, and normalized thigmotaxis distance <div>rows: 4 trials for each day from day 1 to day 5 with 1 probing test each at day 5 and day 8</div> <ul> <li>3. mouse_anatomy.csv: brain region information regarding the connectivity matrix.</li> <li>4. behavior.zip: behavioral data for each mouse from Morris Water Maze experiments.</li> </ul>

Data for: Genetic variants underlying human bisexual behavior are reproductively advantageous

Because human same-sex sexual behavior (SSB) is heritable and leads to fewer offspring, how SSB-associated alleles have persisted and whether they will remain in human populations are of interest. Using the UK Biobank, we address these questions separately for bisexual behavior (BSB) and exclusive SSB (eSSB) after confirming their genetic distinction. We discover that male BSB is genetically positively correlated with the number of offspring. This unexpected phenomenon is attributable to the horizontal pleiotropy of male risk-taking behavior-associated alleles, because male risk-taking behavior is genetically positively correlated with both BSB and the number of offspring and because genetically controlling male risk-taking behavior abolishes the genetic correlation between male BSB and the number of offspring. By contrast, eSSB is genetically negatively correlated with the number of offspring. Our results suggest that male BSB-associated alleles are likely reproductively advantageous, which may explain their past persistence and predict their future maintenance, and that eSSB-associated alleles are likely being selected against at present.

Data from: Multi-generation genetic contributions of immigrants reveal cryptic elevated and sex-biased effective gene flow within a natural meta-population

Impacts of immigration on micro-evolution and population dynamics fundamentally depend on net rates and forms of resulting gene flow into recipient populations. Yet, the degrees to which observed rates and sex ratios of physical immigration translate into multi-generational genetic legacies have not been explicitly quantified in natural meta-populations, precluding inference on how movements translate into effective gene flow and eco-evolutionary outcomes. Our analyses of three decades of complete song sparrow (Melospiza melodia) pedigree data show that multi-generational genetic contributions from regular natural immigrants substantially exceeded those from contemporary natives, consistent with heterosis-enhanced introgression. Further, while contributions from female immigrants exceeded those from female natives by up to three-fold, male immigrants' lineages typically went locally extinct soon after arriving. Both the overall magnitude, and the degree of female bias, of effective gene flow therefore greatly exceeded those which would be inferred from observed physical arrivals, reshaping the eco-evolutionary implications of immigration.

opencc-by-4.0Dec 2023View details →

zenodo36/100

Genetic variants affecting NQO1 protein levels impact on efficacy of idebenone treatment in Leber hereditary optic neuropathy

Fastq files with complete sequencing of NQO1 gene after PCR amplification for cell lines harboring m.11778G>A/MT-ND4 or m.3460A>G/MT-ND1 and controls.

Evidence that genetic drift not adaptation drives fast-Z and large-Z effects in Ficedula flycatchers

The sex chromosomes have been hypothesized to play a key role in driving adaptation and speciation across many taxa. The reason for this is thought to be the hemizygosity of the heteromorphic part of sex chromosomes in the heterogametic sex, which exposes recessive mutations to natural and sexual selection. The exposure of recessive beneficial mutations increases their rate of fixation on the sex chromosomes, which results in a faster rate of evolution. In addition, genetic incompatibilities between sex-linked loci are exposed faster in the genomic background of hybrids of divergent lineages, which makes sex chromosomes contribute disproportionately to reproductive isolation. However, in birds, which show a Z/W sex determination system, the role of adaptation vs. genetic drift as the driving force of the faster differentiation of the Z chromosome (fast-Z effect) and the disproportionate role of the Z chromosome in reproductive isolation (large-Z effect) are still debated. Here, we address this debate in the bird genus Ficedula flycatchers based on population-level whole-genome sequencing data of six species. Our analysis provides evidence for both faster lineage sorting and reduced gene flow on the Z chromosome than the autosomes. However, these patterns appear to be driven primarily by the increased role of genetic drift on the Z chromosome, rather than an increased rate of adaptive evolution. Genomic scans of selective sweeps and fixed differences in fact suggest a reduced action of positive selection on the Z-chromosome. Nevertheless, it is possible that the faster lineage sorting of the Z chromosome due to genetic drift may help drive the evolution of genetic incompatibilities between species.

High sexual display trait diversity without measured genetic divergence in a montane hybrid zone involving young species (Habronattus americanus subgroup, Araneae, Salticidae)

Genetic introgression, allele exchange across species boundaries, is a commonly recognized feature of animal evolution. Under such a paradigm contemporary contact zones provide first-hand and complementary insight into the geographic, phenotypic, and genetic details of introgression. Also, when mate choice phenotypes are conspicuous and variable in hybrids, contact zones provide potential insight into how sexual selection interacts with species boundary maintenance, particularly when postzygotic reproductive isolation is weak. The Habronattus americanus subgroup includes several recently evolved jumping spider species, with an estimated age of about 200,000 years, and substantial evidence for hybridization and introgression. We explored a contact zone involving H. americanus (Keyserling, 1885) and H. kubai (Griswold, 1979) on Mount Shasta, California, in alpine habitats that would have been unavailable (under ice) at the Last Glacial Maximum. We characterized morphological diversity within the contact zone, including the fine-scale geographic distribution of hybrid and parental individuals, and assessed genetic variation using ddRADseq data. Combined results indicate a lack of measured genomic differentiation between specimens with distinct morphologies, including individuals with phenotypes of the parental species. We identified a diverse array of hybrid morphologies, with phenotypic evidence for backcrossing, essentially forming a phenotypic bridge between parental taxa. The study area is characterized by more hybrid than parental individuals, with a significantly larger number of red-palped morphologies than white and/or yellow-palped morphologies; the novel, white-palped phenotype is perhaps transgressive. Overall, these results contribute to a better understanding of the expected ebb and flow of lineage interactions during the early stages of speciation.

Supplementary material: Machine learning and phylogenetic models identify predictors of genetic variation in Neotropical amphibians

Aim: Intraspecific genetic variation is key for adaptation and survival in changing environments and is known to be influenced by many factors, including population size, dispersal, and life history traits. We investigated genetic variation within Neotropical amphibian species to provide insights into how natural history traits, phylogenetic relatedness, climatic, and geographic characteristics can explain intraspecific genetic diversity. Location: Neotropics. Taxon: Amphibians. Methods: We assembled datasets using open-access databases for natural history traits, genetic sequences, phylogenetic trees, climatic, and geographic data. For each species, we calculated overall nucleotide diversity (π) and tested for isolation by distance (IBD) and isolation by environment (IBE). We then identified predictors of π, IBD, and IBE using Random Forest (RF) regression or RF classification. We also fitted phylogenetic generalized linear mixed models (PGLMMs) to predict π, IBD, and IBE. Results: We compiled 4,052 mitochondrial DNA sequences from 256 amphibian species (230 frogs and 26 salamanders), georeferencing 2,477 sequences from 176 species that were not linked to occurrence data. RF regressions and PGLMMs were congruent in identifying range size and precipitation (σ) as the most important predictors of π, influencing it positively. RF classification and PGLMMs identified minimum elevation as an important predictor of IBD; most species without IBD tended to occur at higher elevations. Maximum latitude and precipitation (σ) were the best predictors of IBE, and most species without IBE occur at lower latitudes and in areas with more variable precipitation. Main conclusions: This study identified predictors of genetic variation in Neotropical amphibians using both machine learning and phylogenetic methods. This approach was valuable to determine which predictors were congruent between methods. We found that species with small ranges or living in zones with less variable precipitation tended to have low genetic diversity. We also showed that Western Mesoamerica, Andes, and Atlantic Forest biogeographic units harbor high diversity across many species that should be prioritized for protection. These results could play a key role in the development of conservation strategies for Neotropical amphibians.

Experimental and genetic analysis of selfing reveals no reinforcement in Phlox cuspidata

Reinforcement is the process through which prezygotic reproductive barriers evolve in sympatry due to selection against hybridization between co-occurring, closely related species. The role of self-fertilization in reinforcement and reproductive isolation is uncertain in part because its efficiency as a barrier against heterospecific mating can depend on the timing of autonomous selfing. To investigate whether increased autonomous selfing has evolved as a mechanism for reinforcement, we compared Phlox cuspidata populations across their native Texas range using both estimates of genetic diversity and experimental manipulation with morphological measurements. Specifically, we investigated patterns of variation in floral traits and timing of selfing between individuals from allopatric populations of P. cuspidata and from populations sympatric with the closely related species, P. drummondii. We infer intermediate rates of selfing across field-collected individuals with no significant difference between allopatric and sympatric populations. Among greenhouse grown plants, we find no differences in timing of selfing or other floral traits including anther dehiscence timing, anther-stigma distances, autonomous selfing rate and self-seed count between allopatric and sympatric populations. However, our statistical analyses indicate that P. cuspidata individuals sympatric with P drummondii seem to have generally larger flowers compared to allopatric individuals. Despite strong evidence of costly hybridization with P. drummondii, we find no evidence of trait divergence due to reinforcement in P. cuspidata. Although we document nearly complete autonomous self-seed set in the greenhouse, estimates of selfing rates from genetic data imply realized selfing is much lower in nature suggesting an opportunity for reinforcing selection to act on this trait.

Data from: Distances and their visualization in studies of spatial-temporal genetic variation using single nucleotide polymorphisms (SNPs)

Distance measures are widely used for examining genetic structure in datasets that comprise many individuals scored for a very large number of attributes. Genotype datasets composed of single nucleotide polymorphisms (SNPs) typically contain bi-allelic scores for tens of thousands if not hundreds of thousands of loci. We examine the application of distance measures to SNP genotypes and sequence tag presence-absences (SilicoDArT) and use real datasets and simulated data to illustrate pitfalls in the application of genetic distances and their visualization. The datasets used to illustrate points in the associated review are provided here together with the R script used to analyse the data. Data are either simulated internal to this script or are SNP data generated as part of other studies and included as compressed binary files readily accessable by reading into R using R base function readRDS(). Refer to the analysis script for examples.

Data from: Cross ocean-basin population genetic dynamics in a pelagic top predator of high conservation concern, the oceanic whitetip shark, Carcharhinus longimanus

The oceanic whitetip shark, Carcharhinus longimanus, is a Critically Endangered, circumtropical, and highly migratory, pelagic shark. Yet, little information exists on its population genetic dynamics to guide conservation management practice. We present a first worldwide, mitochondrial and nuclear DNA assessment of the population genetic status of this imperiled species based on sequences of the complete mitochondrial control region (n = 173) and partial ND4 gene (n = 172), and genotypes from 12 nuclear microsatellites (n = 164). Statistically significant mitochondrial and nuclear DNA population genetic differentiation was detected across all marker datasets between Western Atlantic and Indo-Pacific oceanic whitetip sharks. Additionally, our data, combined with previously published, partial (701-base pairs) mitochondrial control region sequences from additional locations in the Atlantic and Indian Oceans, confirmed significant matrilineal population structure between the Western and Eastern Atlantic. The combined data also provisionally (i.e., with FST but not ΦST) indicated differentiation between Western North and Central-South Atlantic sharks, pointing to the need for further assessment in this region. Matrilineal differentiation was also detected between Indian and Pacific Ocean sharks via pairwise analyses, albeit with the ND4 gene sequence only (ΦST = 0.051; FST = 0.092). Limited sampling in the Pacific leaves open questions about the connectivity dynamics in this large region. Despite the presence of geographic population genetic structure, the mitochondrial data showed no evidence of across ocean basin phylogeographic lineages. A provisional assessment of mitochondrial and nuclear genetic diversity indicated the oceanic whitetip shark's status falls in the middle to upper ranges compared to other shark species, potentially lending some optimism for the present adaptability and resiliency of this species if strong conservation measures are effectively implemented.

Patterns in the genetic structure of 49 lowland rain forest tree species co-distributed on opposite sides of the Northern Andes

The Andes are a major dispersal barrier for lowland rain forest plants and animals, yet hundreds of lowland tree species are distributed on both sides of the Northern Andes, raising questions about how the Andes influenced their biogeographic histories and population genetic structure. To explore these questions, we generated standardized datasets of thousands of SNPs from paired populations of 49 tree species co-distributed in rain forest tree communities located in Panama and Amazonian Ecuador and calculated genetic diversity (π) and absolute genetic divergence (dXY) within and between populations, respectively. We predicted (1) higher genetic diversity in the ancestral source region (east or west of the Andes) for each taxon, and (2) correlation of genetic statistics with species attributes, including elevational range and life-history strategy. We found that genetic diversity was higher in putative ancestral source regions, possibly reflecting founder events during colonization. We found little support for a relationship between genetic divergence and species attributes except that species with higher elevational range limits exhibited higher dXY, implying older divergence times. One possible explanation for this pattern is that dispersal through mountain passes declined in importance relative to dispersal via alternative lowland routes as the Andes experienced uplift. We found no difference in mean genetic diversity between populations in Central America and the Amazon. Overall, our results suggest that dispersal across the Andes has left enduring signatures in the genetic structure of widespread rain forest trees. We outline additional hypotheses to be tested with species-specific case studies.

Genetic differentiation and phenotypic plasticity drive troglomorphic character development in European cavefish

The Aach cave loach (Barbatula barbatula), a recently discovered member of the Nemacheilidae family, offers a unique opportunity to understand the mechanisms underlying evolutionary change. In a common garden experiment, we reared groups of laboratory-bred cave, surface, and hybrid loach under different light conditions. Troglomorphic characters varied significantly among the fish, influenced to a different extent by parental origin and light conditions. Cavefish progeny consistently exhibited smaller eyes, lighter pigmentation, longer barbels, and larger olfactory epithelia than surface fish, while hybrids displayed intermediate characteristics. Surface and hybrid fish raised in complete darkness resembled the cavefish phenotype, while cavefish raised under a natural photoperiod approached the surface form. Characters associated with eye degeneration were found to be primarily heritable. Conversely, traits related to chemo- and mechano-reception were enhanced in the surface and hybrid groups reared in complete darkness, suggesting phenotypic plasticity. Our findings offer valuable insights into the interplay between genetic differentiation and phenotypic plasticity to troglomorphic adaption. This contributes to the broader understanding of the early stages of adaptation, where phenotypic plasticity, drift, and selection shape phenotypes. Relatively recently established cavefish, such as the Aach cave loach, are promising candidates for comparative research investigating evolutionary mechanisms.

Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics

Background Hydrangea petiolaris Siebold & Zucc., also known as climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and Sakhalin Island. It is an economically important ornamental plant with fertile and sterile flowers. Despite the recent increase in Hydrangea breeding and interest in germplasm conservation, relatively little is known about the relationships between Hydrangea species. Results We employed Illumina NovaSeq 6000 sequencing technology to generate a total of 39,945,480 reads, which were assembled into 137,715 contigs. A total of 109,092 filtered transcripts were used to identify microsatellites, and 54,587 microsatellite repeat motifs were revealed within 33,556 contigs. Among these, 4,510 transcripts harboring microsatellites had Gene Ontology annotations, and numerous microsatellite-containing transcripts exhibited associations with genes, including those encoding PPR proteins, aldehyde dehydrogenases, and bHLH transcription factors, related to the restorer of fertility (Rf) genes, which play a critical role in restoring fertility in plants with cytoplasmic male sterility. Validation of transcriptomic SSR markers demonstrated high levels of polymorphism, revealing significant genetic diversity within populations. However, null alleles and deviations from Hardy‒Weinberg equilibrium at specific loci suggested caution in genotyping accuracy. Population-level analysis disclosed high genetic differentiation and distinct clustering of populations. Conclusions The H. petiolaris transcriptomic SSR markers offer valuable insight for gaining insights into the population genetics, evolutionary background, and practical strategies for conserving this species. Moreover, the microsatellite loci we have identified and their associations with annotated genes hold promise for creating functional markers specifically tailored for H. petiolaris. These markers include valuable resources of transcriptomic SSR markers suitable for population genetic investigations and have a reasonable degree of applicability across different taxa.

Data from: Ultraviolet signaling in a butterfly is preferred by females and conveys male genetic quality

Indicator models of sexual selection posit that females chose males on the basis of traits that reveal male genetic quality and thereby enjoy increased offspring production. Here we report that females of the butterfly Eurema hecabe receive indirect benefits from choosing males based on their UV wing colouration, a heritable and condition-dependent trait in this species. We first used a large laboratory-bred pedigree to demonstrate a per-family association between inbreeding and male UV trait value. Females exerted choice for UV-bright males within this protocol, and average male UV trait value increased over six consecutive generations presumably due to such selection and despite an increasing rate of pedigree-wide inbreeding. We then experimentally imposed a standard strength of inbreeding upon lines of divergent male UV trait value. Inbreeding depressed the siring performance of low-UV treatment males more severely and resulted in a marginal reduction of their UV brightness, which rebounded sharply following subsequent outcrossing. These findings are consistent with the ornament-based signaling of genetic quality as a function of underlying individual-level mutational load.

Data from: Anti-predator defenses are linked with high levels of genetic differentiation in frogs

Predator-prey interactions have been suggested as drivers of diversity in different lineages, and the presence of anti-predator defences in some clades is linked to higher rates of diversification. Warning signals are some of the most widespread defenses in the animal world, and there is evidence of higher diversification rates in aposematic lineages. The mechanisms behind such species richness, however, are still unclear. Here, we test whether lineages that use aposematism as anti-predator defense exhibit higher levels of genetic differentiation between populations, leading to increased opportunities for divergence. We collated from the literature > 3,000 pairwise genetic differentiation values across more than 700 populations from over 60 amphibian species. We find evidence that, given the same geographic distance, populations of species of aposematic lineages exhibit greater genetic divergence relative to species that are not aposematic. Our results support a scenario where the use of warning signals could restrict gene flow, and suggest that anti-predator defences could impact divergence between populations and potentially have effects at a macro-evolutionary scale.

Shared and distinct patterns of genetic structure in two sympatric large decapods

Aim: Comparing genetic structure in species with shared spatial ranges and ecological niches can help identify how dissimilar aspects of biology can shape differences in population connectivity. Similarly, where species are widely distributed across heterogeneous environments and major topographic barriers, knowledge of the structuring of populations can help reveal the impacts of factors that limit dispersal and/or drive divergence, aiding conservation management. Location: European seas of the northeast Atlantic and Mediterranean. Taxa: European clawed lobster (Homarus gammarus) and European crawfish (Palinurus elephas), two sympatric, heavily-fished decapods with extensive dispersal potential. Methods: By RAD-sequencing 214 H. gammarus from 32 locations, and 349 P. elephas from 15 locations, we isolated 6,340 and 7,681 SNP loci, respectively. Using these data to characterise contemporary population structuring, we investigate potential spatial and environmental drivers of genomic heterogeneity. Results: We found higher levels of differentiation among clawed lobsters than crawfish, both globally and within basins, and demonstrate where known hydrographic and topographic barriers generate shared patterns of divergence, such as a genetic break between the Atlantic and Mediterranean basins. Genetic structure not common to both species is principally apparent in the Atlantic portions of their range, where clawed lobster exhibits a genetic cline and increased differentiation towards range margins, while crawfish appear effectively panmictic throughout this region. Main Conclusions: We attribute the comparative lack of crawfish population structuring to their greater dispersal tendencies via a longer pelagic larval duration and sporadic adult movements. In contrast, genetic connectivity in clawed lobster is relatively restricted, with the correlation of site of origin and temperature to geographic heterogeneity at many divergent loci indicative of both neutral and adaptive processes. Our results help inform how contemporary management can account for likely demographic connectivity and marry the conservation of genomic variation with sustainable fisheries in these ecologically and economically important crustaceans.

Holocene deglaciation drove rapid genetic diversification of Atlantic walrus

Rapid global warming is severely impacting Arctic ecosystems and is predicted to transform the abundance, distribution, and genetic diversity of Arctic species, though these linkages are poorly understood. We address this gap in knowledge using palaeogenomics to examine how earlier periods of global warming influenced the genetic diversity of Atlantic walrus (Odobenus rosmarus rosmarus), a species closely associated with sea ice and shallow-water habitats. We analysed 82 ancient and historical Atlantic walrus mitochondrial genomes (mitogenomes), including now-extinct populations in Iceland and the Canadian Maritimes, to reconstruct the Atlantic walrus' response to Arctic deglaciation. Our results demonstrate that the phylogeography and genetic diversity of Atlantic walrus populations were initially shaped by the Last Glacial Maximum (LGM), surviving in distinct glacial refugia, and subsequently expanding rapidly in multiple migration waves during the late Pleistocene and early Holocene. The timing of diversification and establishment of distinct populations corresponds closely with the chronology of the glacial retreat, pointing to a strong link between walrus phylogeography and sea ice. Our results indicate that accelerated ice loss in the modern Arctic may trigger further dispersal events, likely increasing the connectivity of northern stocks while isolating more southerly stocks putatively caught in small pockets of suitable habitat.