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55 results for “ice ages”
Colonial coral resilience by decreasing size: reaction to increased detrital influx during onset of the late Palaeozoic Ice Age
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Data from: Population genetic consequences of habitat fragmentation in ectomycorrhizal fungi with different dispersal mechanisms: Implications from ice-aged relict forests across the Japanese archipelago
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Maps of anomalies in heavy rainfall across Central Europe from the Little Ice Age to near present
<p>This dataset includes the data displayed in</p> <p>Förster, K., Thiele, L.-B. (2020): Variations in sub-daily precipitation at centennial scale. <em>npj Clim Atmos Sci</em> <strong>3, </strong>13. https://doi.org/10.1038/s41612-020-0117-1</p> <p>For each year, a csv file is provided containing anomalies as xyz point data (latitude, longitude, anomaly), referring to the center of each grid cell (~30 km).</p> <p> </p> <p> </p>
Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska
<p class="CxSpFirst"><i>Larix laricina</i> (eastern larch, tamarack) is a transcontinental North American conifer with a prominent disjunction in the Yukon isolating the Alaskan distribution from the rest of its range. We investigate whether <i>in situ</i> persistence during the Last Glacial Maximum (LGM) or long-distance postglacial migration from south of the ice sheets resulted in the modern-day Alaskan distribution. We analyzed variation in three chloroplast DNA regions of 840 trees from a total of 69 populations (24 new sampling sites situated on both sides of the Yukon range disjunction pooled with 45 populations from a published source) and conducted ensemble species distribution modeling (SDM) throughout Canada and USA to hindcast the potential range of <i>Larix laricina</i> during the LGM. We uncovered the genetic signature of a long-term isolation of larch populations in Alaska, identifying three endemic chlorotypes and low levels of genetic diversity. Range-wide analysis across North America revealed the presence of a distinct Alaskan lineage. Postglacial gene flow across the Yukon divide was unidirectional, from Alaska toward previously glaciated Canadian regions, and with no evidence of immigration into Alaska. Hindcast SDM indicates one of broadest areas of past climate suitability for <i>Larix laricina</i> existed in central Alaska, suggesting possible <i>in situ</i> persistence of larch in Alaska during the LGM. Our results provide the first unambiguous evidence for the long-term isolation of <i>Larix laricina</i> in Alaska that extends beyond the last glacial period and into the present interglacial period. The lack of gene flow into Alaska along with the overall probability of larch occurrence in Alaska being currently lower than during the LGM, suggest that modern-day Alaskan larch populations are isolated climate relicts of broader glacial distributions, and so are particularly vulnerable to current warming trends.</p>
Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
Background: Determining reliable evolutionary rates of molecular markers is essential in illustrating historical episodes with phylogenetic inferences. Although emerging evidence has suggested a high evolutionary rate for intraspecific genetic variation, it is unclear how long such high evolutionary rates persist because a recent calibration point is rarely available. Other than using fossil evidence, it is possible to estimate evolutionary rates by relying on the well-established temporal framework of the Quaternary glacial cycles that would likely have promoted both rapid expansion events and interisland dispersal events. Results: We examined mitochondrial cytochrome b (Cytb) and control region (CR) gene sequences in two Japanese wood mouse species, Apodemus argenteus and A. speciosus, of temperate origin and found signs of rapid expansion in the population from Hokkaido, the northern island of Japan. Assuming that global warming after the last glacial period 7–10 thousand years before present (kyr BP) was associated with the expansion, the evolutionary rates (sites per million years, myr) of Cytb and CR were estimated as 11–16% and 22–32%, respectively, for A. argenteus, and 12–17% and 17–24%, respectively, for A. speciosus. Additionally, the significant signature of rapid expansion detected in the mtDNA sequences of A. speciosus from the remaining southern main islands, Honshu, Shikoku, and Kyushu, provided an estimated Cytb evolutionary rate of 3.1%/site/myr under the assumption of a postglacial population expansion event long ago, most probably at 130 kyr BP. Bayesian analyses using the higher evolutionary rate of 11–17%/site/myr for Cytb supported the recent demographic or divergence events associated with the Last Glacial Maximum. However, the slower evolutionary rate of 3.1%/site/myr would be reasonable for several divergence events that were associated with glacial periods older than 130 kyr BP. Conclusions: The faster and slower evolutionary rates of Cytb can account for divergences associated with the last and earlier glacial maxima, respectively, in the phylogenetic inference of murine rodents. The elevated evolutionary rate seemed to decline within 100,000 years.
Data from: Compositional turnover and ecological changes related to the waxing and waning of glaciers during the Late Paleozoic ice age in ice-proximal regions (Pennsylvanian, western Argentina)
The late Paleozoic ice age (LPIA) had a profound effect on the biota. Despite much research having been focused on paleotropical regions or global-scale analyses, regional ecological changes have seldom been studied in ice-proximal basins. Here, I study the compositional turnover and diversity structure across the main Carboniferous glacial event recorded in western Argentina and the subsequent nonglacial interval. Brachiopod and bivalve data from western Argentina suggest that the transition from glacial to nonglacial climates caused major compositional changes. Turnover, however, was not uniform across the bathymetric gradient, being higher in deep environments. Because extirpation was concentrated in brachiopods, but immigration was similar in both clades, the taxonomic structure of the region was significantly modified. Although regional hierarchical diversity structure and occupancy distributions remained stable, dissecting the analysis in brachiopods and bivalves underscores that both clades had different responses to climate change. Brachiopods, on the one hand, show stability in the diversity structure and a very slight decrease in occupancies of intermediate genera, while bivalves show an important rise in diversity, both at the environment and regional scale, and an increase in genera with intermediate occupancies. The bathymetric diversity gradient was also modified from hump shaped with maximum diversity in the deep subtidal to a linear gradient with maximum values toward the offshore. However, relative compositional differences within environments remained stable, with maximum values at intermediate depths both in glacial and nonglacial intervals. Moreover, local-scale coexistence between brachiopods and bivalves changed in the nonglacial interval, showing significant segregation, which indicates relevant modifications in community assembly dynamics. Results from western Argentina highlight the magnitude of regional-scale ecological changes during the LPIA in ice-proximal regions, suggesting that the waxing and waning of glaciers was able to cause regional taxonomic turnover and medium-scale ecological changes even during intervals of relative macroevolutionary quiescence.
Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age
We investigated how population changes and fluctuations in the pink-footed goose might have been affected by climatic and anthropogenic factors. First, genomic data confirmed the existence of two separate populations: western (Iceland) and eastern (Svalbard/Denmark). Second, emographic inference suggests that the species survived the last glacial period as a single ancestral population with a low population size (100-1,000 individuals) that split into the current populations at the end of the Last Glacial Maximum with Iceland being the most plausible glacial refuge. While population changes during the last glaciation were clearly environmental, we hypothesize that more recent demographic changes are human-related: (1) the inferred population increase in the Neolithic is due to deforestation to establish new lands for agriculture, increasing available habitat for pink-footed geese (2) the decline inferred during the Middle Ages is due to human persecution and (3) improved protection explains the increasing demographic trends during the 20th century. Our results suggest both environmental (during glacial cycles) and anthropogenic effects (more recent) can be a threat to species survival.
Subspecies and Distribution. O.c.cuniculusLinnaeus,1758—N,NE&EIberianPeninsula(Spain). O.c.algirusLoche,1858—S,SW&WIberianPeninsula(Spain,Portugal),NMorocco,NAlgeria(includingHabibasI). O.c.brachyotusTrouessart,1917—SFrance. O.c.cnossiusBate,1906—CreteI. O.c.habetensisCabrera,1923—Tanger-Tetouan-AlHoceimaRegion(NMorocco). O. c. huxleyi Haeckel, 1874 — Mediterranean Is (Balearic Is, Corsica, Sardinia, Sicily and Macaronesia (Azores, Madeira, and Canary Is). Original distribution after last Ice Age restricted to Iberian Peninsula, W France, and N Africa. Ancient introductions of the nominate subspecies probably during the Ro- man period have spread it throughout Europe, and now it is present in most of W, C & E Europe and the Mediterranean and Macaronesian Is (these mostly old introductions are also shaded on the map). During the 20" century it has been released into the steppes of the Black Sea in Ukraine and Russia (N Caucasus); introduced into Australia in 1788 and again in 1859 where it is now widespread; it is found on many Pacific Is, islands off the coast of South Africa and Namibia, and in New Zealand; successfully introduced only since 1936 into South America, nowadays with a limited range in Chile, Argentina, and Falkland Is, it is also present in the Caribbean Is (all these modern introductions not shaded in the map). Worldwide as domesticated forms. in Leporidae
Subspecies and Distribution. O.c.cuniculusLinnaeus,1758—N,NE&EIberianPeninsula(Spain). O.c.algirusLoche,1858—S,SW&WIberianPeninsula(Spain,Portugal),NMorocco,NAlgeria(includingHabibasI). O.c.brachyotusTrouessart,1917—SFrance. O.c.cnossiusBate,1906—CreteI. O.c.habetensisCabrera,1923—Tanger-Tetouan-AlHoceimaRegion(NMorocco). O. c. huxleyi Haeckel, 1874 — Mediterranean Is (Balearic Is, Corsica, Sardinia, Sicily and Macaronesia (Azores, Madeira, and Canary Is). Original distribution after last Ice Age restricted to Iberian Peninsula, W France, and N Africa. Ancient introductions of the nominate subspecies probably during the Ro- man period have spread it throughout Europe, and now it is present in most of W, C & E Europe and the Mediterranean and Macaronesian Is (these mostly old introductions are also shaded on the map). During the 20" century it has been released into the steppes of the Black Sea in Ukraine and Russia (N Caucasus); introduced into Australia in 1788 and again in 1859 where it is now widespread; it is found on many Pacific Is, islands off the coast of South Africa and Namibia, and in New Zealand; successfully introduced only since 1936 into South America, nowadays with a limited range in Chile, Argentina, and Falkland Is, it is also present in the Caribbean Is (all these modern introductions not shaded in the map). Worldwide as domesticated forms.
Elevation-Dependent Warming Identified During the Abrupt Shift at the Last Ice Age Termination
<p>The current Earth’s surface warming rate may increase with elevation, known as Elevation-Dependent Warming, which has profound environmental impacts on the fragile environments in high-elevation mountainous regions. However, Elevation-Dependent Warming has not been well constrained due to the short duration and sparse distribution of available instrumental data. Here we report quantitative paleotemperature reconstructions for three lakes within the elevational range of 1800–3800 m above sea level in the Hengduan Mountains, southeastern Tibetan Plateau, to show that abrupt warming occurred during ~14500–14000 years ago, and the warming rate was higher at higher elevations. We also find a prolonged cold interval from ~24000 to ~14000 years ago at high elevations, which coincides with the timing of the regional mountain glacier advances. We conclude that the observed Elevation-Dependent Warming was probably driven by the surface snow-albedo feedback caused by the rapidly shrinking mountain glaciers, which had a stronger influence at higher elevations.</p>
Genetic datasets, climatic conditions at sampled localities, and occurrence data to: Ice age-driven range shifts of diploids and expanding autotetraploids within a conserved niche (Grünig, Patsiou & Parisod, 2024, New Phytologist)
<div> <h3><strong>This repository includes</strong></h3> - An overview of the raw sequencing reads deposited in the European Nucleotide Archive (ENA) for the 370 individuals sampled in 17 diploid and 19 tetraploid field populations <div>- Scripts used to genotype diploids and autotetraploids samples of <em>Biscutella laevigata</em> from ddRADseq data</div> <div>- Input data (as vcf format) used in population genetic analyses</div> <div>- Scripts used to run the different genetic analyses</div> <div>- Dataset of extracted climatic conditions at sampled localities</div> <div>- Occurrence dataset used for the climatic niche modelling</div> <br> <h3><strong>Description of the data and file structure</strong></h3> <strong>00.ENA_samples_correspondance.txt: </strong>provides ENA project ID, run ID (i.e. raw fastq files), sample ID, and alias for each sample included in the study.<br> <div> </div> <div><strong>1.scripts_reads_to_vcf.zip:</strong> consists of the following:</div> - <strong>1.reads_to_vcf.md: </strong>md file with scripts documenting the read quality check, demultiplexing, mapping, SNP calling using GATK4, and filtering steps<br> <div>- Additional scripts called within <strong>1.reads_to_vcf.md</strong>:</div> <div>-- 1.3. Mapping: <strong>02_run_mapping_XXX.py</strong> and <strong>BWA-mem_bisc1_sg.py</strong> scripts</div> <div>-- 1.4.a. HaplotypeCaller: <strong>03_V1_gvcf.py</strong></div> <div>-- 1.4.b. GDBI + genotypeGVCF: <strong>03_V3_gdbi_genotype_per100scaf.py</strong></div> <br> <div><strong>2.datasets_genetics.tar.gz</strong> consists of the following</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30.vcf.gz</strong>: "Initial SNPs dataset" = biallelic SNPs fulfilling GATK quality hard filtering recommendations, present in at least 50% of samples. Genotypes with DP<15 for diploids and DP<30 for tetraploids are set to no-call. This vcf was used as basis for fastsimcoal dataset preparation, and as basis for subsequent selection of loci fulfilling requirements of each analysis. It includes 2246701 biallelic SNPs for 370 samples</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD05_pruned.vcf.gz:</strong> subset of the "Initial SNPs dataset" retaining SNPs called in at least 50% of samples, and pruned for Linkage disequilibrium. This vcf includes 107574 biallelic SNPs for 370 samples and was used in the analysis of the proportion of diploids diagnostic alleles shared by tetraploids.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD01_pruned.vcf.gz: </strong>subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, and pruned for Linkage disequilibrium. This vcf includes 4444 biallelic SNPs for 370 samples and was used in the analyses of Population diversity and differentiation (SpaGeDi, GenoDive, PCA), and f3-statistics.</div> <br> <div>- <strong>bisc_all370_diminDP15_tetraminDP30_MD0.1_pruned_MAC3rm.vcf.gz:</strong> subset of the "Initial SNPs dataset", retaining SNPs called in at least 90% of samples, pruned for Linkage disequilibrium, and with a minor allele count of 3. This vcf includes 2593 biallelic SNPs for 370 samples and was used in STRUCTURE analysis</div> <br><br> <div><strong>3.pres_2x.txt:</strong> list of the 128 diploid occurrences used in climatic niche modelling</div> <br> <div><strong>3.pres_4x_strat_reg.txt:</strong> list of the 924 tetraploid occurrences used in climatic niche modelling</div> <br> <div><strong>biscall_chelsa_ordered_noDEM.txt:</strong> climatic data extracted from the CHELSA dataset at sampled localities</div> <br> <div><strong>4.plot_GTfreqs.md:</strong> markdown file including scripts to plot allele and genotype frequencies</div> <br> <div> </div> <h3><strong>Sharing/Access information</strong></h3> Raw sequencing reads have been deposited in the European Nucleotide Archive (ENA) at EMBL-EBI under the accession number PRJEB48869:<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB48869"> https://www.ebi.ac.uk/ena/browser/view/PRJEB48869</a></div>
Figure 1 in The genetic legacy of the Quaternary ice ages
Figure 1 The maximum extent of ice and permafrost at the end of the last ice age 20,000 yr BP. The lowered sea level, large deserts and main blocks of tropical forest are indicated. Modified with permission from ref. 2.
Figure 2 in The genetic legacy of the Quaternary ice ages
Figure 2 Three paradigm postglacial colonizations from southern Europe deduced from europeus/concolor, and the bear, Ursos arctos. The main refugial areas, Iberia, Italy, the DNA differences for the grasshopper, Chorthippus parallelus, the hedgehog, Erinaceus Balkans and Caucasus, contributed differently to the repopulation of northern parts.
Figure 3 in The genetic legacy of the Quaternary ice ages
Figure 3 The general position of some wellknown hybrid zones in Europe, which show major clustering in Scandinavia, central Europe and the Alps. Other clusters are apparent in the Pyrenees and the Balkans. These suture zones are caused by commonalities of iceage refugia, rate of postglacial expansion and physical barriers. There is further subdivision in the southern regions.
The Vegetation Dynamics in Response to Cooling Events from the Medieval Warm Period to the Little Ice Age in Southeast China
<p>Full palynological dataset from three-peats (Wangdongyang peat bog: WDY, 27°40′48″N、119°38′15″E, elevation: 1303 m; Xiyaohu peat bog: XYH15, 28°44′N, 115°40′E, elevation: 735m and XYH14 is close to XYH15; Yuhuashan peat bog: YHS2, 27°50′29″N, 115°38′54.98″E, elevation: 882 m) in the southeast of China.</p> <p>The dataset contains raw counts for pollen and ferns.</p>
Using a Web Map Service to map Little Ice Age glacier extents at regional scales
<p>Extending the record of glacier area changes into the past improves our understanding of climate change impacts. Although analogue maps showing historic glacier extents are abundant, digital outlines from before the satellite era are sparse as the digitisation of moraines and trimlines on freely available satellite images is challenging. With the now available very high-resolution images provided by Web Map Services (WMS), new doors are open for the precise digitisation. Here, we used the ESRI WMS to digitise Little Ice Age (LIA) glacier extents and present area changes since the LIA in four selected regions along with a detailed uncertainty analysis. We used modern glacier outlines as a starting point and additionally consulted Sentinel-2 images, the ArcticDEM and historic maps for interpretation. Dating records from the literature allowed calculating area change rates. In total, 493 LIA glaciers (4640 km2, now 891 ice bodies with 3590 km2) were digitised, yielding relative area changes of −20% (−0.14% a−1), −15% (−0.10% a−1), −26% (−0.16% a−1) and −61% (−0.19% a−1) for Alaska, Baffin Island, Novaya Zemlya and the tropics, respectively. The ESRI WMS images are a great asset to precisely map moraines and trimlines, but information about the timing of the related extents requires further sources.</p>
R-ICE Versus R-DHAP in Patients Aged 18-65 With Relapse Diffuse Large B-cell Lymphoma
ClinicalTrials.gov study NCT00137995. IPD Sharing: NO. Countries: 10. Publications: 6.
Data from: Compositional turnover and ecological changes related to the waxing and waning of glaciers during the Late Paleozoic ice age in ice-proximal regions (Pennsylvanian, western Argentina)
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Data from: Estimating the molecular evolutionary rates of mitochondrial genes referring to Quaternary Ice Age events with inferred population expansions and dispersals in Japanese Apodemus
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Data from: Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age
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Ice-age persistence and genetic isolation of the disjunct distribution of larch in Alaska
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Allen Brain Atlas
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DANDI Archive for NWB datasets
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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.