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1,659 results for “structured population”
Data from: Population genetic structure and intraspecific genetic distance of Periplaneta americana (Blattodea: Blattidae) based on mitochondrial and nuclear DNA markers
<p>The American cockroach (<i>Periplaneta americana</i>) is a globally invasive pest that can cause significant economic loss and threaten human health. Although it is abundant and lives in close proximity to humans, few studies have investigated the genetic diversity of <i>P. americana</i>. Our study analyzed 1053 <i>P. americana</i> and other <i>Periplaneta</i> species' samples from different locations in China and the USA. A traditional tree-based method using 17 unique mitochondrial COI haplotypes of <i>P. americana</i> and 20 haplotypes of the other <i>Periplaneta</i> species accurately identified <i>P. americana</i> with a barcoding threshold of 5.1%. To identify the population genetic structure of <i>P. americana,</i> we investigated <i>wingless</i> gene and pooled them with obtained mtDNA data for a combined analysis. Although the genetic diversity of the USA group was relatively higher than the China group, the number of haplotypes and alleles of both groups was small. Molecular variance (AMOVA), intraspecific phylogeny, and haplotype networks indicated that <i>P. americana</i> had very little global genetic differentiation. The weak geographic genetic structure might reflect the human-mediated dispersal of <i>P. americana</i>. Despite no apparent phylogeographic assignment of mtDNA and nuclear lineages was observed in both BI trees, the integrated COI sequence data identified four distinct <i>P. americana</i> haplotype groups, showing four ancient maternal lineages of <i>P. americana</i> in China and the USA.</p>
Genetic structure in populations of Euterpe precatoria Mart. in the Brazilian Amazon
<p><i>Euterpe precatoria</i> is a palm tree belonging to the Arecaceae family, occurring in Western and Central Brazilian Amazonia Its fruit, which is very appreciated in the Amazon region, produces pulp that is consumed in fresh form. Its production is carried out almost exclusively by extractive farmers. In order to establish adequate strategies to sustain this genetic resource. We need knowledge about its diversity and genetic structure in natural populations. This study aimed to evaluate the influence of geographic distance on genetic structure in the main extractive populations of <i>E. precatoria</i> in the Brazilian Amazon. Leaves from 377 plants were collected in 19 populations located in 16 municipalities in the State of Amazonas and three in the State of Rondônia. Twelve microsatellite loci were used to genotype the plants. The diversity and genetic structure among populations were estimated. The average number of alleles per locus was 5.97. The observed heterozygosity means (<i>H<sub>O</sub></i>) were higher than expected (<i>H<sub>E</sub></i>) at the population level (<i>H<sub>O</sub></i> = 0.72, <i>H<sub>E</sub></i> = 0.66) and fixation index (<i>f</i> = -0.100) was negative. The<i> F<sub>ST</sub></i><sub> </sub>value (0.1820) and the AMOVA results (17.961) showed population structure. The populations were clustered into three groups (K = 3) in Bayesian analysis. The Discriminant Analysis of Principal Components (DAPC) confirmed eight clusters, with the populations close to those identified by the Bayesian analysis. The geographic differentiation was confirmed by the groupings obtained in the analyses by the Structure program and the DACP function. Information related to phenotypic, genetic and environmental characterization of populations is important to guide conservation and management strategies and the formulation of public species management policies in Amazonian.</p>
Dataset and code release for "Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia"
<p>This upload contains the raw DArTseq data and code for reproducible analysis and production of output tables and plots to accompany the publication "Current population structure and pathogenicity patterns of <em>Ascochyta rabiei</em> in Australia".<br> The analysis is performed primarily in R and is run using the `A_rabiei_DArT.R` file.</p> <p>A version-controlled repository of this upload is maintained at GitHub at the following link: <a href="https://github.com/IdoBar/A_rabiei_DArT">https://github.com/IdoBar/A_rabiei_DArT</a></p> <p>The archived file is structured as follows:</p> <ul> <li>Main analysis code is in <strong>A_rabiei_DArT.R</strong></li> <li>Raw DArTseq data and <em>A. rabiei</em> isolate metadata can be found in in the <strong><em>data </em></strong>folder</li> <li>Output tables and plots in <em><strong>output</strong></em> folder</li> <li>General information (partial and slightly outdated) in the markdown <strong>A_rabiei_DArT.Rmd </strong>and knitted <strong>A_rabiei_DArT.html </strong>files</li> <li>Australian chickpea production stats and figures in <strong>Chickpea_production.R</strong></li> </ul>
Data from: Continent-wide population genomic structure and phylogeography of North America's most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)
<p>The spruce budworm, <i>Choristoneura fumiferana</i>, is presumed to be panmictic across vast regions of North America. We examined the extent of panmixia by genotyping 3650 single nucleotide polymorphism (SNP) loci in 1975 individuals from 128 collections across the continent. We found three spatially structured subpopulations: Western (Alaska, Yukon), Central (southeastern Yukon to the Manitoba-Ontario border) and Eastern (Manitoba-Ontario border and Atlantic). Additionally, the most diagnostic genetic differentiation between the Central and Eastern subpopulations was chromosomally restricted to a single block of SNPs that may constitute an island of differentiation within the species. Geographic differentiation in the spruce budworm parallels that of its principal larval host, white spruce, <i>Picea glauca</i>, providing evidence that spruce trees survived in the Beringian refugium through the Last Glacial Maximum and that at least two isolated populations diverged with spruce/fir south of the ice sheets. Gene flow in the spruce budworm may also be affected by mountains in western North America, habitat isolation in West Virginia, regional adaptations, factors related to dispersal, and proximity of other species in the spruce budworm species complex. The central and eastern geographic regions contain individuals that assign to Eastern and Central subpopulations, respectively, indicating that these barriers are not complete. Our discovery of previously undetected geographic and genomic structure in the spruce budworm suggests that further population modelling of this ecologically important insect should consider regional differentiation, potentially co-adapted blocks of genes, and gene flow between subpopulations. </p>
Supplementary material 1 from: Guedes GHS, Salgado FLK, Uehara W, de Pavia Ferreira DL, Araújo FG (2020) The recapture of Leptopanchax opalescens (Aplocheiloidei: Rivulidae), a critically endangered seasonal killifish: habitat and aspects of population structure. Zoologia 37: 1-8. https://doi.org/10.3897/zoologia.37.e54982
Figure S1. Photographic records of Leptopanchax opalescens in an aquarium after three hours of capture (Photos 1–3), and record of a male specimen with more exuberant color immediately after capture in its natural habitat (Photos 4–5). Date: March 19th, 2020; Coordinates: 22°42.35'S, 43°41.59'W.
Data from: Large-scale connectivity, cryptic population structure, and relatedness in Eastern Pacific olive ridley sea turtles (Lepidochelys olivacea)
<p>Endangered species are grouped into genetically discrete populations to direct conservation efforts. Mitochondrial Control Region (mtCR) haplotypes are used to elucidate deep divergences between populations, as compared to nuclear microsatellites that can detect recent structuring. When prior populations are unknown, it is useful to subject microsatellite data to clustering and/or ordination population inference. Olive ridley sea turtles (Lepidochelys olivacea) are the most abundant sea turtle, yet few studies have characterized olive ridley population structure. Recently, clustering results of olive ridleys in the Eastern Tropical Pacific Ocean suggested weak structuring (FST=0.02) between Mexico and Central America. We analyzed mtCR haplotypes, new microsatellite genotypes from Costa Rica, and pre-existing microsatellite genotypes from olive ridleys across the Eastern Tropical Pacific, to further explore population structuring in this region. We subjected inferred populations to multiple analyses to explore the mechanisms behind their structuring. We found 10 mtCR haplotypes from 60 turtles nesting at three sites in Costa Rica, but did not detect divergence between Costa Rican sites, or between Central America and Mexico. In Costa Rica, clustering suggested one population with no structuring, but ordination suggested four cryptic clusters with moderate structuring (FST=0.08, p<0.001). Across the Eastern Tropical Pacific, ordination suggested nine cryptic clusters with moderate structuring (FST=0.103, p<0.001) that largely corresponded to Mexican and Central American populations. All ordination clusters displayed significant internal relatedness relative to global relatedness (p<0.001) and contained numerous sibling pairs. This suggests that broadly dispersed family lineages have proliferated in Eastern Tropical Pacific olive ridleys and corroborates previous work showing basin-wide connectivity and shallow population structure in this region. The existence of broadly dispersed kin in Eastern Tropical Pacific olive ridleys has implications for management of olive ridleys in this region, and adds to our understanding of sea turtle ecology and life-history, particularly in light of the natal-homing paradigm.</p>
Population structure of Rosa spinosissima L. on the Frisian Islands and introgression from cultivated material
<i>Rosa spinosissima</i> L. is part of the highly dynamic coastal habitat of the Wadden Sea, between the coast of northwestern continental Europe and the Frisian Islands. Plants of this species grow clonally via root suckers to form large patches, which stabilize dunes and help to protect the islands and used for this purpose locally on the island Sylt. <i>Rosa spinosissima</i> plants are affected by both water and wind in their harsh environment, and are threatened by human impact via habitat destruction and introduction of foreign species. In these northern parts of its range <i>R. spinosissima</i> is categorized as endangered. The population structure of <i>R. spinosissima</i> was investigated using ten microsatellite loci and 195 individuals of Frisian Island populations and European coastal continental samples. DAPC, Kmeans and Structure analyses were conducted to study the genetic composition and integrity of these natural populations relative to cultivated and nursery material mostly consisting of central continental genotypes. The DAPC and Structure analyses differentiated populations of the Frisian Islands between each other and separated them from nursery samples, but some natural populations showing an impact of nursery and cultivated genotypes. In addition, some clonal patches of <i>R. spinosissima</i> were detected. Our results show that the natural Frisian Island populations of <i>R. spinosissima</i> are threatened by the introduction of nonadaptive genotypes into the gene pool.
Microbial Recombination with Population Structure
<p>This collection of data files contains, for each bacterial species:</p> <ol> <li>All raw genome sequence files.</li> <li>The core genome alignment obtained with REALPHY (this is the file with the .phy extension).</li> <li>A file with all SNP columns in the core genome alignment (the file name starts with columns_).</li> <li>A file listing all SNP types sorted from most to least common (the file name starts with snp_stats_)</li> <li>Two files containing the results of the pairwise analysis. First, a file with, for each pair, the histogram of SNP counts per alignment block (the file name ends in _histograms). And second, a file with the results of the mixture modeling (the file with the .pkl extension).</li> </ol> <p>In addition, for M. tuberculosis there is a subfolder with information about which strains have since been retracted from the database.</p> <p> </p> <p>The formats of these files are as follows:</p> <ol> <li>The raw genome sequence files are in FASTA format (.fasta or .fna).</li> <li>The core genome alignment is in PHYLIP multiple alignment format (.phy).</li> <li>The snp_stats file starts with a header line listing the total number of columns in the alignment with 1, 2, 3, and 4 different nucleotides. Each next line in the file corresponds to an observed SNP-type, sorted from most to least common. Each SNP line has the following columns:</li> </ol> <ol> <li>The total amount of genomic DNA associated with these SNP columns (associating each conserved alignment column to its closest SNP).</li> <li>The total number of occurrences of this SNP type.</li> <li>The number of strains sharing the minority allele.</li> <li>A bit-pattern describing the SNP type, with 1 for the strains sharing the minority allele, and zero for the others. The strains are sorted in the same order as in the PHYLIP alignment file.</li> <li>A list of all the strains sharing the minority allele.</li> </ol> <ol> <li>The columns_ file has one SNP per line, giving the position in the alignment plus the bit-pattern describing the SNP.</li> <li>The _histogram file contains, for each pair of strains, a histogram counting the number of 1Kb blocks with 0, 1, 2, etc SNPs. Note that these counts come from 1 kilobase sliding windows along the core genome alignment, sliding the window by 100 bases at a time, i.e. an alignment column will typically occur in 10 blocks.</li> <li>A pickle file with, for each pair, the results of the mixture modeling. Each line corresponds to a pair and has these fields: [spec1, spec2, div, Lpois, r_nomix, Lmix, rho, r, a, lam, mutpois, mutrecomb, cut] which correspond to:</li> </ol> <ol> <li>Name of strain 1.</li> <li>Name of strain 2.</li> <li>Their overall nucleotide divergence.</li> <li>The log-likelihood under a model assuming SNP counts form a simple Poisson distribution.</li> <li>The parameter of this fitted Poisson distribution.</li> <li>The log-likelihood of the mixture of a Poisson and negative binomial</li> <li>The fraction rho assigned to the Poisson part of the mixture.</li> <li>The parameter of the Poisson component.</li> <li>The exponent a of the negative binomial component.</li> <li>The second parameter (lambda) of the negative binomial.</li> <li>The estimated total number of mutations in the Poisson component.</li> <li>The estimated total number of mutations in the negative binomial component.</li> <li>The value at which the likelihood of negative poisson component starts exceeding the likelihood of the negative binomial component.</li> </ol> <p> </p> <p>In addition, for the human data we provide a PHYLIP multiple genome alignment and a file with all SNP columns.</p>
Adaptive population structure shifts in invasive parasitic mites, Varroa destructor
<p>Comparative studies of genetic diversity and population structure can shed light on the ecological and evolutionary factors governing host–parasite interactions. Even though invasive parasites are considered of major biological importance, little is known about their adaptive potential when infesting the new hosts. Here, the genetic diversification of <i>Varroa destructor</i>, a novel parasite of <i>Apis mellifera</i> originating from Asia, was investigated using population genetics to determine how the genetic structure of the parasite changed in distinct European populations of its new host. To do so, mites infesting two categories of hosts in four European regions were compared: (i) adapted hosts surviving through means of natural selection, thereby expected to impose strong selective pressure on the mites, and (ii) treated host populations, surviving mite infestations because acaricides are applied, therefore characterized by a relaxed selection imposed by the host on the mites. Significant genetic divergence was found across regions, partially reflecting the invasion pattern of <i>V. destructor</i> throughout Europe and indicating local adaptation of the mite to the host populations. Additionally, varying degrees of genotypic changes were found between mites from adapted and treated colonies. Altogether, these results indicate that <i>V. destructor</i> managed to overcome the genetic bottlenecks following its introduction in Europe and that host-mediated selection fostered changes in the genetic structure of this mite at diverse geographical scales. These findings highlight the potential of parasites to adapt to their local host populations and confirm that adaptations developed within co-evolutionary dynamics are a major determinant of population genetic changes.</p>
Temporal and spatial variation in population structure among brooding sea stars in the genus Leptasterias
<p>Temporal genetic studies of low-dispersing organisms are rare. Marine invertebrates lacking a planktonic larval stage are expected to have lower dispersal, low gene flow, and a higher potential for local adaptation than organisms with planktonic dispersal. <i>Leptasterias</i> is a genus of brooding sea stars containing several cryptic species complexes. Population genetic methods were used to resolve patterns of fine-scale population structure in central California <i>Leptasterias</i> species using three loci from nuclear and mitochondrial genomes. Historic samples (collected between 1897 and 1998) were compared to contemporary samples (collected between 2008 and 2014) to delineate changes in species distributions in space and time. Phylogenetic analysis of contemporary samples confirmed the presence of a bay-localized clade and revealed an additional bay-localized and previously undescribed clade of <i>Leptasterias</i>. Analysis of contemporary and historic samples indicates two clades are experiencing a constriction in their southern range limit and suggests a decrease in clade-specific abundance at sites at which they were once prevalent. Historic sampling revealed a dramatically different distribution of diversity along the California coastline compared to contemporary sampling and illustrates the importance of temporal genetic sampling in phylogeographic studies. These samples were collected prior to significant impacts of Sea Star Wasting Disease (SSWD) and represent an in-depth analysis of genetic structure over 117 years prior to the SSWD-associated mass die-off of <i>Leptasterias</i>. </p>
Data from: Population structure and persistence of Pacific herring following the Great Tohoku earthquake
We evaluated the effect of the Great Tohoku earthquake, which occurred on March 11, 2011 in Japan, on the genetic diversity and population structure of Pacific herring (Clupea pallasii). Pacific herring (n = 4466) were collected between 2003 and 2014 through more than 20 sampling events during spawning periods at nine spawning sites throughout the Pacific herring distribution range in Japan. We measured them and genotyped 3784 fish at five microsatellite loci. Following the tsunami, the sea-spawning population at the center of the affected area was almost extirpated and was replaced by a genetically distinct lagoon-spawning population from an adjacent brackish lake. However, the pattern of gene flow was stable for populations, with unique admixture proportions in local populations despite the high gene flow (FST = 0.0184). Our results indicate that Pacific herring in Japan spawn in a range of salinities and exchange genes between local populations regardless of the spawning ecotypes. We hypothesize that the combination of constant gene flow between local populations from straying of spawners and spawning fidelity creates weak but significantly differentiated stable population structure. This process can allow restoration of the genetic characteristics of damaged populations over many generations and can thereby promote the long-term viability of marine fishes that have high gene flow.
Data from: Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales
Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study we assess the population genetic structure of the endemic Mediterranean coral Astroides calycularis in the Alboran Sea at local and regional scales, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and Dest statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as one kilometer and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.
Data from: Spatial and temporal genetic structure of Symbiodinium populations within a common reef-building coral on the central Great Barrier Reef
The dinoflagellate photosymbiont Symbiodinium plays a fundamental role in defining the physiological tolerances of coral holobionts, but little is known about the dynamics of these endosymbiotic populations on coral reefs. Sparse data indicate that Symbiodinium populations show limited spatial connectivity; however, no studies have investigated temporal dynamics for in hospite Symbiodinium populations following significant mortality and recruitment events in coral populations. We investigated the combined influences of spatial isolation and disturbance on the population dynamics of the generalist Symbiodinium type C2 (ITS1 rDNA) hosted by the scleractinian coral Acropora millepora in the central Great Barrier Reef. Using eight microsatellite markers, we genotyped Symbiodinium in a total of 401 coral colonies, which were sampled from seven sites across a 12-year period including during flood plume–induced coral bleaching. Genetic differentiation of Symbiodinium was greatest within sites, explaining 70–86% of the total genetic variation. An additional 9–27% of variation was explained by significant differentiation of populations among sites separated by 0.4–13 km, which is consistent with low levels of dispersal via water movement and historical disturbance regimes. Sampling year accounted for 6–7% of total genetic variation and was related to significant coral mortality following severe bleaching in 1998 and a cyclone in 2006. Only 3% of the total genetic variation was related to coral bleaching status, reflecting generally small (8%) reductions in allelic diversity within bleached corals. This reduction probably reflected a loss of genotypes in hospite during bleaching, although no site-wide changes in genetic diversity were observed. Combined, our results indicate the importance of disturbance regimes acting together with limited oceanographic transport to determine the genetic composition of Symbiodinium types within reefs.
Data from: Secondary contact and changes in coastal hydrology influence the nonequilibrium population structure of a salmonid (Oncorhynchus keta)
Numerous empirical studies have reported lack of migration–drift equilibrium in wild populations. Determining the causes of nonequilibrium population structure is challenging because different evolutionary processes acting at a variety of spatiotemporal scales can produce similar patterns. Studies of contemporary populations in northern latitudes suggest that nonequilibrium population structure is probably caused by recent colonization of the region after the last Pleistocene ice age ended ~13 000 years ago. The chum salmon's (Oncorhynchus keta) range was fragmented by dramatic environmental changes during the Pleistocene. We investigated the population structure of chum salmon on the North Alaska Peninsula (NAP) and, using both empirical data and simulations, evaluated the effects of colonization timing and founder population heterogeneity on patterns of genetic differentiation. We screened 161 single nucleotide polymorphisms and found evidence of nonequilibrium population structure when the slope of the isolation-by-distance relationship was examined at incremental spatial scales. In addition, simulations suggested that this pattern closely matched models of recent colonization of the NAP by secondary contact. Our results agree with geological and archaeological data indicating that the NAP was a dynamic landscape that may have been more recently colonized than during the last deglaciation because of dramatic changes in coastal hydrology over the last several thousand years.
Data from: Geographical parthenogenesis and population genetic structure in the alpine species Ranunculus kuepferi (Ranunculaceae)
Geographical parthenogenesis describes the enigmatic phenomenon that asexual organisms have larger distribution areas than their sexual relatives, especially in previously glaciated areas. Classical models suggest temporary advantages to asexuality in colonization scenarios because of uniparental reproduction and clonality. We analyzed population genetic structure and self-fertility of the plant species Ranunculus kuepferi on 59 populations from the whole distribution area (European Alps, Apennines and Corsica). Amplified fragment length polymorphisms (AFLPs) and five microsatellite loci revealed individual genotypes for all populations and mostly insignificant differences between diploid sexuals and tetraploid apomicts in all measures of genetic diversity. Low frequencies of private AFLP fragments/simple sequence repeat alleles, and character incompatibility analyses suggest that facultative recombination explains best the unexpectedly high genotypic diversity of apomicts. STRUCTURE analyses using AFLPs revealed a higher number of partitions and a stronger geographical subdivision for diploids than for tetraploids, which contradicts expectations of standard gene flow models, but indicates a reduction of genetic structure in asexuals. Apomictic populations exhibited high admixture near the sexual area, but appeared rather uniform in remote areas. Bagging experiments and analyses of pollen tube growth confirmed self-fertility for pollen-dependent apomicts, but self-sterility for diploid sexuals. Facultative apomixis combines advantages of both modes of reproduction: uniparental reproduction allows for rapid colonization of remote areas, whereas facultative sexuality and polyploidy maintains genetic diversity within apomictic populations. The density dependence of outcrossing limits range expansions of sexual populations.
Data from: Temporal population-genetic structure of eastern mosquitofish in a dynamic aquatic landscape
We analyzed the effect of periodic drying in the Florida Everglades on spatio-temporal population genetic structure of eastern mosquitofish (Gambusia holbrooki). Severe periodic drying events force individuals from disparate sources to mix in dry-season relatively deep-water refuges. In 1996 (a wet year) and 1999 (a dry year), we sampled mosquitofish at 20 dry-season refuges distributed in three water-management regions and characterized genetic variation for 10 allozyme and 3 microsatellite loci. In 1996, most of the ecosystem did not dry, while in 1999, many of our sampling locations were isolated by expanses of dried marsh surface. In 1996, most spatial genetic variation was attributed to heterogeneity within regions. In 1999, spatial genetic variation within regions was not significant. In both years, a small but significant amount of variation (less than 1% of the total variation) was partitioned among regions. Variance was consistently greater than zero among long-hydroperiod sites within a region, but not among short-hydroperiod sites within a region, where hydroperiod was measured as time since last marsh surface dry-down forcing fishes into local refuges. In 1996, all sites were in Hardy-Weinberg equilibrium. In 1999, we observed fewer heterozygotes than expected for most loci and sites suggesting a Wahlund effect arising from fish leaving areas that dried and mixing in deep-water refuges.
Data from: Low genetic diversity and strong population structure shaped by anthropogenic habitat fragmentation in a critically endangered primate, Trachypithecus leucocephalus
Habitat fragmentation may strongly impact population genetic structure and reduce the genetic diversity and viability of small and isolated populations. The white-headed langur (Trachypithecus leucocephalus) is a critically endangered primate species living in a highly fragmented and human-modified habitat in southern China. We examined the population genetic structure and genetic diversity of the species and investigated the environmental and anthropogenic factors that may have shaped its population structure. We used 214 unique multi-locus genotypes from 41 social groups across the main distribution area of T. leucocephalus, and found strong genetic structure and significant genetic differentiation among local populations. Our landscape genetic analyses using a causal modelling framework suggest that a large habitat gap and geographical distance represent the primary landscape elements shaping genetic structure, yet high levels of genetic differentiation also exist between patches separated by a small habitat gap or road. This is the first comprehensive study that has evaluated the population genetic structure and diversity of T. leucocephalus using nuclear markers. Our results indicate strong negative impacts of anthropogenic land modifications and habitat fragmentation on primate genetic connectivity between forest patches. Our analyses suggest that two management units of the species could be defined, and indicate that habitat continuity should be enforced and restored to reduce genetic isolation and enhance population viability.
Data from: Population structure in Atlantic cod in the eastern North Sea-Skagerrak-Kattegat: early life stage dispersal and adult migration
Background: In marine fish species, where pelagic egg and larvae drift with ocean currents, population structure has been suggested to be maintained by larval retention due to hydrographic structuring and by homing of adult fish to natal areas. Whilst natal homing of adults has been demonstrated for anadromous and coral reef fishes, there are few documented examples of philopatric migration in temperate marine fish species. Results: Here, we demonstrate temporally stable genetic differentiation among spawning populations of Atlantic cod (Gadus morhua L.), and present genetic and behavioural evidence for larval drift and philopatric migration in the eastern North Sea-Skagerrak-Kattegat area. We show that juvenile cod collected in the eastern Skagerrak and central Kattegat are genetically similar to cod from offshore spawning areas in the eastern North Sea. Genetic assignment of individual 2–5 year old fish indicates that cod residing at, or migrating towards, spawning areas in Kattegat and the North Sea display philopatric behaviours. Conclusions: Together these findings suggest a loop between spawning, larval drift and adult return-migrations to spawning areas and underlines that both oceanographic processes and migratory behaviour in the adult phase may be important for stock separation and integrity in marine temperate fishes such as Atlantic cod.
Data from: Fine-scale temperature associated genetic structure between inshore and offshore populations of sea scallop (Placopecten magellanicus)
In the northwest Atlantic Ocean, sea scallop (Placopecten magellanicus) have been characterized by a latitudinal genetic cline with a breakpoint between northern and southern genetic clusters occurring at ~45°N along eastern Nova Scotia, Canada. Using 96 diagnostic single nucleotide polymorphisms (SNPs) capable of discriminating between northern and southern clusters, we examined fine-scale genetic structure of scallops among 27 sample locations, spanning the largest geographic range evaluated in this species to date (~37-51°N). Here, we confirmed previous observations of northern and southern groups, but we show that the boundary between northern and southern clusters is not a discrete latitudinal break. Instead, at latitudes near the previously described boundary, we found unexpected patterns of fine-scale genetic structure occurring between inshore and offshore sites. Scallops from offshore sites, including St. Pierre Bank and the eastern Scotian Shelf, clustered with southern stocks, whereas inshore sites at similar latitudes clustered with northern stocks. Our analyses revealed significant genetic divergence across small spatial scales (i.e., 129 to 221 km distances), and that spatial structure over large and fine scales was strongly associated with temperature during seasonal periods of thermal minima. Clear temperature differences between inshore and offshore locations may explain the fine-scale structuring observed, such as why southern lineages of scallop occur at higher latitudes in deeper, warmer offshore waters. Our study supports growing evidence that fine-scale population structure in marine species is common, often environmentally associated, and that consideration of environmental and genomic data can significantly enhance the identification of marine diversity and management units.
Data from: Murky waters: searching for structure in genetically depauperate blue threadfin populations of Western Australia
The blue threadfin (Eleutheronema tetradactylum) is an exploited fishery species in southeast Asia and Australia. Demographic studies have revealed fine-scale stock structure throughout the Australian coastline, with demographically isolated populations separated by only tens of km. Similarly, population genetic analysis revealed fine-scale structure across most of its Australian range with important implications for fisheries management. However, in northern Western Australia, genetic stock structure analysis showed a contradictory lack of structure. In the present study, one mtDNA marker and a suite of five microsatellite loci were used to further investigate the stock structure of Western Australian blue threadfin populations. By increasing sample sizes from previously investigated areas: Roebuck Bay (n = 93 adults) and Eighty-mile Beach (n = 92 adults and 163 recruits from two settlement cohorts), we were able to detect subtle genetic differentiation that was previously obscured by low levels of genetic polymorphism. Therefore, the same fine-scale stock structure that has been observed elsewhere in this species also appears to exist in Western Australia. This has clear ramifications for a revised management strategy that incorporates the fine scale structuring of northwest Western Australian stocks of the blue threadfin.
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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.