cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j4sf2
title: Data from: The role of diversification in the continental scale community assembly of the American oaks (Quercus)

description: Premise of the study: Evolutionary and biogeographic history, including
 past environmental change and diversification processes, are likely to
 have influenced the expansion, migration, and extinction of populations,
 creating evolutionary legacy effects that influence regional species pools
 and the composition of communities. We consider the consequences of the
 diversification process in shaping trait evolution and assembly of
 oak-dominated communities throughout the continental U.S. Methods: Within
 the US oaks, we tested for phylogenetic and functional trait patterns at
 different spatial scales, taking advantage of a dated phylogenomic
 analysis of American oaks and the US Forest Service Forest Inventory
 Analysis. Key Results: We find 1) phylogenetic overdispersion at small
 grain sizes throughout the US across all spatial extents and 2) a shift
 from overdispersion to clustering with increasing grain sizes. Leaf traits
 have evolved in a convergent manner, and these traits are clustered in
 communities at all spatial scales, except in the far west, where species
 with contrasting leaf types co-occur. Conclusions: Our results support the
 hypotheses that 1) interspecific interactions were important in parallel
 adaptive radiation of the genus into a range of habitats across the
 continent and 2) that the diversification process is a critical driver of
 community assembly. Functional convergence of complementary species from
 distinct clades adapted to the same local habitats is a likely mechanism
 that allows distantly related species to coexist. Our findings contribute
 to an explanation of the long-term maintenance of high oak diversity and
 the dominance of the oak genus in North America.
description: fia.oak.plot.dataForest Inventory Analysis forest plot data for naturally assembled forests; standard plots that have oak trees in them throughout the continental U.S. Data are from the US Forest Service.US.oak.trait.meansSix leaf and stem functional traits for 49 U.S. oak species.Oaks.of.the.Americas.dated.phylogenyDated phylogeny of the Oaks of the Americas from Hipp et al 2018. Dates are in millions of years. Phylogeny was pruned to 49 US tree species.Hipp.et.al.2018.Phylo.tre
DOI: 10.5061/dryad.0rv1m
title: Data from: System-level insights into the cellular interactome of a non-model organism: inferring, modelling and analysing functional gene network of Soybean (Glycine max)

description: Cellular interactome, in which genes and/or their products interact on
 several levels, forming transcriptional regulatory-, protein interaction-,
 metabolic-, signal transduction networks, etc., has attracted decades of
 research focuses. However, such a specific type of network alone can
 hardly explain the various interactive activities among genes. These
 networks characterize different interaction relationships, implying their
 unique intrinsic properties and defects, and covering different slices of
 biological information. Functional gene network (FGN), a consolidated
 interaction network that models fuzzy and more generalized notion of
 gene-gene relations, have been proposed to combine heterogeneous networks
 with the goal of identifying functional modules supported by multiple
 interaction types. There are yet no successful precedents of FGNs on
 sparsely studied non-model organisms, such as soybean (Glycine max), due
 to the absence of sufficient heterogeneous interaction data. We present an
 alternative solution for inferring the FGNs of soybean (SoyFGNs), in a
 pioneering study on the soybean interactome, which is also applicable to
 other organisms. SoyFGNs exhibit the typical characteristics of biological
 networks: scale-free, small-world architecture and modularization.
 Verified by co-expression and KEGG pathways, SoyFGNs are more extensive
 and accurate than an orthology network derived from Arabidopsis. As a case
 study, network-guided disease-resistance gene discovery indicates that
 SoyFGNs can provide system-level studies on gene functions and
 interactions. This work suggests that inferring and modelling the
 interactome of a non-model plant are feasible. It will speed up the
 discovery and definition of the functions and interactions of other genes
 that control important functions, such as nitrogen fixation and protein or
 lipid synthesis. The efforts of the study are the basis of our further
 comprehensive studies on the soybean functional interactome at the genome
 and microRNome levels. Additionally, a web tool for information retrieval
 and analysis of SoyFGNs can be accessed at SoyFN:
 http://nclab.hit.edu.cn/SoyFN.
description: SoyFGNsThe RAR file contains four soybean functional gene networks. The README file describes the file using in details.
DOI: 10.5061/dryad.kh886
title: Data from: aTRAM - automated Target Restricted Assembly Method: a fast method for assembling loci across divergent taxa from next-generation sequencing data

description: Background: Assembling genes from next-generation sequencing data is not
 only time consuming but computationally difficult, particularly for taxa
 without a closely related reference genome. Assembling even a draft genome
 using de novo approaches can take days, even on a powerful computer, and
 these assemblies typically require data from a variety of genomic
 libraries. Here we describe software that will alleviate these issues by
 rapidly assembling genes from distantly related taxa using a single
 library of paired-end reads: aTRAM, automated Target Restricted Assembly
 Method. The aTRAM pipeline uses a reference sequence, BLAST, and an
 iterative approach to target and locally assemble the genes of interest.
 Results: Our results demonstrate that aTRAM rapidly assembles genes across
 distantly related taxa. In comparative tests with a closely related taxon,
 aTRAM assembled the same sequence as reference-based and de novo
 approaches taking on average &lt; 1 min per gene. As a test case with
 divergent sequences, we assembled &gt;1,000 genes from six taxa
 ranging from 25 – 110 million years divergent from the reference taxon.
 The gene recovery was between 97 – 99% from each taxon. Conclusions: aTRAM
 can quickly assemble genes across distantly-related taxa, obviating the
 need for draft genome assembly of all taxa of interest. Because aTRAM uses
 a targeted approach, loci can be assembled in minutes depending on the
 size of the target. Our results suggest that this software will be useful
 in rapidly assembling genes for phylogenomic projects covering a wide
 taxonomic range, as well as other applications. The software is freely
 available: http://www.github.com/juliema/aTRAM
description: Alignments from
 Pediculus schaeffi assembliesThis zip file contains
 folders with alignments from the assembly of Pediculus schaeffi genes
 using aTRAM, reference-based and de novo approaches. The alignments
 include each of these assemblies compared with the reference species
 Pediculus humanus as well as to each of the other assembly
 methods.DRYAD_PedSchaeffi_Data.zipAlignments from aTRAM assemblies across taxaAlignments of 1,107 aTRAM gene assemblies from six taxa. Each gene and each taxon is aligned to the reference sequence of Pediculus humanus.DRYAD_AllTaxon_Alignments.zip
DOI: 10.5061/dryad.bj376f61
title: Data from: Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia

description: Accurate information about the diet of large carnivores that are elusive
 and inhabit inaccessible terrain, is required to properly design
 conservation strategies. Predation on livestock and retaliatory killing of
 predators have become serious issues throughout the range of the snow
 leopard. Several feeding ecology studies of snow leopards have been
 conducted using classical approaches. These techniques have inherent
 limitations in their ability to properly identify both snow leopard feces
 and prey taxa. To examine the frequency of livestock prey and
 nearly-threatened argali in the diet of the snow leopard, we employed the
 recently developed DNA-based diet approach to study a snow leopard
 population located in the Tost Mountains, South Gobi, Mongolia. After DNA
 was extracted from the feces, a region of ~100 bp long from mitochondrial
 12S rRNA gene was amplified, making use of universal primers for
 vertebrates and a blocking oligonucleotide specific to snow leopard DNA.
 The amplicons were then sequenced using a next-generation sequencing
 platform. We observed a total of five different prey items from 81 fecal
 samples. Siberian ibex predominated the diet (in 70.4 % of the feces),
 followed by domestic goat (17.3 %) and argali sheep (8.6 %). The major
 part of the diet was comprised of large ungulates (in 98.8 % of the feces)
 including wild ungulates (79 %) and domestic livestock (19.7 %). The
 findings of the present study will help to understand the feeding ecology
 of the snow leopard, as well as to address the conservation and management
 issues pertaining to this wild cat.
description: uu_bk_uniq#_sortuu_uniq#_sort_sequence_datauu_uniq#_sort_l60c99_clean_rc_tag#uu_bk_uniq#_sort_l60c99_clean_rc_tag#uu_uniq_filtered_datauu_bk_filtered_data
DOI: 10.5061/dryad.gt8b5
title: Data from: Monogamy promotes altruistic sterility in insect societies

description: Monogamy is associated with sibling-directed altruism in multiple animal
 taxa, including insects, birds, and mammals. Inclusive-fitness theory
 readily explains this pattern by identifying high relatedness as a
 promoter of altruism. In keeping with this prediction, monogamy should
 promote the evolution of voluntary sterility in insect societies if
 sterile workers make for better helpers. However, a recent mathematical
 population-genetics analysis failed to identify a consistent effect of
 monogamy on voluntary worker sterility. Here, we revisit that analysis.
 First, we relax genetic assumptions, considering not only alleles of
 extreme effect—encoding either no sterility or complete sterility—but also
 alleles with intermediate effects on worker sterility. Second, we broaden
 the stability analysis—which focused on the invasibility of populations
 where either all workers are fully-sterile or all workers are
 fully-reproductive—to identify where intermediate pure or mixed
 evolutionarily-stable states may occur. Third, we consider a broader range
 of demographically-explicit ecological scenarios relevant to altruistic
 worker non-reproduction and to the evolution of eusociality more
 generally. We find that, in the absence of genetic constraints, monogamy
 always promotes altruistic worker sterility and may inhibit spiteful
 worker sterility. Our extended analysis demonstrates that an exact
 population-genetics approach strongly supports the prediction of
 inclusive-fitness theory that monogamy promotes sib-directed altruism in
 social insects.
description: Worker sterility - Code
 and dataWorker sterility - Code
 and data
DOI: 10.5061/dryad.7s848
title: Data from: Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow and natural selection in shaping patterns of population structure

description: Populus trichocarpa is an ecologically important tree across western North
 America. We used a large population sample of 498 accessions over a wide
 geographical area genotyped with a 34K Populus SNP array to quantify
 geographical patterns of genetic variation in this species (landscape
 genomics). We present evidence that three processes contribute to the
 observed patterns: (1) introgression from the sister species P.
 balsamifera (2) isolation-by-distance and (3) natural selection.
 Introgression was detected only at the margins of the species’
 distribution. Isolation-by-distance was significant across the sampled
 area as a whole, but no evidence of restricted gene flow was detected in a
 core of drainages from southern British Columbia. We identified a large
 number of FST outliers. GO analyses revealed that FST outliers are
 overrepresented in genes involved in circadian rhythm and response to
 red/far-red light when the entire dataset is considered, while in southern
 British Columbia heat response genes are overrepresented. We also
 identified strong correlations between geoclimate variables and allele
 frequencies at FST outlier loci that provide clues regarding the selective
 pressures acting at these loci.
description: FOR_DRYAD_TandB_fwd_june2013_434This file contains genotype data for 499 P. trichocarpa and 10 P. balsamifera accessions genotyped with a 34K SNP chip previously described in Geraldes et al 2013: “A 34K SNP genotyping array for Populus trichocarpa: Design, application to the study of natural populations and transferability to other Populus species.” Molecular Ecology Resources, 13(2):306-23. Details for all accessions genotyped can be found in Supplementary table 1 of “Landscape genomics of Populus trichocarpa: the role of hybridization, limited gene flow and natural selection in shaping patterns of population structure” accepted for publication in Evolution on July 8th 2014. This data file is a matrix with each locus in a row and each accession in a column. Genotypes are given in Illumina’s Forward strand as exported from Illumina’s GenomeStudio software. The numerical value after each genotype is the Genotype Call score. Loci with GenTrain score &lt;0.5 were considered failed assays and were not exported. The file contains data for the remaining 33,070 loci genotyped.
DOI: 10.5061/dryad.73gj4
title: Data from: A role for migration-linked genes and genomic islands in divergence of a songbird

description: Next-generation sequencing has made it possible to begin asking questions
 about the process of divergence at the level of the genome. For example,
 recently there has been a debate around the role of “genomic islands of
 divergence” (i.e. blocks of outlier loci) in facilitating the process of
 speciation-with-gene-flow. The Swainson’s thrush, Catharus ustulatus, is a
 migratory songbird with two genetically-distinct subspecies that differ in
 a number of traits known to be involved in reproductive isolation in birds
 (plumage coloration, song, and migratory behavior), despite contemporary
 gene flow along a secondary contact zone. Here we use RAD-PE sequencing to
 test emerging hypotheses about the process of divergence at the level of
 the genome and identify genes and gene regions involved in differentiation
 in this migratory songbird. Our analyses revealed distinct genomic islands
 on 15 of the 23 chromosomes and levels of differentiation that were 2-3
 orders of magnitude higher on the sex chromosomes than the autosomes.
 Further, an analysis of loci linked to pigmentation, song, and migratory
 behavior showed that genes linked to migration are significantly more
 differentiated then expected by chance, but that these genes lie primarily
 outside of the genomic islands. Overall, our analysis supports the idea
 that genes linked to migration play an important role in divergence in
 migratory songbirds, but we find no compelling evidence that the observed
 genomic islands are facilitating adaptive divergence in migratory
 behavior.
description: MEC-14-0327_Data_and_Scripts.tarData and scripts to reproduce analyses in the paper Data from: A role for migration-linked genes and genomic islands in divergence of a songbird
DOI: 10.5061/dryad.755m2n9
title: Data from: Post-Turing tissue pattern formation: advent of mechanochemistry

description: Chemical and mechanical pattern formation is fundamental during
 embryogenesis and tissue development. Yet, the underlying molecular and
 cellular mechanisms are still elusive in many cases. Most current theories
 assume that tissue development is driven by chemical processes: either as
 a sequence of chemical patterns each depending on the previous one, or by
 patterns spontaneously arising from specific chemical interactions (such
 as “Turing-patterns”). Within both theories, mechanical patterns are
 usually regarded as passive by-products of chemical pre-patters. However,
 several experiments question these theories, and an increasing number of
 studies shows that tissue mechanics can actively influence chemical
 patterns during development. In this study, we thus focus on the interplay
 between chemical and mechanical processes during tissue development. On
 one hand, based on recent experimental data, we develop new
 mechanochemical simulation models of evolving tissues, in which the full
 3D representation of the tissue appears to be critical for obtaining a
 realistic mechanochemical behaviour. The presented modelling approach is
 flexible and numerically studied using state of the art finite element
 methods. Thus, it may serve as a basis to combine simulations with new
 experimental methods in tissue development. On the other hand, we apply
 the developed approach and demonstrate that even simple interactions
 between tissue mechanics and chemistry spontaneously lead to robust and
 complex mechanochemical patterns. Especially, we demonstrate that the main
 contradictions arising in the framework of purely chemical theories are
 naturally and automatically resolved using the mechanochemical patterning
 theory.
description: VTK Data
 fileZIP archive of all
 vtk-Data files underlying the simulation figures as presented in the main
 manuscript as well as in the supporting informationvtk_data.tar.gz
DOI: 10.58053/mapbiomas/vjttbb
title: MapBiomas General “Handbook” - Algorithm Theoretical Basis Document (ATBD) - Collection 10 - Pasture - Appendix

description: This document details the theoretical basis, justification, and methods applied to produce annual maps of land cover and land use (LCLU) specifically for Pasture areas from 1985 to 2024 as part of MapBiomas Collection 10. Additionally, the document presents historical context and background information, a general description of the satellite imagery datasets, feature inputs, and details about the accuracy assessment method applied.
DOI: 10.5061/dryad.54p37
title: Data from: Wolves at the crossroad: fission-fusion range biogeography in the Western Carpathians and Central Europe

description: Aim: Population fragmentation represents a leitmotif of conservation
 biology, but the impact of population reconnection is less well studied.
 The recent recolonization of large carnivores in Europe is a good model
 for studying this phenomenon. We aim to show novel data regarding
 distribution and population genetic structure of the grey wolf in Central
 Europe, a region considered a frequent crossroad and contact zone of
 different phylogeographic lineages, in a biogeographic context. Location:
 Western Carpathians, Central Europe. Methods: In concordance with the
 presumption of a highly mobile mammal, individual-based Bayesian
 clustering and a posteriori definition of populations were used.
 Integrating the frameworks of landscape genetics and biogeography enabled
 the identification of transitions in population architecture. These
 patterns could be ascribed to isolating factors based on historical
 knowledge about species demography. Results: Genetic differentiation
 mirrors population isolation and recognized environmental clusters,
 suggesting ecotypic variation. The east–west split in the Western
 Carpathians likely represents the signature of range fragmentation during
 bottlenecks in the 20th century. Mitochondrial variability is more
 depleted than nuclear variability, indicating founder-flush demography.
 Microsatellites show finer-scale differentiation in the Carpathians
 compared to the European plain, corresponding to topographic
 heterogeneity. Long-range dispersal of a Carpathian wolf (ca. 300 km), the
 establishment of enclaves originated from the lowland population and
 admixture with mountain wolves were ascertained, indicating a population
 fraction producing large-scale gene flow. Main conclusion: Carpathian
 wolves are characterized by periods of population and range decline due to
 eradication, facilitating refugial role of alpine habitats and peripatric
 effects, followed by expansions and fusions probably caused by forest
 transition, population adaptation and efforts in conservation management.
 New occurrence and hybridization events predict further contacts between
 formerly isolated populations, with potential opposing effects of
 heterosis and outbreeding depression. Population recovery might be
 hindered due to isolation by environment and anthropogenic impacts.
description: microsatellite_allele_scoresMicrosatellite allele scores (18 loci) for Canis lupus from Central Europe and Canis lupus familiaris.allele_scores.xlsxwolf_distributionData on current wolf ditribution in Central Europe (updated from Chapron et al. 2014).environmental_clusters_central_europeEnvironmental clusters of Central Europe based on synthesis of climatic & topographical variables.landscape_fragmentationOutputs of landscape fragmentation analysis using method "effective mesh size" (Moser et al. 2007), including data on fragmentation geometry.land_cover_types_slovakiaLand cover types of the Western Carpathians (Slovakia).
DOI: 10.5061/dryad.77563
title: Data from: Cryptic species diversity reveals biogeographic support for the ‘mountain passes are higher in the tropics’ hypothesis

description: The ‘mountain passes are higher in the tropics’ (MPHT) hypothesis posits
 that reduced climate variability at low latitudes should select for
 narrower thermal tolerances, lower dispersal and smaller elevational
 ranges compared with higher latitudes. These latitudinal differences could
 increase species richness at low latitudes, but that increase may be
 largely cryptic, because physiological and dispersal traits isolating
 populations might not correspond to morphological differences. Yet
 previous tests of the MPHT hypothesis have not addressed cryptic
 diversity. We use integrative taxonomy, combining morphology (6136
 specimens) and DNA barcoding (1832 specimens) to compare the species
 richness, cryptic diversity and elevational ranges of mayflies
 (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the
 Andes (Ecuador; approx. 0°). We find higher species richness and smaller
 elevational ranges in Ecuador than Colorado, but only after quantifying
 and accounting for cryptic diversity. The opposite pattern is found when
 comparing diversity based on morphology alone, underscoring the importance
 of uncovering cryptic species to understand global biodiversity patterns.
description: AlignmentsDRYAD Alignments.zipTreesDRYAD Trees.zip