cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4r0t0
title: Data from: Genomic evidence for convergent evolution of a key trait underlying divergence in island birds

description: Reproductive isolation can be initiated by changes in one or a few key
 traits that prevent random mating among individuals in a population.
 During the early stages of speciation, when isolation is often incomplete,
 there will be a heterogeneous pattern of differentiation across regions of
 the genome between diverging populations, with loci controlling these key
 traits appearing the most distinct as a result of strong diversifying
 selection. In this study, we used Illumina-sequenced ddRAD tags to
 identify genome-wide patterns of differentiation in three
 recently-diverged island populations of the Monarcha castaneiventris
 ycatcher of the Solomon Islands. Populations of this species have diverged
 in plumage color, and these differences in plumage color, in turn, are
 used in conspecific recognition and likely important in reproductive
 isolation. Previous candidate gene sequencing identified point mutations
 in MC1R and ASIP, both known pigmentation genes, to be associated with the
 difference in plumage color between islands. Here, we show that background
 levels of genomic differentiation based on over 70,000 SNPs are extremely
 low between populations of distinct plumage color, with no loci reaching
 the level of differentiation found in either candidate gene. Further, we
 found that a phylogenetic analysis based on these SNPs produced a taxonomy
 wherein the two melanic populations appear to have evolved convergently,
 rather than from a single common ancestor, in contrast to their original
 classification as a single subspecies. Finally, we found evidence that the
 pattern of low genomic differentiation is the result of both incomplete
 lineage sorting and gene ow between populations.
description: dadiScriptsSet of Python scripts used to run all dadi analysesRADsysBio_ScriptsSet of all Perl and R scripts used in analysis pipelineMonarcha_nexus_filesSet of nexus input files for running in SNAPP phylogenetic analysis
DOI: 10.5061/dryad.jh87h
title: Data from: Population and life-history consequences of within-cohort individual variation

description: The consequences of within-cohort (i.e., among-individual) variation for
 population dynamics are poorly understood, in particular for the case
 where life history is density dependent. We develop a physiologically
 structured population model that incorporates individual variation among
 and within cohorts and that allows us to explore the intertwined
 relationship between individual life history and population dynamics. Our
 model is parameterized for the lizard Zootoca vivipara and reproduces well
 the species' dynamics and life history. We explore two common
 mechanisms that generate within-cohort variation: variability in food
 intake and variability in birth date. Predicted population dynamics are
 inherently very stable and do not qualitatively change when either of
 these sources of individual variation is introduced. However, increased
 within-cohort variation in food intake leads to changes in morphology with
 longer but skinnier individuals, even though mean food intake does not
 change. Morphological changes result from a seemingly universal non-linear
 relationship between growth and resource availability, but may only become
 apparent in environments with strongly fluctuating resources. Overall, our
 results highlight the importance of using a mechanistic framework to gain
 insights into how different sources of intraspecific variability translate
 into life-history and population dynamic changes.
description: Empirical dataset used
 for parameterizationLarge dataset based on
 &gt;1,200 Zootoca vivipara individuals from a French population. Data
 include individual estimates of: body mass at all ages (including at
 birth), body size measured as snout-vent length, annual survival, sexual
 maturation age for females, and total number of live offspring per
 female.Empirical_dataset_parameterization.zipFood_intake_datasetData from a semi-natural experiment exploring feeding rates in Zootoca vivipara. Feeding rates were explored for diverse age and sex classes under different population densities.Life_history_validationLong-term dataset obtained from a natural population of Zootoca vivipara in the Cévennes, France. These data were used to validate model results. Data include mean, standard deviation, and sample size estimates for body mass, snout-vent length, fecundity, and annual survival rates.
DOI: 10.5061/dryad.t66gq81
title: Data from: The spectre of too many species

description: Recent simulation studies examining the performance of Bayesian species
 delimitation as implemented in the BPP program have suggested that BPP may
 detect population splits but not species divergences and that it tends to
 over-split when data of many loci are analyzed. Here we confirm these
 results and provide the mathematical justifications. We point out that the
 distinction between population and species splits made in the protracted
 speciation model has no influence on the generation of gene trees and
 sequence data, which explains why no method can use such data to
 distinguish between population splits and speciation. We suggest that the
 protracted speciation model is unrealistic as its mechanism for assigning
 species status assumes instantaneous speciation, contradicting prevailing
 taxonomic practice. We confirm the suggestion, based on simulation, that
 in the case of speciation with gene flow, Bayesian model selection as
 implemented in BPP tends to detect population splits when the amount of
 data (the number of loci) increases. We discuss the use of a recently
 proposed empirical genealogical divergence index (gdi) for species
 delimitation and illustrate that parameter estimates produced by a full
 likelihood analysis as implemented in BPP provide much more reliable
 inference under the gdi than the approximate method PHRAPL. We distinguish
 between Bayesian model selection and parameter estimation, and suggest
 that the model selection approach is useful for identifying sympatric
 cryptic species while the parameter estimation approach may be used to
 implement empirical criteria for determining species status among
 allopatric populations.
description: Empirical data for
 analysis of humans, plants, and lizards.The folder contains
 multilocus sequence data for BPP species delimitation analyses of Homo
 sapiens, Scincella lateralis, and Sarracenia alata. Each folder includes
 the data file (formatted for BPP), imap files for assigning samples to
 species, and control files for executing analyses as described in the
 publication. Four replicate control files for each analysis are included
 (each with a different starting seed). The R script is used to summarize
 the results of the BPP analysis by importing the MCMC files, calculating
 the posterior distribution of GDI values, and producing
 graphs.Data.zipSimulation files for hierarchical species delimitation with MSC/GDIFiles for replicating the species delimitation simulation of species ABCD and X, where ABCD is one species with a large geographic distribution, and X is a new species with no gene flow with ABCD. There is gene flow with M = Nm = 2 between the adjacent populations of ABCD (both ancestral and extant populations). The folder includes an MCcoal simulation control file for simulating 100 loci (500 bp each) for populations A, B, C, D, and X. Also included are BPP analysis files for MSC analysis (data files, Imap files, and control files). Four replicate control files are provided for each analysis (with different starting seeds).Simulations.zip
DOI: 10.5061/dryad.f5220r3
title: Data from: Estimating field capacity from volumetric soil water content time series using automated processing algorithms

description: Vadose zone measurements of volumetric soil water content (θ) using soil
 moisture sensors (SMSs) have become more common due to advances in
 technology and reduction of costs. Soil moisture sensor data exhibit a
 characteristic cyclical pattern reflecting water flux dynamics into and
 out of the observed soil volume. Expert review of SMS datasets to
 distinguish valid from corrupt or incomplete soil water cycles is arguably
 the most precise method for determining field capacity (θFC) but is
 impractically cumbersome and time consuming for increasingly large SMS
 datasets. We evaluated competing approaches for automated soil water
 cycles analysis that use widely available R packages based on pattern
 recognition and machine learning (findpeaks [R-FP], symbolic aggregate
 approximation [R-SAX], and density histogram [R-DH]), and a MATLAB code
 based on soil water dynamic principles (SWDP). These approaches were
 applied to three SMS datasets. Our empirical results showed superiority of
 R-SAX for identifying valid soil water cycles, probably due to benefiting
 from training sets to calibrate to correct cycles. Two other approaches
 (SWDP and R-FP) provided similar results without need of training sets or
 preprocessing data. Three approaches for estimating field capacity were
 applied to valid cycles, R-FP, regression of exponential decay (SWDP-R),
 and estimated “knee” of curve (SWDP-K). Each performed similarly to the
 expert defined values, with R-FP and SWDP-R generally performing best
 across analyses. Results of this study also show temporal dynamics of θFC
 within datasets used here. There is potential for optimizing θFC and a
 need for automated, objective analysis to leverage dynamics in irrigation
 management and modeling.
description: Turfgrass with ET
 ControlHourly volumetric water
 content data from soil moisture sensor (Decagon Ech2o EC-5) installed at
 7.6 cm depth below St. Augustine turfgrass (Stenotaphrum secundatum) on
 Krome very gravelly loam soil. Irrigation applications were controlled by
 ET controller.TREC_ET_Online.xlsxTurfgrass with Conventional IrrigationHourly volumetric water content data from soil moisture sensor (Decagon Ech2o EC-5) installed at 7.6 cm depth below St. Augustine turfgrass (Stenotaphrum secundatum) on Krome very gravelly loam soil. Irrigation followed conventional scheduling.TREC_Control_Online.xlsxCitrus Orchard with Conventional Irrigation SchedulingHourly volumetric water content data from soil moisture sensor (Campbell Scientific SC161) installed at 15.2 cm depth below Citrus on well drained sandy soils. Irrigation followed conventional scheduling.FtMeade_VWC_Online.xlsx
DOI: 10.5061/dryad.1j84f
title: Data from: US line-ups outperform UK line-ups

description: In the USA and the UK, many thousands of police suspects are identified by
 eyewitnesses every year. Unfortunately, many of those suspects are
 innocent, which becomes evident when they are exonerated by DNA testing,
 often after having been imprisoned for years. It is, therefore, imperative
 to use identification procedures that best enable eyewitnesses to
 discriminate innocent from guilty suspects. Although police investigators
 in both countries often administer line-up procedures, the details of how
 line-ups are presented are quite different and an important direct
 comparison has yet to be conducted. We investigated whether these two
 line-up procedures differ in terms of (i) discriminability (using receiver
 operating characteristic analysis) and (ii) reliability (using
 confidence–accuracy characteristic analysis). A total of 2249 participants
 watched a video of a crime and were later tested using either a six-person
 simultaneous photo line-up procedure (USA) or a nine-person sequential
 video line-up procedure (UK). US line-up procedure yielded significantly
 higher discriminability and significantly higher reliability. The results
 do not pinpoint the reason for the observed difference between the two
 procedures, but they do suggest that there is much room for improvement
 with the UK line-up.
description: US vs. UK lineup
 dataData for Seale-Carlisle
 & Mickes paper on US vs. UK lineups.USvUKdata.xlsx
DOI: 10.5061/dryad.8dt0gd1
title: Data from: Genetic architecture of traits associated with reproductive barriers in Silene: coupling, sex chromosomes and variation

description: The evolution of reproductive barriers and their underlying genetic
 architecture is of central importance for the formation of new species.
 Reproductive barriers can be controlled either by few large-effect loci
 suggesting strong selection on key traits, or by many small-effect loci,
 consistent with gradual divergence or with selection on polygenic or
 multiple traits. Genetic coupling between reproductive barrier loci
 further promotes divergence, particularly divergence with ongoing gene
 flow. In this study, we investigated the genetic architectures of ten
 morphological, phenological and life history traits associated with
 reproductive barriers between the hybridizing sister species Silene dioica
 and S. latifolia; both are dioecious with XY sex determination. We used
 quantitative trait locus (QTL) mapping in two reciprocal F2 crosses. One
 to six QTLs per trait, including 9 major QTLs (PVE &gt; 20%) were
 detected, in total, on 11 of 12 linkage groups. We found strong evidence
 for coupling of QTLs for uncorrelated traits. QTL clusters occurred both
 on autosomes and on the sex chromosomes. Unexpectedly, QTLs detected in
 the two F2 crosses differed largely, despite limited phenotypic
 differences between them and sufficient statistical power. The widely
 dispersed genetic architectures of traits associated with reproductive
 barriers suggest gradual divergence or multifarious selection and coupling
 of the underlying QTLs likely promoted divergence with gene flow in this
 system. The low congruence of QTLs between the two crosses further points
 to variable and possibly redundant genetic architectures of traits
 associated with reproductive barriers, with important implications for the
 evolutionary dynamics of divergence and speciation.
description: Silene_TraitThe sheet named "data Liu & Karrenberg" contains data of phenotype measurements. The second sheet named "Column_explanation" contains explanation for each column in the first sheet.
DOI: 10.5061/dryad.272c3
title: Data from: Jerzego, a new hisponine jumping spider from Borneo (Araneae: Salticidae)

description: A new genus and species of hisponine jumping spider from Sarawak, Jerzego
 corticicola Maddison sp. nov. are described, representing one of the few
 hisponine jumping spiders known from Asia, and the only whose male is
 known. Although similar to the primarily-Madagascan genus Hispo in having
 an elongate and flat body, sequences of 28s and 16sND1 genes indicate that
 Jerzego is most closely related to Massagris and Tomomingi, a result
 consistent with morphology. Females of Jerzego and other genera of
 Hisponinae were found to have an unusual double copulatory duct, which
 appears to be a synapomorphy of the subfamily. Two species are transferred
 from Hispo, Jerzego bipartitus (Simon) comb. nov. and Jerzego alboguttatus
 (Simon) comb. nov. Diagnostic illustrations and photographs of living
 spiders are provided.
description: Jerzego-DataAndResults28s and 16sND1 alignments for hisponines, other salticids, and outgroups
DOI: 10.5061/dryad.2v10hs6
title: Data from: Mesoscale activity facilitates energy gain in a top predator

description: How animal movement decisions interact with the distribution of resources
 to shape individual performance is a key question in ecology. However,
 links between spatial and behavioural ecology and fitness consequences are
 poorly understood because the outcomes of individual resource selection
 decisions, such as energy intake, are rarely measured. In the open ocean,
 mesoscale features (~10-100 km) such as fronts and eddies can aggregate
 prey and thereby drive the distribution of foraging vertebrates through
 bottom-up biophysical coupling. These productive features are known to
 attract predators, yet their role in facilitating energy transfer to top
 predators is opaque. We investigated the use of mesoscale features by
 migrating northern elephant seals and quantified the corresponding
 energetic gains from the seals’ foraging patterns at a daily resolution.
 Migrating elephant seals modified their diving behaviour and selected for
 mesoscale features when foraging. Daily energy gain increased
 significantly with increasing mesoscale activity, indicating that the
 physical environment can influence predator fitness at fine temporal
 scales. Results show that areas of high mesoscale activity not only
 attract top predators as foraging hotspots, but also lead to increased
 energy transfer across trophic levels. Our study provides evidence that
 the physical environment is an important factor in controlling energy flow
 to top predators by setting the stage for variation in resource
 availability. Such understanding is critical for assessing how changes in
 the environment and resource distribution will affect individual fitness
 and food web dynamics.
description: Northern Elephant Seal
 Lipid EstimatesThis file contains daily
 lipid estimates for 29 adult female northern elephant seals. Lipid
 estimates are derived from a state space model detailed in Schick et al.
 2013, Journal of Animal Ecology.Dryad_Lipid_Data.csv
DOI: 10.5061/dryad.961t3
title: Data from: Diversification in continental island archipelagos: new evidence on the roles of fragmentation, colonization and gene flow on the genetic divergence of Aegean Nigella (Ranunculaceae)

description: Background and Aims: Disentangling the relative roles of past
 fragmentation (vicariance), colonization (dispersal) and post-divergence
 gene flow in the genetic divergence of continental island organisms
 remains a formidable challenge. Amplified fragment length polymorphisms
 (AFLPs) were used to (1) gain further insights into the biogeographical
 processes underlying the Pleistocene diversification of the Aegean Nigella
 arvensis complex; (2) evaluate the role of potential key factors driving
 patterns of population genetic variability (mating system, geographical
 isolation and historical contingencies); and (3) test the robustness of
 conclusions previously drawn from chloroplast (cp) DNA. Methods: Genetic
 diversity was analysed for 235 AFLP markers from 48 populations (497
 individuals) representing 11 taxa of the complex using population genetic
 methods and Bayesian assignment tests. Key Results: Most designated taxa
 are identifiable as genetically distinct units. Both fragmentation and
 dispersal-driven diversification processes occurred at different
 geological time scales, from Early to Late Pleistocene, specifically (1)
 sea barrier-induced vicariant speciation in the Cyclades, the Western
 Cretan Strait and Ikaria; and (2) bi-regional colonizations of the
 ‘Southern Aegean Island Arc’ from the Western vs. Eastern Aegean mainland,
 followed by allopatric divergences in Crete vs. Rhodos and
 Karpathos/Kasos. Outcrossing island taxa experienced drift-related
 demographic processes that are magnified in the two insular selfing
 species. Population genetic differentiation on the mainland seems largely
 driven by dispersal limitation, while in the Central Aegean it may still
 be influenced by historical events (island fragmentation and sporadic
 long-distance colonization). Conclusions: The biogeographical history of
 Aegean Nigella is more complex than expected for a strictly allopatric
 vicariant model of divergence. Nonetheless, the major phylogeographical
 boundaries of this radiation are largely congruent with the geography and
 history of islands, with little evidence for ongoing gene exchange between
 divergent taxa. The present results emphasize the need to investigate
 further biological and landscape features and contemporary vs. historical
 processes in driving population divergence and taxon diversification in
 Aegean plant radiations.
description: Nigella_AFLPSee README file
DOI: 10.5061/dryad.bb8r6
title: Data from: Mother-offspring transmission and age-dependent accumulation of simian foamy virus in wild chimpanzees

description: Simian foamy viruses (SFVs) are thought to infect virtually any adult
 non-human primate (NHP). While much data have accumulated about patterns
 of co-divergence with their hosts and cross-species transmission events,
 little is known about the modalities of SFV transmission within NHP
 species, especially in the wild. Here we provide a detailed investigation
 of the dynamics of SFV circulation in a wild community of Western
 chimpanzees (Pan troglodytes verus). We demonstrate that mother–offspring
 (vertical) SFV transmission is common and hypothesize that it accounts for
 a number of primary infections. We also show that multiple infections with
 several chimpanzee specific SFV strains (i.e., super-infection) commonly
 happen in adult chimpanzees, which might point at adult-specific
 aggressive behaviors as a lifelong source of SFV infection. Our data give
 evidence for complex SFV dynamics in wild chimpanzees, even at a single
 community scale, and show that linking wild NHP social interactions and
 their microorganisms’ dynamics is feasible.
description: Alignment of all clone
 sequences generated in the course of this studyFASTA file comprising
 915 SFV int sequences.complete_data_SFV.fasta
DOI: 10.5061/dryad.5b58400
title: Data from: Mapping the imprint of biotic interactions on β-diversity

description: Investigating how trophic interactions influence the β-diversity of
 meta-communities is of paramount importance to understanding the processes
 shaping biodiversity distribution. Here, we apply a statistical method for
 inferring the strength of spatial dependencies between pairs of species
 groups. Using simulated community data generated from a multi-trophic
 model, we showed that this method can approximate biotic interactions in
 multi-trophic communities based on β-diversity patterns across groups.
 When applied to soil multi-trophic communities along an elevational
 gradient in the French Alps, we found that fungi make a major contribution
 to the structuring of β-diversity across trophic groups. We also
 demonstrated that there were strong spatial dependencies between groups
 known to interact specifically (e.g. plant-symbiotic fungi,
 bacteria-nematodes) and that the influence of environment was less
 important than previously reported in the literature. Our method paves the
 way for a better understanding and mapping of multi-trophic communities
 through space and time.
description: data_ohlmann_etal_2018