cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g9k62
title: Data from: Genomic evidence for ecological divergence against a background of population homogeneity in the marine snail Chlorostoma funebralis

description: The balance between natural selection, gene flow and genetic drift is
 difficult to resolve in marine invertebrates with extensive dispersal and
 fluctuating population sizes. The intertidal snail Chlorostoma funebralis
 has planktonic larvae and previous work using mtDNA polymorphism reported
 no genetic population structure. Nevertheless, recent studies have
 documented differences in thermal tolerance and transcriptomic responses
 to heat stress between northern and southern California, USA, populations.
 To gain insight into the dynamics influencing adaptive divergence, we used
 double-digest restriction site-associated DNA (ddRAD) sequencing to
 identify 1861 genomewide, quality-filtered single-nucleotide polymorphism
 (SNP) loci for C. funebralis collected from three northern and three
 southern California sites (15 individuals per population). Considering all
 SNPs, there was no evidence for genetic differentiation among populations
 or regions (average FST = 0.0042). However, outlier tests revealed 34 loci
 putatively under divergent selection between northern and southern
 populations, and structure and SNP tree analyses based on these outliers
 show clear genetic differentiation between geographic regions. Three of
 these outliers are known or hypothesized to be involved in stress granule
 formation, a response to environmental stress such as heat. Combined with
 previous work that found thermally tolerant southern populations show high
 baseline expression of stress response genes, these results further
 suggest that thermal stress is a strong selective pressure across C.
 funebralis populations. Overall, this study increases our understanding of
 the factors constraining local adaptation in marine organisms, while
 suggesting that ecologically driven, strong differentiation can occur at
 relevant loci in a species with planktonic larvae.
description: C. funebralis multilocus
 SNP genotypesMultilocus SNP genotypes
 for each of 90 Chlorostoma funebralis individuals (45 from northern
 California, USA and 45 from southern California) at all 2371 high quality,
 filtered loci (in Genepop format) obtained from ddRAD
 sequencingbatch_7.genepop
DOI: 10.5061/dryad.j25m2
title: Data from: Adaptation to climate through flowering phenology: a case study in Medicago truncatula

description: Local climatic conditions likely constitute an important selective
 pressure on genes underlying important fitness-related traits such as
 flowering time and in many species flowering phenology and climatic
 gradients strongly covary. To test whether climate shapes genetic
 variation on flowering time genes and to identify candidate flowering
 genes involved in the adaptation to environmental heterogeneity, we used a
 large M. truncatula core collection to examine the association between
 nucleotide polymorphisms at 224 candidate genes and both climate variables
 and flowering phenotypes. Unlike genome-wide studies, candidate gene
 approaches are expected to enrich for the number of meaningful trait
 associations because they specifically target genes that are known to
 affect the trait of interest. We found that flowering time mediates
 adaptation to climatic conditions mainly by variation at genes located
 upstream in the flowering pathways, close to the environmental stimuli.
 Variables related to the annual precipitation regime reflected selective
 constraints on flowering time genes better than the other variables tested
 (temperature, altitude, latitude or longitude). By comparing phenotype and
 climate associations, we identified 12 flowering genes as the most
 promising candidates responsible for phenological adaptation to climate.
 Four of these genes were located in the known flowering time QTL region on
 chromosome 7. However, climate and flowering associations also highlighted
 largely distinct gene sets, suggesting different genetic architectures for
 adaptation to climate and flowering onset.
description: Burgarella_2016_SNP_genotypesGenotypes of 5206 SNPs from 224 candidate flowering genes for 174 Medicago truncatula accessionsBurgarella_2016_SNP_contextChromosome position, gene call, gene product and gene context (I= intron, C=codon, 0=intergenic, 3=3'UTR, 5=5'UTR) for 5206 SNPS from 224 candidate flowering genes in Medicago truncatula.Burgarella_2016_worldclim_dataClimate data for 174 Medicago truncatula accessions obtained from the Worldclim database (http://www.worldclim.org/)Burgarella_2016_kinship_matrixKinship matrix of 174 Medicago truncatula accessions used in association analysis.Burgarella_2016_phenotype_dataFlowering time measures significantly associated with genotypes in Medicago truncatula
DOI: 10.5061/dryad.0mg54
title: Data from: Admixture mapping identifies introgressed genomic regions in North American canids

description: Hybrid zones typically contain novel gene combinations that can be tested
 by natural selection in a unique genetic context. Parental haplotypes that
 increase fitness can introgress beyond the hybrid zone, into the range of
 parental species. We used the Affymetrix canine SNP genotyping array to
 identify genomic regions tagged by multiple ancestry informative markers
 that are more frequent in an admixed population than expected. We surveyed
 a hybrid zone formed in the last 100 years as coyotes expanded their range
 into eastern North America. Concomitant with expansion, coyotes hybridized
 with wolves and some populations became more wolflike, such that coyotes
 in the northeast have the largest body size of any coyote population.
 Using a set of 3102 ancestry informative markers, we identified 60
 differentially introgressed regions in 44 canines across this admixture
 zone. These regions are characterized by an excess of exogenous ancestry
 and, in northeastern coyotes, are enriched for genes affecting body size
 and skeletal proportions. Further, introgressed wolf-derived alleles have
 penetrated into Southern US coyote populations. Because no wolves
 currently exist in this area, these alleles are unlikely to have
 originated from recent hybridization. Instead, they probably originated
 from intraspecific gene flow or ancient admixture. We show that grey wolf
 and coyote admixture has far-reaching effects and, in addition to
 phenotypically transforming admixed populations, allows for the
 differential movement of alleles from different parental species to be
 tested in new genomic backgrounds.
description: Sample_InformationSample information and genome-wide ancestry estimatesAIMS_deltaGenotypes for AIMs, delta values, outlier block detection, and population-specificity
DOI: 10.5061/dryad.5gf06
title: Data from: Anthracycline drugs on modified surface of quercetin-loaded polymer nanoparticles: a dual drug delivery model for cancer treatment

description: Polymer nanoparticles are vehicles used for delivery of hydrophobic
 anti-cancer drugs, like doxorubicin, paclitaxel or chemopreventors like
 quercetin (Q). The present study deals with the synthesis and
 characterisation of nano formulations (NFs) from Q loaded PLGA (poly
 lactic-co-glycolic acid) nano particles (NPs) by surface modification. The
 surface of Q-loaded (NPs) is modified by coating with biopolymers like
 bovine serum albumin (BSA) or histones (His). Conventional
 chemotherapeutic drugs adriamycin (ADR) and mitoxantrone (MTX) are bound
 to BSA and His respectively before being coated on Q-loaded NPs to nano
 formulate NF1 and NF2 respectively. The sizes of these NFs are in the
 range 400-500 nm as ascertained by SEM and DLS measurements. Encapsulation
 of Q in polymer NPs is confirmed from shifts in FT-IR, TGA and DSC traces
 of Q-loaded NPs compared to native PLGA and Q. Surface modification in NFs
 is evidenced by three distinct regions in their TEM images; the core,
 polymer capsule and the coated surface. Negative zeta potential of
 Q-loaded NPs shifted to positive potential on surface modification in NF1
 and NF2. In vitro release of Q from the NFs lasted up to twenty days with
 an early burst release. NF2 is better formulation than NF1 as loading of
 MTX is 85% compared to 23% loading of ADR. Such NFs are expected to
 overcome multi-drug resistance (MDR) by reaching and treating the target
 cancerous cells by virtue of size, charge and retention.
description: FTIR-
 BSAFTIR-NF1FTIR-NF2FTIR-Q NANOFTIR-QFTIR-VOIDDSC-NF1DSC-NF2DSC-QDSC-VOIDTGA-1 pdfTGA-1TGA-2 pdfTGA-2TGA-3 pdfTGA-3Release Kinetics
DOI: 10.5061/dryad.475t2
title: Data from: Phylogeographic concordance factors quantify phylogeographic congruence among co-distributed species in the Sarracenia alata pitcher plant system

description: Comparative phylogeographic investigations have identified congruent
 phylogeographic breaks in co-distributed species in nearly every region of
 the world. The qualitative assessments of phylogeographic patterns
 traditionally used to identify such breaks, however, are limited because
 they rely on identifying monophyletic groups across species and do not
 account for coalescent stochasticity. Only long-standing phylogeographic
 breaks are likely to be obvious; many species could have had a concerted
 response to more recent landscape events, yet possess subtle signs of
 phylogeographic congruence because ancestral polymorphism has not
 completely sorted. Here we introduce Phylogeographic Concordance Factors
 (PCFs), a novel method for quantifying phylogeographic congruence across
 species. We apply this method to the Sarracenia alata pitcher plant
 system, a carnivorous plant with a diverse array of commensal organisms.
 We explore whether a group of ecologically associated arthropods have
 co-diversified with the host pitcher plant, and identify if there is a
 positive correlation between ecological interaction and PCFs. Results
 demonstrate that multiple arthropods share congruent phylogeographic
 breaks with S. alata, and provide evidence that the level of ecological
 association can be used to predict the degree of similarity in the
 phylogeographic pattern. This study outlines an approach for quantifying
 phylogeographic congruence, a central concept in biogeographic research.
description: Satler&Carstens2016
DOI: 10.5061/dryad.q4h2r
title: Data from: Dispersal largely explains the Gondwanan distribution of the ancient tropical clusioid plant clade

description: PREMISE OF THE STUDY: The clusioid clade (Malpighiales) has an ancient
 fossil record (∼90 Ma) and extant representatives exhibit a pantropical
 distribution represented on all former Gondwanan landmasses (Africa,
 Australia, India, Madagascar, and South America) except Antarctica.
 Several biogeographers have hypothesized that the clusioid distribution is
 an example of Gondwanan vicariance. Our aim is to test the hypothesis that
 the modern distribution of the clusioid clade is largely explained by
 Gondwanan fragmentation. METHODS: Using a four gene, 207-taxon data set we
 simultaneously estimated the phylogeny and divergence times of the
 clusioid clade using a Bayesian Markov chain Monte Carlo approach.
 Ancestral Area Reconstructions (AARs) were then conducted on a
 distribution of 1000 trees and summarized on a reduced phylogeny. KEY
 RESULTS: Divergence time estimates and AARs revealed only two or four
 cladogenic events that are potentially consistent with Gondwanan
 vicariance, depending on the placement of the ancient fossil Paleoclusia.
 In contrast, dispersal occurred on &gt; 25% of the branches,
 indicating the current distribution of the clade likely reflects extensive
 recent dispersal during the Cenozoic (&lt; 65 Ma), most of which
 occurred after the beginning of the Eocene (∼56 Ma). CONCLUSIONS: These
 results support growing evidence that suggests many traditionally
 recognized angiosperm clades (families and genera) are too young for their
 distributions to have been influenced strictly by Gondwanan fragmentation.
 Instead, it appears that corridors of dispersal may be the best
 explanation for numerous angiosperm clades with Gondwanan distributions.
description: 4 gene cludioid
 Alignmentnexus alignment file
 with partition informationclusioid4gene_Ruhfel.nexBC_MCCFull_Ruhfel_clusioidsFull maximum clade credibility chronogram of the clusioid clade based on the analysis of a combined four-gene data set (BC placement of Paleoclusia; see text for details). Created by BEAST.CC_MCCFull_Ruhfel_clusioidsFull maximum clade credibility chronogram of the clusioid clade based on the analysis of a combined four-gene data set (CC placement of Paleoclusia; see text for details). Created by BEAST.
DOI: 10.5061/dryad.kk174
title: Data from: Processes of community assembly in an environmentally heterogeneous, high biodiversity region

description: Despite decades of study, the relative importance of niche-based versus
 neutral processes in community assembly remains largely ambiguous. Recent
 work suggests niche-based processes are more easily detectable at coarser
 spatial scales, while neutrality dominates at finer scales. Analyses of
 functional traits with multi-year multi-site biodiversity inventories may
 provide deeper insights into assembly processes and the effects of spatial
 scale. We examined associations between community composition, species
 functional traits, and environmental conditions for plant communities in
 the Kouga-Baviaanskloof region, an area within South Africa's Cape
 Floristic Region (CFR) containing high α and β diversity. This region
 contains strong climatic gradients and topographic heterogeneity, and is
 comprised of distinct vegetation classes with varying fire histories,
 making it an ideal location to assess the role of niche-based
 environmental filtering on community composition by examining how traits
 vary with environment. We combined functional trait measurements for over
 300 species with observations from vegetation surveys carried out in
 1991/1992 and repeated in 2011/2012. We applied redundancy analysis,
 quantile regression, and null model tests to examine trends in species
 turnover and functional traits along environmental gradients in space and
 through time. Functional trait values were weakly associated with most
 spatial environmental gradients and only showed trends with respect to
 vegetation class and time since fire. However, survey plots showed greater
 compositional and functional stability through time than expected based on
 null models. Taken together, we found clear evidence for functional
 distinctions between vegetation classes, suggesting strong environmental
 filtering at this scale, most likely driven by fire dynamics. In contrast,
 there was little evidence of filtering effects along environmental
 gradients within vegetation classes, suggesting that assembly processes
 are largely neutral at this scale, likely the result of very high
 functional redundancy among species in the regional species pool.
description: Baviaanskloof percent
 cover, trait, and environment datasetA dataset combining
 trait measurements for species observed in releve plots in the
 Baviaankloof region of South Africa. Environmental conditions at those
 plots also included.baviaanskloof_data_dryad.csv
DOI: 10.5061/dryad.75876
title: Data from: Analysis of the porcine APOA2 gene expression in liver, polymorphisms identification and association with fatty acid composition traits

description: APOA2 is a protein implicated in triglyceride, fatty acid and glucose
 metabolism. In pigs, the APOA2 gene is located on pig chromosome 4 (SSC4)
 in a QTL region affecting fatty acid composition, fatness and growth
 traits. In this study, we evaluated APOA2 as a candidate gene for meat
 quality traits in an Iberian × Landrace backcross population. The
 APOA2:c.131T&gt;A polymorphism, located in exon 3 of APOA2 and
 determining a missense mutation, was associated with the percentage of
 hexadecenoic acid [C16:1(n–9)], linoleic acid [C18:2(n–6)], α-linolenic
 acid [C18:3(n–3)], dihomo-gamma-linolenic acid [C20:3(n–6)] and
 polyunsaturated fatty acids (PUFAs) in backfat. Furthermore, this SNP was
 associated with the global mRNA expression levels of APOA2 in liver and
 was used as a marker to determine allelic expression imbalance by
 pyrosequencing. We determined an overexpression of the T allele in
 heterozygous samples with a mean ratio of 2.8 (T/A), observing a high
 variability in the allelic expression among individuals. This result
 suggests that complex regulatory mechanisms, beyond a single polymorphism
 (e.g. epigenetic effects or multiple cis-acting polymorphisms), may be
 regulating APOA2 gene expression.
description: Porcine APOA2 gene
 expression in liverData from Analysis of
 the porcine APOA2 gene expression in liver, polymorphisms identification
 and association with fatty acid composition traits. Contains SNP genotypes
 for GWAS and eGWAS studies, mRNA expression of APOA2 in liver, and fatty
 acid composition in backfat and muscle
DOI: 10.5061/dryad.k05qb
title: Data from: Megaphylogenetic specimen-level approaches to the Carex (Cyperaceae) phylogeny using ITS, ETS, and matK sequences: implications for classification

description: We present the first large-scale phylogenetic hypothesis for the genus
 Carex based on 996 of the 1983 accepted species (50.23%). We used a
 supermatrix approach using three DNA regions: ETS, ITS and matK. Every
 concatenated sequence was derived from a single specimen. The topology of
 our phylogenetic reconstruction largely agreed with previous studies. We
 also gained new insights into the early divergence structure of the two
 largest clades, core Carex and Vignea clades, challenging some previous
 evolutionary hypotheses about inflorescence structure. Most sections were
 recovered as non-monophyletic. Homoplasy of characters traditionally
 selected as relevant for classification, historical misunderstanding of
 how morphology varies across Carex, and regional rather than global views
 of Carex diversity seem to be the main reasons for the high levels of
 polyphyly and paraphyly in the current infrageneric classification.
description: Supplemental Data
 5Reference tree. Topology
 revealed by the all-nrDNA matrix of concatenated sequences of ETS, ITS and
 matK. Branches with support below 50% bootstrap are
 collapsed.Supplemental Data 1
 _reference_tree.treeSupplemental Data
 6Query tree. Topology
 revealed by the all-sequences matrix constrained by the reference tree,
 using concatenated sequences of ETS, ITS and matK. Branches with support
 below 75% aLRT are collapsed.Supplemental Data 2
 _query_tree_sections_3_CollapsedUnder75_EDIT.treSupplemental Appendix 1Preliminary assingment to sections according previously published data (see main text for details).Supplemental Appendix 2TDI values recovered for sections when tested on the query tree.Supplemental Data 2ETS sequences matrixSupplemental Data 3ITS sequences matrixSupplemental Data 4matK sequences matrix
DOI: 10.5061/dryad.22n3d
title: Data from: Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (Hystrix cristata) long-lasting and successful invasion?

description: Studying the evolutionary dynamics of an alien species surviving and
 continuing to expand after several generations can provide fundamental
 information on the relevant features of clearly successful invasions.
 Here, we tackle this task by investigating the dynamics of the genetic
 diversity in invasive crested porcupine (Hystrix cristata) populations,
 introduced to Italy about 1500 years ago, which are still growing in size,
 distribution range and ecological niche. Using genome-wide RAD markers, we
 describe the structure of the genetic diversity and the demographic
 dynamics of the H. cristata invasive populations and compare their genetic
 diversity with that of native African populations of both H. cristata and
 its sister species, H. africaeaustralis. First, we demonstrate that
 genetic diversity is lower in both the invasive Italian and the North
 Africa source range relative to other native populations from sub-Saharan
 and South Africa. Second, we find evidence of multiple introduction events
 in the invasive range followed by very limited gene flow. Through
 coalescence-based demographic reconstructions, we also show that the
 bottleneck at introduction was mild and did not affect the introduced
 genetic diversity. Finally, we reveal that the current spatial expansion
 at the northern boundary of the range is following a leading-edge model
 characterized by a general reduction of genetic diversity towards the edge
 of the expanding range. We conclude that the level of genome-wide
 diversity of H. cristata invasive populations is less important in
 explaining its successful invasion than species-specific life-history
 traits or the phylogeographic history in the native source range.
description: Filtered_RADseq_datasets_crested_porcupineThis file contains three datasets of African porcupines (*Hystrix cristata* and *H. africaeaustralis*) samples as presented in the paper "Long live the alien: is high genetic diversity a pivotal aspect of crested porcupine (*Hystrix cristata*) long-lasting and successful invasion?" doi: 10.1111/mec.13698. Data were produced by single-digestion RAD sequencing using SbfI as restriction enzyme and analyzed in Stacks (Catchen et al. 2013) using denovo_map.pl. Catalogs of RAD loci were exported using export_sql.pl script in the Stacks package and further filtered using the custom python script “loci_selector.py” released as Supplementary Material in the above mentioned publication.Dataset_invasive_crested_porcupine_genomics.tar.gz
DOI: 10.5061/dryad.7309c
title: Data from: Mammal madness: is the mammal tree of life not yet resolved?

description: Most molecular phylogenetic studies place all placental mammals into four
 superordinal groups, Laurasiatheria (e.g. dogs, bats, whales),
 Euarchontoglires (e.g. humans, rodents, colugos), Xenarthra (e.g.
 armadillos, anteaters) and Afrotheria (e.g. elephants, sea cows, tenrecs),
 and estimate that these clades last shared a common ancestor 90–110
 million years ago. This phylogeny has provided a framework for numerous
 functional and comparative studies. Despite the high level of congruence
 among most molecular studies, questions still remain regarding the
 position and divergence time of the root of placental mammals, and certain
 ‘hard nodes’ such as the Laurasiatheria polytomy and Paenungulata that
 seem impossible to resolve. Here, we explore recent consensus and conflict
 among mammalian phylogenetic studies and explore the reasons for the
 remaining conflicts. The question of whether the mammal tree of life is or
 can be ever resolved is also addressed.
description: Foley_Springer_Teeling_PRSB2016_AlignmentAlignment and data partitions used to generate the ML tree used for estimating divergence times in PAML.FoleySpringerTeelingPRSB2016_Alignment.nex