cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4k275
title: Data from: Caribou, water, and ice – fine-scale movements of a migratory arctic ungulate in the context of climate change

description: Freshwater lakes and rivers of the Northern Hemisphere have been freezing
 increasingly later and thawing increasingly earlier during the last
 century. With reduced temporal periods during which ice conditions are
 favourable for locomotion, freshwater bodies could become impediments to
 the inter-patch movements, dispersion, or migration of terrestrial animals
 that use ice-covered lakes and rivers to move across their range. Studying
 the fine-scale responses of individuals to broad-scale changes in ice
 availability and phenology would help to understand how animals react to
 ongoing climate change, and contribute to the conservation and management
 of endangered species living in northern environments. Between 2007 and
 2014, we equipped 96 migratory caribou Rangifer tarandus caribou from the
 Rivière-aux-Feuilles herd in northern Québec (Canada) with GPS telemetry
 collars and studied their space use. We measured contemporary (digital
 MODIS maps updated every 8 days, 2000–2014) and historical (annual
 observations, 1947–1985) variations in freshwater-ice availability and
 evaluated the concurrent responses of caribou to these changes.
description: Ice-crossing
 locationsThe GPS locations (n =
 653) of migratory caribou from the Rivière-aux-Feuilles herd that crossed
 lakes on ice from 2007 to 2014 in northern Quebec.IceCross_Data.xlsxWater-crossing locationsThe GPS locations (n = 139) of migratory caribou from the Rivière-aux-Feuilles herd that crossed lakes through water from 2007 to 2014 in northern Quebec.WaterCross_Data.xlsxDetour locationsThe GPS locations (n = 1119) of migratory caribou from the Rivière-aux-Feuilles herd that circumvented lakes from 2007 to 2014 in northern Quebec.Detour_Data.xlsxProportion of ice and waterProportion of ice and water on the largest water bodies used by migratory caribou of the Rivière-aux-Feuilles herd in northern Quebec. Ice and water coverages were estimated using 8-day averaged MODIS values from 2000 to 2014. "Sum lake" and "Sum lake-ice" respectively represent the sum of pixels with values of 37 (ie. freshwater) or 100 (ie. lake ice) on MODIS maps.Ice-Water_Proportion_Data.xlsxNAO and AO dataData used to determine the relationship between the annual breakup and freeze dates of the largest water bodies used by migratory caribou from the Rivière-aux-Feuilles herd in northern Quebec, and monthly values of the North Atlantic and Arctic Oscillations.NAO_AO_Data.xlsxLakes ArcGIS shapefileThe ArcGIS shapefile representing the largest water bodies used by migratory caribou of the Rivière-aux-Feuilles herd in northern Quebec.Lakes_shapefile.zip
DOI: 10.5061/dryad.j9769
title: Data from: Extending ecological niche models to the past 120 000 years corroborates the lack of strong phylogeographic structure in the Crested Drongo (Dicrurus forficatus forficatus) on Madagascar

description: We conduct a phylogeographic study of the Crested Drongo (Dicrurus
 forficatus forficatus), a broadly distributed bird species on Madagascar.
 We first determined the demographic and spatial pattern inferred from
 mitochondrial and nuclear data, and then compared these results with
 predictions from a present to 0.120-Myr-old reconstruction of the spatial
 dynamics of the range of D. f. forficatus on Madagascar, enabling putative
 areas of stability (lineage persistence) to be detected. Weak genetic
 structure along an east–west pattern and comparatively low genetic
 diversity were recovered, with strong evidence of population expansion
 found at all ten loci sampled. The palaeoclimatic distribution models over
 the past 0.120 Myr suggest the presence of extensive areas of suitable
 climate in the east and west for the species since its colonization of
 Madagascar, a result in strong concordance with the spatial and genetic
 signal derived from our multilocus data set.
description: DNA sequence
 alignmentsAlignment of the phased
 dataData
 sets
DOI: 10.5061/dryad.jf3tj
title: Data from: A tale of two phylogenies: comparative analyses of ecological interactions

description: The evolution of traits involved in ecological interactions such as
 predator-prey, host-parasite, and plant-pollinator interactions, are
 likely to be shaped by the phylogenetic history of both parties. We
 develop generalized linear mixed-effects models (GLMM) that estimate the
 effect of both parties’ phylogenetic history on trait evolution, both in
 isolation but also in terms of how the two histories interact. Using data
 on the incidence and abundance of 206 flea species on 121 mammal species,
 we illustrate our method and compare it to previously used methods for
 detecting host-parasite coevolution. At large spatial scales we find that
 the phylogenetic interaction effect was substantial, indicating that
 related parasite species were more likely to be found on related host
 species. At smaller spatial scales, and when sampling effort was not
 controlled for, phylogenetic effects on the number and types of parasite
 species harbored by hosts were found to dominate. We go on to show that in
 situations where these additional phylogenetic effects exist, then
 previous methods have very high Type I error rates when testing for the
 phylogenetic interaction. Our GLMM method represents a robust and reliable
 approach to quantify the phylogenetic effects of traits determined by, or
 defined by, ecological interactions and has the advantage that it can
 easily be extended and interpreted in a broader context than existing
 permutation tests.
description: AnalysesR code for performing all data analyses and Figure generation in Hadfield at al. `A tale of two phylogenies: comparative analyses of ecological interactions'Methods.testR code for simulating data sets and testing the properties of methods covered in Hadfield at al. 'A tale of two phylogenies: comparative analyses of ecological interactions'PQL.testR code for testing the adequacy of PQL approximations for analyses in Hadfield at al. `A tale of two phylogenies: comparative analyses of ecological interactions'DoublePhyloDataCounts of fleas on small mammals in 51 palearctic regions analysed in Hadfield et al. `A tale of two phylogenies: comparative analyses of ecological interactions'HostTreePhylogenetic tree (Newick format) of small mammals used for analyses in Hadfield et al. `A tale of two phylogenies: comparative analyses of ecological interactions'FleaTreePhylogenetic tree (Newick format) of fleas used for analyses in Hadfield et al. `A tale of two phylogenies: comparative analyses of ecological interactions'FleaTreeKPhylogenetic tree (Newick format) of fleas, made ultrametric in Mesquite, and used for analyses in Hadfield et al. `A tale of two phylogenies: comparative analyses of ecological interactions'
DOI: 10.5061/dryad.4m67g
title: Data from: Large-scale, multi-directional larval connectivity among coral reef fish populations in the Great Barrier Reef Marine Park

description: Larval dispersal is the key process by which populations of most marine
 fishes and invertebrates are connected and replenished. Advances in larval
 tagging and genetics have enhanced our capacity to track larval dispersal,
 assess scales of population connectivity, and quantify larval exchange
 among no-take marine reserves and fished areas. Recent studies have found
 that reserves can be a significant source of recruits for populations up
 to 40 km away, but the scale and direction of larval connectivity across
 larger seascapes remain unknown. Here we apply genetic parentage analysis
 to investigate larval dispersal patterns for two exploited coral reef
 groupers (Plectropomus maculatus and P. leopardus) within and among three
 clusters of reefs separated by 60 – 220 km within the Great Barrier Reef
 Marine Park, Australia. A total of 69 juvenile P. maculatus and 17
 juvenile P. leopardus (representing 6% and 9% of the total juveniles
 sampled respectively) were genetically assigned to parent individuals on
 reefs within the study area. We identified both short-distance larval
 dispersal within regions (200 m to 50 km) and long-distance,
 multi-directional dispersal of up to ~250 km among regions. Dispersal
 strength declined significantly with distance, with best-fit dispersal
 kernels estimating median dispersal distances of ~110 km for P. maculatus
 and ~190 km for P. leopardus. Larval exchange among reefs demonstrates
 that established reserves form a highly connected network and contribute
 larvae for the replenishment of fished reefs at multiple spatial scales.
 Our findings highlight the potential for long-distance dispersal in an
 important group of reef fishes, and provide further evidence that
 effectively protected reserves can yield recruitment and sustainability
 benefits for exploited fish populations.
description: Plectropomus leopardus -
 Microsatellite dataMicrosatellite data for
 Plectropomus leopardus in the southern Great Barrier
 ReefPlectropomus maculatus -
 Microsatellite dataMicrosatellite data for
 Plectropomus maculatus in the southern Great Barrier
 Reef
DOI: 10.5061/dryad.h422c
title: Data from: The evolution of post-pairing male mate choice

description: An increasing number of empirical studies in animals have demonstrated
 male mate choice. However, little is known about the evolution of
 post-pairing male choice, specifically that which occurs by differential
 allocation of male parental care in response to female signals. We use a
 population genetic model to examine whether such post-pairing male mate
 choice can evolve when males face a trade-off between parental care and
 extra-pair copulations (EPCs). Specifically, we assume that males allocate
 more effort to providing parental care when mated to preferred (signaling)
 females, but they are then unable to allocate additional effort to seek
 EPCs. We find that both male preference and female signaling can evolve in
 this situation, under certain conditions. First, this evolution requires a
 relatively large difference in parental investment between males mated to
 preferred versus non-preferred females. Second, whether male choice and
 female signaling alleles become fixed in a population versus cycle in
 their frequencies depends on the additional fecundity benefits from EPCs
 that are gained by choosy males. Third, less costly female signals enable
 both signaling and choice alleles to evolve under more relaxed conditions.
 Our results also provide a new insight into the evolution of sexual
 conflict over parental care.
description: PMMC_eigenvaluesCalculating the equilibrium and the corresponding eigenvalues.PMMC_simulationsNumerical simulations.PMMC_constantCalculating the equilibrium and the corresponding eigenvalues when d_c1=d_c2=d, delta1=delta2=delta and theta is a constant.
DOI: 10.5061/dryad.qr7f5
title: Data from: Spatial and temporal patterns of larval dispersal in a coral-reef fish metapopulation: evidence of variable reproductive success

description: Many marine organisms can be transported hundreds of kilometers during
 their pelagic larval stage, yet little is known about spatial and temporal
 patterns of larval dispersal. Although traditional population-genetic
 tools can be applied to infer movement of larvae on an evolutionary time
 scale, large effective population sizes and high rates of gene-flow
 present serious challenges to documenting dispersal patterns over shorter,
 ecologically-relevant, time scales. Here, we address these challenges by
 combining direct parentage analysis and indirect genetic analyses over a
 four-year period to document spatial and temporal patterns of larval
 dispersal in a common coral-reef fish: the bicolor damselfish (Stegastes
 partitus). At four island locations surrounding Exuma Sound, Bahamas,
 including a long-established marine reserve, we collected 3,278
 individuals and genotyped them at 10 microsatellite loci. Using Bayesian
 parentage analysis, we identified eight parent-offspring pairs, thereby
 directly documenting dispersal distances ranging from 0 km (i.e.,
 self-recruitment) to 129 km (i.e., larval connectivity). Despite
 documenting substantial dispersal and gene-flow between islands, we
 observed more self-recruitment events than expected if the larvae were
 drawn from a common, well-mixed pool (i.e., a completely open population).
 Additionally, we detected both spatial and temporal variation in
 signatures of sweepstakes and Wahlund effects. The high variance in
 reproductive success (i.e., “sweepstakes”) we observed may be influenced
 by seasonal mesoscale gyres present in the Exuma Sound, which play a
 prominent role in shaping local oceanographic patterns. This study
 documents the complex nature of larval dispersal in a coral-reef fish, and
 highlights the importance of sampling multiple cohorts and coupling both
 direct and indirect genetic methods in order disentangle patterns of
 dispersal, gene-flow, and variable reproductive success.
description: 05to08Bicolor_Genotypes_Final_PopulationsThis data file contains the genotypes of all adult and recruit bicolor damselfish, which were genotyped at 10 microsatellite loci.Probability self recruitment patternThis file contains a script to be used in the R statistical environment, and it calculates the probability of parentage patterns resulting from a common 'well-mixed' pool of larvaeCalculateProbabilitesofSiblingsThis file contains a script to be used in the R statistical environment, and calculates how likely individuals that share alleles at all 10 loci are some first-order relative such as siblings.
DOI: 10.5061/dryad.r6b3s
title: Data from: Density dependence and population regulation in marine fish: a large-scale, long-term field manipulation

description: Do small-scale experiments showing spatial density dependence in marine
 fishes scale-up to temporal density dependence and regulation of
 relatively large local populations? If so, what are the causative
 mechanisms and their implications? We conducted an 8-year multi-generation
 study of population dynamics of bicolor damselfish (Stegastes partitus)
 inhabiting four large coral reefs in the Bahamas. After a 4-year baseline
 period, it was clear that two populations naturally received very few
 settlement-stage larvae, so recruitment of recently settled fish was
 artificially enhanced at one low-settlement reef and reduced at one
 high-settlement reef to ensure a broad range of population sizes over
 which to test for regulation. Over all 8 years, populations on the two
 naturally high-settlement reefs experienced temporal density dependence in
 multiple per capita demographic rates mortality, survival to adulthood,
 and fecundity. These local populations also displayed components of
 regulation persistence, boundedness, and return tendency. Reefs supporting
 regulated populations were structurally complex, providing sufficient prey
 refuges that ensured high survival at low densities. In contrast,
 populations at low-settlement reefs experienced either density-independent
 or slightly inversely density-dependent demographic rates, even though
 recruitment was artificially augmented to high levels at one reef. There
 was no evidence of regulation at these reefs, and indeed, one local
 population suffered temporary extirpation. Here, habitat complexity was
 relatively low, increasing the risk of predation, especially at low
 population densities when fish would have to travel longer distances when
 finding mates or home sites inhabited by conspecifics. Among all
 demographic parameters, density dependence in individual growth (an
 indicator of within-species competition for food) was least correlated
 with the presence or absence of local population regulation. We conclude
 that, for systems like these, the environmental context of a local
 population -- especially predation risk and the distribution and abundance
 of spatial refuges -- is more important than the magnitude of larval
 supply alone in determining the existence of regulating density
 dependence. At the broader metapopulation scale, density dependence in
 both survival and fecundity exogenously caused by predation may provide
 regulation for the entire stock, even when endogenous within-species
 competition (assumed to be important in most fisheries models) is weak.
description: Hixon et al Ecol Mongr
 MS 11-1525Data files for Hixon et
 al Ecol Mongr MS 11-1525.
DOI: 10.5061/dryad.hm550
title: Data from: The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America

description: A comprehensive study of the phylogeography and population genetics of the
 largest wild artiodactyl in the arid and cold-temperate South American
 environments, the guanaco (Lama guanicoe), was conducted to detail
 patterns of molecular genetic structure related with phylogeographic
 history, barriers to gene flow, to describe and contrast the evolutionary
 history and patterns of gene flow among populations. Analyses of 514 bp of
 mtDNA sequence and 14 biparentally-inherited microsatellite markers of 314
 individuals from 17 localities throughout their current distribution
 across Peru, Bolivia, Argentina and Chile confirm the well-defined genetic
 differentiation and subspecies designation of populations geographically
 separated to the northwest (L. g. cacsilensis) and southeast (L. g.
 guanicoe) of the central Andes plateau. However, these populations are not
 completely isolated, as shown by admixture prevalent throughout a limited
 contact zone and a strong signal of expansion from north-to-south in the
 beginning of Holocene. Microsatellite analyses differentiated 3
 northwestern and 4-5 southeastern populations, suggesting patterns of
 genetic contact among these populations, and identified possible genetic
 refuges and source-sink patterns of gene flow at historical and recent
 time scales. These results confirm that conservation and management of
 guanaco should be implemented with an understanding of local population
 dynamics while considering the preservation of broader adaptive variation
 and evolutionary processes.
description: Unique mtDNA haplotypes
 (n=35)Nexus file containing
 the sequences (514 bp) of the 35 unique parcial sequences of Control
 Region mtDNA haplotypes discovered among 306 guanacos
 samples.FinalHap.nexMicrosat_datesMicrosatellites dates by populationsIndividual mtDNA sequences (n=306)Nexus file containing the 514 bp mtDNA Control Region parcial sequences for each of the 306 guanacos samples analyzed (Lama guanicoe, Genbank accession JX678291 - JX678596).FinalSeq.nexSamples_informationInformation of Lama guanicoe samples used in the analyses, including localities, geographic positions, type of sample, Haplotype and GenBank accessions numbers.Supplementary TableTable 6: Prior distributions used for the analysis of the Lama guanicoe data (popABC analysis)
DOI: 10.5061/dryad.jq989
title: Data from: Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest

description: Comparisons of nematode communities among ecosystems have indicated that,
 unlike many organisms, nematode communities have less diversity in the
 tropics than in temperate ecosystems. There are, however, few studies of
 tropical nematode diversity on which to base conclusions of global
 patterns of diversity. This study reports an attempt to estimate nematode
 diversity in the lowland tropical rainforest of La Selva Biological
 Research Station in Costa Rica. We suggest that one reason previous
 estimates of tropical nematode diversity were low is that habitats above
 the mineral soil are seldom sampled. As much as 62% of the overall genetic
 diversity, measured by an 18S ribosomal barcode, exists in litter and
 understory habitats and not in soil. A maximum likelihood tree of barcodes
 from 360 individual nematodes indicates most major terrestrial nematode
 lineages were represented in the samples. Estimated â speciesâ richness
 ranges from 464 to 502 within the four 40 by 40 m plots. Directed sampling
 of insects and their associated nematodes produced a second set of
 barcodes that were not recovered by habitat sampling, yet may constitute a
 major class of tropical nematode diversity. While the generation of novel
 nematode barcodes proved relatively easy, their identity remains obscure
 due to deficiencies in existing taxonomic databases. Specimens of
 Criconematina, a monophyletic group of soil-dwelling plant-parasitic
 nematodes were examined in detail to assess the steps necessary for
 associating barcodes with nominal species. Our results highlight the
 difficulties associated with studying poorly understood organisms in an
 understudied ecosystem using a destructive (barcode) sampling method.
description: MOTUs - nematode
 diversity in a lowland tropical rainforestSequence data. See
 ReadMe file for details.Powers_etal(MolEcol2009).txt
DOI: 10.5061/dryad.87v3v
title: Data from: Detecting an elusive invasive species: a diagnostic PCR to detect Burmese python in Florida waters and an assessment of persistence of environmental DNA

description: Recent studies have demonstrated that detection of environmental DNA
 (eDNA) from aquatic vertebrates in water bodies is possible. The Burmese
 python, Python bivittatus, is a semi-aquatic, invasive species in Florida
 where its elusive nature and cryptic coloration make its detection
 difficult. Our goal was to develop a diagnostic PCR to detect P.
 bivittatus from water-borne eDNA, which could assist managers in
 monitoring this invasive species. First, we used captive P. bivittatus to
 determine whether reptilian DNA could be isolated and amplified from water
 samples. We also evaluated the efficacy of two DNA isolation methods and
 two DNA extraction kits commonly used in eDNA preparation. A fragment of
 the mitochondrial cytochrome b gene from P. bivittatus was detected in all
 water samples isolated with the sodium acetate precipitate and the QIAamp
 DNA Micro Kit. Next, we designed P. bivittatus-specific primers and
 assessed the degradation rate of eDNA in water. Our primers did not
 amplify DNA from closely related species, and we found that P. bivittatus
 DNA was consistently detectable up to 96 h. Finally, we sampled water from
 six field sites in south Florida. Samples from five sites, where P.
 bivittatus has been observed, tested positive for eDNA. The final site was
 negative and had no prior documented evidence of P. bivittatus. This study
 shows P. bivittatus eDNA can be isolated from water samples; thus, this
 method is a new and promising technique for the management of invasive
 reptiles.
description: ABI Fragment analysis
 PybiCB3 Pentest II 6-18-13_15 minutes onlyABI fragment analysis
 screen shot to show peaks generated when using the primers we developed in
 Pen test II plus flourescent labels.Gel PybiCB3 Pentest II
 6-18-13_15 minutes onlyPicture of bands
 generated by running PCR product using the primers we dveloped in Pen test
 II (unlabeled) on agarose gel.PybiCB3 primers full
 sequenceFASTA file showing
 sequence produced from PCR product using primers we develeoped in Pen Test
 IIQA-1950 Python all
 results 6-25-2013