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48 results for “post-glacial”
Seismic profiles, diatom and microfossil assemblages, and radiocarbon ages for constructing a post-glacial sea level curve from Fiordland, New Zealand
Two research cruises (12PL027 and 13PL018) were conducted aboard the University of Otago RV Polaris II in 2012 and 2013 to collect marine sediment cores and 2d seismic data as part of a collaborative research effort to study late-Pleistocene and Holocene environmental change in New Zealand. Data includes 4 Boomer seismic profiles, 4 CHIRP seismic profiles, seismic line GPS tracks, diatom assemblages (raw counts and relative abundances) and microfossil assemblages (raw counts and relative abundances), and radiocarbon ages from 4 marine sediment cores. The data used to construct a post-glacial sea level curve for Fiordland, New Zealand are also included, as well as data from published literature plotted for global comparisons. These data accompany the publication: Dlabola. E.K., Wilson, G.S., Gorman, A.R., Riesselman, C.R., and Moy, C.M. 2015. A post-glacial sea-level curve from Fiordland, New Zealand. Global and Planetary Change, 131, 101-114. https://doi.org/10.1016/j.gloplacha.2015.05.010
Data from: Differential patterns of floristic phylogenetic diversity across a post-glacial landscape
<p>Abstract: Aim: In this study, we explored spatial patterns of phylogenetic diversity and endemism in the flora of Norway and tested hypothesized post-glacial environmental drivers of phylogenetic diversity, including temperature, precipitation, edaphic factors, and time since glacial retreat.<br> <br> Location: Norway.<br> <br> Taxon: Vascular plants (Trachaeophyta).<br> <br> Methods: We produced a multi-locus Maximum Likelihood (ML) phylogeny using a combination of newly produced DNA sequences from herbarium specimens and sequences available from public repositories. We combined the phylogeny with species occurrence data to estimate phylogenetic diversity and phylogenetic endemism across Norway, using a spatial randomization to judge statistical significance. We used multiple-model inference to identify environmental variables that contributed the most to the patterns of phylogenetic diversity. Finally, we estimated phylogenetic turnover and used this to identify Norwegian plant assemblages in terms of composition and evolutionary history.<br> <br> Results: Our ML phylogeny contained 87% of all currently described native Norwegian vascular plants. Assemblages were phylogenetically overdispersed in warmer and wetter regions of Norway, as well as in regions with a longer post-glacial history. In cold and dry regions, plant assemblages were phylogenetically clustered, and characterised by neo-endemism, while the mild and wet regions were characterised by both paleo- and neo-endemism. Phylogenetic diversity was positively correlated with summer temperature and habitat heterogeneity, and peaked in the southeast of Norway.<br> <br> Main conclusions: Both contemporary ecological factors (climate and habitat heterogeneity), and post-glacial history seem to have shaped the phylogenetic structure of the flora of Norway. The flora in the far north of Norway appear to be a result of recent diversification while the coastal regions are assemblages of deeper lineages. Our results suggest that there is an evolutionary signal in the distribution of the Norwegian vascular flora.</p>
Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe
Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense using various mitochondrial DNA markers on modern and/or ancient specimens. This tends to confound the identification of refugial areas and post-glacial colonization patterns in this group. In this study we used Genotyping-by-Sequencing (GBS) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), in Europe by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g. Iberia) and sources of post-glacial re-expansion (e.g. Carpathians and Balkans) across northern regions of the continent. In addition, we tested multiple post-glacial re-colonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach. We identified the role of ancient and temporary land-bridges in the colonization of Scandinavia and the British Isles, with a natural colonization of Ireland deemed more likely than an ancient human-mediated introduction as has previously been proposed. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not always evident from using more limited marker sets.
Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus)
Cycles of glacial expansion and contraction throughout the Pleistocene drove increases and decreases, respectively, in the geographical range and population size of many animal species. Genetic data have revealed that during glacial maxima the distribution of many Eurasian animals was restricted to small refugial areas, from which species expanded to reoccupy parts of their former range as the climate warmed. It has been suggested that the extinct eastern moa (Emeus crassus)—a large, flightless bird from New Zealand—behaved analogously during glacial maxima, possibly surviving only in a restricted area of lowland habitat in the southern South Island of New Zealand during the Last Glacial Maximum (LGM). However, previous studies have lacked the power and geographic sampling to explicitly test this hypothesis using genetic data. Here we analyse 46 ancient mitochondrial genomes from Late Pleistocene and Holocene bones of the eastern moa from across their post-LGM distribution. Our results are consistent with a post-LGM increase in the population size and genetic diversity of eastern moa. We also demonstrate that genetic diversity was higher in eastern moa from the southern extent of their range, supporting the hypothesis that they expanded from a single glacial refugium following the LGM.
Post-glacial colonization of the Fennoscandian coast by a plant parasitic insect with an unusual life history
<p><span>Species that exhibit very peculiar ecological traits combined with limited dispersal ability pose a challenge to our understanding of ecological and evolutionary mechanisms. This is especially true when they have managed to spread over long distances, overcome physical barriers and colonise large areas. Climate and landscape changes, trophic web relations as well as life history all interact to shape migration routes and present-day species distributions and their population genetic structures. Here we analysed the post-glacial colonization of northern Europe by the gall midge <em>Contarinia</em> <em>vincetoxici</em>, which is a monophagous parasite on the perennial herb White swallowwort (<em>Vincetoxicum</em> <em>hirundinaria</em>). This insect not only has a narrow feeding niche but also limited dispersal ability and an exceptionally long dormancy. Gall midge larvae (n = 329) were collected from 16 sites along its distribution range in Denmark, Sweden, and Finland. Using microsatellite loci and knowledge of the species and the regions' history, we investigated the role of landscape change, host plant distribution, insect population dynamics, and life history in shaping the population genetic structure of the insect. We devoted particular interest to the role of the insect's presumed poor dispersal capacity in combination with its exceptionally extended diapause. We found significant levels of local inbreeding (95% highest posterior density interval = 0.42–0.47), low level within-population heterozygosity (mean HE = 0.45, range 0.20–0.61) with private alleles in all populations except two. We also found significant (p < 0.001) regional isolation-by-distance patterns, suggesting regularly recurring mainly short-distance dispersal. According to approximate Bayesian computations, <em>C. vincetoxici</em> appears to have colonized the study area via wind-aided flights from remote areas approximately 4600 to 700 years before present when the land has gradually risen above the sea level. Extremely long dormancy periods have allowed the species to "disperse in time", thereby aiding population persistence despite generally low census population sizes.</span></p>
Post-glacial colonization of the Fennoscandian coast by a plant parasitic insect with an unusual life history
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Data from: High dispersal ability versus migratory traditions: Fine-scale population structure and post-glacial colonization in bar-tailed godwits
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Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe
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Data from: Which ecological factors influence the level of intraspecific diversity within post-glacial fishes? A case study using Coregonus and Salvelinus
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Genetic evidence for post-glacial expansion from a southern refugium in the eastern moa (Emeus crassus)
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Data from: The influence of post-glacial migration and hybridization on the gene pool of marginal Quercus pubescens populations in Central Europe
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Data from: The limited legacy of post-glacial recolonization in the floristic patterns of the European Alps
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Data from: Geography best explains global patterns of genetic diversity and post-glacial co-expansion in marine turtles
For many species, climate oscillations drove cycles of population contraction during cool glacial periods followed by expansion during interglacials. Some groups, however, show evidence of uniform and synchronous expansion while others display differences in the timing and extent of demographic change. We compared demographic histories inferred from genetic data across marine turtle species to identify responses to post-glacial warming shared across taxa and to examine drivers of past demographic change at the global scale. Using coalescent simulations and approximate Bayesian computation (ABC), we estimated demographic parameters, including the likelihood of past population expansion, from a mitochondrial dataset encompassing 23 previously identified lineages from all 7 marine turtle species. For lineages with a high posterior probability of expansion, we conducted a hierarchical ABC analysis to estimate the proportion of lineages expanding synchronously and the timing of synchronous expansion. We used Bayesian Model Averaging to identify variables associated with expansion and genetic diversity. Approximately 60% of extant marine turtle lineages showed evidence of expansion, with the rest mainly exhibiting patterns of genetic diversity most consistent with population stability. For lineages showing expansion, there was a strong signal of synchronous expansion after the Last Glacial Maximum. Expansion and genetic diversity were best explained by ocean basin and the degree of endemism for a given lineage. Geographic differences in sensitivity to climate change have implications for prioritizing conservation actions in marine turtles as well as for identifying areas of past demographic stability and potential resilience to future climate change for broadly distributed taxa.
Data from: Sea-level driven glacial-age refugia and post-glacial mixing on subtropical coasts, a palaeohabitat and genetic study
Using a novel combination of palaeohabitat modelling and genetic mixture analyses, we identify and assess a sea-level-driven recolonization process following the Last Glacial Maximum (LGM). Our palaeohabitat modelling reveals dramatic changes in estuarine habitat distribution along the coast of California (USA) and Baja California (Mexico). At the LGM (approx. 20 kya), when sea level was approximately 130 m lower, the palaeo-shoreline was too steep for tidal estuarine habitat formation, eliminating this habitat type from regions where it is currently most abundant, and limiting such estuaries to a northern and a southern refugium separated by 1000 km. We assess the recolonization of estuaries formed during post-LGM sea-level rise through examination of refugium-associated alleles and approximate Bayesian computation in three species of estuarine fishes. Results reveal sourcing of modern populations from both refugia, which admix in the newly formed habitat between the refuges. We infer a dramatic peak in habitat area between 15 and 10 kya with subsequent decline. Overall, this approach revealed a previously undocumented dynamic and integrated relationship between sea-level change, coastal processes and population genetics. These results extend glacial refugial dynamics to unglaciated subtropical coasts and have significant implications for biotic response to predicted sea-level rise.
Data from: Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring and autumn-spawners confined to early post-glacial arrival
Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.
Data from: Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish
Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of 'redfish' occurring in the North Atlantic – which is known for a widely distributed 'shallow-pelagic' oceanic type inhabiting waters between 250 and 550 m, and a more localized 'deep-pelagic' population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an 'hourglass' to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.
Data from: Post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus): genetic evidence of multiple northern refugia and hybridization between glacial lineages
Aims: We investigated post-glacial recolonization of the North American Arctic by Arctic char (Salvelinus alpinus) and examined potential hybridization between different glacial lineages upon secondary contact. Location: North American Arctic and adjacent areas. Methods: We collected mtDNA sequence data from 1355 individuals from 110 sampling locations and data from nine microsatellite loci from 931 individuals from 37 locations. We assessed the phylogenetic relationships and geographical distribution of mtDNA haplotypes and conducted historical demographic analyses. We used a Bayesian clustering analysis method to detect potential hybridization between glacial lineages. Results: Two highly divergent mtDNA lineages were identified in the Arctic region with distinct but overlapping geographic distributions: one in Beringia and the other over the entire Arctic Archipelago and coastal mainland east of Alaska. The microsatellite data also implied the existence of these two lineages. Evidence of hybridization was detected between the Arctic lineage and an Atlantic lineage in eastern North America. Main conclusions: Our data suggested survival and recolonization from two northern glacial refugia: one in Beringia and another in a smaller refugium, perhaps in the Arctic Archipelago itself or a separate refugium within Beringia. Patterns of hybridization detected supported the presence of a secondary contact zone between glacial lineages in the eastern Canadian Arctic.
Traversing the Great Lakes: Post-glacial colonization by a widespread terrestrial salamander
<p><strong>Aims:</strong> Glacial retreat at the end of the Pleistocene epoch opened vast expanses of emergent habitat in the northern hemisphere that were colonized by opportunistic taxa. However, species that undergo post-glacial expansion may have originated from one or several glacial refugia. We inferred the post-glacial expansion history of the Eastern Red-backed Salamander (<em>Plethodon cinereus</em>), a fully terrestrial species with a vast distribution despite severe dispersal limitations. Previous studies indicated populations south of the glacial boundary at the eastern and western limits of the distribution were closely related, suggesting either multiple refugia or an extraordinary post-glacial expansion event.</p> <p><strong>Location:</strong> Eastern North America.</p> <p><strong>Taxon:</strong> <em>Plethodon cinereus</em> (Green, 1818), Caudata: Plethodontidae.</p> <p><strong>Methods: </strong>We collected ddRAD-seq data from 106 individuals throughout the distribution of <em>P. cinereus</em>. We estimated phylogeographic structure, including finer-scale structure among the post-glacial populations. To test the origins and routes of colonization, we used ecological niche modeling, population trees, and analyses of directional range expansion.</p> <p><strong>Results: </strong>Analyses supported our hypothesis of a southeastern glacial refugium, with northward expansion along the Eastern Seaboard prior to westward invasion into the Great Lakes region, including southwestern expansion into unglaciated areas at the western end of the distribution. However, a distinct subgroup in the northwestern portion of the range raises the possibility of a second refugium near the ice-free Driftless Area.</p> <p><strong>Main conclusions:</strong> Based on our results, we hypothesize a southeastern refugium from which most of today's northern populations undertook extensive post-glacial colonization. Our results indicate a geographically non-linear colonization history for <em>P. cinereus</em>.</p>
Data from: Phylogeography and post-glacial dynamics in the clonal-sexual orchid Cypripedium calceolus L.
Aim: We investigated the phylogeographic history of a clonal-sexual orchid, to test the hypothesis that current patterns of genetic diversity and differentiation retain the traces of climatic fluctuations and of the species reproductive system. Location: Europe, Siberia and Russian Far East. Taxon: Cypripedium calceolus L. (Orchidaceae). Methods: Samples (>900, from 56 locations) were genotyped at eleven nuclear microsatellite loci and plastid sequences were obtained for a subset of them. Analysis of genetic structure and approximate Bayesian computations were performed. Species distribution modelling was used to explore the effects of past climatic fluctuations on the species range. Results: Analysis of genetic diversity reveals high heterozygosity and allele diversity, with no geographical trend. Three genetic clusters are identified with extant gene pools derived from ancestral demes in glacial refugia. Siberian populations exhibit different plastid haplotypes, supporting an early divergence for the Asian gene pool. Demographic results based on genetic data are compatible with an admixture event explaining differentiation in Estonia and Romania and they are consistent with past climatic dynamics inferred through species distribution modelling. Current population differentiation does not follow an isolation by distance model and is compatible with a model of isolation by colonisation. Main conclusions: The genetic differentiation observed today in C. calceolus preserves the signature of climatic fluctuations in the historical distribution range of the species. Our findings support the central role of clonal reproduction in in reducing loss of diversity through genetic drift. The dynamics of the clonal-sexual reproduction are responsible for the persistence of ancestral variation and stability during glacial periods and post-glacial expansion.
Data from: Post-glacial habitat release and incipient speciation in the genus Delphinus
The role of ecological and changing environmental factors in the radiation of species diversity is a fundamental question in evolutionary biology. Of particular interest is the potential for these factors to determine the boundary between what we would consider differentiation among populations and incipient speciation. Dolphins in the genus Delphinus provide a useful test case, exhibiting morphological variation in beak length, coloration and body size across their wide geographic distribution, and in particular among coastal and more pelagic habitats. Two species have been proposed, D. delphis and D. capensis, but morphologically similar allopatric populations are not monophyletic, indicating that the mostly coastal 'long-beaked' D. capensis form is not a single globally distributed species. However, the sympatric populations in the Eastern North Pacific currently designated as these two species are both morphologically and genetically differentiated. Here we use microsatellite DNA and mitochondrial DNA markers to investigate the evolutionary mechanisms that led to this incipient speciation event. We used coalescent and assignment methods to investigate the timing and extent of reproductive isolation. Our data indicate that although there is some level of on-going gene flow, the putative species found in the Eastern North Pacific are reciprocally monophyletic. The timing of isolation appears to be associated with regional changes in paleoceanographic conditions within the Holocene timeframe.
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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.
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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
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