cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7dk42
title: Data from: Sex matters in massive parallel sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

description: Using massively parallel sequencing data from two species with different
 life history traits, American lobster (Homarus americanus) and Arctic Char
 (Salvelinus alpinus), we highlight how an unbalanced sex ratio in the
 samples and a few sex-linked markers may lead to false interpretations of
 population structure and thus to potentially erroneous management
 recommendations. Here, multivariate analyses revealed two genetic clusters
 separating samples by sex instead of by expected spatial variation;
 inshore and offshore locations in lobster, or east and west locations in
 Arctic Char. To further investigate this, we created several subsamples
 artificially varying the sex ratio in the inshore/offshore and east/west
 groups, and then demonstrated that significant genetic differentiation
 could be observed despite panmixia in lobster, and that Fst values were
 overestimated in Arctic Char. This pattern was due to 12 and 94 sex-linked
 markers driving differentiation for lobster and Arctic Char, respectively.
 Removing sex-linked markers led to non-significant genetic structure in
 lobster and a more accurate estimation of Fst in Arctic Char. The
 locations of these markers and putative identities of genes containing, or
 nearby the markers were determined using available transcriptomic and
 genomic data, and this provided new information related to sex
 determination in both species. Given that only 9.6% of all
 marine/diadromous population genomic studies to date have reported sex
 information, we urge researchers to collect and consider individual sex
 information. Sex information is therefore relevant for avoiding unexpected
 biases due to sex-linked markers as well as for improving our knowledge of
 sex determination systems in non-model species.
description: 1717snps-203ind-gender.recodeAmerican lobster SNP genotypespopulation-map-female-maleAmerican lobster sex information samples.290ind-6230snps-salmo.recodeArctic char SNPs genotypes.SexPopDefArctic char sex information samples.
DOI: 10.5061/dryad.f8n5j
title: Data from: The computer program structure for assigning individuals to populations: easy to use but easier to misuse

description: The computer program Structure implements a Bayesian method, based on a
 population genetics model, to assign individuals to their source
 populations using genetic marker data. It is widely applied in the fields
 of ecology, evolutionary biology, human genetics and conservation biology
 for detecting hidden genetic structures, inferring the most likely number
 of populations (K), assigning individuals to source populations and
 estimating admixture and migration rates. Recently, several simulation
 studies repeatedly concluded that the program yields erroneous inferences
 when samples from different populations are highly unbalanced in size.
 Analysing both simulated and empirical data sets, this study confirms that
 Structure indeed yields poor individual assignments to source populations
 and gives frequently incorrect estimates of K when sampling is unbalanced.
 However, this poor performance is mainly caused by the adoption of the
 default ancestry prior, which assumes all source populations contribute
 equally to the pooled sample of individuals. When the alternative ancestry
 prior, which allows for unequal representations of the source populations
 by the sample, is adopted, accurate individual assignments could be
 obtained even if sampling is highly unbalanced. The alternative prior also
 improves the inference of K by two estimators, albeit the improvement is
 not as much as that in individual assignments to populations. For the
 difficult case of many populations and unbalanced sampling, a rarely used
 parameter combination of the alternative ancestry prior, an initial ALPHA
 value much smaller than the default and the uncorrelated allele frequency
 model is required for Structure to yield accurate inferences. I conclude
 that Structure is easy to use but is easier to misuse because of its
 complicated genetic model and many parameter (prior) options which may not
 be obvious to choose, and suggest using multiple plausible models
 (parameters) and K estimators in conducting comparative and exploratory
 Structure analysis.
description: Program for simulating
 and analyzing genotype data by StructureThe zipped file contains
 a number of files used to (1) simulate genotype data, (2) run Structure to
 analyze simulated data. A ReadMe file is also included.simu.zipProgram for bootstrapping human genotype dataThe zipped file contains a number of files to do bootstrapping of the human genotype data (included), and to run Structure on the data. A ReadMe file is included in the package.sampling.zip
DOI: 10.5061/dryad.36rn7
title: Data from: Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

description: Differential gene expression can play an important role in phenotypic
 evolution and divergent adaptation. Although differential gene expression
 can be caused by both local- and distant-regulatory changes, we know
 little about their relative contribution to transcriptome evolution in
 natural populations. Here, we conducted expression quantitative trait loci
 (eQTL) analysis to investigate the genetic architecture underlying
 transcriptome divergence between marine and stream ecotypes of threespine
 sticklebacks (Gasterosteus aculeatus). We identified both local and
 distant eQTLs, some of which constitute hotspots, regions with a
 disproportionate number of significant eQTLs relative to the genomic
 background. The majority of local eQTLs including those in the hotspots
 caused expression changes consistent with the direction of transcriptomic
 divergence between ecotypes. Genome scan analysis showed that many local
 eQTLs overlapped with genomic regions of high differentiation. In
 contrast, nearly half of the distant eQTLs including those in the hotspots
 caused opposite expression changes, and few overlapped with regions of
 high differentiation, indicating that distant eQTLs may act as a
 constraint of transcriptome evolution. Finally, a comparison between two
 salinity conditions revealed that nearly half of eQTL hotspots were
 environment-specific, suggesting that analysis of genetic architecture in
 multiple conditions is essential for predicting response to selection.
description: MicroarrayBrain microarray data of parental crosses. Normalized fluorescent signals for each gene are shown.LCF2_genotype_rna_combined_SDeQTL input file under 10%SW condition.LCF2_genotype_rna_combined_SWeQTL input file under 100%SW-challenge condition.
DOI: 10.5061/dryad.dk34k
title: Data from: First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)

description: Standard Sanger chloroplast markers provide limited information to resolve
 species level relationships within plants, in particular within large
 genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of
 angiosperms with ∼750 species occurring in the tropics and subtropics
 worldwide. Figs, in addition to being a keystone food resource in
 rainforests, are well-known for the mutualistic interactions with their
 pollinating wasps. It is regarded as a model system for understanding
 co-evolution dating back more than 75 million years. However, despite
 significant taxon sampling, combinations of low copy nuclear, nuclear
 ribosomal and chloroplast regions have not been able to confidently
 resolve relationships among major groups of figs. Using a high throughput
 sequencing approach we attempted to resolve the major lineages of Ficus
 based on plastome data. In this study, we show that the use of a de novo
 assembled plastome from within the genus provides less ambiguity and
 higher coverage across the 59 Ficus and 6 outgroup plastome assemblies
 compared to using the nearest available reference plastome outside the
 genus resulting in improved resolution and higher support of the
 phylogenetic relationships within Ficus inferred from plastome data.
 Chloroplast genome data confidently resolved relationships among major
 groups of figs and largely support current understanding based on nuclear
 sequence data including passively pollinated Neotropical section
 Pharmacosycea as sister lineage to all other Ficus. However, conflicts
 between the new plastome topology and previous nuclear studies are
 observed for both individual species as well as relationships among some
 sections at deeper levels. Conflicts could be caused by lack of resolution
 in the nuclear data or may indicate potential cyto-nuclear discordance as
 previously observed in an African lineage of Ficus.
description: Ficus plastid genome
 alignmentMAFFT alignment of 59
 near-complete Ficus plastid genomes and 6 Castilleae plastid genomes as
 outgroup produced by high throughput sequencing.Ficus plastome Dryad-sub (59
 ficus and 6 outgroup).nexBayesian majority-rule
 consensus tree reconstructed from near-complete plastome sequences for 59
 species of Ficus and outgroup.Bayesian majority-rule
 consensus tree depicted in Figure 1 and described in
 publication.Bayesian_tree.nexus
DOI: 10.5061/dryad.dg154
title: Data from: Sex-specific association patterns in bonobos and chimpanzees reflect species differences in cooperation

description: In several group-living species, individuals' social preferences are
 thought to be influenced by cooperation. For some societies with
 fission–fusion dynamics, sex-specific association patterns reflect sex
 differences in cooperation in within- and between-group contexts. In our
 study, we investigated this hypothesis further by comparing sex-specific
 association patterns in two closely related species, chimpanzees and
 bonobos, which differ in the level of between-group competition and in the
 degree to which sex and kinship influence dyadic cooperation. Here, we
 used long-term party composition data collected on five chimpanzee and two
 bonobo communities and assessed, for each individual of 10 years and
 older, the sex of its top associate and of all conspecifics with whom it
 associated more frequently than expected by chance. We found clear species
 differences in association patterns. While in all chimpanzee communities
 males and females associated more with same-sex partners, in bonobos males
 and females tended to associate preferentially with females, but the
 female association preference for other females is lower than in
 chimpanzees. Our results also show that, for bonobos (but not for
 chimpanzees), association patterns were predominantly driven by
 mother–offspring relationships. These species differences in association
 patterns reflect the high levels of male–male cooperation in chimpanzees
 and of mother–son cooperation in bonobos. Finally, female chimpanzees
 showed intense association with a few other females, and male chimpanzees
 showed more uniform association across males. In bonobos, the most
 differentiated associations were from males towards females. Chimpanzee
 male association patterns mirror fundamental human male social traits and,
 as in humans, may have evolved as a response to strong between-group
 competition. The lack of such a pattern in a closely related species with
 a lower degree of between-group competition further supports this notion.
description: All PAV
 dataset
DOI: 10.5061/dryad.7f91m
title: Data from: Locomotor activity and body temperature patterns over a temperature gradient in the highveld mole-rat (Cryptomys hottentotus pretoriae)

description: African mole-rats are strictly subterranean mammals that live in extensive
 burrow systems. High humidity levels in the burrows prevent mole-rats from
 thermoregulating using evaporative cooling. However, the relatively stable
 environment of the burrows promotes moderate temperatures and small daily
 temperature fluctuations. Mole-rats therefore display a relatively wide
 range of thermoregulation abilities. Some species cannot maintain their
 body temperatures at a constant level, whereas others employ behavioural
 thermoregulation. Here we test the effect of ambient temperature on
 locomotor activity and body temperature, and the relationship between the
 two parameters, in the highveld mole-rat. We exposed mole-rats to a
 12L:12D and a DD light cycle at ambient temperatures of 30°C, 25°C and
 20°C while locomotor activity and body temperature were measured
 simultaneously. In addition, we investigated the endogenous rhythms of
 locomotor activity and body temperature at different ambient temperatures.
 Mole-rats displayed nocturnal activity at all three ambient temperatures
 and were most active at 20°C, but least active at 30°C. Body temperature
 was highest at 30°C and lowest at 20°C, and the daily cycle was highly
 correlated with locomotor activity. We show that the mole-rats have
 endogenous rhythms for both locomotor activity and body temperature.
 However, the endogenous body temperature rhythm appears to be less robust
 compared to the locomotor activity rhythm. Female mole-rats appear to be
 more sensitive to temperature changes than males, increased heterothermy
 is evident at lower ambient temperatures, whilst males show smaller
 variation in their body temperatures with changing ambient temperatures.
 Mole-rats may rely more heavily on behavioural thermoregulation as it is
 more energy efficient in an already challenging environment.
description: Body temperature
 dataHourly body temperatures
 for all animals at 30LD, 30DD, 25LD, 25DD, 20LD and
 20DD.Activity
 dataPer minute locomotor
 activity data for all animals at 30LD, 30DD, 25LD, 25DD, 20LD and
 20DDsoil
 tempSoil temperatures for 5
 consecutive days.
DOI: 10.5061/dryad.4pm73
title: Data from: Extinction vs. rapid radiation: the juxtaposed evolutionary histories of coelotine spiders support the Eocene–Oligocene orogenesis of the Tibetan Plateau

description: Evolutionary biology has long been concerned with how changing
 environments affect and drive the spatiotemporal development of organisms.
 Coelotine spiders (Agelenidae: Coelotinae) are common species in the
 temperate and subtropical areas of the Northern Hemisphere. Their long
 evolutionary history and the extremely imbalanced distribution of species
 richness suggest that Eurasian environments, especially since the
 Cenozoic, are the drivers of their diversification. We use phylogenetics,
 molecular dating, ancestral area reconstructions, diversity and ecological
 niche analyses to investigate the spatiotemporal evolution of 286
 coelotine species from throughout the region. Based on eight genes (6.5
 kb) and 2323 de novo DNA sequences, analyses suggest an Eocene South China
 origin for them. Most extant, widespread species belong to the southern
 (SCG) or northern (NCG) clades. The origin of coelotine spiders appears to
 associate with either the Paleocene–Eocene Thermal Maximum or the hot
 period in early Eocene. Tibetan uplifting events influenced the current
 diversity patterns of coelotines. The origin of SCG lies outside of the
 Tibetan Plateau. Uplifting in the southeastern area of the plateau blocked
 dispersal since the Late Eocene. Continuous orogenesis appears to have
 created localized vicariant events, which drove rapid radiation in SCG.
 North-central Tibet is the likely location of origin for NCG and many
 lineages likely experienced extinction owing to uplifting since early
 Oligocene. Their evolutionary histories correspond with recent geological
 evidence that high-elevation orographical features existed in the Tibetan
 region as early as 40 to 35 Ma. Our discoveries may be the first empirical
 evidence that links the evolution of organisms to the Eocene–Oligocene
 uplifting of the Tibetan Plateau.
description: Supplementary
 Data_20170324
DOI: 10.5061/dryad.170rb
title: Data from: Inference of evolutionary jumps in large phylogenies using Lévy processes

description: While it is now widely accepted that the rate of phenotypic evolution may
 not necessarily be constant across large phylogenies, the frequency and
 phylogenetic position of periods of rapid evolution remain unclear. In his
 highly influential view of evolution, G. G. Simpson supposed that such
 evolutionary jumps occur when organisms transition into so called new
 adaptive zones, for instance after dispersal into a new geographic area,
 after rapid climatic changes, or following the appearance of an
 evolutionary novelty. Only recently, large, accurate and well calibrated
 phylogenies have become available that allow testing this hypothesis
 directly, yet inferring evolutionary jumps remains computationally very
 challenging. Here, we develop a computationally highly efficient algorithm
 to accurately infer the rate and strength of evolutionary jumps as well as
 their phylogenetic location. Following previous work we model evolutionary
 jumps as a compound process, but introduce a novel approach to sample jump
 configurations that does not require matrix inversions and thus naturally
 scales to large trees. We then make use of this development to infer
 evolutionary jumps in Anolis lizards and Loriinii parrots where we find
 strong signal for such jumps at the basis of clades that transitioned into
 new adaptive zones, just as postulated by Simpson's hypothesis.
description: Supplementary
 FiguressupInfo_resubmission.pdf
DOI: 10.5061/dryad.qc10g
title: Data from: Natural selection on MHC IIβ in parapatric lake and stream stickleback: balancing, divergent, both or neither?

description: Major histocompatibility (MHC) genes encode proteins that play a central
 role in vertebrates’ adaptive immunity to parasites. MHC loci are among
 the most polymorphic in vertebrates’ genomes, inspiring many studies to
 identify evolutionary processes driving MHC polymorphism within
 populations, and divergence between populations. Leading hypotheses
 include balancing selection favoring rare alleles within populations, and
 spatially divergent selection. These hypotheses do not always produce
 diagnosably distinct predictions, causing many studies of MHC to yield
 inconsistent or ambiguous results. We suggest a novel strategy to
 distinguish balancing versus divergent selection on MHC, taking advantage
 of natural admixture between parapatric populations. With divergent
 selection, individuals with immigrant alleles will be more infected and
 less fit because they are susceptible to novel parasites in their new
 habitat. With balancing selection, individuals with locally-rare immigrant
 alleles will be more fit (less infected). We tested these contrasting
 predictions using threespine stickleback from three replicate pairs of
 parapatric lake and stream habitats. We found numerous positive and
 negative associations between particular MHC IIβ alleles and particular
 parasite taxa. A few allele-parasite comparisons supported balancing
 selection, others supported divergent selection between habitats. But,
 there was no overall tendency for fish with immigrant MHC alleles to be
 more or less heavily infected. Instead, locally rare MHC alleles (not
 necessarily immigrants) were associated with heavier infections. Our
 results illustrate the complex relationship between MHC IIβ allelic
 variation and spatially varying multi-species parasite communities:
 different hypotheses may be concurrently true for different
 allele-parasite combinations.
description: StutzBolnickDataData to recreate results, including genotype scores and parasite infection and geographic locations.AllelesFASTA file with inferred true MHC IIb alleles (removing sequencing error via Stepwise Threshold Clustering)MHC_master
DOI: 10.5061/dryad.4m7m1
title: Data from: DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes

description: Microeukaryotic plankton (0.2–200 μm) are critical components of aquatic
 ecosystems and key players in global ecological processes. High-throughput
 sequencing is currently revolutionizing their study on an unprecedented
 scale. However, it is currently unclear whether we can accurately,
 effectively and quantitatively depict the microeukaryotic plankton
 communities using traditional size-fractionated filtering combined with
 molecular methods. To address this, we analysed the eukaryotic plankton
 communities both with, and without, prefiltering with a 200 μm pore-size
 sieve –by using SSU rDNA-based high-throughput sequencing on 16 samples
 with three replicates in each sample from two subtropical reservoirs
 sampled from January to October in 2013. We found that ~25% reads were
 classified as metazoan in both size groups. The species richness, alpha
 and beta diversity of plankton community and relative abundance of reads
 in 99.2% eukaryotic OTUs showed no significant changes after prefiltering
 with a 200 μm pore-size sieve. We further found that both &gt;0.2 μm
 and 0.2–200 μm eukaryotic plankton communities, especially the abundant
 plankton subcommunities, exhibited very similar, and synchronous,
 spatiotemporal patterns and processes associated with almost identical
 environmental drivers. The lack of an effect on community structure from
 prefiltering suggests that environmental DNA from larger metazoa is
 introduced into the smaller size class. Therefore, size-fractionated
 filtering with 200 μm is insufficient to discriminate between the
 eukaryotic plankton size groups in metabarcoding approaches. Our results
 also highlight the importance of sequencing depth, and strict quality
 filtering of reads, when designing studies to characterize microeukaryotic
 plankton communities.
description: raw data
 size-fractionated 20161206OTU table (97% sequence
 similarity threshold after quality filtered) and the raw physico-chemical
 parameters
DOI: 10.5061/dryad.kc65r
title: Data from: Variation in growth drives the duration of parental care: a test of Ydenberg's model

description: The duration of parental care in animals varies widely, from none to
 lifelong. Such variation is typically thought to represent a trade-off
 between growth and safety. Seabirds show wide variation in the age at
 which offspring leave the nest, making them ideal to test the idea that a
 trade-off between high energy gain at sea and high safety at the nest
 drives variation in departure age (Ydenberg’s model). To directly test the
 model assumptions, we attached time-depth recorders to murre parents
 (fathers [which do all parental care at sea] and mothers; of each). Except
 for the initial mortality experienced by chicks departing from the colony,
 the mortality rate at sea was similar to the mortality rate at the colony.
 However, energy gained by the chick per day was ∼2.1 times as high at sea
 compared with at the colony because the father spent more time foraging,
 since he no longer needed to spend time commuting to and from the colony.
 Compared with the mother, the father spent ∼2.6 times as much time diving
 per day and dived in lower-quality foraging patches. We provide a simple
 model for optimal departure date based on only (1) the difference in
 growth rate at sea relative to the colony and (2) the assumption that
 transition mortality from one life-history stage to the other is size
 dependent. Apparently, large variation in the duration of parental care
 can arise simply as a result of variation in energy gain without any
 trade-off with safety.
description: Common Murre data
 fileDescription of Common
 Murre data fileMaster_Dives_COMU.txtDaily summary fileIncludes all dives from Coats Island; Daily summary for all birds; meta data associated with all birds.Daily summary.xlsxCoats Island data filesOverwinter dive files for Coats Island42_2_183-189_Overwinter_Files.zip
DOI: 10.5281/zenodo.17426548
title: Earthquake data and cluster analysis along the Mid-Atlantic Ridge (2000-2024)

description: Dataset and Juptyer code for identifying swarms of earthquakes along the Mid-Atlantic Ridge (2000-2024).