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opencc-zeroApr 2021View details →

Historical translocations and stocking alter the genetic structure of a Mediterranean lobster fishery

Stocking is often used to supplement wild populations that are overexploited or have collapsed, yet it is unclear how this affects the genetic diversity of marine invertebrate populations. During the 1970s, a lobster stock enhancement programme was carried out around the island of Corsica in the Mediterranean using individuals translocated from the Atlantic coast of France. This included the release of thousands of hatchery-reared post-larval lobsters and several adult individuals, but no monitoring plan was established to assess whether these animals survived and recruited to the population. In this study, we sampled European lobster (Homarus gammarus) individuals caught around Corsica and tested whether they showed Atlantic ancestry. Due to a natural marked phylogeographic break between Atlantic and Mediterranean lobsters, we hypothesised that lobsters with dominant (>0.50) Atlantic ancestry were descended from historical stocking releases. Twenty Corsican lobsters were genotyped at 79 single nucleotide polymorphisms and assignment analysis showed that the majority (13) had dominant Atlantic ancestry. This suggests that the hatchery stocking programme carried out in Corsica during the 1970s, using individuals translocated from the Atlantic coast of France, has likely augmented local recruitment but at a cost of altering the genetic structure of the Corsican lobster population.

opencc-zeroDec 2015View details →

Data from: Comparative analysis indicates historical persistence and contrasting contemporary structure in sympatric woody perennials of semi-arid south-west Western Australia

We used a comparative approach to assess congruence of phylogeographic and genetic structure and diversity, demographic signals, and ratios of pollen to seed dispersal, in the context of species-specific life-history traits, for two widespread sympatric perennial plant species. We sampled Grevillea paradoxa and Melaleuca nematophylla across the species' ranges throughout the Transitional Rainfall Zone and extending slightly into the Arid Zone of south-west Western Australia. Both species exhibited range-wide phylogeographic and contemporary genetic structure. Moderate haplotype diversity centred in populations on Banded Ironstone Formation (BIF) outcrops and within the Murchison River gorge supports a hypothesis of historical persistence and evolution in these mesic refugia. These features are likely to play important roles in evolutionary persistence with ongoing climate change. There was little evidence of particularly complex demographic histories for the region. More limited haplotype diversity, as well as more limited nuclear genetic diversity and connectivity, in G. paradoxa was consistent with predictions from life-history traits of shorter lifespan, lower fecundity, more limited seed dispersal, and shorter plants, but inconsistent with a prediction of greater pollen dispersal by bird pollinators. Low pollen to seed dispersal ratios suggest seed dispersal plays a greater than expected role in maintaining connectivity in this semi-arid landscape. The study highlights a need for research that integrates aspects of seed ecology and seed and pollen dispersal as well as phylogeographic and genetic patterns in Gondwanan shrublands and other semi-arid landscapes globally.

opencc-zeroDec 2013View details →

Data from: Range-wide analysis of genetic structure in a widespread, highly mobile species (Odocoileus hemionus) reveals the importance of historical biogeography

Highly mobile species that thrive in a wide range of habitats are expected to show little genetic differentiation across their range. A limited but growing number of studies have revealed that patterns of broad-scale genetic differentiation can and do emerge in vagile, continuously distributed species. However, these patterns are complex and often shaped by both historical and ecological factors. Comprehensive surveys of genetic variation at a broad scale and at high resolution are useful for detecting cryptic spatial genetic structure, and for investigating the relative roles of historical and ecological processes in structuring widespread, highly mobile species. In this study, we analyzed 10 microsatellite loci from over 1,900 samples collected across the full range of mule deer (Odocoileus hemionus), one of the most widely distributed and abundant of all large mammal species in North America. Through both individual- and population-based analyses we found evidence for three main genetic lineages, one corresponding to the 'mule deer' morphological type and two to the 'black-tailed deer' type. Historical biogeographic events likely are the primary drivers of genetic divergence in this species; boundaries of the three lineages correspond well with predictions based on Pleistocene glacial cycles and substructure within each lineage demonstrates island vicariance. However, across large geographic areas, including the entire mule deer lineage, we found that genetic variation fit an isolation-by-distance pattern rather than discrete clusters. A lack of genetic structure across wide geographic areas of the continental west indicates that ecological processes have not resulted in restrictions to gene flow sufficient for spatial genetic structure to emerge. Our results have important implications for our understanding of evolutionary mechanisms of divergence, as well as for taxonomy, conservation, and management.

opencc-zeroDec 2013View details →

Data from: Genetic structure of populations of whale sharks among ocean basins and evidence for their historic rise and recent decline

This study presents genetic evidence that whale sharks, Rhincodon typus, are comprised of at least two populations that rarely mix and is the first to document a population expansion. Relatively high genetic structure is found when comparing sharks from the Gulf of Mexico with sharks from the Indo-Pacific. If mixing occurs between the Indian and Atlantic Oceans, it is not sufficient to counter genetic drift. This suggests whale sharks are not all part of a single global meta-population. The significant population expansion we found was indicated by both microsatellite and mitochondrial DNA. The expansion likely happened during the Holocene, when tropical species could expand their range due to sea level rise eliminating dispersal barriers. However, the historic trend of population increase may have reversed recently. Declines in genetic diversity are found for 6 consecutive years at Ningaloo Reef in Australia. The declines in genetic diversity being seen now are likely due to commercial-scale harvesting of whale sharks and collision with boats in past decades in other countries in the Indo-Pacific. Whale shark hunting is banned in Australia but continues in other countries despite bans in places like China. The study findings have implications for models of population connectivity for whale sharks and advocate for continued focus on effective protection of the world's largest fish at multiple spatial scales.

opencc-zeroDec 2012View details →

Data from: The influence of contemporary and historic landscape features on the genetic structure of the sand dune endemic, Cirsium pitcheri (Asteraceae)

Narrow endemics are at risk from climate change due to their restricted habitat preferences, lower colonization ability and dispersal distances. Landscape genetics combines new tools and analyses that allow us to test how both past and present landscape features have facilitated or hindered previous range expansion and local migration patterns, and thereby identifying potential limitations to future range shifts. We have compared current and historic habitat corridors in Cirsium pitcheri, an endemic of the linear dune ecosystem of the Great Lakes, to determine the relative contributions of contemporary migration and post-glacial range expansion on genetic structure. We used seven microsatellite loci to characterize the genetic structure for 24 populations of Cirsium pitcheri, spanning the center to periphery of the range. We tested genetic distance against different measures of geographic distance and landscape permeability, based on contemporary and historic landscape features. We found moderate genetic structure (ave Fst =0.14), and a north -south pattern to the distribution of genetic diversity and inbreeding, with northern populations having the highest diversity and lowest levels of inbreeding. High allelic diversity, small average pairwise distances and mixed genetic clusters identified in Structure suggest populations in the center of the range represent the point of entry to the Lake Michigan and a refugia of diversity for this species. A strong association between genetic distances and lake level changes suggests that historic lake fluctuations best explain the broad geographic patterns, and sandy habitat best explain local patterns or movement.

opennotspecifiedDec 2003View details →

FIGURES 2027. Crozetia larval structures. 20 in Crozetia Davies (Diptera: Simuliidae): redescription of Cr. crozetensis, Cr. seguyi, number of larval instars, phylogenetic relationships and historical biogeography

FIGURES 2027. Crozetia larval structures. 20. Cr. crozetensis, LM of last instar larval hypostoma. Scale bar = 0.1 mm. 21. Cr. seguyi, SEM of last instar larval hypostoma. Image foreshortened see Fig 23. Scale bar = 0.05 mm. 22. Cr. crozetensis, LM of last instar larval hypostoma and postgenal cleft. Scale bar = 0.1 mm. 23. Cr. seguyi, LM of last instar larval hypostoma and postgenal cleft. Scale bar = 0.1 mm. 24. Cr. crozetensis, LM of abdomen, last instar larvae. Scale bar = 1.0 mm. 25. Cr. seguyi, LM of abdomen, last instar larvae. Scale bar = 1.0 mm. 26. Cr. crozetensis, last instar, anal sclerites. Scale bar = 0.1 mm. 27. Cr. seguyi, last instar, anal sclerites. Scale bar = 0.1 mm.

opencc-byJul 2022View details →

Historical stone masonry road structure

These structures seem to be frequently built next to roads Source: Objaverse 1.0 / Sketchfab

FIGURE 6 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features

FIGURE 6. Species Distribution Model (SDM) of D. ensatus based on museum records. Increased shading towards green represents increasing suitable habitat.

FIGURE 2 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features

FIGURE 2. Relationships between Dicamptodon ensatus populations and distribution of those lineages along the coast of the California region. Major mtDNA lineages are color coded and branch lengths are proportional. Support values on branches follow the format (coalescent analysis�posterior probability / Bayesian inference analysis posterior probability / bootstrap proportions maximum-likelihood analysis). The tree is a consensus gene tree from the coalescent analysis with deeper weakly supported relationships collapsed. The color bar represents nuclear genotype groups. Geographic range denoted by green shading. Stars on map denote likely ancestral haplotype regions as determined by the BPEC analysis. The approximate region of the former Wilson Grove embayment is overlaid onto the map in transparent blue.

FIGURE 1 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features

FIGURE 1. Range map from the IUCN Red List in transparent green with sampling localities from this study marked.

FIGURE 5 in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features

FIGURE 5. Isolation by distance plot. P value calculated by Mantel test. (y = 0.00292 x + 0.07696, r2 = 0.809, P = 0.007).

FIGURE 3. a in Phylogeography and Genetic Structure in the California Giant Salamander (Dicamptodon ensatus): Impacts of current and historic landscape features

FIGURE 3. a) mtDNA TCS haplotype network of the control region. b) nuDNA haplotype TCS network of E16C7. Colors of clusters are coded to match the coalescent tree clade branches. Circle size is proportional to haplotype occurrence and numbers refer to occurrence sampled if greater then one.

opencc-zeroDec 2018View details →

Data from: The influence of historical dispersal on the phylogenetic structure of tree communities in the tropical Andes

We test for evidence of the Tropical Niche Conservatism or the Out of The Tropics hypotheses in structuring patterns of tree community composition along a 2000+ meter elevational gradient in the northern tropical Andes. By collecting and integrating data on the presence-absence of tree species within plots with phylogenetic information, we analyzed: 1) patterns of phylogenetic dispersion and species diversity along the elevational gradient based on indexes of net relatedness, nearest taxon relatedness, and species richness (α-diversity); and 2) the replacement of lineages along the gradient using the PhyloSorensen metric (β-diversity). More specifically, we established 20 0.25-ha permanent tree inventory plots between 750 and 2802 m asl where all individuals with Diameter at Breast Height (DBH) ≥ 10 cm were measured and identified. We then used a series of linear models to test for changes in α and β diversity between plots in relation to elevation. Neither the net relatedness index nor the nearest taxon index showed a significant relationship with elevation. However, there was greater phylogenetic over-dispersion at intermediate elevations; this likely reflects the mixing of species with contrasting origins from tropical and temperate lineages. β-diversity between plots was negatively related to the corresponding difference in elevation, indicating that closely related lineages occupy similar ranges of elevation and temperature. We conclude that the immigration of lineages from extra-tropical regions have significant effects in determining the phylogenetic structure of tree communities in tropical Andean forests.

opencc-zeroAug 2022View details →

Raw data and alignments for: Application of palaeogenetic techniques to historic mollusc shells reveals phylogeographic structure in a New Zealand abalone

Natural history collections worldwide contain a plethora of mollusc shells. Recent studies have detailed the sequencing of DNA extracted from shells up to thousands of years old and from various taphonomic and preservational contexts. However, previous approaches have largely addressed methodological rather than evolutionary research questions. Here we report the generation of DNA sequence data from mollusc shells using such techniques, applied to Haliotis virginea Gmelin, 1791, a New Zealand abalone, in which morphological variation has led to the recognition of several forms and subspecies. We successfully recovered near-complete mitogenomes from 22 specimens including 12 dry-preserved shells up to 60 years old. We used a combination of palaeogenetic techniques that have not previously been applied to shell, including DNA extraction optimized for ultra-short fragments and hybridization-capture of single-stranded DNA libraries. Phylogenetic analyses revealed three major, well-supported clades comprising samples from: 1) the Three Kings Islands; 2) the Auckland, Chatham and Antipodes Islands; and 3) mainland New Zealand and Campbell Island. This phylogeographic structure does not correspond to the currently recognized forms. Critically, our non-reliance on freshly collected or ethanol-preserved samples enabled inclusion of topotypes of all recognized subspecies as well as additional difficult-to-sample populations. Broader application of these comparatively cost-effective and reliable methods to modern, historical, archaeological and palaeontological shell samples has the potential to revolutionize invertebrate genetic research.

opennotspecifiedJan 2017View details →

Fig. 1 Mitochondrial genome structure and genes variability. a in Historical biogeography and mitogenomics of two endemic Mediterranean gorgonians (Holaxonia, Plexauridae)

Fig. 1 Mitochondrial genome structure and genes variability. a Mitogenomes of Paramuricea clavata and Paramuricea macrospina with genome size and gene annotation. GC-content and AT-content are shown in blue and green on the inner and outer surface of the ring, respectively. b Sliding window analysis of the complete mitochondrial genomes of P. clavata and P. macrospina. The black line indicates

opencc-zeroDec 2015View details →

Data from: Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

Understanding the causes of population decline is crucial for conservation management. We therefore used genetic analysis both to provide baseline data on population structure and to evaluate hypotheses for the catastrophic decline of the South American sea lion (Otaria flavescens) at the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259 animals from 23 colonies across the Falklands at 281 bp of the mitochondrial hypervariable region and 22 microsatellites. A weak signature of population structure was detected, genetic diversity was moderately high in comparison with other pinniped species, and no evidence was found for the decline being associated with a strong demographic bottleneck. By combining our mitochondrial data with published sequences from Argentina, Brazil, Chile and Peru, we also uncovered strong maternally directed population structure across the geographical range of the species. In particular, very few shared haplotypes were found between the Falklands and South America, and this was reflected in correspondingly low migration rate estimates. These findings do not support the prominent hypothesis that the decline was caused by migration to Argentina, where large-scale commercial harvesting operations claimed over half a million animals. Thus, our study not only provides baseline data for conservation management but also reveals the potential for genetic studies to shed light upon long-standing questions pertaining to the history and fate of natural populations.

opencc-zeroDec 2011View details →

Data from: The interplay of dispersal limitation, rivers, and historical events shapes the genetic structure of an Amazonian frog

Disentangling the impact of landscape features such as rivers and historical events on dispersal is a challenging but necessary task to gain a comprehensive picture of the evolution of diverse biota such as that found in Amazonia. Adenomera andreae, a small, territorial, terrestrial frog species of the Amazonian forest represents a good model for such studies. We combined Cytochrome b sequences with 12 microsatellites to investigate the genetic structure at two contrasted spatial scales in French Guiana: along a ~6 km transect to evaluate dispersal ability and between paired bank populations along a ~65 km stretch of the Approuague river to test the effect of rivers as barriers to dispersal. We observed significant spatial genetic structure between individuals at a remarkably small geographical scale and conclude that the species has a restricted dispersal ability likely tied to its life history traits. Mitochondrial and microsatellite data also indicate a high level of differentiation among populations on opposite banks of the river and, in some cases, among populations on the same riverbank. These results suggest that the observed population structure in A. andreae is due to restricted dispersal abilities combined with the action of rivers and Quaternary population isolation. Given that Amazonia hosts a great portion of anurans, as well as other small vertebrates, that display life history traits comparable to Adenomera andreae, we argue that our analyses provide new insights into the complex interactions among evolutionary processes shaping Amazonian biodiversity.