Find research datasets worth reusing

opencc-by-4.0Feb 2018View details →

Datasets and Scripts: Full-length mRNA sequencing uncovers a widespread coupling between transcription and mRNA processing

The multilayered control of gene expression requires tight coordination of regulatory mechanisms at the transcriptional and post-transcriptional level. In this study, we studied the interdependence of transcription, splicing and polyadenylation events on single mRNA molecules by full-length mRNA sequencing. In MCF-7 breast cancer cells and three human tissues, we found an unforeseen number of genes that demonstrate mutually inclusive or exclusive alternative transcription and mRNA processing events, which can span the entire length of mRNA molecules. Furthermore, alternative poly(A) sites that are coupled with alternative splicing events are depleted for known poly(A) signals and enriched for MBNL binding motifs, supporting a dual role of MBNL proteins in regulating splicing and polyadenylation. We predict thousands of open-reading frames from the sequence of full-length mRNAs, allowing for a more sensitive proteogenomics analysis of MCF-7 mass-spectrometry data. Our findings demonstrate that our understanding of transcriptome complexity is far from complete and provides a framework to reveal largely unresolved mechanisms that coordinate transcription and mRNA processing.

opencc-by-4.0Oct 2019View details →

Spectral Evidence for Widespread Acid-Altered Surfaces in Acidalia Planitia, Mars

Spectral data set from manuscript entitled, Spectral Evidence for Widespread Acid-Altered Surfaces in Acidalia Planitia, Mars. Submitted to JGR-Planets for publication. The data includes mid-infrared emission spectra and visible/near-infrared reflectance spectra for Irvine, Backstay, Pathfinder Soil Glass, and Pathfinder Rock Glass laboratory materials.

opencc-by-4.0Sep 2024View details →

Table 1 in Mitochondrial DNA reveals the impact of Pleistocene glaciations on a widespread palearctic bat species

Table 1 Average values of detected genetic p-distances (±SD) in percentage per lineage of H. savii s.l. according to used marker set<table><tbody><tr><th></th><th></th><th>A</th><th>B</th><th>C</th><th>D</th><th>E</th></tr></tbody><tbody><tr><th>A</th><td>ND1:</td><td>0.46± 0.12</td><td></td><td></td><td></td><td></td></tr><tr><td>CytB:</td><td>0.32± 0.21</td><td></td><td></td><td></td><td></td></tr><tr><td>COI:</td><td>0.28± 0.24</td><td></td><td></td><td></td><td></td></tr><tr><td>16 S:</td><td>0.13± 0.11</td><td></td><td></td><td></td><td></td></tr><tr><th>B</th><td>ND1:</td><td>9.14± 0.28</td><td>0.47± 0.57</td><td></td><td></td><td></td></tr><tr><td>CytB:</td><td>8.03± 1.31</td><td>1.68± 0.96</td><td></td><td></td><td></td></tr><tr><td>COI:</td><td>7.90± 0.24</td><td>0.18± 0.19</td><td></td><td></td><td></td></tr><tr><td>16 S:</td><td>3.90± 0.27</td><td>0.34± 0.41</td><td></td><td></td><td></td></tr><tr><th>C</th><td>ND1:</td><td>6.79± 0.51</td><td>8.46± 0.35</td><td>0.62 ±0.68</td><td></td><td></td></tr><tr><td>CytB:</td><td>8.27± 0.68</td><td>9.01± 1.06</td><td>1.44 ±0.71</td><td></td><td></td></tr><tr><td>COI:</td><td>7.36± 0.25</td><td>8.92± 0.24</td><td>0.83 ±0.61</td><td></td><td></td></tr><tr><td>16 S:</td><td>/</td><td>/</td><td>/</td><td></td><td></td></tr><tr><th>D</th><td>ND1:</td><td>9.19± 0.30</td><td>9.12± 0.24</td><td>8.55 ±0.64</td><td>0.42±0.54</td><td></td></tr><tr><td>CytB:</td><td>/</td><td>/</td><td>/</td><td>/</td><td></td></tr><tr><td>COI:</td><td>8.91± 0.18</td><td>7.36± 0.28</td><td>10.15 ±0.38</td><td>0</td><td></td></tr><tr><td>16 S:</td><td>/</td><td>/</td><td>/</td><td>/</td><td></td></tr><tr><th>E</th><td>ND1:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>CytB:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>COI:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>16 S:</td><td>12.8± 0.65</td><td>11.81 ±0.89</td><td>/</td><td>/</td><td>0.59± 0.30</td></tr><tr><th>X</th><td>ND1:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>CytB:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>COI:</td><td>/</td><td>/</td><td>/</td><td>/</td><td>/</td></tr><tr><td>16 S:</td><td>4.62± 0.23</td><td>5.12± 0.29</td><td>/</td><td>/</td><td>9.97± 0.31</td></tr></tbody></table>

opencc-by-4.0Sep 2024View details →

Table 2 in Mitochondrial DNA reveals the impact of Pleistocene glaciations on a widespread palearctic bat species

Table 2 Estimated divergence times (in MYa) between mitochondrial lineages, obtained by BI analysis of the different marker datasets. Node heights (mean ages) are given, with 95% HPD intervals in square brackets. FIS indicates the first internal split within what we consider H. savii s.l. (including all four lineages – A, B, C and D), while SNN denotes the split from its nearest neighbour in the tree (most commonly H. alaschanicus). In the case of 16 S dataset, SNN does not include lineage E, as it is placed significantly more basal (see Fig. 2d). E is also excluded from H. savii, alongside X (Fig. 1c), in case of concatenated dataset. (C1, C2) refers to dating of the split within lineage C. Hstu – H. stubbei, Hara – H. arabicus, sc – sister clade<table><tbody><tr><th></th><th>ND1</th><th>CytB</th><th>COI</th><th>16 S</th><th>Conc.</th></tr></tbody><tbody><tr><th>(A, C)</th><td>2.17 [1.62–2.70]</td><td>2.16 [1.75–2.60]</td><td>2.58 [1.94–3.30]</td><td></td><td>3.21 [2.56–3.89]</td></tr><tr><th>(A, B)</th><td></td><td></td><td></td><td>3.31 [2.13–4.52]</td><td></td></tr><tr><th>(B, D/Hstu)</th><td>2.38 [1.89–2.92]</td><td></td><td>2.54 [1.87–3.24]</td><td></td><td>3.12 [2.46–3.82]</td></tr><tr><th>(B, (A, C))</th><td></td><td>2.50 [2.08–2.94]</td><td></td><td></td><td></td></tr><tr><th>(C1,C2)</th><td>0.51 [0.32–0.70]</td><td>0.54 [0.36–0.73]</td><td>0.44 [0.24–0.66]</td><td></td><td>0.64 [0.43–0.85]</td></tr><tr><th>(E, sc)</th><td></td><td></td><td></td><td>11.18 [8.15–14.39]</td><td>9.93 [7.79–12.19]</td></tr><tr><th>(X, (A, B))</th><td></td><td></td><td></td><td>4.31 [2.97–5.76]</td><td></td></tr><tr><th>(X, Hara)</th><td></td><td></td><td></td><td></td><td>2.47 [0.00-5.44]</td></tr><tr><th>FIS</th><td>2.79 [2.32–3.28]</td><td></td><td>3.29 [2.67–3.95]</td><td></td><td>3.89 [3.22–4.62]</td></tr><tr><th>SNN</th><td>3.12 [2.58–3.67]</td><td>3.36 [2.81–3.93]</td><td>3.61 [2.95–4.34]</td><td>5.96 [4.68–7.37]</td><td>4.51 [3.72–5.30]</td></tr></tbody></table>

opencc-by-4.0Oct 2024View details →

Dataset for "Early Jurassic rift-related low-pressure-high–temperature granulite facies metamorphism generates widespread peraluminous crustal melts"

This repository contains data for the manuscript "Early Jurassic rift-related low-pressure-high–temperature granulite facies metamorphism generates widespread peraluminous crustal melts" by Anthony Ramírez-Salazar, Mattia Parolari, Arturo Gómez-Tuena, Fernando Ortega-Gutiérrez, and Mariano Elías-Herrera submitted for publication to Geochemistry, Geophysics, Geosystem. The file contains geochemical, isotopic and geochronological data collected from the metapelitic xenoliths of Pepechuca, southern Mexico. All xenoliths were collected between the coordinates 18° 47´ 17.36´´N, 100° 04´ 07.92´´W and 18° 47´ 12.47´´N, 100° 04´ 05.00´´W. The dataset is divided in four tables: Table S1 Xenoliths' Bulk rock major elements Table S2 Xenoliths' trace elements Table S3 Xenoliths'  Sr, Nd, Hf and Pb isotopic compositions Table S4 U-Pb and trace element data of the xenoliths Anthony Ramírez-Salazar. e-mail: r.s.anthonyy@gmail.com; anthony@geologia.unam.mx

opencc-zeroAug 2019View details →

Data from: Widespread selection and gene flow shape the genomic landscape during a radiation of monkeyflowers

Speciation genomic studies aim to interpret patterns of genome-wide variation in light of the processes that give rise to new species. However, interpreting the genomic 'landscape' of speciation is difficult, because many evolutionary processes can impact levels of variation. Facilitated by the first chromosome-level assembly for the group, we use whole-genome sequencing and simulations to shed light on the processes that have shaped the genomic landscape during a radiation of monkeyflowers. After inferring the phylogenetic relationships among the nine taxa in this radiation, we show that highly similar diversity (π) and differentiation (FST) landscapes have emerged across the group. Variation in these landscapes was strongly predicted by the local density of functional elements and the recombination rate, suggesting that the landscapes have been shaped by widespread natural selection. Using the varying divergence times between pairs of taxa, we show that the correlations between FST and genome features arose almost immediately after a population split and have become stronger over time. Simulations of genomic landscape evolution suggest that background selection (i.e., selection against deleterious mutations) alone is too subtle to generate the observed patterns, but scenarios that involve positive selection and genetic incompatibilities are plausible alternative explanations. Finally, tests for introgression among these taxa reveal widespread evidence of heterogeneous selection against gene flow during this radiation. Combined with previous evidence for adaptation in this system, we conclude that the correlation in FST among these taxa informs us about the processes contributing to adaptation and speciation during a rapid radiation.

opencc-by-4.0Oct 2009View details →

Figure 1 in Combined phylogenetic analysis of a new North American fossil species confirms widespread Eocene distribution for stem rollers (Aves, Coracii)

Figure 1. Map showing the distribution of extant and extinct Coracii.

opencc-zeroOct 2022View details →

Illumina next generation ddRAD sequencing SNP data from: Contrasting genetic diversity and structure between endemic and widespread damselfishes are related to differing adaptive strategies

Aim: Discerning when, where, and how processes of isolation lead to differing biogeography is especially complex for marine species with similar ecological niches and within the same geographic location. We assessed population genetics of congeneric and ecologically similar damselfishes within their overlapping distributions and across potential barriers to geneflow. Taxon: Dascyllus marginatus (endemic) and Dascyllus abudafur (widespread). Location: Coral reefs from the Red Sea, Djibouti, Yemen, Oman, and Madagascar. Methods: We used RADseq derived SNPs to investigate key differences in population genetics between both species and discuss barriers shaping genetic differentiation (neutral vs. selective) and biogeography. Results: Dascyllus marginatus inhabited the Red Sea, the coasts of Yemen (including Socotra), and the Gulf of Oman. Dascyllus abudafur species was present from the Red Sea to Madagascar but was absent from Yemen and Oman. Populations of D. marginatus had an order of magnitude higher genetic differentiation compared to D. abudafur, as well as several outlier loci (suggesting selective pressure), which were absent in D. abudafur despite equal sampling locations. In both species, specimens from the Red Sea and Djibouti formed one genetic cluster separated from all other locations. Main conclusions: The stronger genetic structure at smaller geographic scale of the endemic species seems associated to faster adaptation to environmental differences; whereas the widespread species only experienced reduced geneflow and neutral differentiation at much larger geographic scales. Restrictive transitions (between the Gulf of Aqaba and the Red Sea or the Red Sea and the Gulf of Aden) did not affect the genetic architecture of either species, while the environmental shift within the Red Sea (at 22°N/20°N) affected the endemic but not the widespread species. Samples from continental Yemen revealed that a genetic break in the Gulf of Aden likely reflects historical colonization processes and not contemporary environmental regimes.

opencc-zeroNov 2022View details →

Data from: Hedging at the rear edge: Intraspecific trait variability drives the trajectory of marginal populations in a widespread boreal tree species

Rear-edge populations at the warm margin of species distribution are small, isolated and face environmental conditions at the limit of species bioclimatic envelope. Intraspecific phenotypic variation contributing to the persistence of peripheral populations is expected to become increasingly important under future climate conditions in order to avoid local extirpation where range shifts lag behind climate change velocity. We investigated the putative role of intraspecific phenotypic variation for the maintenance of rear-edge populations of fire-prone jack pine (Pinus banksiana), an obligate pyriscent boreal species. We assessed whether variation in cone serotiny is associated with the population trajectory of marginal stands located south of the boreal biome, in the temperate forest where natural wildfires are infrequent and unpredictable. To this end, we estimated stand-scale serotiny, minimal age and tree size structure in 26 jack pine stands from the rear edge (n = 17 sites) and the core (n = 9 sites) of the species' range in eastern Canada. On average, rear-edge jack pine populations are less serotinous albeit more variably compared to range-core populations where serotiny is more uniformly high. Rear-edge stands are generally older and display reverse J-shape tree size structure indicative of a multi-aged demographic equilibrium, whereas range-core stands are younger and show a unimodal stand structure depicting a single aging cohort generally lacking interfire recruitment. Eco-evolutionary dynamics shifts from a dependency on wildfires in range-core populations to stands that can regenerate and persist without recurrent fires at the rear edge, where stand-scale serotiny reaches values below 85%. Synthesis: Unlike range-core populations, rear-edge jack pine populations can locally rely on a dual life-history strategy to ensure both steady recruitment during fire-free intervals and successful postfire regeneration. This capacity to cope with infrequent and unpredictable fire regime should increase the resilience and resistance of jack pine populations as global changes alter fire dynamics of the boreal forest. More generally, unique intraspecific phenotypic variation in rear-edge populations contributes to long-term species persistence in marginal environmental conditions that might scale up with global changes. The conservation of rear-edge populations and their genetic legacy appears crucial for the resilience of species.

opencc-zeroJan 2023View details →

Phenotypic and ecological data from: Widespread convergent morphological evolution within the largest family of songbirds

Although convergence is a common evolutionary phenomenon, few studies have quantified its prevalence across a large, densely sampled clade. Large-scale phylogenies and the advent of novel computational methods facilitate more robust identification of convergent events and their statistical significance. The tanagers (Aves: Thraupidae), the largest family of songbirds, offer an excellent opportunity to study the extent of phenotypic convergence in response to similar ecological pressures on a continental scale. To investigate convergence in the group, we used the largest phylogenetic and multivariate morphological dataset to date for the clade. First, we used phylogenetic comparative analyses to show a correlation between diet and aspects of bill shape. We then investigated our dataset for the presence and magnitude of convergent events and assessed significance through simulations and modeling analyses. Overall, we found that around half (45.3%) of species and clades we tested have converged in morphological space more than would be expected by chance alone. Our study shows that across Thraupidae, various bill shapes have evolved convergently to fill multiple distinct sections of ecological niche space, reflecting a signal of ecological opportunity and structural constraints.

opencc-zeroJan 2023View details →

Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

Coloration is an important phenotypic trait for taxonomic studies and has been widely used for identifying insect species and populations. However, coloration can be a poor diagnostic character for insect species that exhibit high polymorphism in this trait, which can lead to over-splitting of taxonomic units. In orchid bees, color variation has been interpreted by different taxonomists as either polymorphism associated with Mullerian mimicry complexes or diagnostic traits for species identification. Despite this uncertainty, integrative approaches that incorporate multiple independent datasets to test the validity of hair coloration as a character that identifies independent evolutionary units have not been used. Here, we use phylogenomic data from Ultraconserved Elements (UCEs) to explore whether color phenotypes in the widespread orchid bee species complexes Eulaema meriana and Eulaema bombiformis (Hymenoptera: Apidae: Euglossini) correspond to independent lineages or polymorphic trait variation within species. We find that lineages within both species are structured according to geography and that color morphs are generally unassociated with evolutionarily independent groups except for populations located in the Atlantic Forest of Brazil. We conclude that there is compelling evidence that E. atleticana and E. niveofasciata are subspecies of E. meriana and E. bombiformis, respectively, and not different species as previously suggested. Therefore, we recognize Eulaema meriana atleticana comb. n. and Eulaema bombiformis niveofasciata comb. n. and discuss their morphological characteristics. We make recommendations on the use of color traits for orchid bee taxonomy and discuss the significance of subspecies as evolutionary units relevant for conservation efforts.

Effects of environmental factors on the ecology and survival of a widespread, endemic Cerrado frog

Understanding the mechanisms that affect habitat use by vertebrates is critical for understanding how species are distributed across landscapes and how they cope with habitat change. The Brazilian Savanna (the Cerrado) has vegetation ranging from grassland to woodland savannas and harbors a rich and diverse amphibian fauna impacted by accelerated habitat loss. Here, we test the influence of vegetation type (from grassy scrubland to woodland) and distance from breeding sites (ephemeral water bodies) on body size, abundance, and survival of the frog Physalaemus nattereri in a natural metapopulation system of south-central Brazil. We also test whether body size is a significant predictor of population abundance. We found that the abundance of P. nattereri varies according to the mean snout-vent length of each metapopulation (sampling unit), as well as a higher estimated mortality rate in woodlands compared to typical Cerrado. Furthermore, we found no difference in estimated mortality among sampling units located far or close to ephemeral water bodies. Thus, our results highlight variable responses of P. nattereri metapopulations to environmental factors, despite the observed high heterogeneity among sampled habitats and the importance of ephemeral water bodies for reproduction. These findings highlight that land cover and availability of breeding sites might not always interact to explain population persistence of Cerrado frogs.

Data from: Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos

Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyze geographic variation in genome size, genetic diversity, and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity, and increased self-fertilization, but we show that this is not the case for Poa annua. Microsatellite data indicated low population genetic structure and lack of isolation-by-distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality, and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of autogamy declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are likely tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy likely benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.

Data from: Contrasting long-term trends in juvenile abundance of a widespread cold-water salmonid along a latitudinal gradient: Effects of climate, stream size and migration strategy

A changing climate reshapes the range distribution of many organisms, and species with relatively low thermal optima, like many salmonids, are increasingly expected to face local population extinctions at lower latitudes. Understanding where and how fast these changes are happening is of pivotal importance for successful mitigation and conservation efforts. We used an extensive electrofishing database to explore temporal trends of brown trout juveniles (Salmo trutta L.) in 218 locations from 174 Swedish streams, over the last 30 years (1991–2020). We hypothesized that 1) declines in abundance have occurred predominately in the warmer, southern regions, while increases have occurred in the colder, northern regions, 2) larger stream sizes may partly offset negative effects of climate, and 3) migrating and resident populations are affected differently by a warming climate. We found that abundance of brown trout juveniles generally declined in warmer regions, especially in smaller streams (≤ 6 m wide), while the abundance increased in colder regions. In larger streams, negative effects of higher temperatures were seemingly buffered, as we found lower rates of decline or even positive trends. The rate of change (i.e. the slopes of the trends in abundance) was more pronounced towards the climate extremes and was on average zero in regions with a normal annual air temperature (average temperature over 30-year period) around 5–6 ºC. Warmer climate had stronger effects on migrating compared to resident populations, suggesting that climate-induced loss of stream connectivity could be an additional factor that hinders recruitment in anadromous populations in a changing climate. Considering predictions of increasing temperatures and frequency of summer droughts, management of cold-water salmonid populations should focus on conserving and restoring riparian vegetation, wetlands, climate and thermal refugia, and habitat integrity overall. Such measures may, however, not suffice for small streams at lower latitudes, unless hydrological connectivity is maintained.

Singing on the nest is a widespread behavior in incubating Northern Mockingbirds and increases probability of nest predation

In this study, we documented for the first time singing on the nest (SOTN) in 74% of 65 Northern Mockingbird (Mimus polyglottos) nests that were monitored with continuous-running video cameras (8,353.9 hrs sampled). As predicted, higher rates of SOTN significantly decreased daily survival rates of nests. SOTN occurred almost exclusively by females during the egg stage and in 86% (48/56) of nests for which we had sampling from the egg stage. While extensive at the population level, the average rate of SOTN per individual was very low (5.24 ± 1.24 s SOTN per hr video sampled). We found mixed support for the hypothesis that SOTN functions in territory maintenance. We found no support for the hypotheses that SOTN functions to coordinate parental care, defend nests, or aid in vocal learning. Given the limited attention SOTN has received and the mostly anecdotal accounts of it, our understanding of its costs and benefits is lacking. We conclude that while individual rates of SOTN are quite low, SOTN may be more widespread in populations than previously thought and that studies specifically designed to test hypotheses regarding potential functions are critically needed.

opencc-zeroDec 2021View details →

Identification of microbial taxa present in Ctenocephalides felis (cat flea) reveals widespread co-infection and associations with vector phylogeny

Background Ctenocephalides felis, the cat flea, is the most common ectoparasite of cats and dogs worldwide. As a cause of flea allergy dermatitis and a vector for two genera of zoonotic pathogens (Bartonella and Rickettsia spp.), the effect of the C. felis microbiome on pathogen transmission and vector survival is of substantial medical importance to both human and veterinary medicine. The aim of this study was to assay the pathogenic and commensal eubacterial microbial communities of individual C. felis from multiple geographic locations and analyze these findings by location, qPCR pathogen prevalence, and flea genetic diversity. Methods 16S Next Generation Sequencing (NGS) was utilized to sequence the microbiome of fleas collected from free-roaming cats, and the cox1 gene was used for flea phylogenetic analysis. NGS data were analyzed for 168 individual fleas from seven locations within the US and UK. Given inconsistency in the genera historically reported to constitute the C. felis microbiome, we utilized the decontam prevalence method followed by literature review to separate contaminants from true microbiome members. Results NGS identified a single dominant and cosmopolitan amplicon sequence variant (ASV) from Rickettsia and Wolbachia while identifying one dominant Bartonella clarridgeiae and one dominant Bartonella henselae/Bartonella koehlerae ASV. Multiple less common ASVs from these genera were detected within restricted geographical ranges. Co-detection of two or more genera (Bartonella, Rickettsia, and/or Wolbachia) or multiple ASVs from a single genus in a single flea was common. Achromobacter, Peptoniphilus, and Rhodococcus were identified as additional candidate members of the C. felis microbiome on the basis of decontam analysis and literature review. Ctenocephalides felis phylogenetic diversity as assessed by the cox1 gene fell within currently characterized clades while identifying seven novel haplotypes. NGS sensitivity and specificity for Bartonella and Rickettsia spp. DNA detection was compared to targeted qPCR. Conclusions Our findings confirm the widespread coinfection of fleas with multiple bacterial genera and strains, proposing three additional microbiome members. The presence of minor Bartonella, Rickettsia, and Wolbachia ASVs was found to vary by location and flea haplotype. These findings have important implications for flea-borne pathogen transmission and control.

opencc-by-4.0Feb 2023View details →

Widespread flood severity index time series for Germany

The dataset provides time series from 1951 to 2013 of monthly flood severity index and mean monthly precipitation derived for Germany (DE) and its three hydroclimatic regions (NW: North-Western region; NE: North-Eastern region; South: Southern region). The dataset also provides most frequent event type recorded in Germany for each months.  The dataset was used to train and test a dilated Convolutional Neural Network for forecasting monthly flood severity in Germany (Tarasova et al., submitted to Earth's Future).

opencc-zeroMar 2023View details →

Drivers of strong isolation and small effective population size at a leading range edge of a widespread plant

Climate change has influenced species distributions worldwide with upward elevational shifts observed in many systems. Leading range edge populations, like those at upper elevation limits, are crucial for climate change responses but can exhibit low genetic diversity due to founder effects, isolation, or limited outbreeding. These factors can hamper local adaptation at range limits. Using the widespread herb, Argentina anserina, we measured ecological attributes (population density on the landscape, area of population occupancy, and plant and flower density) spanning a 1000m elevation gradient, with high elevation populations at the range limit. We measured vegetative clonal potential in the greenhouse for populations spanning the gradient. We combined these data with a ddRAD-seq dataset to test the hypotheses that high-elevation populations would exhibit ecological and genomic signatures of leading range edge populations. We found that population density on the landscape declined towards the high elevation limit, as is expected towards range edges. However, plant density was elevated within edge populations. In the greenhouse, high-elevation plants exhibited stronger clonal potential than low-elevation plants, likely explaining increased plant density in the field. Phylogeographic analysis supported more recent colonization of high-elevation populations which were also more genetically isolated, had more extreme heterozygote excess, and had smaller effective population size than low. Results support that colonization of high elevations was likely accompanied by increased asexuality, contributing to a decline in effective population size. Despite high plant density in leading-edge populations, their small effective size, isolation, and clonality could constrain adaptive potential.

opencc-zeroMar 2023View details →

Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass

This raw data set contains multilocus genotypes for 1,312 individual samples from 44 locations. Aim: Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterise intraspecific genetic diversity and its spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia. Location: Temperate Australian coastal waters Methods: Predictive modelling was used to contrast the current Posidonia australis distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. Results: Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognised biogeographic provinces and largely consistent with the finer-scale IMCRA bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional bioregions. Clonal diversity was highly variable, but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance. Main conclusions: Our approach suggests how shared seascape drivers have influenced the capacity of P. australis to effectively track sea level changes associated with natural climate cycles over millennia, and in particular, the recolonisation of meadows across the Continental Shelf following the LGM. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure.