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1,598 results for “genetic diversity”
Colony fitness increases in the honey bee at queen mating frequencies higher than genetic diversity asymptote
Abstract Across the eusocial Hymenoptera, a queen's mating frequency is positively associated with her workers' genetic diversity and colony's fitness. Over 90% of a colony's diversity potential is achieved by its mother's tenth effective mating (me); however, many females mate at levels of me > 10, a zone we here call hyperpolyandry. We compared honey bee colony fitness at mating levels near and above this genetic diversity asymptote. We were interested in how hyperpolyandry affects colony phenotypes arising from both common tasks (brood care) and rare specialized tasks (parasite resistance). We used an unselected wild line of bees and a Varroa Sensitive Hygiene (VSH) line selected to resist the parasite Varroa destructor. Virgin queens were instrumentally inseminated to replicate the following queen/colony conditions: (1) VSH semen/low polyandry (observed mating number = mo = 9), (2) VSH semen/high polyandry (mo = 54), (3) wild type semen/low polyandry, or (4) wild semen/high polyandry. There was a positive effect of polyandry on brood survival, an outcome of common tasks, with highest values at mo = 54. There was an interaction between polyandry and genetics such that differences between genetic lines expressed only at mo = 54, with fewer mites in VSH colonies. These results are consistent with two hypotheses for the evolution of mating levels in excess of the genetic diversity asymptote: hyperpolyandry improves colony fitness by (1) optimizing genotype compositions for common tasks and (2) by capturing rare specialist allele combinations, resisting cliff-edge ecological catastrophes. Significance statement Polyandry is a female's practice of mating with several males, storing their sperm, and using it to produce one or more clutches of genetically diverse offspring. In the social Hymenoptera, polyandry increases the genetic diversity and task efficiency of workers, leading to improved colony fitness. Over 90% of the increase in a colony's diversity potential is achieved by its mother's tenth mating; however, many females practice hyperpolyandry, a term we reserve here for mating levels above this genetic diversity asymptote. We show that a token of colony fitness arising from common tasks, brood survival, improves universally as one moves from sub- to hyperpolyandrous mating levels. However, a colony phenotype arising from a rare parasite resistance task is only expressed in the presence of the controlling alleles and under conditions of hyperpolyandry. These results suggest adaptive mechanisms by which hyperpolyandry could evolve.
Genetic diversity and the origins of parthenogenesis in the teiid lizard Aspidoscelis laredoensis
<p><span><span><span><span><span><span><span><span><span><span><span>Unisexual vertebrates typically form through hybridization events between sexual species in which reproductive mode transitions occur in the hybrid offspring. This evolutionary history is thought to have important consequences for the ecology of unisexual lineages and their interactions with congeners in natural communities. However, these consequences have proven challenging to study owing to uncertainty about patterns of population genetic diversity in unisexual lineages. Of particular interest is resolving the contribution of historical hybridization events vs. postformational mutation to patterns of genetic diversity in nature. Here we use restriction site associated DNA genotyping to evaluate genetic diversity and demographic history in <i>Aspidoscelis laredoensis</i>, a diploid unisexual lizard species from the vicinity of the Rio Grande River in southern Texas and northern Mexico. The sexual progenitor species from which one or more lineages are derived also occur in the Rio Grande Valley region, although patterns of distribution across individual sites are quite variable. Results from population genetic and phylogenetic analyses resolved the major axes of genetic variation in this species and highlight how these match predictions based on historical patterns of hybridization. We also found discordance between results of demographic modelling using different statistical approaches with the genomic data. We discuss these insights within the context of the ecological and evolutionary mechanisms that generate and maintain lineage diversity in unisexual species. As one of the most dynamic, intriguing, and geographically well investigated groups of whiptail lizards, these species hold substantial promise for future studies on the constraints of diversification in unisexual vertebrates.</span></span></span></span></span></span></span></span></span></span></span></p>
Strong population genetic structure and cryptic diversity in the Florida bonneted bat (Eumops floridanus)
<p>Knowledge of genetic structure is essential for the long-term management and conservation of endangered species. We report the results from a genetic examination of the federally endangered Florida bonneted bat (<i>Eumops floridanus</i>) sampled from its range in southern Florida, USA. Bonneted bats are primarily found in four regions separated by approximately 100 to 250 kms, including three western natural areas (BW, PC, and CC) and one urban population on the east coast [Miami-Dade County (MD)]. We used 22 microsatellite loci and cytochrome <i>b</i> sequences to assess the extent of connectivity and levels of genetic diversity. Regional populations were highly differentiated (<i>F</i><sub>ST</sub> = 0.178) and model-based and multivariate analyses showed that MD was the most distinct among pairwise comparisons. Regional populations are small (i.e., <i>N<sub>e</sub></i><sub> </sub>< 100) but demographically stable. Estimates of contemporary migration and historic gene flow suggest that regional populations do not frequently exchange migrants, but simulations suggest that the divergence among western regions is likely a result of recent genetic drift rather than long-term isolation. Significantly, mitochondrial DNA revealed that haplotypes from MD were similar or shared with those recognized as <i>Eumops ferox</i> from Cuba and Jamaica, and divergent (1.5%) from the remainder of bonneted bats in Florida. Our data support the management of each of the four populations as distinct population segments, and that BW, PC and CC combined are on an independent evolutionary trajectory from bats in MD. Critically, bonneted bats in Florida appear to harbor cryptic diversity that will require a reassessment of their taxonomy.</p>
Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies
<p class="MsoNormal"><strong><u><span>Aim:</span></u></strong><span> Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow.</span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Taxon:</span></u></strong><span> <em>Dascyllus marginatus </em>(endemic) and <em>Dascyllus abudafur </em>(widespread)<em>.</em></span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Location:</span></u></strong><span> Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Methods:</span></u></strong><span> We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Results:</span></u></strong><strong><span> </span></strong><em><span>Dascyllus marginatus </span></em><span>inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. <em>Dascyllus abudafur</em> species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of <em>D. marginatus </em>had an order of magnitude higher genetic differentiation compared to <em>D. abudafur</em>, as well as several outlier loci (suggesting selective pressure), which were absent in <em>D. abudafur</em> despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. </span></p> <p class="MsoNormal"> </p> <p class="MsoNormal"><strong><u><span>Main conclusions:</span></u></strong><span> The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.</span></p>
Male diversity matters: Genetic structuring of insular male date palm (Phoenix dactylifera L.) revealed valuable breeding and conservation resources
Most male date palms available for pollinating different female cultivars have mainly originated from seed propagation resulting in many different local males that represent a source of genetic diversity. Favorable fruit production is related to quality of pollen and its compatibility with a certain female variety. Therefore, the genetic characterization of the male pollen as a superior one for each female cultivar should be the first step to establish an intensive program to produce superior males through different procedures. In this study, the genetic diversity and population structure of 72 male date palm accessions were investigated using 15 microsatellite loci. A total number of 125 alleles was detected with an average of 8.33 alleles per locus. Bayesian model-based clustering analysis indicated the presence of two differentiated endemic male date palm genetic clusters, continental and insular, with the presence of introduced accessions originating from the Middle East. The diversity analysis in the insular region of Tunisia, which had never been performed before, revealed that this germplasm enclosed valuable endemic resources supporting the hypothesis of the presence of wild material. These findings are crucial for identifying interesting genotypes that can be integrated into international coordinated actions of Phoenix dactylifera L. breeding programs as well as for the protection and conservation of valuable resources.
Complex patterns shape immune genes diversity during invasion of common raccoon in Europe – selection in action despite genetic drift
<p>Rapid adaptation is common in invasive populations and is crucial to their long-term success. The primary target of selection in the invasive species' new range is standing genetic variation. Therefore, genetic drift and natural selection acting on existing variation are key evolutionary processes through which invaders will evolve over a short timescale. In this study, we used the case of the raccoon <em>Procyon</em> <em>lotor</em> invasion in Europe to identify the forces shaping the diversity of immune genes during invasion. The genes involved in the defence against infection should be under intense selection pressure in the invasive range where novel pathogens are expected to occur. To disentangle the selective and demographic processes shaping the adaptive immune diversity of its invasive and expanding populations, we have developed species-specific SNP markers located in the coding regions of targeted immune-related genes. We characterised the genetic diversity of 110 functionally important immune genes in two invasive and one native raccoon genetic clusters, each presenting a different demographic history. Despite the strong effect of demographic processes in the invasive clusters, we detected a subset of genes exhibiting the diversity pattern suggestive of selection. The most likely process shaping the variation in those genes was balancing selection. The selected genes belong to toll-like receptors and cytokine-related genes. Our results suggest that the prevalence of selection depends on the level of diversity, i.e. – less genetically diverse invasive population from Czech Republic displayed fewer signs of selection. Our results highlight the role of standing genetic variation in adapting to a new environment. Understanding the evolutionary mechanisms behind invasion success would enable predicting how populations may respond to environmental change.</p>
Methodological challenges in the genomic analysis of an endangered mammal population with low genetic diversity
<p><span>Recently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (<em>Galemys</em> <em>pyrenaicus</em>). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research.</span></p>
Data and R scripts for: Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse (Lyrurus tetrix)
<p>While intensive hunting activities, such as commercial fishing and trophy hunting, can have profound influences on natural populations, less intensive recreational hunting can also have more subtle effects on animal behaviour, habitat use and movement, with implications for population persistence. Lekking species such as the black grouse (<em>Lyrurus</em> <em>tetrix</em>) may be especially prone to hunting as leks are temporally and spatially predictable, making them easy targets. Furthermore, inbreeding in black grouse is mainly avoided through female-biased dispersal, so any disruptions to dispersal caused by hunting could lead to changes in gene flow, leading to an increasing risk of inbreeding. We therefore investigated the impact of hunting on genetic diversity, inbreeding and dispersal on a metapopulation of black grouse in Central Finland. We genotyped 1,065 adult males and 813 adult females from twelve lekking sites (six hunted, six unhunted) and 200 unrelated chicks from seven sites (two hunted, five unhunted) at up to thirteen microsatellite loci. Our initial confirmatory analysis of sex-specific fine-scale population structure revealed little genetic structure in the metapopulation. Levels of inbreeding did not differ significantly between hunted and unhunted sites in both adults and chicks. However, immigration rates into hunted sites were significantly higher among adults compared to immigration into unhunted sites. We conclude that the influx of migrants into hunted sites may compensate for the loss of harvested individuals, thereby increasing gene flow and mitigating inbreeding. Given the absence of any obvious potential barriers to gene flow in Central Finland, a spatially heterogeneous matrix of hunted and unhunted regions may be crucial to ensure sustainable harvests into the future.</p>
Data for: Geographic isolation reduces genetic diversity of a wide-ranging terrestrial vertebrate, Canis lupus
<p>Genetic diversity is theorized to decrease in populations closer to a species' range edge, where habitat may be suboptimal. However, generalist species capable of long-range dispersal may maintain sufficient gene flow to counteract this, though the presence of significant barriers to dispersal (e.g., large water bodies, human-dominated landscapes) may still lead to, and exacerbate, the edge effect. We used microsatellite data for 2,426 gray wolves (<em>Canis</em> <em>lupus</em>) from 24 sub-populations (groups) to model how allelic richness and expected heterozygosity varied with two measures of range edge (mainland-island position, latitude, and distance from range center) across >7.3 million km<sup>2</sup> of northern North America. We found that allelic richness and expected heterozygosity of island groups was measurably less than that of mainland groups and that these differences increased with the island's distance to the species' range center in the study area. Our results demonstrate how multiple axes of geographic isolation (distance from range center and island habitation) can act synergistically to erode the genetic diversity of wide-ranging terrestrial vertebrate populations despite the counteracting influence of long-range dispersal ability. These findings emphasize how geographic isolation is a potential threat to the genetic diversity and viability of terrestrial vertebrate populations even among species capable of long-range dispersal. </p> <p>This dataset is comprised of four separate sub-datasets, sourced from Carmichael et al. (2007), Musiani et al. (2007), McNay (2006), and a manuscript in progress (referred to as "MacNulty" in the data files, to be first published in Frevol et al. 2023). The raw data are comprised of sample IDs, latitude and longitude points indicating where the sample was collected or recorded, and microsatellite genetic information. To aid in re-use, the raw genetic data has also been formatted and presented for use with common population genetics software (Genepop, MICROCHECKER, Genetix, FSTAT). The dataset also includes spatial data files of the sub-populations described in the study, allelic richness and expected heterozygosity data derived from the raw and spatial data, and the R script used to create the models. </p> <ul> <li>Carmichael LE, Krizan J, Nagy JA, et al (2007) Historical and ecological determinants of genetic structure in arctic canids. Molecular Ecology 16:3466–3483. https://doi.org/10.1111/j.1365-294X.2007.03381.x</li> <li>McNay ME (2006) Preliminary results of parentage analysis using microsatellite markers from an exploited wolf population in central Alaska. Alaska Department of Fish and Game, Division of Wildlife Conservation, Juneau, Alaska</li> <li>Musiani M, Leonard JA, Cluff HD, et al (2007) Differentiation of tundra/taiga and boreal coniferous forest wolves: genetics, coat colour and association with migratory caribou. Molecular Ecology 16:4149–4170. https://doi.org/10.1111/j.1365-294X.2007.03458.x</li> </ul>
Data from: Population connectivity patterns of genetic diversity, immune responses and exposure to infectious pneumonia in a metapopulation of desert bighorn sheep
<p>Habitat fragmentation is an important driver of biodiversity loss and can be remediated through management actions aimed at maintenance of natural connectivity in metapopulations. Connectivity may protect populations from infectious diseases by preserving immunogenetic diversity and disease resistance. However, connectivity could exacerbate the risk of infectious disease spread across vulnerable populations.</p> <p>We tracked the spread of a novel strain of <em>Mycoplasma ovipneumoniae</em> in a metapopulation of desert bighorn sheep (<em>Ovis canadensis nelsoni</em>) in the Mojave desert to investigate how variation in connectivity among populations influenced disease outcomes.</p> <p><em>M. ovipneumoniae</em> was detected throughout the metapopulation, indicating that the relative isolation of many of these populations did not protect them from pathogen invasion. However, we show that connectivity among bighorn sheep populations was correlated with higher immunogenetic diversity, a protective immune response and lower disease prevalence. Variation in protective immunity predicted infection risk in individual bighorn sheep and was associated with heterozygosity at genetic loci linked to adaptive and innate immune signalling.</p> <p>Together, these findings may indicate that population connectivity maintains immunogenetic diversity in bighorn sheep populations in this system and has direct effects on immune responses in individual bighorn sheep and their susceptibility to infection by a deadly pathogen.</p> <p>Our study suggests that the genetic benefits of population connectivity could outweigh the risk of infectious disease spread and supports conservation management that maintains natural connectivity in metapopulations.</p>
Data from: Tree species and genetic diversity increase productivity via functional diversity and trophic feedbacks
<p><span>This data was collected in the species × genetic diversity experiment of the Biodiversity–Ecosystem Functioning Experiment China Platform (BEF-China, <a href="http://www.bef-china.com/">www.bef-china.com</a>). This data set includes four species (<em>Alniphyllum fortunei</em>, <em>Cinnamanum camphora</em>, <em>Daphniphyllum oldhamii</em>, and <em>Idesia polycarpa</em>) with the mother trees of all tree individuals known, and </span><span>the offspring from the same mother tree was defined as a seed family. In total, 92 subplots with 4 tree diversity levels were included: species diversity (1 or 4 species) and genetic diversity (1 or 4 seed families per species) which resulted in four tree diversity levels: one species with one seed family (1.1), one species with four seed families (1.4), four species with one seed family per species (4.1) and four species with four seed families per species (4.4). For tree functional traits, five leaf functional traits were measured in 2017 and 2018, including leaf area (LA), specific leaf area (SLA), chlorophyll content (CHL), leaf nitrogen content (LN), and leaf carbon content (LC). Herbivory was visually recorded as leaf damage in 2017. Soil fungal diversity was used as proxies for unspecified trophic interactions. Soil samples were taken on subplot level for the 1.1 and 1.4 diversity treatments, but on plot level for the 4.1 and 4.4 diversity treatments in 2017. Tree community productivity was summed by the biomass of individual trees in each subplot and individual tree biomass (kg) was calculated using the biomass equation (H × BA × CV) of the BEF-China experiment, where CV is a correction factor for stem shape and wood density.</span></p>
The timings of host diapause and epidemic progression mediate host genetic diversity and future epidemic size in Daphnia-parasite populations
<p>Epidemics commonly exert parasite-mediated selection and cause declines in host population genetic diversity. This could lead to evolution of resistance in the long-term and smaller subsequent epidemics. Alternatively, the loss of genetic diversity could increase host vulnerability to future disease spread and larger future epidemics. Matters are made more complex by the fact that a great many host organisms produce diapausing life stages in response to environmental change (often as a result of sexual reproduction) e.g., plant seeds and invertebrate resting eggs. These diapausing stages can disrupt the relationship between past epidemics, host genetic diversity and future epidemics because they allow host dispersal through time. Specifically, temporally dispersing hosts avoid infection and thus selection from contemporary parasites, and also archive genetic variation for the future. We studied 80 epidemics in 20 semi-natural populations of the temporally dispersing crustacean Daphnia magna and its sterilising bacterial parasite Pasteuria ramosa, and half of these populations experienced a simulated environmental disturbance treatment. We found that early initiation of diapause relative to the timing of the epidemic led to greater host genetic diversity and reduced epidemic size in the subsequent year, but this was unaffected by environmental disturbance.</p>
A common resequencing‐based genetic marker dataset for global maize diversity
<p>Maize (<em>Zea mays ssp. mays</em>) populations exhibit vast amounts of genetic and phenotypic diversity. As sequencing costs have declined, an increasing number of projects have sought to measure genetic differences between and within maize populations using whole genome resequencing strategies, identifying millions of segregating single-nucleotide polymorphisms (SNPs) and insertions/deletions (InDels). Unlike older genotyping strategies like microarrays and genotyping by sequencing, resequencing should, in principle, frequently identify and score common genetic variants. However, in practice, different projects frequently employ different analytical pipelines, often employ different reference genome assemblies, and consistently filter for minor allele frequency within the study population. This constrains the potential to reuse and remix data on genetic diversity generated from different projects to address new biological questions in new ways. Here we employ resequencing data from 1,276 previously published maize samples and 239 newly resequenced maize samples to generate a single unified marker set of ~366 million segregating variants and ~46 million high confidence variants scored across crop wild relatives, landraces as well as tropical and temperate lines from different breeding eras. We demonstrate that the new variant set provides increased power to identify known causal flowering time genes using previously published trait datasets, as well as the potential to track changes in the frequency of functionally distinct alleles across the global distribution of modern maize.</p>
Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos
<p><span>Biological invasions in remote</span> <span>areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To </span><span>analyze</span><span> geographic variation in genome size, genetic diversity, and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity, and increased self-fertilization, but we show that this is not the case for Poa annua. Microsatellite data indicated low population genetic structure and lack of isolation-by-distance</span> <span>among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality, and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of autogamy declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are likely tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which</span> <span>promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy likely benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.</span></p>
Genetic diversity and population structure from a Peruvian nucleus cattle herd using SNP data
<p>New-generation sequencing technologies, among them SNP chips for massive genotyping, have proven to be useful for the effective management of genetic resources. Also, developing nucleus herds is an effective method for genetic improvement work. To date, molecular studies in Peruvian cattle are still in their infancy. To close this gap, we here employed two SNP panels (BovineHD and Bovine100K) to determine for the first time the Peruvian nucleus herd's genetic diversity and population structure that belong to INIA. This nucleus comprises Brahman (N=16), Braunvieh (N=14), Gyr (N=11), and Fleckvieh (N=22) breeds. Additionally, samples from a locally adapted creole cattle, the Arequipa Fighting Bull (AFB, N=12), were incorporated into the study. The genetic diversity indices in all breeds showed a high proportion of polymorphic SNPs, varying from 69.37% in Gyr to 80.81% in Braunvieh. Also, Braunvieh possessed the highest observed heterozygosity (0.53±0.17), while Brahman possessed the lowest (0.44±0.10), indicating that the former is more diverse compared to the other cattle breed groups. According to the molecular variance analysis, 83.92% of the variance occurs within individuals, whereas 16.0% occurs between populations. The pairwise FST estimates between breeds showed values that ranged from 0.054 (Braunvieh vs AFB) to 0.266 (Brahman vs AFB). Pairwise Reynold's distance showed a pattern similar to the one obtained with the FST statistics, with values ranging from 0.058 to 0.309. A dendrogram was constructed using the Neighbor-Joining clustering algorithm, and similar to the principal coordinate analysis, three groups were identified. Results showed a clear separation between <em>Bos</em> <em>indicus</em> (Brahman and Gyr) and <em>B</em>. <em>taurus</em> breeds (Braunvieh and Fleckvieh). For Fleckvieh and Braunvieh, there were two subgroups each one of them grouping with the AFB group. Similar results were obtained with ADMIXTURE analysis with K= 3 as the most optimal number for the inferred genetic structure of the populations. The results from the current study would contribute to the appropriate management avoiding loss of genetic variability in these breeds and to future improvements for this nucleus. Additional work is needed to speed up the breeding process in the Peruvian cattle system.</p>
Assessment of the Genetic Diversity and Population Structure of the Peruvian Andean Legume, Tarwi (Lupinus mutabilis), with High Quality SNPs
<p><em>Lupinus mutabilis</em> Sweet (Fabaceae), “tarwi” or “chocho”, is an important grain legume in the Andean region. In Peru, studies on tarwi have mainly focused on morphological features; however, they have not been molecularly characterized. Currently, it is possible to explore the genetic parameters of plants with reliable and modern methods such as genotyping by sequencing (GBS). Here, for the first time, we used single nucleotide polymorphism (SNP) markers to infer the genetic diversity and population structure of 89 accessions of tarwi from nine Andean regions of Peru. A total of 5922 SNPs distributed along all chromosomes of tarwi were identified. STRUCTURE analysis revealed that this crop is grouped into two clusters. A dendrogram was generated using the UPGMA clustering algorithm and, like the principal coordinate analysis (PCoA), it showed two groups that correspond to the geographic origin of the tarwi samples. AMOVA showed a reduced variation between clusters (7.59%) and indicated that variability within populations is 92.41%. Population divergence (F<sub>st</sub>) between clusters 1 and 2 revealed low genetic difference (0.019). We also detected a negative F<sub>is</sub> for both populations, demonstrating that, like other <em>Lupinus</em> species, tarwi also depends on cross-pollination. SNP markers were powerful and effective for the genotyping process in this germplasm. We hope that this information is the beginning of the path towards a modern genetic improvement and conservation strategies of this important Andean legume.</p>
Impacts of ecological restoration on the genetic diversity of plant species: A global meta-analysis
<p>1. In contrast to the depth of knowledge available for the enhancement of plant species diversity and ecosystem services through ecological restoration, our understanding of how ecological restoration impacts genetic diversity (GD) of plant species has not yet been synthesized.</p> <p>2. We performed a global meta-analysis to examine whether ecological restoration improved GD of plant species in restored populations. First, we compared the GD of restored populations with reference or degraded populations. Second, we explored whether the influence of ecological restoration on plant GD varies between species with different characteristics (life form and threat status), between different restoration strategies (active/passive, seeding/planting, mixture/non-mixture) or between different restoration times (<50 and ≥50 years; with an average of 29.3 years).</p> <p>3. The GD of restored populations was significantly lower (HE, 1.06%; PPB, 5.10%, and SWI, 4.95%) than in reference populations but was comparable to degraded populations. The inbreeding coefficient (FIS, the proportion by which the heterozygosity of an individual is reduced by inbreeding) was consistently comparable between restored populations and reference or degraded populations.</p> <p>4. Woody species but not herbs had significantly lower GD in restored populations than in reference populations. Forest but not grassland ecosystem had significantly lower GD in restored populations than in reference populations. Passive but not active restoration, seeding rather than planting, and mixing materials from different sources rather than using a single source, all significantly increased the GD of restored populations. When the restoration time was ≥50 years, in contrast to <50 years, GD was comparable between the restored and reference populations.</p> <p>5. Synthesis and applications. In general, ecological restoration did not significantly improve the GD of plant species compared to reference or degraded populations. This might be due in part to the relatively short restoration time. Using passive restoration, seeding, and mixed sources could significantly increase the GD of restored populations. We emphasize that GD should not be treated as a minor cobenefit of ecological restoration for other purposes and that the recovery of GD should be listed as a vital goal in future ecological restoration with plant species.</p>
Data from: A self-transmissible plasmid from a hyperthermophile that facilitates genetic modification of diverse Archaea
<p><span>Conjugative plasmids (CP) are self-transmissible mobile genetic elements which transfer DNA between host cells via Type IV Secretion Systems (T4SS). While T4SS-mediated conjugation has been well-studied in bacteria, information is sparse in Archaea and known representatives exist only in the Sulfolobales order of Crenarchaeota. Here we present the first self-transmissible plasmid identified in a Euryarchaeon, Thermococcus sp. 33-3. The 103 kbp plasmid, pT33-3, is seen in CRISPR-spacers throughout the Thermococcales order. We demonstrate that pT33-3 is a bona fide conjugative plasmid that requires cell-to-cell contact, and is dependent upon canonical, plasmid-encoded T4SS-like genes. Under laboratory conditions pT33-3 transfers to various Thermococcales, and transconjugants propagate at 100°C. Using pT33-3, we developed a genetic toolkit which allows modification of phylogenetically diverse Archaeal genomes. We demonstrate pT33-3–mediated plasmid mobilization and subsequent targeted genome modification in previously untransformable Thermococcales species, and extend this process to interphylum transfer to a Crenarchaeon.</span></p>
Genetic diversity and sperm characteristics are not associated in two bluethroat (Luscinia svecica) populations
<p>Individual heterozygosity may influence the expression of fitness-related traits, via genome-wide or local genetic effects. Earlier studies have shown negative relationships between heterozygosity and sperm variation, predominantly in captive, highly inbred populations. Little is known about the possible influence of variation in heterozygosity on sperm traits in wild, outbred populations. We studied two populations of the bluethroat, one from the widely distributed northern subspecies (<em>Luscinia</em>. <em>s</em>. <em>svecica</em>) and the other from the smaller, more patchily distributed subspecies breeding along the French coast of Brittany (<em>L. s. namnetum</em>). The two subspecies differed significantly in body size, plumage colour, sperm traits and the degree of genetic diversity. However, there was no evidence that sperm traits (total length and motility) were influenced by the degree of heterozygosity at the individual level. In contrast, we found that male body size was positively related to heterozygosity across both populations, indicating a possible relationship between overall genetic diversity and general vigour or ability to obtain food. We conclude that sperm traits are unrelated to levels of heterozygosity in the studied outbred and weakly genetically depauperate bluethroat populations.</p>
Obuasi case study data: Performance of neutral SNP barcodes to determine genetic diversity and structure of Plasmodium falciparum in Africa
<p>A small number of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the genotyping and relatedness analysis of <em>Plasmodium</em> <em>falciparum</em> in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries characterised by moderate-to-high transmission. Using haplotypes generated from the MalariaGEN <em>P. falciparum</em> Community Project version 6 database, 52.3% of infections were multiclonal, generating high frequencies of mixed-allele calls (MACs) per isolate. Both multiclonality and low heterozygosity of SNPs impeded haplotype construction for analyses of relatedness. Although fewer SNPs provided usable data, these SNP barcodes weakly identified genetic differentiation across large geographic distances. However, both minor and major alleles' frequencies were temporally unstable. We conclude that these standardised SNP barcodes are vulnerable to ascertainment bias. While large numbers of SNPs acquired by whole-genome sequencing and computational methods to construct haplotypes present a way forward, these approaches may not be practical or cost-effective for surveillance on large scales in malaria-endemic areas. </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.