cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mn643
title: Data from: The counterintuitive role of sexual selection in species maintenance and speciation

description: The pronounced and elaborate displays that often differ between closely
 related animal species have led to the common assumption that sexual
 selection is important in speciation, especially in geographically
 separated populations. We use population genetic models to examine the
 ability of Fisherian sexual selection to contribute to lasting species
 differentiation by isolating its effect after the onset of gene flow
 between allopatric populations. We show that when sexually selected traits
 are under ecologically divergent selection, the situation most favorable
 to speciation, mating preferences tend to introgress faster than trait
 alleles, causing sexual selection to counter the effects of local
 adaptation. As a consequence, the net amount of trait divergence often
 drops with stronger Fisherian sexual selection. Furthermore, alleles for
 progressively weaker preferences spread in this context until sexual
 selection is removed. The effects of pure Fisherian sexual selection on
 species maintenance are thus much more inhibitory than previously assumed.
description: Basic model, multilocus
 notation, and QLEDevelops recursions for
 basic model in standard and multilocus notation. Develops a quasi-linkage
 equilibrium approximation with weak selectionPreference-trait
 expression of trait in both sexesDevelops recursion
 equations for version of the model with trait expression in both
 sexes.Preference-trait with
 search costsDevelops the model and
 provides simulation code for version of the model with search
 costsPreference-trait
 simulation basic modelSimulation code for the
 basic modelPreference-trait
 simulation best-of-nSimulation code for
 version of the model with best-of-n mating algorithmEvolution of preference
 strengthDevelopment of
 recursions and simulation code for model of evolution of preference
 strength.Preference-trait
 simulation both sexesSimulation code for
 version of the model with expression of the trait in both
 sexes.Approx large
 alphaDerivations of the
 approximate equilibrium with strong selection
DOI: 10.5061/dryad.d9s74
title: Data from: Early back-to-Africa migration into the Horn of Africa

description: Genetic studies have identified substantial non-African admixture in the
 Horn of Africa (HOA). In the most recent genomic studies, this non-African
 ancestry has been attributed to admixture with Middle Eastern populations
 during the last few thousand years. However, mitochondrial and Y
 chromosome data are suggestive of earlier episodes of admixture. To
 investigate this further, we generated new genome-wide SNP data for a
 Yemeni population sample and merged these new data with published
 genome-wide genetic data from the HOA and a broad selection of surrounding
 populations. We used multidimensional scaling and ADMIXTURE methods in an
 exploratory data analysis to develop hypotheses on admixture and
 population structure in HOA populations. These analyses suggested that
 there might be distinct, differentiated African and non-African ancestries
 in the HOA. After partitioning the SNP data into African and non-African
 origin chromosome segments, we found support for a distinct African
 (Ethiopic) ancestry and a distinct non-African (Ethio-Somali) ancestry in
 HOA populations. The African Ethiopic ancestry is tightly restricted to
 HOA populations and likely represents an autochthonous HOA population. The
 non-African ancestry in the HOA, which is primarily attributed to a novel
 Ethio-Somali inferred ancestry component, is significantly differentiated
 from all neighboring non-African ancestries in North Africa, the Levant,
 and Arabia. The Ethio-Somali ancestry is found in all admixed HOA ethnic
 groups, shows little inter-individual variance within these ethnic groups,
 is estimated to have diverged from all other non-African ancestries by at
 least 23 ka, and does not carry the unique Arabian lactase persistence
 allele that arose about 4 ka. Taking into account published mitochondrial,
 Y chromosome, paleoclimate, and archaeological data, we find that the time
 of the Ethio-Somali back-to-Africa migration is most likely
 pre-agricultural.
description: New SNP data for 64
 YemeniContains the complete
 unfiltered new genotype data from 64 Yemeni samples in a binary PED (BED)
 file format (compatible with PLINK). These samples were collected by
 Connie Mulligan, Ali Al-Meeri, and Ryan Raaum in the spring of 2007 in
 Yemen with grant support from NSF BCS-0518530 to Connie Mulligan. These
 samples were genotyped on the Illumina Human CNV370-Quad V3.0 Beadchip.
 The chromosome and map location information in the bed map file are as
 provided in the Illumina documentation for this chip. As of April 22,
 2014, Illumina has information on this chip at:
 http://support.illumina.com/downloads/humancnv370-quad_v30_product_files.ilmnyemen.zip
DOI: 10.5061/dryad.t7t5r
title: Data from: Sexual antagonism for resistance and tolerance to infection in Drosophila melanogaster

description: A critical task in evolutionary genetics is to explain the persistence of
 heritable variation in fitness-related traits such as immunity. Ecological
 factors can maintain genetic variation in immunity, but less is known
 about the role of other factors, such as antagonistic pleiotropy, on
 immunity. Sexually dimorphic immunity—with females often being more
 immune-competent—may maintain variation in immunity in dioecious
 populations. Most eco-immunological studies assess host resistance to
 parasites rather than the host's ability to maintain fitness during
 infection (tolerance). Distinguishing between resistance and tolerance is
 important as they are thought to have markedly different evolutionary and
 epidemiological outcomes. Few studies have investigated tolerance in
 animals, and the extent of sexual dimorphism in tolerance is unknown.
 Using males and females from 50 Drosophila melanogaster genotypes, we
 investigated possible sources of genetic variation for immunity by
 assessing both resistance and tolerance to the common bacterial pathogen
 Pseudomonas aeruginosa. We found evidence of sexual dimorphism and sexual
 antagonism for resistance and tolerance, and a trade-off between the two
 traits. Our findings suggest that antagonistic pleiotropy may be a major
 contributor to variation in immunity, with implications for host–parasite
 coevolution.
description: MA-P Resistance
 DataMAPfitnessdataDrosophila Tolerance Data Entry
DOI: 10.5061/dryad.3c5r8
title: Data from: Species distribution models of an endangered rodent offer conflicting measures of habitat quality at multiple scales

description: 1. The high cost of directly measuring habitat quality has led ecologists
 to test alternate methods for estimating and predicting this critically
 important ecological variable. In particular, it is frequently assumed but
 rarely tested that models of habitat suitability (“species distribution
 models”, SDMs) may provide useful indices of habitat quality, either from
 an individual animal or manager’s perspective. Critically, SDMs are
 increasingly used to estimate species’ ranges, with an implicit assumption
 that areas of high suitability will result in higher probability of
 persistence. This assumption underlies efforts to use SDMs to design
 protected areas, assess the status of cryptic species, or manage responses
 to climate change. Recent tests of this relationship have provided mixed
 results, suggesting SDMs may predict abundance but not other measures of
 high quality habitat (e.g., survival, persistence). 2. In this study, we
 created a suite of SDMs for the endangered giant kangaroo rat Dipodomys
 ingens at three distinct scales using the machine-learning method Maxent.
 We compared these models with three measures of habitat quality: survival,
 abundance, and body condition. 3. SDMs were not correlated with survival,
 while models at all scales were positively correlated with abundance.
 Finer-scale models were more closely correlated with abundance than the
 largest scale. Body condition was not correlated with habitat suitability
 at any scale. The inability of models to predict survival may be due to a
 lack of information in environmental covariates; unmeasured community
 processes or stochastic events; or the inadequacy of using models that
 predict species presence to also predict demography. Synthesis and
 applications: SDMs, especially fine scale ones, may be useful for
 longer-term management goals, such as identifying high quality habitat for
 protection. However, short-term management decisions should be based only
 on models that use covariates appropriate for the necessary temporal and
 spatial scales. Assumptions about the relationship between habitat
 suitability and habitat quality must be made explicit. Even then, care
 should be taken in inferring multiple types of habitat quality from SDMs.
description: GKR Capture
 HistoriesCapture histories at
 each trapping grid, formatted for analysis in Program MARK or
 rMarkcaphists_combined.csvEnvironmental Predictors for Giant Kangaroo Rats in Carrizo PlainASCII rasters of environmental predictors used to produce species distribution model for giant kangaroo rats (Dipodomys ingens) in the Carrizo Plain National Monument.SDM_ASCII.zipEstimate of giant kangaroo rat burrow densityCount of active and inactive giant kangaroo rat burrows in 10m x 50m transect at sites across GKR range.burrow.mean.rangewide.csv
DOI: 10.7927/606k-d497
title: IPCC AR6 Synthesis Report SPM.4 (a) and LR Figure 3.3 (a) (Linear graph): Global surface temperature change relative to 1850-1900

description: Global surface temperature changes in °C relative to 1850–1900. These changes were obtained by combining CMIP6 model simulations with observational constraints based on past simulated warming, as well as an updated assessment of equilibrium climate sensitivity. Very likely ranges are shown for the low and high GHG emissions scenarios (SSP1-2.6 and SSP3-7.0).
DOI: 10.5061/dryad.g7g0n
title: Data from: Genetic distance for a general non-stationary Markov substitution process

description: The genetic distance between biological sequences is a fundamental
 quantity in molecular evolution. It pertains to questions of rates of
 evolution, existence of a molecular clock, and phylogenetic inference.
 Under the class of continuous-time substitution models, the distance is
 commonly defined as the expected number of substitutions at any site in
 the sequence. We eschew the almost ubiquitous assumptions of evolution
 under stationarity and time-reversible conditions and extend the concept
 of the expected number of substitutions to non-stationary Markov models
 where the only remaining constraint is of time homogeneity between nodes
 in the tree. Our measure of genetic distance reduces to the standard
 formulation if the data in question are consistent with the stationarity
 assumption. We apply this general model to samples from across the tree of
 life to compare distances so obtained with those from the general
 time-reversible model, with and without rate heterogeneity across sites,
 and the paralinear distance, an empirical pairwise method explicitly
 designed to address non-stationarity. We discover that estimates from both
 variants of the general time-reversible model and the paralinear distance
 systematically overestimate genetic distance and departure from the
 molecular clock. The magnitude of the distance bias is proportional to
 departure from stationarity, which we demonstrate to be associated with
 longer edge lengths. The marked improvement in consistency between the
 general non-stationary Markov model and sequence alignments leads us to
 conclude that analyses of evolutionary rates and phylogenies will be
 substantively improved by application of this model.
description: mitochondrialNexus alignments of mtDNA protein coding sequences from one-to-one orthologs of Mouse, Human and Opossum. The Ensembl release 68 stable ID for the Human gene is used as the filename. Species common names are used as the sequence labels.mtDNA.tar.gznuclearNexus alignments of nuclear protein coding sequences from one-to-one orthologs of Mouse, Human and Opossum. The Ensembl release 68 stable ID for the Human gene is used as the filename. Species common names are used as the sequence labels.microbialNexus formatted alignments of 16S rRNA sequences from 3 microbial species. Files differ in species triples present. These alignments were derived from http://www.secondgenome.com/go/2011-greengenes-taxonomy/. File names are the greengenes sequence identifiers.Online appendixSupplementary figures and table.evo_time_online_appendix.pdfAnalysis source codeCode used to perform the analyses.PyCogent libraryThe git repo for PyCogent. Capabilities required for this project were included in https://github.com/pycogent/pycogent commit 6fb91188d4ced898c66529ef85a43e742d5b39b5.
DOI: 10.5061/dryad.v0v83
title: Data from: A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution

description: Detailed linkage and recombination rate maps are necessary to use the full
 potential of genome sequencing and population genomic analyses. We used a
 custom collared flycatcher 50 K SNP array to develop a high-density
 linkage map with 37 262 markers assigned to 34 linkage groups in 33
 autosomes and the Z chromosome. The best-order map contained 4215 markers,
 with a total distance of 3132 cM and a mean genetic distance between
 markers of 0.12 cM. Facilitated by the array being designed to include
 markers from most scaffolds, we obtained a second-generation assembly of
 the flycatcher genome that approaches full chromosome sequences (N50
 super-scaffold size 20.2 Mb and with 1.042 Gb (of 1.116 Gb) anchored to
 and mostly ordered and oriented along chromosomes). We found that
 flycatcher and zebra finch chromosomes are entirely syntenic but that
 inversions at mean rates of 1.5–2.0 event (6.6–7.5 Mb) per My have changed
 the organization within chromosomes, rates high enough for inversions to
 potentially have been involved with many speciation events during avian
 evolution. The mean recombination rate was 3.1 cM/Mb and correlated
 closely with chromosome size, from 2 cM/Mb for chromosomes &gt;100 Mb
 to &gt;10 cM/Mb for chromosomes &lt;10 Mb. This size dependence
 seemed entirely due to an obligate recombination event per chromosome; if
 50 cM was subtracted from the genetic lengths of chromosomes, the rate per
 physical unit DNA was constant across chromosomes. Flycatcher
 recombination rate showed similar variation along chromosomes as chicken
 but lacked the large interior recombination deserts characteristic of
 zebra finch chromosomes.
description: FlycatcherGenotypeThese are the genotype files of collared flycatcher used for linkage analysis. Please see README.txt for more details.
DOI: 10.5061/dryad.vf210
title: Data from: Ecological and evolutionary effects of fragmentation on infectious disease

description: Ecological theory predicts that disease incidence increases with
 increasing density of host networks, yet evolutionary theory suggests that
 host resistance increases accordingly. To test the combined effects of
 ecological and evolutionary forces on host-pathogen systems, we analyzed
 the spatiotemporal dynamics of a plant (Plantago lanceolata)–fungal
 pathogen (Podosphaera plantaginis)relationship for 12 years in over 4000
 host populations. Disease prevalence at the metapopulation level was low,
 with high annual pathogen extinction rates balanced by frequent
 (re-)colonizations. Highly connected host populations experienced less
 pathogen colonization and higher pathogen extinction rates than expected;
 a laboratory assay confirmed that this phenomenon was caused by higher
 levels of disease resistance in highly connected host populations.
description: ALL_FINAL
DOI: 10.5061/dryad.9ht88
title: Data from: Fruiting bodies of the social amoeba Dictyostelium discoideum increase spore transport by Drosophila

description: Background: Many microbial phenotypes are the product of cooperative
 interactions among cells, but their putative fitness benefits are often
 not well understood. In the cellular slime mold Dictyostelium discoideum,
 unicellular amoebae aggregate when starved and form multicellular fruiting
 bodies in which stress-resistant spores are held aloft by dead stalk
 cells. Fruiting bodies are thought to be adaptations for dispersing spores
 to new feeding sites, but this has not been directly tested. Here we
 experimentally test whether fruiting bodies increase the rate at which
 spores are acquired by passing invertebrates. Results: Drosophila
 melanogaster accumulate spores on their surfaces more quickly when exposed
 to intact fruiting bodies than when exposed to fruiting bodies physically
 disrupted to dislodge spore masses from stalks. Flies also ingest and
 excrete spores that still express a red fluorescent protein marker.
 Conclusions: Multicellular fruiting bodies created by D. discoideum
 increase the likelihood that invertebrates acquire spores that can then be
 transported to new feeding sites. These results thus support the
 long-hypothesized dispersal benefits of altruism in a model system for
 microbial cooperation.
description: Data: Spore carriage by
 fliesData for experiment on
 spore carriage by flies after exposure to fruiting bodies. Formatted as
 tab-delimited text file for use with R. Columns and values described in
 comments (lines beginning with #).data_dispersal.txtAnalysis: Spore carriage by fliesScript for analyzing data and producing figures using R with ggplot2 package.stats_dispersal.RFig. 2 - Images of flies carrying sporesHigh resolution version of Figure 2, showing composite images of D. melanogaster after exposure to fruiting bodies of D. discoideum genetically marked to express red fluorescent protein.figure2.pdf
DOI: 10.5061/dryad.t342m
title: Data from: A novel Bayesian method for inferring and interpreting the dynamics of adaptive landscapes from phylogenetic comparative data

description: Our understanding of macroevolutionary patterns of adaptive evolution has
 greatly increased with the advent of large-scale phylogenetic comparative
 methods. Widely used Ornstein-Uhlenbeck (OU) models can describe an
 adaptive process of divergence and selection. However, inference of the
 dynamics of adaptive landscapes from comparative data is complicated by
 interpretational difficulties, lack of identifiability among parameter
 values and the common requirement that adaptive hypotheses must be
 assigned a priori. Here we develop a reversible-jump Bayesian method of
 fitting multi-optima OU models to phylogenetic comparative data that
 estimates the placement and magnitude of adaptive shifts directly from the
 data. We show how biologically informed hypotheses can be tested against
 this inferred posterior of shift locations using Bayes Factors to
 establish whether our a priori models adequately describe the dynamics of
 adaptive peak shifts. Furthermore, we show how the inclusion of
 informative priors can be used to restrict models to biologically
 realistic parameter space and test particular biological interpretations
 of evolutionary models. We argue that Bayesian model-fitting of OU models
 to comparative data provides a framework for integrating of multiple
 sources of biological data–such as microevolutionary estimates of
 selection parameters and paleontological timeseries–allowing inference of
 adaptive landscape dynamics with explicit, process-based biological
 interpretations.
description: Online_Appendices
DOI: 10.5281/zenodo.18390499
title: Data and code for: Survival and reproduction of reintroduced Crested Ibis (Nipponia nippon) in Henan Province, China.

description: Data and R code supporting the analyses in the associated manuscript.
DOI: 10.5281/zenodo.18390498
title: Data and code for: Survival and reproduction of reintroduced Crested Ibis (Nipponia nippon) in Henan Province, China.

description: Data and R code supporting the analyses in the associated manuscript.
DOI: 10.5061/dryad.fm573
title: Data from: Estimation of migration rates from marker based parentage analysis

description: Coupled with rapid developments of efficient genetic markers, powerful
 population genetics methods were proposed to estimate migration rates (m)
 in natural populations in much broader spatial and temporal scales than
 the traditional mark-release-recapture (MRR) methods. Highly polymorphic
 (e.g. microsatellites) and genomic wide (e.g. SNPs) markers provide
 sufficient information to assign individuals to their populations or
 parents of origin, and thereby to estimate directly m in a way similar to
 MRR. Such direct estimates of current migration rates are particularly
 useful in understanding the ecology and microevolution of wild populations
 and in managing the populations in the future. In this study I proposed
 and implemented, in the software MigEst, a likelihood method to use marker
 based parentage assignments in jointly estimating m and candidate parent
 sampling proportions (x) in a subset of populations, investigated its
 power and accuracy using data simulated in various scenarios of population
 properties (e.g. the actual m, number, size and differentiation of
 populations) and sampling properties (e.g. the numbers of sampled parent
 candidates, offspring, and markers), compared it with the population
 assignment approach implemented in the software BayesAss, and demonstrated
 its usefulness by analysing a microsatellite dataset from three natural
 populations of Brazilian bats. Simulations showed that MigEst provides
 unbiased and accurate estimates of m, and performs better than BayesAss
 except when populations are highly differentiated with very small and
 ecologically insignificant migration rates. A valuable property of MigEst
 is that in the presence of unsampled populations, it gives good estimates
 of the rate of migration among sampled populations as well as of the rate
 of migration into each sampled population from the pooled unsampled
 populations.
description: Input and output
 filesThis zipped file
 contains all input files for simulations, all input files for the bat
 dataset, and output files from the analyses of simulated data and the bat
 dataDataResults.zipSimuMigEstThe simulation package containing all of the programs and associated files needed to run the simulations