cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6301dq0
title: Data from: Cracking the case: seed traits and phylogeny predict time to germination in prairie restoration species

description: 1. Traits are important for understanding how plant communities assemble
 and function, providing a common currency for studying ecological
 processes across species, locations, and habitat types. However, most
 studies relating species traits to community assembly rely upon vegetative
 traits of mature plants. Seed traits, which are understudied relative to
 whole-plant traits, are key to understanding assembly of plant
 communities. This is particularly true in restored communities, which are
 typically started from seed, making germination a critical first step in
 community assembly. 2. We experimentally tested effects of seed traits
 (mass, shape, and embryo to seed size ratio) and phylogeny on germination
 in 32 species commonly used in prairie restoration in the Midwestern USA,
 analyzing data using time-to-event (survival) analysis. Since germination
 is influenced by seed dormancy, and dormancy-break treatments are commonly
 employed in restoration, we also tested the effects of two pre-treatments
 (cold stratification and gibberellic acid application) on time to
 germination. 3. Seed traits, phylogenetic position and seed pre-treatments
 affected time to germination. Of all traits tested, variables related to
 seed shape (height and shape variance) best predicted germination
 response, with high-variance (i.e., narrower) seeds germinating faster.
 Phylogenetic position (location of species on the phylogenetic tree
 relative to other tested species) was also an important predictor of
 germination. Closely related species showed similar patterns in time to
 germination. This was true even though all measured traits showed
 phylogenetic signal. 4. Seed traits, phylogenetic position and germination
 pre-treatments were important predictors of germination response for
 species commonly used in grassland restoration. Shape traits were
 especially important, while mass, often the only seed trait used to study
 community assembly, was not a strong predictor of germination timing.
 These findings illustrate the ecological importance of seed traits that
 are rarely studied in plant communities. This information can also be used
 to guide restoration planning and seed mix design.
description: Seed trait and
 germination dataMeasured traits of
 individual seeds (mass, shape and embryo measurements), and germination
 date for seeds of 32 prairie species under three germination
 pre-treatments. Also contains data from unmeasured control seeds under
 three germination pre-treatments.Barak_trait_germ.xlsxPhylogenetic treePhylogenetic tree of 32 prairie species.Barak_small_tree.tre
DOI: 10.5061/dryad.t3n50
title: Data from: Minimal variation in eutherian brain growth rates during fetal neurogenesis

description: A central question in the evolution of brain development is whether
 species differ in rates of brain growth during fetal neurogenesis. Studies
 of neonatal data have found allometric evidence for brain growth rate
 differences according to physiological variables such as relative
 metabolism and placental invasiveness, but these findings have not been
 tested against fetal data directly. Here, we measure rates of exponential
 brain growth acceleration in 10 eutherian mammals, two marsupials, and two
 birds. Eutherian brain acceleration exhibits minimal variation relative to
 body and visceral organ growth, varies independently of correlated growth
 patterns in other organs, and is unrelated to proposed physiological
 constraints such as metabolic rate or placental invasiveness. Brain growth
 rates in two birds overlap with eutherian variation, while marsupial brain
 growth is exceptionally slow. Peak brain growth velocity is linked in time
 with forebrain myelination and eye opening, reliably separates altricial
 species born before it from precocial species born afterwards, and is an
 excellent predictor of adult brain size (r2 = 0.98). Species with faster
 body growth exhibit larger relative brain size in early ontogeny, while
 brain growth is unrelated to allometric measures. These findings indicate
 a surprising conservation of brain growth rates during fetal neurogenesis
 in eutherian mammals, clarify sources of variation in neonatal brain size,
 and suggest that slow body growth rates cause species to be more
 encephalized at birth.
description: Halley_2017_DatasetData on fetal and perinatal growth (i.e. organ size at known age post-conception) in ten eutherian, two marsupial, and two bird species. Model estimates on neurodevelopmental event timing from Workman et al., 2013 (translatingtime.net). This file also includes life history and physiological variables used in statistical tests.
DOI: 10.5061/dryad.7tb527m3
title: Data from: Population divergence with or without admixture: selecting models using an ABC approach

description: Genetic data have been widely used to reconstruct the demographic history
 of populations, including the estimation of migration rates, divergence
 times and relative admixture contribution from different populations.
 Recently, increasing interest has been given to the ability of genetic
 data to distinguish alternative models. One of the issues that has plagued
 this kind of inference is that ancestral shared polymorphism is often
 difficult to separate from admixture or gene flow. Here, we applied an
 Approximate Bayesian Computation (ABC) approach to select the model that
 best fits microsatellite data among alternative splitting and admixture
 models. We performed a simulation study and showed that with reasonably
 large data sets (20 loci) it is possible to identify with a high level of
 accuracy the model that generated the data. This suggests that it is
 possible to distinguish genetic patterns due to past admixture events from
 those due to shared polymorphism (population split without admixture). We
 then apply this approach to microsatellite data from an endangered and
 endemic Iberian freshwater fish species, in which a clustering analysis
 suggested that one of the populations could be admixed. In contrast, our
 results suggest that the observed genetic patterns are better explained by
 a population split model without admixture.
description: Heredity_Sousaetal_HDY-11-OR0127RThis compressed file contains the files used for the simulation study and analysis of Iberochondrostoma lusitanicum microsatellite data performed in V Sousa, MA Beaumont, P Fernandes, MM Coelho, L Chikhi (2011) "Population divergence with or without admixture: selecting models using an ABC approach", Heredity.
DOI: 10.5061/dryad.kg4mq
title: Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)

description: Background: Phylogeography is an important tool that can be used to reveal
 cryptic biodiversity and to better understand the processes that promote
 lineage diversification. We studied the phylogeographic history of the
 Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to
 the California floristic province. We used multi-locus data to reconstruct
 the evolutionary history of A. lugubris and to discover the geographic
 location of major genetic breaks within the species. We also used species
 distribution modeling and comparative phylogeography to better understand
 the environmental factors that have shaped the genetic history of A.
 lugubris. Results: We found six major mitochondrial clades in A. lugubris.
 Nuclear loci supported the existence of at least three genetically
 distinct groups, corresponding to populations north of the San Francisco
 Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the
 central coast and southern California. All of the genetic breaks in
 mitochondrial and nuclear loci corresponded to regions where historical
 barriers to dispersal have been observed in other species. Geologic or
 water barriers likely were the most important factors restricting gene
 flow among clades. Climatic unsuitability during glacial maximum may have
 contributed to the isolation of the mitochondrial clades in the central
 coast and southern California. A projection of our species distribution
 model to a future scenario with a moderate amount of climate change
 suggests that most of the range of A. lugubris will remain climatically
 suitable, but climatic conditions in the Sierra Nevada and low elevation
 areas in Southern California are likely to deteriorate. Conclusions:
 Aneides lugubris contains substantial cryptic genetic diversity as a
 result of historical isolation of populations. At least two (and perhaps
 three) evolutionarily significant units in A. lugubris merit protection;
 all six mitochondrial clades should be considered as management units
 within the species.
description: A.lugubris_STRUCTURE_inputSTRUCTURE input fileA.lugubris_BEAST_mtDNA_combinedBEAST treeA.lugubris_ND4+cytbAlignment of mtDNA genes (ND4+cytb)A.lugubris_CXCR4_unphasedCXCR4 alignmentA.lugubris_KIAA2013_unphasedKIAA2013 alignmentA.lugubris_RAG2_unphasedRAG2 alignmentA.lugubris_SVEP1_unphasedSVEP1 alignmentA.lugubris_ZEB1_unphasedZEB1 alignmentA.lugubris_StarBEAST_4geneStarBEAST tree utilizing the ND4, cytb, CXCR4, and KIAA2013 genesA.lugubris_StarBEAST_5geneStarBEAST tree utilizing the nuclear genes CXCR4, KIAA2013, RAG2, SVEP1, and ZEB1A.lugubris_StarBEAST_7geneStarBEAST tree utilizing the mitochondrial ND4 and cytb genes, and the nuclear genes CXCR4, KIAA2013, RAG2, SVEP1, and ZEB1
DOI: 10.5061/dryad.ns1st0v2
title: Data from: Multi-locus analysis of Pristionchus pacificus on La Réunion Island reveals an evolutionary history shaped by multiple introductions, constrained dispersal events, and rare out-crossing

description: Pristionchus pacificus, recently established as a model organism in
 evolutionary biology, is a cosmopolitan nematode that has a necromenic
 association with scarab beetles. The diverse array of host beetle species
 and habitat types occupied by P. pacificus make it a good model for
 investigating local adaptation to novel environments. The presence of P.
 pacificus on La Réunion Island, a young volcanic island with a dynamic
 geological history and a wide variety of ecozones, facilitates such
 investigation in an island biogeographical setting. Microsatellite data
 from 20 markers and 223 strains, and mitochondrial sequence data from 272
 strains, reveal rich genetic diversity among La Réunion P. pacificus
 isolates, shaped by differentially timed introductions from diverse
 sources and in association with different beetle species. Distinctions
 between volcanic zones, and between arid western and wet eastern climatic
 zones, have likely limited westwards dispersal of recently colonised
 lineages, and maintained a genetic distinction between eastern and western
 clades. The highly selfing lifestyle of P. pacificus contributes to the
 strong fine-scale population structure detected, with each beetle host
 harbouring strongly differentiated assemblages of strains. Periodic
 out-crossing generates admixture between genetically diverse lineages,
 creating a diverse array of allelic combinations likely to increase the
 evolutionary potential of the species and facilitate adaptation to local
 environments and beetle hosts.
description: microsatellite
 genotypesA spreadsheet including
 the identifier of each strain, and the genotype at each microsatellite.
 For details of primers used, and strain collection, see
 manuscript.Collection
 recordDetails of the sampling
 localities and host beetles from which nematodes were
 obtained.Supplementary
 S1.docxSupplementary
 S1.pdfPrimer
 detailsDetails of the primers
 used to genotype microsatellites.supplementary
 S2.docXsupplementary
 S2.pdfGenBank
 JN812789-JN812965Mitochondrial sequence
 data is in GenBank with accessions JN812789-JN812965.JN812789-JN812965.txt
DOI: 10.5061/dryad.t8t25
title: Data from: Personality-matching habitat choice, rather than behavioural plasticity, is a likely driver of a phenotype–environment covariance

description: An emerging hypothesis of animal personality posits that animals choose
 the habitat that best fits their personality, and that the match between
 habitat and personality can facilitate population differentiation, and
 eventually speciation. However, behavioural plasticity and the adjustment
 of behaviours to new environments have been a classical explanation for
 such matching patterns. Using a population of dunnocks (Prunella
 modularis), we empirically tested whether personality or behavioural
 plasticity is responsible for the non-random distribution of shy and bold
 individuals in a heterogeneous environment. We found evidence for bold
 individuals settling in areas with high human disturbance, but also that
 birds became bolder with increasing age. Importantly, personality
 primarily determines the distribution of individuals, and behavioural
 adjustment over time contributes very little to the observed patterns. We
 cannot, however, exclude a possibility of very early behavioural
 plasticity (a type of developmental plasticity) shaping what we refer to
 as ‘personality’. Nonetheless, our findings highlight the role personality
 plays in shaping population structure, lending support to the theory of
 personality-mediated speciation. Moreover, personality-matching habitat
 choice has important implications for population management and
 conservation.
description: Territories and assigned
 squaresFor each breeding
 season, individuals were assigned to a grid of 141 squares covering the
 whole study area.Territories_squares_data.xlsxVisitor survey February 2014To quantify the levels of human disturbance in the study area, we counted the number of visitors in each of the 141 squares that covered our study area. In total, we conducted three surveys (February 2014, August 2014, February 2015), each over a period of 24 consecutive days.Visitor_survey_February_2014.xlsxVisitor survey August 2014To quantify the levels of human disturbance in the study area, we counted the number of visitors in each of the 141 squares that covered our study area. In total, we conducted three surveys (February 2014, August 2014, February 2015), each over a period of 24 consecutive days.Visitor_survey_August_2014.xlsxVisitor survey February 2015To quantify the levels of human disturbance in the study area, we counted the number of visitors in each of the 141 squares that covered our study area. In total, we conducted three surveys (February 2014, August 2014, February 2015), each over a period of 24 consecutive days.Visitor_survey_February_2015.xlsxFlight-initiation-distance, age, and sampling interval dataFlight-initiation distance measurements, age, and sampling interval of 99 individuals used in 'Personality-matching habitat choice, rather than behavioural plasticity, is a likely driver of a phenotype-environment covariance'.Flight-initiation-distance_data.xlsx
DOI: 10.5061/dryad.404rm
title: Data from: Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo-Australian Archipelago

description: Understanding spatial patterns of gene flow and genetic structure is
 essential for the conservation of marine ecosystems. Contemporary ocean
 currents and historical isolation due to Pleistocene sea-level
 fluctuations have been predicted to influence the genetic structure in
 marine populations. In the Indo-Australian Archipelago (IAA), the
 world's hotspot of marine biodiversity, seagrasses are a vital
 component but population genetic information is very limited. Here, we
 reconstructed the phylogeography of the seagrass Thalassia hemprichii in
 the IAA based on single nucleotide polymorphisms (SNPs) and then
 characterised the genetic structure based on a panel of 16 microsatellite
 markers. We further examined the relative importance of historical
 isolation and contemporary ocean currents in driving the patterns of
 genetic structure. Results from SNPs revealed three population groups:
 eastern Indonesia, western Indonesia (Sunda Shelf), and Indian Ocean;
 while the microsatellites supported five population groups (eastern
 Indonesia, Sunda Shelf, Lesser Sunda, Western Australia, and Indian
 Ocean). Both SNPs and microsatellites showed asymmetrical gene flow among
 population groups with a trend of south-westward migration from eastern
 Indonesia. Genetic diversity was generally higher in eastern Indonesia and
 decreased southwestward. The pattern of genetic structure and connectivity
 is attributed partly to the Pleistocene sea level fluctuations modified to
 a smaller level by contemporary ocean currents.
description: SNP_seq_dataSequence data is in phylip format. Site ID name for each sample can be found the sampling site GPS coordinate fileTh_SNP_data_UdhiHernawan_Chapter3.phyGenotype_msatsGenotype data is in GeAlEx format. Site ID for each sample can be found in the sampling site GPS coordinate file.Genalex_Th3all_IAA.xlsxSampling site GPS coordinatesGPS site IAA.xlsx
DOI: 10.5061/dryad.6vr28
title: Data from: Mapping habitats in a marine reserve showed how a 30-year trophic cascade altered ecosystem structure

description: Time-series studies have reported trophic cascades in land, freshwater and
 marine environments in many geographic areas. However, the spatial extent
 of habitats, a key metric of ecosystem structure, has not been mapped in
 these studies. Marine reserves can provide experimental, before-after and
 inside-outside (control-impacted), situations for assessing the impact of
 fishing on ecosystems. We mapped seabed habitats and their associated
 communities (biotopes) in New Zealand’s oldest marine reserve for
 comparison with pre-reserve maps created about 30 years previously. Areas
 grazed bare by sea urchins were entirely replaced in the centre of the
 reserve by kelp, or alga turf, an intermediate biotope between heavily
 grazed encrusting algae and lightly grazed kelp. Urchins declined
 following increased abundance and body size of spiny (rock) lobsters and
 fish (especially snapper) in the reserve but maintained bare rock outside.
 While this gradient in habitat change matched the gradient of predator
 abundance, it also matched the extent of reef habitat area. Thus the
 trophic cascade may be influenced by the effect of habitat on the
 abundance and behavioural interactions of urchins and their predators.
 Further ecosystem changes may arise should the abundance of
 mega-predators, such as seals, cetaceans and large sharks, increase in the
 region; if parasites become pathogenic; and/or when invasive species reach
 the reserve. No-take Marine Reserves provide real-world experiments that
 show the importance of species in food webs, and the consequences of
 fishing for ecosystems. Because these changes in ecosystem structure may
 continue, and will vary with environment, climate and species
 distributions, reserves need to be permanent and replicated
 geographically. Habitat maps should be produced for all reserves to enable
 ecological changes in the ecosystem to be spatially quantified.
description: Seabed habitat
 mapsThe files contain maps
 and ArcGIS shapefiles of the seabed habitats and biotopes at the Cape
 Rodney – Okakari Point Marine Reserve (also called Goat Island) adjacent
 to Leigh Marine Laboratory, North Island, New Zealand. There are two maps:
 The first was digitized from a map published by Ayling, A.M., Cumming, A.,
 Ballantine, W.J. (1981). Map of shore and sub-tidal habitats of the Cape
 Rodney-Okakari Point Marine Reserve, North Island, New Zealand in 3
 sheets, scale 1:2000. Department of Lands and Survey, Wellington, New
 Zealand. The second was remapped in 2006. A full description of the 2006
 methods and comparison of both maps is available in Leleu K, Remy-Zephir
 B., Grace R., Costello M.J. 2012. Mapping habitats in a marine reserve
 showed how a 30-year trophic cascade altered ecosystem structure.
 Biological Conservation , in press. The maps were created to quantify the
 area of seabed habitats and biotopes in the reserve and adjacent areas in
 each map.GIS_files_website.zip
DOI: 10.5061/dryad.1j292
title: Data from: Medically important differences in snake venom composition are dictated by distinct postgenomic mechanisms

description: Variation in venom composition is a ubiquitous phenomenon in snakes and
 occurs both interspecifically and intraspecifically. Venom variation can
 have severe outcomes for snakebite victims by rendering the specific
 antibodies found in antivenoms ineffective against heterologous toxins
 found in different venoms. The rapid evolutionary expansion of different
 toxin-encoding gene families in different snake lineages is widely
 perceived as the main cause of venom variation. However, this view is
 simplistic and disregards the understudied influence that processes acting
 on gene transcription and translation may have on the production of the
 venom proteome. Here, we assess the venom composition of six related
 viperid snakes and compare interspecific changes in the number of toxin
 genes, their transcription in the venom gland, and their translation into
 proteins secreted in venom. Our results reveal that multiple levels of
 regulation are responsible for generating variation in venom composition
 between related snake species. We demonstrate that differential levels of
 toxin transcription, translation, and their posttranslational modification
 have a substantial impact upon the resulting venom protein mixture.
 Notably, these processes act to varying extents on different toxin
 paralogs found in different snakes and are therefore likely to be as
 important as ancestral gene duplication events for generating
 compositionally distinct venom proteomes. Our results suggest that these
 processes may also contribute to altering the toxicity of snake venoms,
 and we demonstrate how this variability can undermine the treatment of a
 neglected tropical disease, snakebite.
description: crisp_dnaDNA alignment of the cysteine rich secretory protein (CRISP) toxin familyLAAO_dnaDNA alignment of the L-amino acid oxidase (LAAO) toxin familylectin_dnaDNA alignment of the C-type lectin (CTL) toxin familypla2_dnaDNA alignment of the phospholipase A2 (PLA2) toxin familyserine_protease_dnaDNA alignment of the serine protease (SP) toxin familysvmp_dnaDNA alignment of the snake venom metalloproteinase (SVMP) toxin family