cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vf0t2
title: Data from: Benefits of turbid river plume habitat for Lake Erie yellow perch (Perca flavescens) recruitment determined by juvenile to larval genotype assignment

description: Nutrient-rich, turbid river plumes that are common to large lakes and
 coastal marine ecosystems have been hypothesized to benefit survival of
 fish during early life stages by increasing food availability and (or)
 reducing vulnerability to visual predators. However, evidence that river
 plumes truly benefit the recruitment process remains meager for both
 freshwater and marine fishes. Here, we use genotype assignment between
 juvenile and larval yellow perch (Perca flavescens) from western Lake Erie
 to estimate and compare recruitment to the age-0 juvenile stage for larvae
 residing inside the highly turbid, south-shore Maumee River plume versus
 those occupying the less turbid, more northerly Detroit River plume.
 Bayesian genotype assignment of a mixed assemblage of juvenile (age-0)
 yellow perch to putative larval source populations established that
 recruitment of larvae was higher from the turbid Maumee River plume than
 for the less turbid Detroit River plume during 2006 and 2007, but not in
 2008. Our findings add to the growing evidence that turbid river plumes
 can indeed enhance survival of fish larvae to recruited life stages, and
 also demonstrate how novel population genetic analyses of early life
 stages can contribute to determining critical early life stage processes
 in the fish recruitment process.
description: Yellow perch larvae and
 juvenile microsatellite dataGenePop file of
 genotypes (12 microsatellites) for larval and juvenile Yellow perch
 collected from the Detroit and Maumee River plumes, and Western Lake Erie
 in 2006, 2007, 2008YP_PONE-D-14-52289R1_GP.txtGeneland_06_coordsGeographic coordinates (decimal degrees) for Yellow perch larvae 2006, Geneland formatGeneland_07_coordsGeographic coordinates (decimal degrees) for Yellow perch larvae 2007, Geneland formatGeneland_08_coordsGeographic coordinates (decimal degrees) for Yellow perch larvae 2008, Geneland formatGeneland_06_dataMicrosatellite data (12 loci) for Yellow perch larvae 2006, Geneland formatGeneland_07_dataMicrosatellite data (12 loci) for Yellow perch larvae 2007, Geneland formatGeneland_08_dataMicrosatellite data (12 loci) for Yellow perch larvae 2008, Geneland format
DOI: 10.5061/dryad.h5346
title: Data from: Sexual conflict over remating interval is modulated by the sex peptide pathway

description: Sexual conflict, in which the evolutionary interests of males and females
 diverge, shapes the evolution of reproductive systems across diverse taxa.
 Here, we used the fruit fly to study sexual conflict in natural, three-way
 interactions comprising a female, her current and previous mates. We
 manipulated the potential for sexual conflict by using sex peptide
 receptor (SPR) null females and by varying remating from 3 to 48 h, a
 period during which natural rematings frequently occur. SPR-lacking
 females do not respond to sex peptide (SP) transferred during mating and
 maintain virgin levels of high receptivity and low fecundity. In the
 absence of SPR, there was a convergence of fitness interests, with all
 individuals gaining highest productivity at 5 h remating. This suggests
 that the expression of sexual conflict was reduced. We observed an
 unexpected second male-specific advantage to early remating, resulting
 from an increase in the efficiency of second male sperm use. This early
 window of opportunity for exploitation by second males depended on the
 presence of SPR. The results suggest that the SP pathway can modulate the
 expression of sexual conflict in this system, and show how variation in
 the selective forces that shape conflict and cooperation can be
 maintained.
description: Smith et al.
 RSPB-2016-2394 DRYADExcel file containing
 metadata and all raw data in the paper.
DOI: 10.5061/dryad.ns34t
title: Data from: Cryptic diversity hides host and habitat specialization In a gorgonian-algal symbiosis

description: Shallow water anthozoans, the major builders of modern coral reefs,
 enhance their metabolic and calcification rates with algal symbionts.
 Controversy exists over whether these anthozoan-algae associations are
 flexible over the lifetimes of individual hosts, promoting acclimative
 plasticity, or are closely linked, such that hosts and symbionts coevolve
 across generations. Given the diversity of algal symbionts and the
 morphological plasticity of many host species, cryptic variation within
 either partner could potentially confound studies of anthozoan-algal
 associations. Here, we used ribosomal, organelle, and nuclear sequences,
 along with microsatellite variation, to study the relationship between
 lineages of a common Caribbean gorgonian and its algal symbionts. The
 gorgonian Eunicea flexuosa is a broadcast spawner, composed of two
 recently diverged, genetically distinct lineages largely segregated by
 depth. We sampled colonies of the two lineages across depth gradients at
 three Caribbean locations. We find that each host lineage is associated
 with a unique Symbiodinium B1/184 phylotype. This relationship between
 host and symbiont is maintained when host colonies are reciprocally
 transplanted, although cases of within phylotype switching were also
 observed. Even when the phylotypes of both partners are present at
 intermediate depths, the specificity between host and symbiont lineages
 remained absolute. Unrecognized cryptic diversity may mask host-symbiont
 specificity and change the inference of evolutionary processes in
 mutualistic associations. Symbiotic specificity thus likely contributes to
 the ecological divergence of the two partners, generating species
 diversity within coral reefs.
description: cp23s fragment
 analysisRaw fragment length data
 for cp32s-rDNAReduced microsatellite
 data 4 loci from 7 populationsReduced microsatellite
 data 4 loci from 7 populationsmicrostats
 reducedExtended microsatellite
 data 4 loci from 7 populationsExtended microsatellite
 data 4 loci from 7 populationsmicrosats
 extended2ITS2 fasta
 aligmentits2.fastaB7SYM15 fasta aligmentSequences for the flanking region of microsatellite B7SYM15B7SYM15.fastacp23s fasta aligmentcp23s.fastapsbA fasta aligmentCoding region of the chloroplast psbApsbA.fasta
DOI: 10.5061/dryad.s6t70
title: Data from: Preliminary molecular phylogenetics of Sobralia and relatives (Orchidaceae: Sobralieae)

description: With over 200 species, the orchid tribe Sobralieae is a major constituent
 of the Neotropical flora. As currently circumscribed, the tribe includes
 four genera: Elleanthus, Epilyna, Sertifera, and Sobralia. Most species of
 these four genera typically produce long, cane-like stems but differ
 drastically in flower size and inflorescence structure. DNA sequence data
 support the monophyly of Elleanthus, Epilyna, and Sertifera but not
 Sobralia, which is a polyphyletic assemblage traditionally placed together
 due to relatively large flower size. Details of inflorescence structure
 provide characters that can easily distinguish the different clades of
 Sobralia. The misleading characteristic of flower size is probably due to
 at least several shifts in pollination syndrome within the tribe. With few
 exceptions, species of Sobralia predominantly offer no reward and are
 pollinated by bees. Elleanthus and Sertifera are small-flowered and mostly
 pollinated by hummingbirds with legitimate rewards. Nothing is known of
 pollination in Epilyna. Understanding the evolution of shifts in
 pollination syndrome will require more empirical observations of
 pollination within Sobralieae. In addition, increased taxon sampling and
 improved phylogenetic resolution are needed before generic realignments
 are made.
description: Sobralieae3geneNexus matrix of nrITS, trnS-G, and ycf1 sequences of various Sobralieae (Orchidaceae)
DOI: 10.5061/dryad.66rd8
title: Data from: Caves as microrefugia: Pleistocene phylogeography of the troglophilic North American scorpion Pseudouroctonus reddelli

description: Background: Survival in microrefugia represents an important paradigm in
 phylogeography for explaining rapid postglacial re-colonization by species
 in temperate regions. Microrefugia may allow populations to persist in
 areas where the climatic conditions on the surface have become
 unfavourable. Caves generally contain stable microclimates and may
 represent microrefugia for species capable of exploiting both cave and
 surface habitats (troglophiles). We examine the phylogeography of the
 troglophilic North American vaejovid scorpion Pseudouroctonus reddelli
 using 1,993 base pairs of mitochondrial and nuclear DNA sequence data
 generated from 12 populations. We use (i) descriptive measures of genetic
 diversity and population genetics statistics, (ii) reconstructions of
 phylogeographical structure, spatial diffusion during diversification, and
 population sizes through time, and (iii) species distribution modelling to
 test predictions of the hypothesis that caves serve as microrefugia. We
 compare phylogeographical patterns in P. reddelli with other troglophilic
 species across the Edwards Plateau karst region of Texas. Results: Results
 revealed high haplotype and nucleotide diversity and substantial
 phylogeographical structure, probably generated during the Pleistocene.
 Spatial diffusion occurred along the southern edge of the Edwards Plateau
 from multiple refugia along the Balcones Escarpment. There was little
 evidence for population and geographical expansion. Species distribution
 models predicted substantial reductions in suitable epigean habitat for P.
 reddelli at the Last Glacial Maximum (LGM). Conclusions: High genetic
 diversity, strong phylogeographical structure, diffusion from multiple
 refugia, and unfavourable climatic conditions at the LGM collectively
 support the hypothesis that caves served as microrefugia for P. reddelli.
 Similar patterns of genetic structure in P. reddelli and other
 troglophilic species across the Edwards Plateau karst region of Texas
 suggest that caves serving as microrefugia are important for the
 formation, maintenance, and future survival of troglophilic species in
 temperate karst regions.
description: Pseudouroctonus reddelli
 and P. sprousei, COI dataNexus file with aligned
 COI sequences. See ReadMe file to match sample names with species and
 voucher specimens.reddelliCOI.nexPseudouroctonus reddelli and P. sprousei, 16S dataNexus file with aligned 16S sequences. See ReadMe file to match sample names with species and voucher specimens.reddelli16S.nexPseudouroctonus reddelli and P. sprousei, phased ITS dataNexus file with final alignment of phased ITS sequences. See ReadMe file to match sample names with species and voucher specimens.reddelliITS.nex
DOI: 10.5061/dryad.8768
title: Data from: The molecular genetics of clinal variation: a case study of ebony and thoracic trident pigmentation in Drosophila melanogaster from eastern Australia

description: Widespread pigmentation diversity coupled with a well-defined genetic
 system of melanin synthesis and patterning in Drosophila provides an
 excellent opportunity to study phenotypes undergoing evolutionary change.
 Pigmentation variation is highly correlated with different ecological
 variables and is thought to reflect adaptations to different environments.
 Several studies have linked candidate genes from D. melanogaster to
 intra-population variation and interspecific morphological divergence, but
 less clearly to variation among populations forming pigmentation clines.
 We characterised a new thoracic trident pigmentation cline in D.
 melanogaster populations from eastern Australia, and applied a candidate
 gene approach to explain the majority of the geographically structured
 phenotypic variation. More melanised populations from higher latitudes
 tended to express less ebony than their tropical counterparts, and an
 independent artificial selection experiment confirmed this association. By
 partitioning temperature dependent effects, we showed that the genetic
 differences underlying clinal patterns for trident variation at 25°C do
 not explain the patterns observed at 16°C. Changes in thoracic trident
 pigmentation could be a common evolutionary response to
 climatically-mediated environmental pressures. On the Australian east
 coast most of the changes appear to be associated with regulatory
 divergence of the ebony gene but this depends on temperature.
description: raw_pigmentation_data_east_australiaThis data file contains raw thoracic trident pigmentation scores for three replicates of 35 individuals of two sexes at two rearing temperatures from eighteen populations collected along the Australian East Coast.raw_pcr_data_east_australiaThis data file contains the raw realtime PCR results for ebony expression in females from eighteen populations collected from the Australian East Coast (three replicates). The twodeltacp is the normalised ebony transcript abundance relative to the housekeeping control RPL11.average_pcr_pigmentation_east_australiaThis data file contains the population averages of the ebony expression data and the thoracic trident scores used for linear regression analysis in females from eighteen populations from the Australian east Coast.selection_study_pcr_pigmentation_dataThis data file contains the average pigmentation scores and ebony PCR data for the artificial selection study. twodeltacp is the normalised ebony expression scores relative to the housekeepking gene RpL11.
DOI: 10.5061/dryad.41sn4
title: Data from: Adaptive strategies in nocturnally migrating insects and songbirds: contrasting responses to wind

description: 1. Animals that use flight as their mode of transportation must cope with
 the fact that their migration and orientation performance is strongly
 affected by the flow of the medium they are moving in, i.e. by the winds.
 Different strategies can be used to mitigate the negative effects and
 benefit from the positive effects of a moving flow. The strategies an
 animal can use will be constrained by the relationship between the speed
 of the flow and the speed of the animal's own propulsion in relation
 to the surrounding air. 2. Here we analyse entomological and
 ornithological radar data from north-western Europe to investigate how two
 different nocturnal migrant taxa, the noctuid moth Autographa gamma and
 songbirds, deal with wind by analysing variation in resulting flight
 directions in relation to the wind-dependent angle between the
 animal's heading and track direction. 3. Our results, from fixed
 locations along the migratory journey, reveal different global strategies
 used by moths and songbirds during their migratory journeys. As expected,
 nocturnally migrating moths experienced a greater degree of wind drift
 than nocturnally migrating songbirds, but both groups were more affected
 by wind in autumn than in spring. 4. The songbirds’ strategies involve
 elements of both drift and compensation, providing some benefits from wind
 in combination with destination and time control. In contrast, moths
 expose themselves to a significantly higher degree of drift in order to
 obtain strong wind assistance, surpassing the songbirds in mean ground
 speed, at the cost of a comparatively lower spatiotemporal migratory
 precision. 5. Moths and songbirds show contrasting but adaptive responses
 to migrating through a moving flow, which are fine-tuned to the respective
 flight capabilities of each group in relation to the wind currents they
 travel within.
description: Bird radar data_Lund_J
 Anim Ecol paper_for DryadFlight data from
 individual radar-tracked nocturnal passerines (songbirds) migrating over
 southern Sweden.Moth radar data_UK_J
 Anim Ecol paper_for DryadFlight data for
 individual radar-tracked nocturnal noctuid moths Autographa gamma
 migrating over southern UK
DOI: 10.5061/dryad.1v1k6rj
title: Data from: A combinatorial analysis using observational data identifies species that govern ecosystem functioning

description: Understanding the relationship between biodiversity and ecosystem
 functioning has so far resulted from two main approaches: the analysis of
 species' functional traits, and the analysis of species interaction
 networks. Here we propose a third approach, based on the association
 between combinations of species or of functional groups, which we term
 assembly motifs, and observed ecosystem functioning. Each assembly motif
 describes a biotic environment in which species interactions have
 particular effects on a given ecosystem function. Clustering species in
 functional groups generates a classification of ecosystems based on their
 assembly motif. We evaluate the quality of each species clustering, that
 is its ability to predict an ecosystem function, by the coefficient of
 determination of the ecosystem classification. An iterative process then
 enables identifying the species clustering in functional groups that best
 accounts for the functioning of the observed ecosystems. We test this
 approach using experimental and simulated datasets. We show that our
 combinatorial analysis makes it possible to identify the combinations of
 functional groups of species whose interactions govern ecosystem
 functioning without any a priori knowledge of the species themselves or
 their interactions. Our combinatorial approach reproduces the associative
 learning of empirical ecologists, and proves to be powerful and
 parsimonious.
description: Jaillard_et_al.PlosOneR codes and datasets
DOI: 10.5061/dryad.n618q
title: Data from: A new durophagous stem cheloniid turtle from the lower Paleocene of Cabinda, Angola

description: A new stem cheloniid turtle, Cabindachelys landanensis, gen. et sp. nov.,
 is represented by a nearly complete skull and partial hyoid collected in
 lower Paleocene shallow marine deposits, equivalent to the offshore
 Landana Formation, near the town of Landana in Cabinda, Angola. A partial
 chelonioid carapace previously reported from this locality is referred
 here to C. landanensis. Cabindachelys landanensis possesses clear
 synapomorphies of Pan-Cheloniidae, including a rod-like rostrum
 basisphenoidale, V-shaped basisphenoid crest, and secondary palate, but
 differs from most other pan-cheloniids in that the foramen palatinum
 posterius is present. Phylogenetic analysis suggests that C. landanensis
 forms a weakly-supported clade with Erquelinnesia gosseleti, Euclastes
 acutirostris, Euclastes wielandi, and Terlinguachelys fischbecki, although
 a close relationship between the protostegid T. fischbecki and these
 durophagous pan-cheloniids is unlikely. The Paleocene–Eocene strata near
 Landana have produced a number of turtle fossils, including the holotype
 specimen of the pleurodire Taphrosphys congolensis. A turtle humerus
 collected approximately 1 meter above the holotype skull of C. landanensis
 differs from humeri of chelonioids and Taphrosphys, indicating that a
 third turtle taxon is present at Landana. Cheloniid fossil material is
 rare in the Landana assemblage, in comparison with the abundant remains of
 Taphrosphys congolensis found throughout the stratigraphic section. This
 disparity implies that C. landanensis preferred open marine habitats,
 whereas Taphrosphys congolensis spent more time in nearshore environments.
 The appearance of new durophagous species such as C. landanensis in the
 early Paleocene reflects the rapid radiation of pan-chelonioids as they
 diversified into open niches following the K–Pg extinction.
description: Table of character
 codings for Cabindachelys landanensis and Angolachelys
 mbaxiThis table shows the
 character codings for Cabindachelys landanensis, including both the
 holotype skull and referred carapace material, as well as modified codings
 for Angolachelys mbaxi. Character numbering corresponds to that of the
 original matrix in Cadena and Parham (2015).Turtle Appendix
 S1.docTNT file for
 phylogenetic analysis of TestudinataThis TNT file contains a
 modified version of the matrix presented by Cadena and Parham (2015) with
 155 taxa and 256 characters. The matrix includes character codings for
 both the holotype skull and the carapace material referred to
 Cabindachelys landanensis.Turtle Appendix S2 Testudinata
 TNT.tntStrict consensus tree
 from analysis of TestudinataStrict consensus of
 50,000 MPTs from the analysis of Testudinata using a modified version of
 the matrix in Cadena and Parham (2015).Turtle Appendix
 S3.pdf
DOI: 10.5061/dryad.k2qc1
title: Data from: Landscape genetics of a top neotropical predator

description: Habitat loss and fragmentation as a consequence of human activities is a
 worldwide phenomenon and one of the major threats to global biodiversity.
 Habitat loss and fragmentation is particularly a concern in the biodiverse
 tropics, where deforestation is occurring at unprecedented rates. Although
 insects are one of the most diverse and functionally important groups in
 tropical ecosystems, the quantitative effect of landscape features on
 their gene flow remains unknown. Here, we used a robust landscape genetics
 approach to quantify the effect of ten landscape features (deforestation,
 mature forests, other forest types, the River Chagres, streams, stream
 banks, roads, sea, lakes and swamps) and interactions between them, on the
 gene flow of a neotropical forest keystone species, the army ant Eciton
 burchellii. The influence of landscape on E. burchellii's gene flow
 reflected the different dispersal capability of its sexes; aerial for
 males and pedestrian for females, and the different depths of population
 history inferred from microsatellites and mitochondrial DNA. In contrast
 to the gene flow-facilitating effect of mature forests, deforested areas
 were found to be strong barriers for E. burchellii's gene flow. Other
 forest types were found to be gene flow facilitators but only when
 interacting with mature secondary forests, therefore indicating the
 importance of mature forests for the survival of E. burchelii and its
 associate species. The River Chagres was identified as a major historical
 gene flow barrier for E. burchellii, suggesting that an important loss of
 connectivity may occur because of large artificial waterways such as the
 Panama Canal.
description: Data_file_MEC-12_0649Data_file_MEC-12-0649 contains the microsatellite data, coordinates and landscape genetics data (univariate and bivariate) associated with study entitled 'Landscape genetics of a top neotropical predator'
DOI: 10.5061/dryad.43j31
title: Data from: The quantitative genetic basis of clinal divergence in phenotypic plasticity

description: Phenotypic plasticity is thought to be an important mechanism for adapting
 to environmental heterogeneity. Nonetheless, the genetic basis of
 plasticity is still not well understood. In Drosophila melanogaster and D.
 simulans, body size and thermal stress resistance show clinal patterns
 along the east coast of Australia, and exhibit plastic responses to
 different developmental temperatures. The genetic basis of thermal
 plasticity, and whether the genetic effects underlying clinal variation in
 traits and their plasticity are similar, remains unknown. Here we use
 line-cross analyses between a tropical and temperate population of D.
 melanogaster and D. simulans developed at three constant temperatures (18,
 25 and 29°C) to investigate the quantitative genetic basis of clinal
 divergence in mean thermal response (elevation) and plasticity (slope and
 curvature) for thermal stress and body size traits. Generally, the genetic
 effects underlying divergence in mean response and plasticity differed,
 suggesting that different genetic models may be required to understand the
 evolution of trait means and plasticity. Furthermore, our results suggest
 that non-additive genetic effects, in particular epistasis, may commonly
 underlie plastic responses, indicating that current models that ignore
 epistasis may be insufficient to understand and predict evolutionary
 responses to environmental change.
description: Data for
 DRYAD