cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.68s5c1r4
title: Data from: Pleistocene speciation with and without gene flow in Euphaea damselflies of subtropical and tropical East Asian islands

description: Climatic oscillations during the Pleistocene period could have had a
 profound impact on the origin of tropical species by the alternation of
 allopatric isolation and inter-population gene flow cycles. However,
 whether tropical speciation involves strictly allopatric isolation, or
 proceeds in the face of homogenizing gene flow, is relatively unclear.
 Here, we investigated geographical modes of speciation in four
 closely-related Euphaea damselfly species endemic to the subtropical and
 tropical East Asian islands using coalescent analyses of a multi-locus
 data set. The reconstructed phylogenies demonstrated distinct species
 status for each of the four species and the existence of two sister
 species pairs, E. formosa/E. yayeyamana and E. decorata/E. ornata. The
 species divergence time of the sibling Euphaea damselflies dates back to
 within the last one Mya of the Middle to Lower Pleistocene. The speciation
 between the populous E. formosa of Taiwan and the less numerous E.
 yayeyamana of the Yaeyama islands occurred despite significant
 bidirectional, asymmetric gene flow, which is strongly inconsistent with a
 strictly allopatric model. In contrast, speciation of the approximately
 equal-sized populations of E. decorata of the south-east Asian mainland
 and E. ornata of Hainan is inferred to have involved allopatric divergence
 without gene flow. Our findings suggest that differential selection of
 natural or sexual environments is a prominent driver of species divergence
 in subtropical E. formosa and E. yayeyamana; whereas for tropical E.
 decorata and E. ornata at lower latitudes, allopatric isolation may well
 be a pivotal promoter of species formation.
description: EDOIMa2Full data set for IMa2 analyses of Euphaea decorata and Euphaea ornata.EFYIMa2Full data set for IMa2 analyses of Euphaea formosa and Euphaea yayeyamana.
DOI: 10.5061/dryad.6tb1702
title: Data from: Prednisolone induces osteoporosis-like phenotypes via focal adhesion signaling pathway in zebrafish larvae

description: Patients taking glucocorticoid or glucocorticoid-like drugs for an
 extended period of time may develop osteoporosis, termed
 glucocorticoid-induced osteoporosis (GIOP). GIOP is the most common form
 of secondary osteoporosis, but the mechanism underlying its development is
 unclear. In the present study, we used prednisolone to treat zebrafish
 larvae to investigate GIOP. Our RNA deep-sequencing (RNA-seq) results show
 that prednisolone affects genes known to act in the extracellular region.
 Therefore the extracellular region, extracellular matrix, and collagen
 trimer might be involved in glucocorticoid-induced osteoporosis. Kyoto
 Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that
 the focal adhesion signaling pathway is the most enriched signaling
 pathway in terms of differentially expressed genes (DEGs). In this
 pathway, integrin subunit alpha 10 (itga10) and integrin subunit beta like
 1 (itgbl1), genes encoding two adapter proteins, were down-regulated in
 the prednisolone-treated larvae. Further experiments showed that
 prednisolone contributes to GIOP by down-regulating itga10 and itgbl1.
description: gene expression
 dataThis file contains data
 of gene expression data from qRT-PCR. This file was made with Microsoft
 excel 2010.Supplementary excel
 1This
 file contains all the difference expression genes from RNA-seq analysis.
 This file was made with excel 2010Supplementary excel
 2This
 file contains GO results which enriched by DEGs of RNA-seq. This file was
 made with Microsoft excel 2010Supplementary excel
 3This
 file contains KEGG pathway results which enriched by DEGs of RNA-seq. This
 file was made with Microsoft excel 2010
DOI: 10.5061/dryad.m6t4j
title: Data from: An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles

description: Predicting functions of proteins and alternatively spliced isoforms
 encoded in a genome is one of the important applications of bioinformatics
 in the post-genome era. Due to the practical limitation of experimental
 characterization of all proteins encoded in a genome using biochemical
 studies, bioinformatics methods provide powerful tools for function
 annotation and prediction. These methods also help minimize the growing
 sequence-to-function gap. Phylogenetic profiling is a bioinformatics
 approach to identify the influence of a trait across species and can be
 employed to infer the evolutionary history of proteins encoded in genomes.
 Here we propose an improved phylogenetic profile-based method which
 considers the co-evolution of the reference genome to derive the basic
 similarity measure, the background phylogeny of target genomes for profile
 generation and assigning weights to target genomes. The ordering of
 genomes and the runs of consecutive matches between the proteins were used
 to define phylogenetic relationships in the approach. We used Escherichia
 coli K12 genome as the reference genome and its 4195 proteins were used in
 the current analysis. We compared our approach with two existing methods
 and our initial results show that the predictions have outperformed two of
 the existing approaches. In addition, we have validated our method using a
 targeted protein-protein interaction network derived from protein-protein
 interaction database STRING. Our preliminary results indicates that
 improvement in function prediction can be attained by using
 coevolution-based similarity measures and the runs on to the same scale
 instead of computing them in different scales. Our method can be applied
 at the whole-genome level for annotating hypothetical proteins from
 prokaryotic genomes.
description: SupplementaryFile_Benchmark_PairsAll pairs of proteins with a probability score &gt; 0.5 were considered for evaluation in our study. A total of 100, 000 protein pairs were evaluated and provided in Supplementary Material.
DOI: 10.15468/dl.9trwwb
title: Occurrence Download

description: A dataset containing 153590 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Specimen",
 "DatasetKey is Malacology Collection at the Academy of Natural Sciences of Philadelphia",
 "OccurrenceStatus is Present",
 "TaxonKey is Stylommatophora"
 ]
}

 The dataset includes 153590 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000488-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.864rv
title: Data from: Genotyping-by-sequencing of genome-wide microsatellite loci reveals fine-scale harvest composition in a coastal Atlantic salmon fishery

description: Individual assignment and genetic mixture analysis are commonly utilized
 in contemporary wildlife and fisheries management. Although microsatellite
 loci provide unparalleled numbers of alleles per locus, their use in
 assignment applications is increasingly limited. However, next-generation
 sequencing, in conjunction with novel bioinformatic tools allows large
 numbers of microsatellite loci to be simultaneously genotyped, presenting
 new opportunities for individual assignment and genetic mixture analysis.
 Here we scanned the published Atlantic salmon genome to identify 706
 microsatellite loci, from which we developed a final panel of 101
 microsatellites distributed across the genome (average 3.4 loci per
 chromosome). Using samples from 35 Atlantic salmon populations (n=1485
 individuals) from coastal Labrador, Canada, a region characterized by low
 levels of differentiation in this species, this panel identified 844
 alleles (average of 8.4 alleles per locus). Simulation-based evaluations
 of assignment and mixture identification accuracy revealed unprecedented
 resolution, clearly identifying 26 rivers or groups of rivers spanning 500
 km of coastline. This baseline was used to examine the stock composition
 of 696 individuals harvested in the Labrador Atlantic salmon fishery and
 revealed that coastal fisheries largely targeted regional groups
 (&lt;300km). This work suggests that the development and application
 of large sequenced microsatellite panels presents great potential for
 stock resolution in Atlantic salmon and more broadly in other exploited
 anadromous and marine species.
description: Labrador Atlantic Salmon
 Sequenced Microsatellite DataGenepop file of
 sequenced microsatellite genotype data for 35 salmon populations in
 Labrador Canada.
DOI: 10.5061/dryad.k5c8v
title: Data from: ‘Becoming a species by becoming a pest’ or how two maize pests of the genus Ostrinia possibly evolved through parallel ecological speciation events

description: New agricultural pest species attacking introduced crops may evolve from
 pre-existing local herbivores by ecological speciation, thereby becoming a
 species by becoming a pest. We compare the evolutionary pathways by which
 two maize pests (the Asian and the European corn borers, ACB and ECB) in
 the genus Ostrinia (Lepidoptera, Crambidae) probably diverged from an
 ancestral species close to the current Adzuki bean borer (ABB). We typed
 larval Ostrinia populations collected on maize and dicotyledons across
 China and eastern Siberia, at microsatellite and mitochondrial loci. We
 found only two clusters: one on maize (as expected) and a single one on
 dicotyledons despite differences in male mid-tibia morphology, suggesting
 that all individuals from dicotyledons belonged to the ABB. We found
 evidence for migrants and hybrids on both host plant types. Hybrids
 suggest that field reproductive isolation is incomplete between ACB and
 ABB. Interestingly, a few individuals with an ‘ABB-like’ microsatellite
 profile collected on dicotyledons had ‘ACB’ mtDNA rather than ‘ABB-like’
 mtDNA, whereas the reverse was never found on maize. This suggests
 asymmetrical gene flow directed from the ACB towards the ABB. Hybrids and
 backcrosses in all directions were obtained in no-choice tests. In
 laboratory conditions, they survived as well as parental strain
 individuals. In Xinjiang, we found ACB and ECB in sympatry, but no
 hybrids. Altogether, our results suggest that reproductive isolation
 between ACB and ABB is incomplete and mostly prezygotic. This points to
 ecological speciation as a possible evolutionary scenario, as previously
 found for ECB and ABB in Europe.
description: Comparison COI Ostrinia
 nubilalis - furnacalisComparison of the
 sequence of the COI of O. nubilalis and O. scapulalis showing the ClaI and
 VspI restriction used to differentiate these two
 speciesComplete Dataset
 ChinaThis file include the
 microsatellite and well as the mt genotypes of all chinese
 individualsMicrosatellite dataset
 used in Frolov et al. 2012Microsatellite-dataset-used-in-Frolov-et-al.-2012.xls
DOI: 10.5061/dryad.pm5rt
title: Data from: Anchors and snorkels: heterochrony, development and form in functionally-constrained fossil crassatellid bivalves

description: New growth-rate estimates for nine species from three genera of New
 Zealand Crassatellidae (Mollusca; Bivalvia), combined with existing
 morphometric ontogenetic descriptions, allow identification of
 heterochronic processes in the evolution of these genera. Both
 paedomorphosis (progenesis and neoteny) and peramorphosis (hypermorphosis
 and acceleration) have occurred within the clade. Overall, morphological
 variability and response to environmental pressure in this non-siphonate
 group is restricted by the interplay of anatomical and life-habit
 constraints. Stability in the substrate, predator avoidance, sluggish
 burrowing speed and inability to escape by deep burial are suggested as
 key drivers of, or constraints on, morphological change. Two groups of
 shell characters are identified: heavy, armoured “anchors” and elongate
 “snorkels”, which combine juvenile and adult traits in shells of different
 sizes and ages, produced by heterochronic variation in developmental
 timing. Anchors and snorkels both represent different ‘solutions’ to the
 problems of life as a non-siphonate, infaunal bivalve.
description: Collins et al SOM -
 isotopesIsotope data from
 crassatellid bivalves, associated with analyses of
 heterochrony
DOI: 10.5061/dryad.vj2nn
title: Data from: Competition between sympatric wolf taxa: an example involving African and Ethiopian Wolves

description: Carnivore populations are declining globally due to range contraction,
 persecution and prey depletion. One consequence of these patterns is
 increased range and niche overlap with other carnivores, and thus an
 elevated potential for competitive exclusion. Here we document competition
 between an endangered canid, the Ethiopian wolf (EW), and the newly
 discovered African wolf (AW) in central Ethiopia. The diet of the
 ecological specialist EW was dominated by rodents whereas the AW consumed
 more diverse diet also including insects and non-rodent mammals. EWs used
 predominantly intact habitat whereas AWs used mostly areas disturbed by
 humans and their livestock. Still, we observed 82 encounters between the
 two species, of which 94% were agonistic. The outcomes of agonistic
 encounters followed a territory-specific dominance pattern, with EWs
 dominating in intact habitat and AWs in human-disturbed areas. For AWs,
 the likelihood of winning encounters also increased with group size.
 Trapping data indicated that rodent species consumed by EWs were also
 available in the human-disturbed areas, suggesting that these areas could
 be suitable habitat for EWs if AWs were not territorially dominant there.
 Increasing human encroachment not only affects the prey base of EWs, but
 also may impact their survival by intensifying competition with sympatric
 AWs.
description: African wolf and
 Ethiopian wolf localitiesLocation of African wolf
 and Ethiopian wolf in respect to the buffer and core zone of the study
 area, Guassa mountainsEthiopian wolf-African
 wolf interaction-INT1African wolf-Ethiopian
 wolf interaction: Key for each of activity is given in the second sheet of
 the excel.Mole rat
 surveyMole rat survey on
 random plotsRodent Abundance
 dataResults from rodent
 trappingRodent diversity-buffer
 to core areaFour scripts used in
 this paper 1) interaction outcomes, 2) rodent abundance and 3) mole rat
 abundance in core area compared to the buffer zone
DOI: 10.5281/zenodo.17210526
title: White-fronted Woodpeckers select exotic trees with low wood density for cavity excavation in a Neotropical city

description: Urbanization alters ecological resources for cavity‐nesting communities. This transformation often reduces suitable substrates for excavation, such as standing deadwood, which is commonly removed for safety or aesthetic purposes. We examined tree selection for cavity excavation by the White‐fronted Woodpecker (Melanerpes cactorum) in urban parks of Córdoba, Argentina, a temperate, highly populated Neotropical city. Across 279 ha in 89 parks, we located 49 excavated trees and compared their attributes with paired control trees. Using generalized linear mixed models, we assessed the effects of wood density, decay class, diameter at breast height, tree height, canopy cover, and local tree density on tree selection. Substrate hardness, determined by wood density and decay, strongly shaped excavation patterns. Woodpeckers predominantly excavated live trees with low wood density, especially the exotic tree Melia azedarach, which represented nearly 80% of excavated trees despite comprising only 4% of available trees. White‐fronted Woodpeckers selected live trees only for species with low wood density, whereas higher wood-density species were increasingly chosen as decay advanced. No significant selection occurred for tree height, diameter, canopy cover, or local tree density. Current urban management may filter out deadwood‐dependent bird species, but exotic plantings may benefit woodpeckers if their wood properties fall within the woodpeckers’ biomechanical limits and preferences. Management strategies that retain some deadwood and also include tree species within the suitable hardness range when living could enhance diversity and resilience in urban cavity‐nesting communities.
DOI: 10.5281/zenodo.18381284
title: White-fronted Woodpeckers select exotic trees with low wood density for cavity excavation in a Neotropical city

description: Urbanization alters ecological resources for cavity‐nesting communities. This transformation often reduces suitable substrates for excavation, such as standing deadwood, which is commonly removed for safety or aesthetic purposes. We examined tree selection for cavity excavation by the White‐fronted Woodpecker (Melanerpes cactorum) in urban parks of Córdoba, Argentina, a temperate, highly populated Neotropical city. Across 279 ha in 89 parks, we located 49 excavated trees and compared their attributes with paired control trees. Using generalized linear mixed models, we assessed the effects of wood density, decay class, diameter at breast height, tree height, canopy cover, and local tree density on tree selection. Substrate hardness, determined by wood density and decay, strongly shaped excavation patterns. Woodpeckers predominantly excavated live trees with low wood density, especially the exotic tree Melia azedarach, which represented nearly 80% of excavated trees despite comprising only 4% of available trees. White‐fronted Woodpeckers selected live trees only for species with low wood density, whereas higher wood-density species were increasingly chosen as decay advanced. No significant selection occurred for tree height, diameter, canopy cover, or local tree density. Current urban management may filter out deadwood‐dependent bird species, but exotic plantings may benefit woodpeckers if their wood properties fall within the woodpeckers’ biomechanical limits and preferences. Management strategies that retain some deadwood and also include tree species within the suitable hardness range when living could enhance diversity and resilience in urban cavity‐nesting communities.
DOI: 10.5061/dryad.k47b2
title: Data from: Where do animals come from during post-fire population recovery? Implications for ecological and genetic patterns in post-fire landscapes

description: Identifying where animals come from during population recovery can help to
 understand the impacts of disturbance events and regimes on species
 distributions and genetic diversity. Alternative recovery processes for
 animal populations affected by fire include external recolonization,
 nucleated recovery from refuges, or in situ survival and population
 growth. We used simulations to develop hypotheses about ecological and
 genetic patterns corresponding to these alternative models. We tested
 these hypotheses in a study of the recovery of two small mammals, the
 Australian bush rat and the agile antechinus, after a large
 (&gt;50,000 ha), severe wildfire. The abundance of both species was
 severely reduced by fire and recovered to near or above pre-fire levels
 within two generations, yet we rejected a hypothesis of recovery by
 external recolonization. While the agile antechinus showed genetic
 evidence for far greater dispersal capacity than the bush rat, neither
 species showed gradients in abundance or genetic diversity with distance
 from unburnt forest during population recovery. Population recovery was
 driven by local-scale processes. However, the mechanisms differed between
 species, resulting from the spatial impacts of fire on habitat
 suitability. Agile antechinus populations recovered through population
 growth from in situ survivors. The bush rat followed a model of nucleated
 recovery, involving local recolonization from micro-refuges in topographic
 drainage lines. Nucleated recovery by the bush rat was associated with
 changes in dispersal, and fine-scale patterns of genetic admixture. We
 identified increased dispersal by females during recovery, contrasting
 with male-biased dispersal in unburnt forest. Such flexibility in
 dispersal can potentially increase recovery rates compared to expectations
 based on dispersal behavior within undisturbed populations. Our study
 shows how the initial distribution of survivors, determined by fire
 effects on resource distribution, determines the subsequent scaling of
 population recovery patterns, and the sensitivity of population
 distribution and genetic diversity to changing disturbance regimes.
description: Site-level abundance
 dataAbundance data at site
 levelTrap_level_trapping_dataCapture data at trap level for binomial modelling of capture patternsGenotypesGenotype data in Genalex format (http://biology-assets.anu.edu.au/GenAlEx/Welcome.html).
DOI: 10.5061/dryad.g216n
title: Data from: No evidence for nuclear introgression despite complete mtDNA replacement in the Carpathian newt (Lissotriton montandoni)

description: Patterns of interspecific introgression may vary geographically, and the
 distribution of introgressed variants can yield insight into the
 historical dynamics of genetic interactions between hybridizing species.
 Urodele amphibians, often characterized by limited mobility, deep
 intraspecific genetic structuring and vulnerability to climatic changes,
 constitute suitable models for such historical inferences. Here, we
 combine an extensive survey of the mitochondrial (mtDNA) and nuclear (15
 microsatellites) genomes in the Carpathian newt, Lissotriton montandoni
 (Lm) with species distribution modelling (SDM). Populations of the smooth
 newt, L. vulgaris (Lv) from the areas surrounding the Lm range were also
 sampled to test whether gene flow between these hybridizing species
 extends beyond the area of strict syntopy. The extent of introgression
 differs dramatically between the mitochondrial genome and the nuclear
 genome. While multiple, spatially and temporally distinct introgression
 events from Lv resulted in complete mtDNA replacement in Lm, there was
 little evidence of recent interspecific nuclear gene flow in the assayed
 markers. Microsatellite differentiation within Lm defines three units,
 probably derived from separate glacial refugia, located in the northern,
 eastern and southern part of the Carpathians. In situ survival and range
 fragmentation of Lm are supported by SDM, corroborating the role of the
 Carpathians as a major refugial area. Our results, in combination with
 previous reports of extensive introgression of the major
 histocompatibility complex (MHC) genes, emphasize the complexity of
 historical gene exchange between Lm and Lv.
description: IMa2 input file, mtDNA
 lineage J, Lissotriton montandoni and L. vulgarisJ_mon_vul_input.txtIMa2 input file, mtDNA lineage G, Lissotriton montandoni and L. vulgarisG_mon_vul_input.txtGPS coordinates of Lissotriton montandoni localities used for species distribution modelingMontandoni_localities.xlsxMicrosatellite genotypesGenepop format; 000000 - missing data (may inbclude null homozygotes); 999999 - confirmed null homozygotesNewts_ms_data.xlsMicrosatellite genotypes and mtDNA haplotypesGenepop-like format; 000000 - missing data (may inbclude null homozygotes); 999999 - confirmed null homozygotes; for individuals with sequenced mtDNA haplotype and GenBank Accession are givenNewts_ms_data_IndID_GenbankAcc.xlsClimatic data used in species distribution modellingThe input layers used to make the Maxent modelInput_layer.zip