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29 results for “Panmixia”
Data from: Demographic expansion and panmixia in a St. Martin endemic, Anolis pogus, coincides with the decline of a competitor
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Panmixia across elevation in thermally sensitive Andean dung beetles
Janzen's seasonality hypothesis predicts that organisms inhabiting environments with limited climatic variability will evolve a reduced thermal tolerance breadth compared with organisms experiencing greater climatic variability. In turn, narrow tolerance breadth may select against dispersal across strong temperature gradients, such as those found across elevation. This can result in narrow elevational ranges and generate a pattern of isolation-by-environment, or neutral genetic differentiation correlated with environmental variables that is independent of geographic distance. We tested for signatures of isolation-by-environment across elevation using genome-wide SNP data from five species of Andean dung beetles (subfamily Scarabaeinae) with well-characterized, narrow thermal physiologies and narrow elevational distributions. Contrary to our expectations, we found no evidence of population genetic structure associated with elevation and little signal of isolation-by-environment. Further, elevational ranges for four of five species appear to be at equilibrium and show no evidence of demographic constraints at range limits. Taken together, these results suggest physiological constraints on dispersal may primarily operate outside of a stable realized niche, and point to a lower bound on the spatial scale of local adaptation.
Data from: Genomic evidence for panmixia of eastern and western North American migratory monarch butterflies
Monarch butterflies are known for their spectacular annual migration in eastern North America, with millions of monarchs flying up to 4,500 kilometers to overwintering sites in central Mexico. Monarchs also live west of the Rocky Mountains, where they travel shorter distances to overwinter along the Pacific Coast. Monarch numbers have recently dwindled, and monarch migration may be on the brink of extinction. It is often assumed that eastern and western monarchs form distinct evolutionary units that require specific protection, but genomic studies to support this notion are lacking. We used a tethered flight mill to show that migratory eastern monarchs have greater flight performance than western monarchs. However, analyzing more than 20 million SNPs in 43 monarch genomes, we found no evidence for genomic differentiation between eastern and western monarchs, suggesting the existence of one panmictic migratory population. Our genomic analysis also showed identical and low levels of genetic diversity, and a lack of singleton alleles, indicating a shared history of decline of eastern and western monarchs. Gene expression analysis of a subset of candidate genes during active flight revealed differential gene expression related to non-muscular motor activity. Our results demonstrate that North American monarchs form one panmictic and declining population, and that differences in migration distance and destination are therefore likely driven by environmentally induced differential gene expression. Our study indicates that eastern and western monarchs do not form distinct genetic populations, suggesting that preservation of eastern monarchs could potentially rescue western migration and vice versa.
Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers
<p>Dataset for the paper named "Panmixia and active colonisation of the invasive palm Trachycarpus fortunei (Arecaceae) in Southern Switzerland and Northern Italy as inferred by microsatellites and SNP markers"</p> <p>GBS analysis:</p> <p>- variants.vcf.gz : compressed non filtered VCF file with 208 samples and 73685 markers on 36195 loci</p> <p>- variants.filt.vcf.gz: Filtered Variant call file (compressed) - Samples with > 50% missing genotypes, and variants with genotype calls in less than 80% of samples are removed; variants with maf < 1% are removed -207 samples and 31312 markers on 19301 loci - 1 samples removed 6CL</p> <p>Microsatellites:</p> <p>TFT.fortunei_Microsatellites_FSTATFINAL_Pop.dat</p> <p>Samples file</p> <p>-Trachycarpus_Samples_sheet.xlsx : list of samples used (lab extractions) </p> <p> </p> <p> </p>
Panmixia across elevation in thermally sensitive Andean dung beetles
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Data from: Genomic evidence for panmixia of eastern and western North American migratory monarch butterflies
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Data from: Large-scale genetic panmixia in the blue shark (Prionace glauca): a single worldwide population, or a genetic lag-time effect of the "grey zone" of differentiation?
The blue shark Prionace glauca, among the most common and widely studied pelagic sharks, is a top predator, exhibiting the widest distribution range. However, little is known about its population structure and spatial dynamics. With an estimated removal of 10 to 20 million individuals per year by fisheries, the species is classified as "Near Threatened" by International Union for Conservation of Nature. We lack the knowledge to forecast the long-term consequences of such a huge removal on this top predator itself and on its trophic network. The genetic analysis of more than 200 samples collected at broad scale (from Mediterranean Sea, North Atlantic and Pacific Oceans) using mtDNA and nine microsatellite markers allowed to detect signatures of genetic bottlenecks but a nearly complete genetic homogeneity across the entire studied range. This apparent panmixia could be explained by a genetic lag-time effect illustrated by simulations of demographic changes that were not detectable through standard genetic analysis before a long transitional phase here introduced as the "population grey zone". The results presented here can thus encompass distinct explanatory scenarios spanning from a single demographic population to several independent populations. This limitation prevents the genetic-based delineation of stocks and thus the ability to anticipate the consequences of severe depletions at all scales. More information is required for the conservation of population(s) and managements of stocks, which may be provided by large scale sampling not only of individuals worldwide, but also of loci genome-wide.
Data from: Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species
Phylogeographical studies have shown that some shallow-water marine organisms, such as certain coral reef fishes, lack spatial population structure at oceanic scales, despite vast distances of pelagic habitat between reefs and other dispersal barriers. However, whether these dispersive widespread taxa constitute long-term panmictic populations across their species ranges remains unknown. Conventional phylogeographical inferences frequently fail to distinguish between long-term panmixia and metapopulations connected by gene flow. Moreover, marine organisms have notoriously large effective population sizes that confound population structure detection. Therefore, at what spatial scale marine populations experience independent evolutionary trajectories and ultimately species divergence is still unclear. Here, we present a phylogeographical study of a cosmopolitan Indo-Pacific coral reef fish Naso hexacanthus and its sister species Naso caesius, using two mtDNA and two nDNA markers. The purpose of this study was two-fold: first, to test for broad-scale panmixia in N. hexacanthus by fitting the data to various phylogeographical models within a Bayesian statistical framework, and second, to explore patterns of genetic divergence between the two broadly sympatric species. We report that N. hexacanthus shows little population structure across the Indo-Pacific and a range-wide, long-term panmictic population model best fit the data. Hence, this species presently comprises a single evolutionary unit across much of the tropical Indian and Pacific Oceans. Naso hexacanthus and N. caesius were not reciprocally monophyletic in the mtDNA markers but showed varying degrees of population level divergence in the two nuclear introns. Overall, patterns are consistent with secondary introgression following a period of isolation, which may be attributed to oceanographic conditions of the mid to late Pleistocene, when these two species appear to have diverged.
Data from: Maintaining genetic diversity and population panmixia through dispersal and not gene flow in a holocyclic heteroecious aphid species
Heteroecious holocyclic aphids exhibit both sexual and asexual reproduction and alternate among primary and secondary hosts. Most of these aphids can feed on several related hosts, and invasions to new habitats may limit the number of suitable hosts. For example, the aphid specialist Aphis glycines survives only on the primary host buckthorn (Rhamnus spp.) and the secondary host soybean (Glycine max) in North America where it is invasive. Owing to this specialization and sparse primary host distribution, host colonization events could be localized and involve founder effects, impacting genetic diversity, population structure and adaptation. We characterized changes in the genetic diversity and structure across time among A. glycines populations. Populations were sampled from secondary hosts twice in the same geographical location: once after secondary colonization (early season), and again immediately before primary host colonization (late season). We tested for evidence of founder effects and genetic isolation in early season populations, and whether or not late-season dispersal restored genetic diversity and reduced fragmentation. A total of 24 single-nucleotide polymorphisms and 6 microsatellites were used for population genetic statistics. We found significantly lower levels of genotypic diversity and more genetic isolation among early season collections, indicating secondary host colonization occurred locally and involved founder effects. Pairwise FST decreased from 0.046 to 0.017 in early and late collections, respectively, and while genetic relatedness significantly decreased with geographical distance in early season collections, no spatial structure was observed in late-season collections. Thus, late-season dispersal counteracts the secondary host colonization through homogenization and increases genetic diversity before primary host colonization.
Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water
Antarctic krill (Euphausia superba; hereafter krill) are an incredibly abundant pelagic crustacean which has a wide, but patchy, distribution in the Southern Ocean. Several studies have examined the potential for population genetic structuring in krill, but DNA-based analyses have focused on a limited number of markers and have covered only part of their circum-Antarctic range. We used mitochondrial DNA and restriction site-associated DNA sequencing (RAD-seq) to investigate genetic differences between krill from five sites, including two from East Antarctica. Our mtDNA results show no discernible genetic structuring between sites separated by thousands of kilometres, which is consistent with previous studies. Using standard RAD-seq methodology, we obtained over a billion sequences from >140 krill, and thousands of variable nucleotides were identified at hundreds of loci. However, downstream analysis found that markers with sufficient coverage were primarily from multicopy genomic regions. Careful examination of these data highlights the complexity of the RAD-seq approach in organisms with very large genomes. To characterize the multicopy markers, we recorded sequence counts from variable nucleotide sites rather than the derived genotypes; we also examined a small number of manually curated genotypes. Although these analyses effectively fingerprinted individuals, and uncovered a minor laboratory batch effect, no population structuring was observed. Overall, our results are consistent with panmixia of krill throughout their distribution. This result may indicate ongoing gene flow. However, krill's enormous population size creates substantial panmictic inertia, so genetic differentiation may not occur on an ecologically relevant timescale even if demographically separate populations exist.
Data from: Restriction to large-scale gene flow versus regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae)
The history of colonization and dispersal in fauna distributed among deep-sea chemosynthetic ecosystems remains enigmatic and poorly understood because of an inability to mark and track individuals. A combination of molecular, morphological and environmental data improves understanding of spatial and temporal scales at which panmixia, disruption of gene flow or even speciation may occur. Vestimentiferan tubeworms of the genus Escarpia are important components of deep -sea cold seep ecosystems, as they provide long-term habitat for many other taxa. Three species of Escarpia, Escarpia spicata [Gulf of California (GoC)], Escarpia laminata [Gulf of Mexico (GoM)] and Escarpia southwardae (West African Cold Seeps), have been described based on morphology, but are not discriminated through the use of mitochondrial markers (cytochrome oxidase subunit 1; large ribosomal subunit rDNA, 16S; cytochrome b). Here, we also sequenced the exon-primed intron-crossing Haemoglobin subunit B2 intron and genotyped 28 microsatellites to (i) determine the level of genetic differentiation, if any, among the three geographically separated entities and (ii) identify possible population structure at the regional scale within the GoM and West Africa. Results at the global scale support the occurrence of three genetically distinct groups. At the regional scale among eight sampling sites of E. laminata (n = 129) and among three sampling sites of E. southwardae (n = 80), no population structure was detected. These findings suggest that despite the patchiness and isolation of seep habitats, connectivity is high on regional scales.
Data from: Beyond the Coral Triangle: high genetic diversity and near panmixia in Singapore's populations of the broadcast spawning sea star Protoreaster nodosus
The Coral Triangle is widely considered the most important centre of marine biodiversity in Asia while areas on its periphery such as the South China Sea, have received much less interest. Here, we demonstrate that a small population of the knobbly sea star Protoreaster nodosus in Singapore has similarly high levels of genetic diversity as comparable Indonesian populations from the Coral Triangle. The high genetic diversity of this population is remarkable because it is maintained despite decades of continued anthropogenic disturbance. We postulate that it is probably due to broadcast spawning which is likely to maintain high levels of population connectivity. To test this, we analysed 6140 genome-wide single nucleotide polymorphism (SNP) loci for Singapore's populations and demonstrate a pattern of near panmixia. We here document a second case of high genetic diversity and low genetic structure for a broadcast spawner in Singapore, which suggests that such species have high resilience against anthropogenic disturbances. The study demonstrates the feasibility and power of using genome-wide SNPs for connectivity studies of marine invertebrates without a sequenced genome.
Data from: Antarctic krill population genomics: apparent panmixia, but genome complexity and large population size muddies the water
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Data from: Maintaining genetic diversity and population panmixia through dispersal and not gene flow in a holocyclic heteroecious aphid species
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Data from: Panmixia supports divergence with gene flow in Darwin’s small ground finch, Geospiza fuliginosa, on Santa Cruz, Galápagos Islands
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Data from: Restriction to large-scale gene flow versus regional panmixia among cold seep Escarpia spp. (Polychaeta, Siboglinidae)
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Data from: Panmixia and limited interspecific introgression in coyotes (Canis latrans) from West Virginia and Virginia, USA
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Data from: All roads lead to home: panmixia of European eel in the Sargasso Sea
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Data from: Long-term panmixia in a cosmopolitan Indo-Pacific coral reef fish and a nebulous genetic boundary with its broadly sympatric sister species
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Data from: Panmixia in a critically endangered fish: the totoaba (Totoaba macdonaldi) in the Gulf of California
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