cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3qq01
title: Data from: Assessing the spatial ecology and resource use of a mobile and endangered species in an urbanized landscape using satellite telemetry and DNA faecal metabarcoding

description: The conservation of highly mobile species presents challenges to managers
 for assessment of threats to survival, given the difficulties in locating
 and observing such species. Here we evaluate satellite telemetry, DNA
 faecal metabarcoding and traditional field observations as three
 complementary techniques to acquire critical management information for an
 endangered species, Carnaby's Cockatoo Calyptorhynchus latirostris.
 Satellite telemetry of 23 birds resulted in 6026 location fixes accurate
 to within 500 m, and combined with extensive field observations and DNA
 faecal metabarcoding resulted in a more detailed understanding of how this
 species survives in an urbanised landscape. We identified 168 night
 roosts, 75% of which were previously unknown, which will contribute
 towards a more accurate population size estimate based on annual counts of
 roosting birds. We also determined the scale of daily movements (morning
 5.4 ± 3.4 km from roost, afternoon 5.5 ± 3.3 km to roost; maximum distance
 between consecutive roosts 69.7 km) and the size of foraging areas around
 roosts (range 17 to 276 km2), and identified dependence on a variety of
 native and exotic food sources. Field observations identified 11
 food-plant families, but combined with DNA faecal metabarcoding this was
 extended to 21 food-plant families. The three techniques were compared to
 assess their individual and collective values. By combining spatial
 ecology information from satellite telemetry with ecological knowledge
 from field observation and DNA faecal analysis, we gained deeper insights
 into the ecology of the species than would have been possible from any one
 technique alone. This information will lead to more strategic conservation
 planning to allow this species to persist within a rapidly expanding urban
 environment.
description: Unique_IT_Run27_WTBCPool1_trnLc66_47RUnique_IT_RUN27_WTBCPool2_trnLc68_47RUnique_IT_Run27_WTBCPool3_trnLc69_47RUnique_IT_Run27_WTBCPool4_trnLc70_47RUnique_IT_Run27_WTBCPool5_trnLc61_48RUnique_IT_Run27_WTBCPool6_trnLc62_48RUnique_IT_Run27_WTBCPool7_trnLc63_48RUnique_IT_Run27_WTBCPool8_trnLc64_48RUnique_IT_Run27_WTBCPool9_trnLc65_48RUnique_IT_Run27_WTBCPool10_trnLc66_48RUnique_IT_Run27_WTBCPool11_trnLc68_48R
DOI: 10.5061/dryad.kt364
title: Data from: Cryptic lineages of a common alpine mayfly show strong life-history divergence

description: Understanding ecological divergence of morphologically similar but
 genetically distinct species – previously considered as a single
 morphospecies – is of key importance in evolutionary ecology and
 conservation biology. Despite their morphological similarity, cryptic
 species may have evolved distinct adaptations. If such ecological
 divergence is unaccounted for, any predictions about their responses to
 environmental change and biodiversity loss may be biased. We used
 spatio-temporally replicated field surveys of larval cohort structure and
 population genetic analyses (using nuclear microsatellite markers) to test
 for life-history divergence between two cryptic lineages of the alpine
 mayfly Baetis alpinus in the Swiss Alps. We found that the more widespread
 and abundant cryptic lineage represents a ‘generalist’ with at least two
 cohorts per year, whereas the less abundant lineage is restricted to
 higher elevations and represents a ‘specialist’ with a single cohort per
 year. Importantly, our results indicate partial temporal segregation in
 reproductive periods between these lineages, potentially facilitating
 local coexistence and reproductive isolation. Taken together, our findings
 emphasize the need for a taxonomic revision: widespread and apparently
 generalist morphospecies can hide cryptic lineages with much narrower
 ecological niches and distribution ranges.
description: Nuclear genotypes at 10
 microsatellite loci and additional information regarding the larvae
 samplednuclear data (10
 microsatellites) of Baetis alpinus larvae sampled on several
 dates/assigned to different cohorts in two basins of the Swiss Alps (Val
 Roseg and Lötschental).Nuclear_SSRs_Leys_et_al_MolEcol.txtlife history dataLarval size measurements of Baetis alpinus species group individuals collected in Roseg and Lötschental (2012 and 2013)Larval sizes_Leys_et_al_MolEcol.txtStream temperature dataTributary (hourly logged) and glacial main-stream (predicted from hydrological station) temperature estimates at Val Roseg and Lötschental sitesStream Temperature_Leys_et_al_MolEcol.txtPeriphyton biomass estimatesPeriphyton biomass estimates in Val Roseg and Lötschental (2013)Periphyton_Leys_et_al_MolEcol.txtWater Chemistry, conductivity and monthly mean temperaturesWater Chemistry, conductivity and monthly mean temperatures in Val Roseg and Lötschental (mostly 2013)Water Chemistry_Leys_et_al_MolEcol.txt
DOI: 10.5061/dryad.1hs2m
title: Data from: In the shadows: phylogenomics and coalescent species delimitation unveil cryptic diversity in a Cerrado endemic lizard (Squamata: Tropidurus)

description: The recognition of cryptic diversity within geographically widespread
 species is gradually becoming a trend in the highly speciose Neotropical
 biomes. The statistical methods to recognise such cryptic lineages are
 rapidly advancing, but have rarely been applied to genomic-scale datasets.
 Herein, we used phylogenomic data to investigate phylogenetic history and
 cryptic diversity within Tropidurus itambere, a lizard endemic to the
 Cerrado biodiversity hotspot. We applied a series of phylogenetic methods
 to reconstruct evolutionary relationships and a coalescent Bayesian
 species delimitation approach (BPP) to clarify species limits. The BPP
 results suggest that the widespread nominal taxon comprises a complex of 5
 highly supported and geographically structured cryptic species. We
 highlight and discuss the different topological patterns recovered by
 concatenated and coalescent species tree methods for these closely related
 lineages. Finally, we suggest that the existence of cryptic lineages in
 the Cerrado is much more common than traditionally thought, highlighting
 the value of using NGS data and coalescent techniques to investigate
 patterns of species diversity.
description: AHE_BPP_alignmentsText file containing the alignments of all captured AHE loci used in the BPP analysesAHE_concatenated_alignment_partitionsPartitions of the AHE concatenated dataset used in phylogenetic analyses, as estimated by PartitionFinder2AHE_concatenated_alignmentPhylip file with concatenated AHE loci used in phylogenetic analysesCytb_aligmentPhylip file with cytb alignments
DOI: 10.5061/dryad.1k79k
title: Data from: High monetary reward rates and caloric rewards decrease temporal persistence

description: Temporal persistence refers to an individual's capacity to wait for
 future rewards, while forgoing possible alternatives. This requires a
 trade-off between the potential value of delayed rewards and opportunity
 costs, and is relevant to many real-world decisions, such as dieting.
 Theoretical models have previously suggested that high monetary reward
 rates, or positive energy balance, may result in decreased temporal
 persistence. In our study, 50 fasted participants engaged in a temporal
 persistence task, incentivised with monetary rewards. In alternating
 blocks of this task, rewards were delivered at delays drawn randomly from
 distributions with either a lower or higher maximum reward rate. During
 some blocks participants received either a caloric drink or water. We used
 survival analysis to estimate participants' probability of quitting
 conditional on the delay distribution and the consumed liquid.
 Participants had a higher probability of quitting in blocks with the
 higher reward rate. Furthermore, participants who consumed the caloric
 drink had a higher probability of quitting than those who consumed water.
 Our results support the predictions from the theoretical models, and
 importantly, suggest that both higher monetary reward rates and
 physiologically relevant rewards can decrease temporal persistence, which
 is a crucial determinant for survival in many species.
description: DataThis file contains the
 raw data for all analyses involved in the study. Variable names should be
 self-identifying, and all analyses from the study should be reproducible.
 Please contact Bowen J Fung (bowenjfung@gmail.com) if you require
 clarification or more information.trialData.csv
DOI: 10.5061/dryad.3k3m2
title: Data from: Genetic structure of coral-Symbiodinium symbioses on the world’s warmest reefs

description: Corals in the Arabian/Persian Gulf (PAG) survive extreme sea temperatures
 (summer mean: &gt;34°C), and it is unclear whether these corals have
 genetically adapted or physiologically acclimated to these conditions. In
 order to elucidate the processes involved in the thermal tolerance of PAG
 corals, it is essential to understand the connectivity between reefs
 within and outside of the PAG. To this end, this study set out to
 investigate the genetic structure of the coral, Platygyra daedalea, and
 its symbiotic algae in the PAG and neighbouring Gulf of Oman. Using
 nuclear markers (the ITS region and an intron of the Pax-C gene), this
 study demonstrates genetic divergence of P. daedalea on reefs within the
 thermally extreme PAG compared with those in the neighbouring Gulf of
 Oman. Isolation by distance of P. daedalea was supported by the ITS
 dataset but not the Pax-C intron. In addition, the symbiont community
 within the PAG was dominated by C3 symbionts, while the purportedly
 thermotolerant clade D was extremely rare and was common only at sites
 outside of the PAG. Analysis of the psbAncr indicates that the C3 variant
 hosted by P. daedalea in the PAG belongs to the newly described species,
 Symbiodinium thermophilum. The structuring of the coral and symbiont
 populations suggests that both partners of the symbiosis may contribute to
 the high bleaching thresholds of PAG corals. While limited gene flow has
 likely played a role in local adaptation within the PAG, it also indicates
 limited potential for natural export of thermal tolerance traits to reefs
 elsewhere in the Indian Ocean threatened by climate change.
description: Pax-C and ITS sequencing
 chromatograms from Platygyra daedalea in the Arabian
 GulfAB1 files for Platygyra
 daedalea Pax-C intron and ITS region markers.PDAE_CHROM.zip
DOI: 10.5061/dryad.484m0
title: Data from: Programmed and flexible: long-term Zugunruhe data highlight the many axes of variation in avian migratory behaviour

description: Studies of Zugunruhe – the ‘migratory restlessness’ behaviour of captive
 birds – have been integral to our understanding of animal migration,
 revealing an inherited propensity to migrate and an endogenous timing and
 navigation system. However, differences between Zugunruhe in captivity and
 migration in the wild call for more data, in particular on variation
 within and among taxa with diverse migration strategies. Here, we
 characterise Zugunruhe in a long-term dataset of activity profiles from
 stonechats (genus Saxicola) with diverse migratory phenotypes (976
 migration periods from 414 birds), using a flexible and consistent
 quantitative approach based on changepoint analysis. For east African,
 Austrian, Irish, and Siberian stonechats and hybrids, we report key
 inter-population differences in the occurrence, timing, and intensity of
 Zugunruhe. In line with expectations, we found the highest Zugunruhe
 intensity in the longest-distance migrants, more variable patterns in
 short-distance migrants, and intermediate characteristics of hybrids
 relative to their parental groups. Inter-population differences imply high
 evolutionary lability of Zugunruhe timing within a robustly structured
 annual cycle. However, counter to theory, Irish partial migrants showed no
 segregation between migrant and resident individuals, and previously
 reported nocturnal restlessness was confirmed for resident African
 stonechats. Further features of nocturnal restlessness that did not align
 with migratory behaviour of stonechats were juvenile nocturnal
 restlessness even prior to postjuvenile moult, and protandry in spring,
 although stonechats winter in heterosexual pairs. Importantly, Zugunruhe
 of all populations declined with age, and the intensity of an individual
 bird's Zugunruhe was correlated with activity levels during other
 parts of the annual cycle. Our results confirm endogenous,
 population-specific migration programmes but also reveal apparent
 discrepancies between Zugunruhe and migration in the wild. We thus
 highlight both the continued potential of Zugunruhe study and the need for
 circumspect interpretation when using migratory restlessness to make
 inferences about migration in the wild.
description: Migratory restlessness
 data from stonechats with example processing scriptsThis zip archive
 contains nocturnal and diurnal activity data (and associated metadata)
 from stonechats. Also included are example data processing
 scripts.Raw_Data_and_Example_Scripts.zip
DOI: 10.5061/dryad.b12kk
title: Data from: Spatial detection of outlier loci with Moran eigenvector maps (MEM)

description: The spatial signature of microevolutionary processes structuring genetic
 variation may play an important role in the detection of loci under
 selection. However, the spatial location of samples has not yet been used
 to quantify this. Here, we present a new two-step method of spatial
 outlier detection at the individual and deme levels using the power
 spectrum of Moran eigenvector maps (MEM). The MEM power spectrum
 quantifies how the variation in a variable, such as the frequency of an
 allele at a SNP locus, is distributed across a range of spatial scales
 defined by MEM spatial eigenvectors. The first step (Moran spectral
 outlier detection: MSOD) uses genetic and spatial information to identify
 outlier loci by their unusual power spectrum. The second step uses Moran
 spectral randomization (MSR) to test the association between outlier loci
 and environmental predictors, accounting for spatial autocorrelation.
 Using simulated data from two published papers, we tested this two-step
 method in different scenarios of landscape configuration, selection
 strength, dispersal capacity and sampling design. Under scenarios that
 included spatial structure, MSOD alone was sufficient to detect outlier
 loci at the individual and deme levels without the need for incorporating
 environmental predictors. Follow-up with MSR generally reduced (already
 low) false-positive rates, though in some cases led to a reduction in
 power. The results were surprisingly robust to differences in sample size
 and sampling design. Our method represents a new tool for detecting
 potential loci under selection with individual-based and population-based
 sampling by leveraging spatial information that has hitherto been
 neglected.
description: R
 scriptsR scripts for analyzing
 both sets of simulations (individual and deme level), and additional
 spatial coordinate files for Lotterhos & Whitlock (2015) data at
 http://dx.doi.org/10.5061/dryad.mh67vR_scripts_Wagner_et_al_MER.zip
DOI: 10.5061/dryad.1g304
title: Data from: Transcriptomic imprints of adaptation to fresh water: parallel evolution of osmoregulatory gene expression in the Alewife

description: Comparative approaches in physiological genomics offer an opportunity to
 understand the functional importance of genes involved in niche
 exploitation. We used populations of Alewife (Alosa pseudoharengus) to
 explore the transcriptional mechanisms that underlie adaptation to fresh
 water. Ancestrally anadromous Alewives have recently formed multiple,
 independently derived, landlocked populations, which exhibit reduced
 tolerance of saltwater and enhanced tolerance of fresh water. Using
 RNA-seq, we compared transcriptional responses of an anadromous Alewife
 population to two landlocked populations after acclimation to fresh (0
 ppt) and saltwater (35 ppt). Our results suggest that the gill
 transcriptome has evolved in primarily discordant ways between independent
 landlocked populations and their anadromous ancestor. By contrast, evolved
 shifts in the transcription of a small suite of well-characterized
 osmoregulatory genes exhibited a strong degree of parallelism. In
 particular, transcription of genes that regulate gill ion exchange has
 diverged in accordance with functional predictions: freshwater ion-uptake
 genes (most notably, the ‘freshwater paralog’ of Na+/K+-ATPase α-subunit)
 were more highly expressed in landlocked forms, whereas genes that
 regulate saltwater ion secretion (e.g. the ‘saltwater paralog’ of NKAα)
 exhibited a blunted response to saltwater. Parallel divergence of ion
 transport gene expression is associated with shifts in salinity tolerance
 limits among landlocked forms, suggesting that changes to the gill's
 transcriptional response to salinity facilitate freshwater adaptation.
description: CombinedAnnotation_alewife_nrAlewife gill transcriptome annotations
DOI: 10.15468/dl.5ts7bw
title: Occurrence Download

description: A dataset containing 1843466 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is India",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 1843466 records from 901 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001451-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.mt28k
title: Data from: One foot out the door: limb function during swimming in terrestrial versus aquatic turtles

description: Specialization for a new habitat often entails a cost to performance in
 the ancestral habitat. Although aquatic lifestyles are ancestral among
 extant cryptodiran turtles, multiple lineages, including tortoises
 (Testudinidae) and emydid box turtles (genus Terrapene), independently
 specialized for terrestrial habitats. To what extent is swimming function
 retained in such lineages despite terrestrial specialization? Because
 tortoises diverged from other turtles over 50 Ma, but box turtles did so
 only 5 Ma, we hypothesized that swimming kinematics for box turtles would
 more closely resemble those of aquatic relatives than those of tortoises.
 To test this prediction, we compared high-speed video of swimming Russian
 tortoises (Testudo horsfieldii), box turtles (Terrapene carolina) and two
 semi-aquatic emydid species: sliders (Trachemys scripta) and painted
 turtles (Chrysemys picta). We identified different kinematic patterns
 between limbs. In the forelimb, box turtle strokes most resemble those of
 tortoises; for the hindlimb, box turtles are more similar to semi-aquatic
 species. Such patterns indicate functional convergence of the forelimb of
 terrestrial species, whereas the box turtle hindlimb exhibits greater
 retention of ancestral swimming motions.
description: Kinematic_Divergence_AnglesRaw data for calculating kinematic divergence angles and generating plots for Figure 2: mean kinematic profiles for forelimb and hindlimb variables during swimming in four turtle species.Kine_Divergence_Angles.xlsxRaw Kinematic Profile DataRaw data for generating plots for Figure 2: mean kinematic profiles for forelimb and hindlimb variables during swimming in four species of turtle.4spp_rawdata.xlsForelimb Kinematic VariablesRaw data for generating plots for Figure 1(a): plots of the first two principal components axes for ten variables from swimming kinematics in the forelimb.4spp_forelimbkinematicvars_forR.csvHindlimb Kinematic VariablesRaw data for generating plots for Figure 1(b): plots of the first two principal components axes for ten variables from swimming kinematics in the hindlimb.4spp_nhindlimbkinematicvars_forR.csv
DOI: 10.5061/dryad.s4td3
title: Data from: Keeping things local: subpopulation Nb and Ne in a stream network with partial barriers to fish migration

description: For organisms with overlapping generations that occur in metapopulations,
 uncertainty remains regarding the spatio-temporal scale of inference of
 estimates of the effective number of breeders (N^b)and whether these
 estimates can be used to predict generational Ne. We conducted a series of
 tests of the spatio-temporal scale of inference of estimates of Nb in nine
 consecutive cohorts within a long-term study of brook trout (Salvelinus
 fontinalis). We also tested a recently developed approach to estimate
 generational Ne from N^b and compared this to an alternative approach for
 estimating N^e that also accounts for age structure. Multiple lines of
 evidence were consistent with N^b corresponding to the local
 (subpopulation) spatial scale and the cohort-specific temporal scale. We
 found that at least four consecutive cohort-specific estimates of N^b were
 necessary to obtain reliable estimates of harmonic mean N^b for a
 subpopulation. Generational N^e derived from cohort-specific N^b were
 within 7 - 50% of an alternative approach to obtain, N^e suggesting some
 population-specificity for concordance between approaches. Our results
 regarding the spatio-temporal scale of inference for Nb should apply
 broadly to many taxa that exhibit overlapping generations and
 metapopulation structure and point to promising avenues for using
 cohort-specific N^b for local-scale genetic monitoring.
description: WB 2001-2009
 dryadIndividual information
 for fish from each of the 2001 to 2009 brook trout cohorts from West
 Brook, Massachusetts. Information includes: sample location, length, sex,
 full-sib family assignment, 12 microsatellite genotypes. See ReadMe file
 for more information.
DOI: 10.5061/dryad.g0hd8
title: Data from: Range expansion underlies historical introgressive hybridization in the Iberian hare

description: Introgressive hybridization is an important and widespread evolutionary
 process, but the relative roles of neutral demography and natural
 selection in promoting massive introgression are difficult to assess and
 an important matter of debate. Hares from the Iberian Peninsula provide an
 appropriate system to study this question. In its northern range, the
 Iberian hare, Lepus granatensis, shows a northwards gradient of increasing
 mitochondrial DNA (mtDNA) introgression from the arctic/boreal L. timidus,
 which it presumably replaced after the last glacial maximum. Here, we
 asked whether a south-north expansion wave of L. granatensis into L.
 timidus territory could underlie mtDNA introgression, and whether nuclear
 genes interacting with mitochondria (“mitonuc” genes) were affected. We
 extended previous RNA-sequencing and produced a comprehensive annotated
 transcriptome assembly for L. granatensis. We then genotyped 100
 discovered nuclear SNPs in 317 specimens spanning the species range. The
 distribution of allele frequencies across populations suggests a
 northwards range expansion, particularly in the region of mtDNA
 introgression. We found no correlation between variants at 39 mitonuc
 genes and mtDNA introgression frequency. Whether the nuclear and
 mitochondrial genomes coevolved will need a thorough investigation of the
 hundreds of mitonuc genes, but range expansion and species replacement
 likely promoted massive mtDNA introgression.
description: Lepus granatensis
 transcriptomeDe novo transcriptome
 assembly of the Iberian hare, Lepus granatensis.gra.transcriptome.annotated-or-orf.faSNPs inferred from RNA-sequencing data.SNPs inferred from RNA-sequencing data of the Iberian hare, Lepus granatensis.snps_from_RNA-seq.xlsxGenotyped SNPsSNPs genotyped in Iberian hare, Lepus granatensis, and mountain hare, Lepus timidus.genotyped_snps.xlsx