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19,493 results for “Populism”
Data from: Complex selection on a regulator of social cognition: evidence of balancing selection, regulatory interactions and population differentiation in the prairie vole Avpr1a locus
Adaptive variation in social behavior depends upon standing genetic variation, but we know little about how evolutionary forces shape genetic diversity relevant to brain and behavior. In prairie voles (Microtus ochrogaster), variants at the Avpr1a locus predict expression of the vasopressin 1a receptor in the retrosplenial cortex (RSC), a brain region that mediates spatial and contextual memory; cortical V1aR abundance in turn predicts diversity in space-use and sexual fidelity in the field. To examine the potential contributions of adaptive and neutral forces to variation at the Avpr1a locus, we explore sequence diversity at the Avpr1a locus and throughout the genome in two populations of wild prairie voles. First, we refine results demonstrating balancing selection at the locus by comparing the frequency spectrum of variants at the locus to a random sample of the genome. Next, we find that the four SNPs that predict high V1aR expression in the RSC are in stronger linkage disequilibrium than expected by chance despite high recombination among intervening variants, suggesting that epistatic selection maintains their association despite recombination. Analysis of population structure and a haplotype network for two populations revealed that this excessive LD was unlikely to be due to admixture alone. Furthermore, the two populations differed considerably in the region shown to be a regulator of V1aR expression despite the extremely low levels of genome-wide genetic differentiation. Together, our data suggest that complex selection on Avpr1a locus favors specific combinations of regulatory polymorphisms, maintains the resulting alleles at populations-specific frequencies, and may contribute to unique patterns of spatial cognition and sexual fidelity among populations.
Data from: Genomic signatures of population bottleneck and recovery in Northwest Atlantic pinnipeds
Population increases over the past several decades provide natural settings in which to study the evolutionary processes that occur during bottleneck, growth, and spatial expansion. We used parallel natural experiments of historical decline and subsequent recovery in two sympatric pinniped species in the Northwest Atlantic, the gray seal (Halichoerus grypus atlantica) and harbor seal (Phoca vitulina vitulina), to study the impact of recent demographic change in genomic diversity. Using restriction site‐associated DNA sequencing, we assessed genomic diversity at over 8,700 polymorphic gray seal loci and 3,700 polymorphic harbor seal loci in samples from multiple cohorts collected throughout recovery over the past half‐century. Despite significant differences in the degree of genetic diversity assessed in the two species, we found signatures of historical bottlenecks in the contemporary genomes of both gray and harbor seals. We evaluated temporal trends in diversity across cohorts, as well as compared samples from sites at both the center and edge of a recent gray seal range expansion, but found no significant change in genomewide diversity following recovery. We did, however, find that the variance and degree of allele frequency change measured over the past several decades were significantly different from neutral expectations of drift under population growth. These two cases of well‐described demographic history provide opportunities for critical evaluation of current approaches to simulating and understanding the genetic effects of historical demographic change in natural populations.
Data from: Pollen competition between morphs in a pollen-color dimorphic herb and the loss of phenotypic polymorphism within populations
Flower color polymorphism is relatively uncommon in natural flowering plants, suggesting that maintenance of different color morphs within populations is difficult. To address the selective mechanisms shaping pollen-color dimorphism, pollinator preferences and reproductive performance were studied over three years in Epimedium pubescens in which some populations had plants with either green or yellow pollen (and anthers). Visitation rate and pollen removal and receipt by the bee pollinator (Andrena emeishanica) did not differ between the two color morphs. Compared to the green morph, siring success of the yellow morph's pollen was lower, but that of mixtures of pollen from green and yellow morphs was lowest. This difference, corresponding to in and ex vivo experiments on pollen performance, indicated that pollen germination, rather than tube growth, of the green morph was higher than that of the yellow morph and was seriously constrained in both morphs if a pollen competitor was present. A rare green morph may invade a yellow-morph population, but the co-existence of pollen color variants is complicated by the reduced siring success of mixed pollinations. Potential pollen competition between morphs may have discouraged the maintenance of multiple phenotypes within populations, a cryptic mechanism of competitive exclusion.
Data from: Phoretic dispersal influences parasite population genetic structure
Dispersal is a fundamental component of the life history of most species. Dispersal influences fitness, population dynamics, gene flow, genetic drift, and population genetic structure. Even small differences in dispersal can alter ecological interactions and trigger an evolutionary cascade. Linking such ecological processes with evolutionary patterns is difficult, but can be done in the proper comparative context. Here we investigate how differences in phoretic dispersal influence the population genetic structure of two different parasites of the same host species. We focus on two species of host-specific feather lice (Phthiraptera: Ischnocera) that co-occur on feral rock pigeons (Columba livia). Although these lice are ecologically very similar, "wing lice" (Columbicola columbae) disperse phoretically by "hitchhiking" on pigeon flies (Diptera: Hippoboscidae), while "body lice" (Campanulotes compar) do not. Differences in the phoretic dispersal of these species are thought to underlie observed differences in host specificity, as well as the degree of host-parasite cospeciation. These ecological and macroevolutionary patterns suggest that body lice should exhibit more genetic differentiation than wing lice. We tested this prediction among lice on individual birds and among lice on birds from three pigeon flocks. We found higher levels of genetic differentiation in body lice compared to wing lice at two spatial scales. Our results indicate that differences in phoretic dispersal can explain microevolutionary differences in population genetic structure and are consistent with macroevolutionary differences in the degree of host-parasite cospeciation.
Data from: Genetic basis of photosynthetic responses to cold in two locally adapted populations of Arabidopsis thaliana
Local adaptation is common, but the traits and genes involved are often unknown. Physiological responses to cold probably contribute to local adaptation in wide-ranging species, but the genetic basis underlying natural variation in these traits has rarely been studied. Using a recombinant inbred (495 lines) mapping population from locally adapted populations of Arabidopsis thaliana from Sweden and Italy, we grew plants at low temperature and mapped quantitative trait loci (QTLs) for traits related to photosynthesis: maximal quantum efficiency (Fv/Fm), rapidly reversible photoprotection (NPQfast), and photoinhibition of PSII (NPQslow) using high-throughput, whole-plant measures of chlorophyll fluorescence. In response to cold, the Swedish line had greater values for all traits, and for every trait, large effect QTLs contributed to parental differences. We found one major QTL affecting all traits, as well as unique major QTLs for each trait. Six trait QTLs overlapped with previously published locally adaptive QTLs based on fitness measured in the native environments over 3 years. Our results demonstrate that photosynthetic responses to cold can vary dramatically within a species, and may predominantly be caused by a few QTLs of large effect. Some photosynthesis traits and QTLs probably contribute to local adaptation in this system.
Data from: Plasticity of plant defense and its evolutionary implications in wild populations of Boechera stricta
Phenotypic plasticity is thought to impact evolutionary trajectories by shifting trait values in a direction that is either favored by natural selection ("adaptive plasticity") or disfavored ("nonadaptive" plasticity). However, it is unclear how commonly each of these types of plasticity occurs in natural populations. To answer this question, we measured glucosinolate defensive chemistry and reproductive fitness in over 1,500 individuals of the wild perennial mustard Boechera stricta, planted in four common gardens across central Idaho, USA. Glucosinolate profiles—including total glucosinolate concentration as well as the relative abundances and overall diversity of different compounds—were strongly plastic both among habitats and within habitats. Patterns of glucosinolate plasticity varied greatly among genotypes. Plasticity among sites was predicted to affect fitness in 27.1% of cases; more often than expected by chance, glucosinolate plasticity increased rather than decreased relative fitness. In contrast, we found no evidence for within-habitat selection on glucosinolate reaction norm slopes (i.e., plasticity along a continuous environmental gradient). Together, our results indicate that glucosinolate plasticity may improve the ability of B. stricta populations to persist after migration to new habitats.
Environment dependent costs and benefits of recombination in independently evolved populations of Escherichia coli
Understanding of the causes by which reproductive isolation arises remains limited. We examine the role of adaptation in driving reproductive isolation among 12 Escherichia coli populations evolved in two different environments. We found that, regardless of whether parents were selected in the same or different environments, the average fitness of recombinants was lower than the expected, consistent with a prevailing influence of incompatibility between independently accumulated mutations. Exceptions to this pattern occurred among recombinants of some parents evolved in different environments. These recombinants were less fit than expected in the selective environment of one parent, but more fit than expected in the selective environment of the other parent. Our results indicate that both parallel and divergent adaptation can quickly lead to intrinsic genetic barriers contributing to the initial stages of speciation and show that these barriers can be complex, for example, depending on the environment in which recombinant offspring are tested.
Using a coalescent approach to assess gene flow and effective population size of Acrocomia aculeata (Jacq.) Lodd. Ex Mart. in the Brazilian Atlantic Forest
<p><i>Acrocomia aculeata</i> is a tropical palm tree native to Central and South America that has significant economic, social, and environmental potential. However, land encroachment due to the expansion of agribusiness, and other factors such as urban sprawl, have resulted in the fragmentation and destruction of its habitat, leading to the loss of genes and genotypes in <i>A. aculeata</i> populations. In this context, the objective of this study was to characterize the genetic variability of <i>A. aculeata</i> populations by estimating gene flow and effective population size using an approach based on coalescent theory. Four populations located in the municipalities of Teodoro Sampaio (TSI and TSII), Rosana (RA), and Amparo (AP) in São Paulo State, Brazil, were genotyped with nine microsatellite markers. Gene flow and effective population size were estimated using a coalescent-based Bayesian inference implemented in the MIGRATE-N software. The effective population size (<i>N<sub>e</sub></i>) was obtained considering an assumed mutation rate of <a name="_Hlk6565387">5x10<sup>-5</sup>. </a>Gene flow (<i>Nm</i>) for pairwise populations ranged from 0.28 to 1.17, with higher levels of migration between the three geographically proximal locations (TSI, TSII, and RA). The estimates of effective population size (<i>N<sub>e</sub></i>) were 444, 835, 838, and 874 for AP, TSII, RA, and TSI, respectively, showing that the effects caused by genetic drift may be more pronounced when <i>N<sub>e</sub></i> is smaller. The coalescent-based results add to our understanding of <i>A. aculeata</i> population genetics and suggest that some traditional assessment methods may be ineffective in characterizing historical evolutionary processes.</p>
Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities
Urbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (< 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.
Reduced avian body condition due to global warming has little reproductive or population consequences
<p><span>Climate change has strong effects on traits such as phenology and physiology. Studies typically assume that climate-induced trait changes will have consequences for population dynamics, but explicit tests are rare. Body condition reflects energy storage and may directly affect how much can be invested in reproduction and survival. <a name="_Hlk2255083">However, the causal pathway by which decreased body condition impacts population dynamics has never been quantified across multiple populations and species. </a>Therefore, we lack a general understanding of the consequences of changes in condition for variables more relevant for conservation, such as population size. Using structural equation modeling, we investigate how temperature-induced changes in body condition affect reproduction, and the subsequent impact on population growth rates of 19 bird species across 80 Dutch sites over a 21-year period. Warmer temperatures were associated with decreased body condition, which led to both decreased and increased reproduction at different sites, cancelling out any overall effect. <a name="_Hlk21968494">The indirect effect of temperature on population growth (via body condition and reproduction) only explained within-species variation in the total effects of temperature on population growth. </a><a name="_Hlk2256206">Instead, the direct effect of temperature on population growth (unrelated to condition and reproduction) was the most important pathway underlying the total effects of temperature on population growth, suggesting that unknown variables are mediating this effect. </a>About half of the species are expected to increase under global warming, but this variation was not associated with any species characteristic.<a name="_Hlk1222971"> </a><a name="_Hlk1223032">Overall, body condition responses to global warming are common, but their consequences on reproduction and subsequently population growth contribute relatively little to the total temperature impacts on population dynamics</a>. <a name="_Hlk2255609">Given that warming temperatures have strong effects on population dynamics, understanding the pathways via which temperature impacts population dynamics will be crucial for our ability to predict climate change effects in the future and improve conservation efforts.</a></span></p>
Genetic analyses reveal population structure and recent decline in leopards (Panthera pardus fusca) across Indian subcontinent
<p><span><span><b><i>Background </i></b></span></span></p> <p><span><span>Large carnivores maintain the stability and functioning of ecosystems. Currently, many carnivore species face declining population sizes due to natural and anthropogenic pressures. The leopard, <i>Panthera pardus</i>, is probably the most widely distributed and highly adaptable large felid globally, still persisting in most of its historic range. However, we lack subspecies-level data on country or regional scale on population trends, as ecological monitoring approaches are difficult to apply on such wide-ranging species. We used genetic data from leopards sampled across the Indian subcontinent to investigate population structure and patterns of demographic decline. </span></span></p> <p><span><span><b><i>Methods </i></b></span></span></p> <p><span><span>We collected faecal samples from the Terai-Arc landscape of north India and identified 56 unique individuals using a panel of 13 microsatellite markers. We merged this data with already available 143 leopard individuals and assessed genetic structure at country scale. Subsequently, we investigated the demographic history of each identified subpopulations and compared genetic decline analyses with countrywide local extinction probabilities. </span></span></p> <p><span><span><b><i>Results </i></b></span></span></p> <p><span><span>Our genetic analyses revealed four distinct subpopulations corresponding to Western Ghats, Deccan Plateau-Semi Arid, Shivalik and Terai region of the north Indian landscape, each with high genetic variation. Coalescent simulations with microsatellite loci revealed a possibly human-induced 75-90% population decline between ∼120-200 years ago across India. Population-specific estimates of genetic decline are in concordance with ecological estimates of local extinction probabilities in these subpopulations obtained from occupancy modeling of the historic and current distribution of leopards in India. </span></span></p> <p><span><span><b><i>Conclusions </i></b></span></span></p> <p><span><span>Our results confirm the population decline of a widely distributed, adaptable large carnivore. We re-iterate the relevance of indirect genetic methods for such species in conjunction with occupancy assessment and recommend that detailed, landscape-level ecological studies on leopard populations are critical to future conservation efforts. Our approaches and inference are relevant to other widely distributed, seemingly unaffected carnivores such as the leopard.</span></span></p>
Rapid adaptation (or not) in restored plant populations
<p>Mismatches between the traits of a colonizing population and a novel habitat can generate strong selection, potentially resulting in rapid adaptation. However, for most colonization events, it can be difficult to detect rapid adaptation or distinguish it from non-adaptive evolutionary changes. Here I take advantage of a replicated prairie restoration experiment to compare recently established plant populations in two closely-located restored prairies to each other and to their shared source population to test for rapid adaptation. Using a reciprocal transplant experiment six years after the populations were established, I found that one restored plant population showed evidence of adaptation, outperforming the other restored population when grown at its home site. In contrast, I detected no evidence for adaptation at the other site. These findings demonstrate that while rapid adaptation can occur in colonizing plant populations, it may not be the rule. Better understanding of when adaptation may or may not occur in these contexts may help us use evolution to our advantage, potentially improving establishment of desirable species in restored habitats.</p>
Data from: Intraspecific DNA contamination distorts subtle population structure in a marine fish: decontamination of herring samples before restriction-site associated (RAD) sequencing and its effects on population genetic statistics
Wild specimens are often collected in challenging field conditions, where samples may be contaminated with the DNA of conspecific individuals. This contamination can result in false genotype calls, which are difficult to detect, but may also cause inaccurate estimates of heterozygosity, allele frequencies, and genetic differentiation. Marine broadcast spawners are especially problematic, because population genetic differentiation is low and samples are often collected in bulk and sometimes from active spawning aggregations. Here, we used contaminated and clean Pacific herring (Clupea pallasi) samples to test (i) the efficacy of bleach decontamination, (ii) the effect of decontamination on RAD genotypes, and (iii) the consequences of contaminated samples on population genetic analyses. We collected fin tissue samples from actively spawning (and thus contaminated) wild herring and non-spawning (uncontaminated) herring. Samples were soaked for 10 minutes in bleach or left untreated, and extracted DNA was used to prepare DNA libraries using a restriction-site associated DNA (RAD) approach. Our results demonstrate that intraspecific DNA contamination affects patterns of individual and population variability, causes an excess of heterozygotes, and biases estimates of population structure. Bleach decontamination was effective at removing intraspecific DNA contamination and compatible with RAD sequencing, producing high-quality sequences, reproducible genotypes, and low levels of missing data. Although sperm contamination may be specific to broadcast spawners, intraspecific contamination of samples may be common and difficult to detect from high-throughput sequencing data, and can impact downstream analyses.
Genetic diversity and thermal performance in invasive and native populations of African fig flies
<p>During biological invasions, invasive populations can suffer losses of genetic diversity that are predicted to negatively impact their fitness/performance. Despite examples of invasive populations harboring lower diversity than conspecific populations in their native range, few studies have linked this lower diversity to a decrease in fitness. Using genome sequences, we show that invasive populations of the African fig fly, <i>Zaprionus indianus</i>, have less genetic diversity than conspecific populations in their native range and that diversity is proportionally lower in regions of the genome experiencing low recombination rates. This result suggests that selection may have played a role in lowering diversity in the invasive populations. We next use interspecific comparisons to show that genetic diversity remains relatively high in invasive populations of <i>Z. indianus</i> when compared to other closely related species. By comparing genetic diversity in orthologous gene regions, we also show that the genome-wide landscape of genetic diversity differs between invasive and native populations of <i>Z. indianus</i>, indicating that invasion not only affects amounts of genetic diversity, but also how that diversity is distributed across the genome. Finally, we use parameter estimates from thermal performance curves measured for 13 species of <i>Zaprionus</i> to show that <i>Z. indianus</i> has the broadest thermal niche of measured species, and that performance does not differ between invasive and native populations. These results illustrate how aspects of genetic diversity in invasive species can be decoupled from measures of fitness, and that a broad thermal niche may have helped facilitate <i>Z. indianus's</i> range expansion.</p>
Data from: Evaluating shell variation across different populations of a freshwater snail
The freshwater snail Potamopyrgus antipodarum has become a model system for studying invasion ecology, host–parasite coevolution, the maintenance of sexual reproduction and ecotoxicology. One understudied aspect of this snail is the variation in morphology within and among populations, which could provide insights into ecological differences across its native range. In this study of 17 New Zealand lake populations of P. antipodarum we used linear measurements and geometric morphometrics to compare several aspects of shell size and shape. We found that, except for those from Lake Te Anau, most lake populations of P. antipodarum differ slightly in shape, but differ significantly in size and in the presence of spines, where larger and spinier snails are found in deeper regions. These striking distinctions in size and shell armature, but not in shape, suggest that the various components of form are under different selective regimes. Snails from Lake Te Anau are different in both shape and size, implying that this population is diverging from the rest of the species in multiple ways, making it an interesting study population for further research.
Data from: Population genetic structure between Yap and Palau for the coral Acropora hyacinthus
Information on connectivity is becoming increasingly in demand as marine protected areas are being designed as an integral part of a network to protect marine resources at the ecosystem level. Larval dispersal and population structure, however, remain very difficult to assess. Here, we tested the predictions of a detailed oceanographic connectivity model of larval dispersal and coral recruitment within Palau and between Palau and Yap, which was developed to support the review of the existing network of marine protected areas in Palau. We used high throughput microsatellite genotyping of the coral Acropora hyacinthus to characterize population genetic structure. Pairwise F′ST values between Palau and Yap (0.10), Palau and Ngulu (0.09) and Yap and Ngulu (0.09) were all significant and similar to pairwise F′ST values of sites within Palau (0.02–0.12) and within Yap (0.02–0.09) highlighting structure at island scale and indicating that recruitment may be even more localized than previously anticipated. A bottleneck test did not reveal any signs of a founder effect between Yap and Palau. Overall, the data supports the idea that recovery of A. hyacinthus in Palau did not come exclusively from a single source but most likely came from a combination of areas, including sites within Palau. In light of these results there seems to be very little connectivity around the barrier reef and management recommendation would be to increase the number or the size of MPAs within Palau.
Population structure in landrace barley (Hordeum vulgare L.) during the late 19th century crop failures in Fennoscandia
<p><span><span><span><span><span><span><span><span><span><span><span>Agricultural disasters and the subsequent need for supply of relief seed can be expected to influence the genetic composition of crop plant populations. The consequences of disasters and seed relief have, however, rarely been studied since specimens sampled before the events are seldomly available. A series of crop failures struck northern Fennoscandia (Norway, Sweden and Finland) during the second half of the 19<sup>th</sup> century. In order to assess population genetic dynamics of landrace barley (<i>Hordeum vulgare</i>), and consequences of crop failure and possible seed relief during this time period, we genotyped seeds from 16 historical accessions originating from two time periods spanning the period of repeated crop failure. Reliable identification of genetic structuring is highly dependent on sampling regimes and detecting fine-scale geographic or temporal differentiation requires large sample sizes. The robustness of the results under different sampling regimes was evaluated by analyzing subsets of the data and an artificially pooled dataset. The results led to the conclusion that six individuals per accession were insufficient for reliable detection of the observed genetic structure. We found that population structure among the data was best explained by collection year of accessions, rather than geographic origin. The correlation with collection year indicated a change in genetic composition of landrace barley in the area after repeated crop failures, likely a consequence of introgression of relief seed in local populations. Identical genotypes were found to be shared among some accessions, suggesting founder effects and local seed exchange along known routes for trade and cultural exchange. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Reticulate evolution within a spruce (Picea) species complex revealed by population genomic analysis
The role of reticulation in the rapid diversification of organisms is attracting greater attention in evolutionary biology. Here, we report a population genomics approach to test the role of hybridization and introgression in the evolution of the Picea likiangensis species complex. Based on 84,793 SNPs detected in transcriptomes of 82 trees collected from 35 localities, we identified 18 hybrids (including backcrosses) distributed within the range boundaries of the four taxa. Coalescent simulations, for each pair of taxa and for all taxa taken together, rejected several tree-like divergence models and supported instead a reticulate evolution model with secondary contacts occurring during Pleistocene glacial cycles after initial divergence in the late Pliocene. Significant gene flow occurred among some taxa after secondary contact according to an analysis based on modified ABBA-BABA statistics that accommodated a rapid diversification scenario. A novel finding was that introgression between certain taxa can contribute to increasing divergence (and possibly reproductive isolation) between those taxa and other taxa within a complex at some loci. These results illuminate the reticulate nature of evolution within the P. likiangensis complex and highlight the value of population genomic data in detecting the effects of introgression in the rapid diversification of related taxa.
Data from: Expression of additive genetic variance for fitness in a population of partridge pea in two field sites
Despite the importance of adaptation in shaping biological diversity over many generations, little is known about populations' capacities to adapt at any particular time. Theory predicts that a population's rate of ongoing adaptation is the ratio of its additive genetic variance for fitness, VA (W), to its mean absolute fitness, W̅. We conducted a transplant study to quantify W̅ and standing VA (W) for a population of the annual legume Chamaecrista fasciculata in one field site from which we initially sampled it and another site where it does not currently occur naturally. We also examined genotype‐by‐environment interactions, G x E, as well as its components, differences between sites in VA (W) and in rank of breeding values for fitness. The mean fitness indicated population persistence in both sites, and there was substantial VA (W) for ongoing adaptation at both sites. Statistically significant G x E indicated that the adaptive process would differ between sites. We found a positive correlation between fitness of genotypes in the "home" and "away" environments, and G x E was more pronounced as the life cycle proceeds. This study exemplifies an approach to assessing whether there is sufficient VA (W) to support evolutionary rescue in populations that are declining.
Linked-read sequencing enables haplotype-resolved resequencing at population scale
The feasibility to sequence entire genomes of virtually any organism provides unprecedented insights into the evolutionary history of populations and species. Nevertheless, many population genomic inferences – including the quantification and dating of admixture, introgression and demographic events, and inference of selective sweeps – are still limited by the lack of high-quality haplotype information. The newest generation of sequencing technology now promises significant progress. To establish the feasibility of haplotype-resolved genome resequencing at population scale, we investigated properties of linked-read sequencing data of songbirds of the genus Oenanthe across a range of sequencing depths. Our results based on the comparison of downsampled (25x, 20x, 15x, 10x, 7x, and 5x) with high-coverage data (46-68x) of seven bird genomes mapped to a reference suggest that phasing contiguities and accuracies adequate for most population genomic analyses can be reached already with moderate sequencing effort. At 15x coverage, phased haplotypes span about 90% of the genome assembly, with 50 and 90 percent of phased sequences located in phase blocks longer than 1.25-4.6 Mb (N50) and 0.27-0.72 Mb (N90). Phasing accuracy reaches beyond 99% starting from 15x coverage. Higher coverages yielded higher contiguities (up to about 7 Mb/1Mb (N50/N90) at 25x coverage), but only marginally improved phasing accuracy. Phase block contiguity improved with input DNA molecule length; thus, higher-quality DNA may help keeping sequencing costs at bay. In conclusion, even for organisms with gigabase-sized genomes like birds, linked-read sequencing at moderate depth opens an affordable avenue towards haplotype-resolved genome resequencing at population scale.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.