cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h4g74
title: Data from: Social role specialization promotes cooperation between parents

description: Biparental care of offspring is a widespread social behavior, and various
 ecological, life-history and demographic factors have been proposed to
 explain its evolution and maintenance. Raising offspring generally
 requires several types of care (e.g. feeding, brooding, defense), and
 males and females often specialize in providing different types of care.
 However, theoretical models of care often assume that 'care' is
 a single variable, and hence that a unit of care by the mother is
 interchangeable with a unit of care by the father. We hypothesize that the
 ability of one parent to provide all types of care may be limited by
 non-additive costs, or by sex-based asymmetries in the costs of particular
 care types. Using an individual-based simulation, we show that synergistic
 costs of investing in two tasks, or a negligible sex-based cost asymmetry,
 select for task specialization and biparental care. Biparental care
 persists despite intense sexual selection and sex-biased mortality,
 suggesting that previous models make overly restrictive predictions of the
 conditions under which cooperation can be maintained. Our model provides a
 mechanistic underpinning for published models that show synergistic
 benefits of individuals cooperating can stabilize cooperation, both in the
 context of parental care and in other social scenarios.
description: Data and R scripts for
 simulation showing that role specialisation promotes parental
 cooperationSimulation data and R
 scripts from which figures in Barta et al American Naturalist 2014
 "Social role specialization promotes cooperation between
 parents" were prepared.BartaAmNat2014_RoleSpecialisation.zip
DOI: 10.5883/bold:aek5477
title: Overview of Barcode Index Number - BOLD:AEK5477

description: DNA barcode data hosted in the Data Portal of the Barcode of Life Data Systems. Records consist of specimen metadata, specimen images, and sequence data.
DOI: 10.5061/dryad.v77j2
title: Data from: A relationship between attractiveness and performance in professional cyclists

description: Females often prefer to mate with high quality males, and one aspect of
 quality is physical performance. Although a preference for physically
 fitter males is therefore predicted, the relationship between
 attractiveness and performance has rarely been quantified. Here, I test
 for such a relationship in humans and ask whether variation in (endurance)
 performance is associated with variation in facial attractiveness within
 elite professional cyclists that finished the 2012 Tour de France. I show
 that riders that performed better were more attractive, and that this
 preference was strongest in women not using a hormonal contraceptive.
 Thereby, I show that, within this preselected but relatively homogeneous
 sample of the male population, facial attractiveness signals endurance
 performance. Provided that there is a relationship between
 performance-mediated attractiveness and reproductive success, this
 suggests that human endurance capacity has been subject to sexual
 selection in our evolutionary past.
description: Data
 fileContains all rater- and
 rider specific data.postma_data.txt
DOI: 10.5061/dryad.hn1vn
title: Data from: Automatic detection of key innovations, rate shifts, and diversity-dependence on phylogenetic trees

description: A number of methods have been developed to infer differential rates of
 species diversification through time and among clades using
 time-calibrated phylogenetic trees. However, we lack a general framework
 that can delineate and quantify heterogeneous mixtures of dynamic
 processes within single phylogenies. I developed a method that can
 identify arbitrary numbers of time-varying diversification processes on
 phylogenies without specifying their locations in advance. The method uses
 reversible-jump Markov Chain Monte Carlo to move between model subspaces
 that vary in the number of distinct diversification regimes. The model
 assumes that changes in evolutionary regimes occur across the branches of
 phylogenetic trees under a compound Poisson process and explicitly
 accounts for rate variation through time and among lineages. Using
 simulated datasets, I demonstrate that the method can be used to quantify
 complex mixtures of time-dependent, diversity-dependent, and constant-rate
 diversification processes. I compared the performance of the method to the
 MEDUSA model of rate variation among lineages. As an empirical example, I
 analyzed the history of speciation and extinction during the radiation of
 modern whales. The method described here will greatly facilitate the
 exploration of macroevolutionary dynamics across large phylogenetic trees,
 which may have been shaped by heterogeneous mixtures of distinct
 evolutionary processes.
description: Phylogenetic trees
 simulated under multi-process macroevolutionary models for analysis with
 BAMMThis file contains
 simulated datasets analyzed as part of Rabosky (2014). There are 6 general
 simulation scenarios, described at length in the manuscript. These include
 500 phylogenetic trees simulated under each macroevolutionary scenario.
 Each batch of simulated datasets was analyzed with BAMM. This dataset
 contains the simulated datasets, and also the parameters underlying the
 simulations. For example, the subdirectory "constant" contains
 the 500 constant-rate birth-death process phylogenies that were analyzed
 with BAMM. These trees are stored in the fild "simtrees.txt".
 Another file in this directory, "cr_truerates.txt", contains the
 actual simulation parameters. For example, the first row of that file
 gives the speciation and extinction parameters that were used to simulate
 the first tree in the "simtrees.txt" file. The same general idea
 holds for the other subdirectories. dd_k1 for example is a pure-birth
 background process with a shift to a single diversity-dependent regime on
 one descendant lineage. The simulation scenarios are detailed in the
 master file "DESCRIPTION.txt".BAMM-TestSIms.zip
DOI: 10.5061/dryad.65t6n
title: Data from: Molecular phylogeny and chromosomal evolution of Alcelaphini (Antilopinae)

description: Robertsonian (Rb) translocations, in particular centric fusions, are
 thought to play a primary role in evolution and speciation of the Bovidae
 family. However, Rb fusions are often polymorphic within species, being
 suggested as phylogenetically uninformative characters. This work studies
 chromosome variation in 72 captive individuals of 6 species of Alcelaphini
 (Antilopinae): The hartebeest (genus Alcelaphus), hirola (Beatragus),
 black and blue wildebeests (Connochaetes), and the topi and bontebok
 (Damaliscus). We infer the phylogenic relationships among Alcelaphini
 species and determine patterns of chromosomal evolution using G-banded
 karyotypes and complete mitochondrial genome sequences. The molecular
 phylogeny showed an early divergence of Connochaetes, followed by the
 split of Alcelaphus plus Beatragus + Damaliscus as sister taxa.
 Mitochondrial and chromosomal phylogenies only differed in the position of
 the critically endangered Beatragus, likely due to homoplasic chromosome
 characters. Patterns of chromosome evolution, reconstructed using a
 probabilistic approach, suggest that chromosome changes leading to
 speciation in Alcelaphini do not exclusively involve consecutive reduction
 of diploid number through centric fusion but also the losses and
 reversions of Rb translocations in Beatragus and Damaliscus lineages. Our
 results provide evidence that complex scenarios of chromosomal
 rearrangements can be detected in relatively recent-diverged bovids, as in
 this group of antelopes.
description: Concatened_MrBNexus file of concatenated mitochondrial partitions used to perform the Bayesian phylogenetic analysis of Alcelaphini. Five partitions were considered: tRNAs (1-1512 nucleotide positions), rRNA (1513-4039), and first, second and third codon sites of the protein coding genes (4040-15439). The Bayesian inference consisted of ten million generations analysis (sampled every 1,000 generations), and a 50% burn-in.Chromosome_MPNexus files of 23 chromosome characters used to perform maximum parsimony phylogenetic analysis of Alcelaphini. The data matrix was established by assigning 0 or 1 values for the absence or presence of characters. MP trees were generated using a heuristic search option and phylogenetic support for each node was assessed using 1000 bootstrap replicates.ChraALLNexus file of 5 ambiguous chromosomal characters used to estimate ancestral states and chromosome evolution in Alcelaphini via SIMMAP.BurninMrBNexus file containing the 4999 post-burning Bayesian trees used to estimated the posterior probability distribution of the rate of change of 5 ambiguous chromosome characters in Alcelaphini. SIMMAP estimated ancestral states by averaging the posterior distribution over multiple trees. The number of changes is proportional to branch lengths.
DOI: 10.15159/phytop.159
title: Jaanuse

description: Phytoplankton biomass, diversity and abundance in samples collected from Lake Jaanuse during the period 1999 and 2016.
DOI: 10.5061/dryad.d85ng
title: Data from: Domestication and the mitochondrial genome: comparing patterns and rates of molecular evolution in domesticated mammals and birds and their wild relatives

description: Studies of domesticated animals have led to the suggestion that
 domestication could have significant effects on patterns of molecular
 evolution. In particular, analyses of mitochondrial genome sequences from
 domestic dogs and yaks have yielded higher ratios of non-synonymous to
 synonymous substitutions in the domesticated lineages than in their wild
 relatives. These results are important because they imply that changes to
 selection or population size operating over a short timescale can cause
 significant changes to the patterns of mitochondrial molecular evolution.
 In this study, our aim is to test whether the impact on mitochondrial
 genome evolution is a general feature of domestication, or whether it is
 specific to particular examples. We test whether domesticated mammals and
 birds have consistently different patterns of molecular evolution than
 their wild relatives for 16 phylogenetically independent comparisons of
 mitochondrial genome sequences. We find no consistent difference in branch
 lengths or dN/dS between domesticated and wild lineages. We also find no
 evidence that our failure to detect a consistent pattern is due to the
 short timescales involved, or low genetic distance between domesticated
 lineages and their wild relatives. However, removing comparisons where the
 wild relative may also have undergone a bottleneck does reveal a pattern
 consistent with reduced effective population size in domesticated
 lineages. Our results suggest that, while some domesticated lineages may
 have undergone changes to selective regime or effective population size
 that could have affected mitochondrial evolution, it is not possible to
 generalise these patterns over all domesticated mammals and birds.
description: Data and analysis files
 for Domestication and the Mitochondrial Genome, Moray et al.,
 GBEPlease see README file
 for details.
DOI: 10.5061/dryad.75j12
title: Data from: Lower Jurassic foraminifera from the Llanbedr (Mochras Farm) Borehole, North Wales, UK

description: The complete, fully cored Lower Jurassic (Hettangian, Sinemurian,
 Pliensbachian, Toarcian) succession from the Llanbedr (Mochras Farm)
 Borehole, North Wales, the thickest known British section, has yielded a
 diverse and well preserved foraminiferal fauna, comprising 270 species and
 subspecies which are described and illustrated. An additional nine taxa,
 not encountered at Mochras, are also described. This typical European
 Boreal Atlantic foraminiferal fauna is dominated by members of the
 Lagenida, with the Ceratobuliminoidea, Miliolida, Spirillinina,
 Involutinina, Buliminida and Textulariida as important accessory groups.
 The Ceratobuliminoidea and Miliolida are unusually diverse, with
 Reinholdella and Ophthalmidium being notably abundant. The presence of the
 family Oberhauserellidae is significant. A benthonic foraminiferal
 biozonation scheme for the Lower Jurassic, comprising 16 biozones and tied
 to the standard ammonite-based chronostratigraphy, is described in detail.
 It is recognizable across the northern European Boreal province and as far
 south as Spain and France, and is applicable to subsurface hydrocarbon
 exploration of the UK continental shelf and onshore Europe. Three new
 genera (Duoplanum, Extonia and Haynesella) are described as well as 19 new
 species (Citharina sherringtoni, Duoplanum inaequale, D. leve,
 Glomospirella liassica, Lagena? haeusleri, L. semisulcata, Lagenammina
 pseudofusiformis, L. tangentia, Loxostomum liassicum, Marginulina turneri,
 Neobulimina bangae, Nodosaria pseudoclaviformis, Ophthalmidium strictum,
 Reinholdella? mochrasensis, R. robusta, Reussoolina? lacrimaforma,
 Semiiinvoluta excelsa, Tubinella pseudoinornata, and Vinelloidea lordi),
 and 10 new subspecies (Berthelinella involuta striata, Ichthyolaria
 terquemi barnardi, I. terquemi mediumcostata, Lenticulina varians
 barnardi, Loxostomum liassicum liassicum, L. liassicum teres,
 Ophthalmidium macfadyeni tenuiloculare, Paralingulina cernua ssp. A,
 Reinholdella margarita dorsoplana, and R. pachyderma humilis). Two further
 species are renamed as Nodosaria whittakeri and Paralingulina
 paranodosaria .
description: Mochras Borehole
 Foraminifera Distribution Charts (Supplementary Data)The data file comprises
 two large scale charts, in pdf format, showing the distribution and
 abundances of all recorded foraminifera from the Lower Jurassic section of
 the Llanbedr (Mochras Farm) Borehole, North Wales, United Kingdom. These
 data are supplementary to the publication COPESTAKE, P & JOHNSON, B.
 2014. Lower Jurassic Foraminifera from the Llanbedr (Mochras Farm)
 Borehole, North Wales, UK. Monograph of the Palaeontographical Society,
 London: 1-000, pls 1-21. (Publ.641, part of Vol. 000 for
 2013).MochrasBoreholeForamDistCharts_Copestake&Johnson_15Jan2014.pdf
DOI: 10.5061/dryad.9kh1b
title: Data from: Sequential adaptive introgression of the mitochondrial genome in Drosophila yakuba and D. santomea

description: Interspecific hybridization provides the unique opportunity for species to
 tap into genetic variation present in a closely related species and
 potentially take advantage of beneficial alleles. It has become
 increasingly clear that when hybridization occurs, mitochondrial DNA
 (mtDNA) often crosses species boundaries, raising the possibility that it
 could serve as a recurrent target of natural selection and source of
 species’ adaptations. Here we report the sequences of 46 complete
 mitochondrial genomes of Drosophila yakuba and D. santomea, two sister
 species known to produce hybrids in nature (~3%). At least two independent
 events of mtDNA introgression were uncovered in this study, including an
 early invasion of the D. yakuba mitochondrial genome that fully replaced
 the D. santomea mtDNA native haplotypes and a more recent, ongoing event
 centered in the hybrid zone. Interestingly, this recent introgression
 event bears the signature of Darwinian natural selection and the selective
 haplotype can be found at low frequency in Africa mainland populations of
 D. yakuba. We put forward the possibility that, because the effective
 population size of D. santomea is smaller than that of D. yakuba, the
 faster accumulation of mildly deleterious mutations associated with
 Muller’s ratchet in the former species may have facilitated the
 replacement of the mutationally loaded mitochondrial genome of D. santomea
 by that of D. yakuba.
description: IMa2 input file (2
 populations, mtDNA)Input file used in the
 simulations of the Isolation-with-Migration (IM) model with 2 populations
 (D. yakuba and D. santomea) performed with the program IMa2 and the
 dataset of complete mitochondrial DNA sequencesLlopart_et_al_IMa2_2_pop.txtIMa2 input file (3 populations, mtDNA)Input file used in the simulations of the Isolation-with-Migration (IM) model with 3 populations (D. yakuba mainland, D. yakuba island and D. santomea) performed with the program IMa2 and the dataset of complete mitochondrial DNA sequencesLlopart_et_al_IMa2_3_pop.txtIMa2 input file (2 populations, mtDNA and Y chromosome)Input file used in the simulations of the Isolation-with-Migration (IM) model with 2 populations (D. yakuba and D. santomea) performed with the program IMa2 and the dataset of complete mitochondrial and partial Y chromosome DNA sequencesLlopart_et_al_IMa2_with_Y.txtGene tree fileInput file in MEGA format used to obtain the gene tree shown in Fig. 3Llopart_et_al_Tree.meg
DOI: 10.5061/dryad.t91v2
title: Data from: Muscle tradeoffs in a power-amplified prey capture system

description: Should animals operating at great speeds and accelerations use fast or
 slow muscles? The answer hinges on a fundamental tradeoff: muscles can be
 maximally fast or forceful, but not both. Direct lever systems offer a
 straightforward manifestation of this tradeoff, yet the fastest organisms
 use power amplification, not direct lever action. Power-amplified systems
 typically use slow, forceful muscles to pre-load springs which then
 rapidly release elastic potential energy to generate high speeds and
 accelerations. However, a fast response to a stimulus may necessitate fast
 spring-loading. Across 22 mantis shrimp species (Stomatopoda), this study
 examined how muscle anatomy correlates with spring mechanics and appendage
 type. We found that muscle force is maximized through physiological
 cross-sectional area, but not through sarcomere length. Sit-and-wait
 predators had the shortest sarcomere lengths (fastest contractions) and
 the slowest strike speeds. The species that crush shells (“smashers”) had
 the fastest speeds, most forceful springs and longest sarcomeres. The
 origin of the smasher clade yielded dazzlingly high accelerations, perhaps
 due to the release from fast spring-loading for evasive prey capture. This
 study offers a new window into the dynamics of force-speed tradeoffs in
 muscles in the biomechanical, comparative evolutionary framework of
 power-amplified systems.
description: muscledatasetRaw data for muscle analysisspringdatasetData for spring analysisAnalyses in RR analyses used in studyMendozaBlancoPatek_muscleanalyses.R
DOI: 10.5061/dryad.67md0
title: Data from: Sensory drive does not explain reproductive character displacement of male acoustic signals in the Upland Chorus Frog (Pseudacris feriarum)

description: Biotic and abiotic factors have been proposed to explain patterns of
 reproductive character displacement, but which factor is most important to
 character displacement of acoustic signals is not clear. Male
 vocalizations of the frog Pseudacris feriarum are known to undergo
 reproductive character displacement in areas of sympatry with P. brimleyi
 and P. nigrita. Despite evidence for reinforcement as an important
 mechanism, local adaptation via sensory drive might explain this pattern
 because Pseudacris breed in different habitat types and mating signals are
 exposed to a variety of environments. We tested the sensory drive
 hypothesis by playing synthesized vocalizations representing the spectrum
 of variation in P. feriarum at 12 different study sites. If sensory drive
 has occurred, then vocalizations should transmit better in the site of
 origin or at ecologically similar sites. We found that variation in
 acoustic signals did not produce better transmission in particular sites,
 the effect of site was uniform, and acoustic signals often transmitted
 better in habitats external to their origin. Ecological variation among
 habitats did not explain signal degradation. Our playback experiments,
 ecological analyses, and comparisons of different habitat types provide no
 support for sensory drive as a process promoting reproductive character
 displacement in this system. Reinforcement is the more likely primary
 mechanism.
description: Malone_etal_2014_Evolution_SuperMasterFileThis is the master file that contains information about the acoustic stimuli used, cross correlations, and ecological data.
DOI: 10.5061/dryad.6c45t
title: Data from: Social forces can impact the circadian clocks of cohabiting hamsters

description: A number of field and laboratory studies have shown that the social
 environment influences daily rhythms in numerous species. However,
 underlying mechanisms, including the circadian system’s role, are not
 known. Obstacles to this research have been the inability to track and
 objectively analyse rhythms of individual animals housed together. Here,
 we employed temperature dataloggers to track individual body temperature
 rhythms of pairs of cohabiting male Syrian hamsters (Mesocricetus auratus)
 in constant darkness and applied a continuous wavelet transform to
 determine the phase of rhythm onset before, during, and after
 cohabitation. Cohabitation altered the predicted trajectory of rhythm
 onsets in 34% of individuals, representing 58% of pairs, compared to 12%
 of hamsters single-housed as ‘virtual pair’ controls. Deviation from the
 predicted trajectory was by a change in circadian period (t), which tended
 to be asymmetric—affecting one individual of the pair in nine of 11
 affected pairs—with hints that dominance might play a role. These data
 implicate a change in the speed of the circadian clock as one mechanism
 whereby social factors can alter daily rhythms. Miniature dataloggers
 coupled with wavelet analyses should provide powerful tools for future
 studies investigating the principles and mechanisms mediating social
 influences on daily timing.
description: body temperature
 filesText files containing
 the body temperature recordings from individual Syrian hamsters co-housed
 in pairs or single-housed as 'virtual pairs' in laboratory
 cages. Temperature is in Celsius (C = Celsius) and was recorded using
 iButton temperature dataloggers. Each line contains the date and time of
 the body temperature recording. The first number in the filename
 represents the hamster ID for that file. Co-housed hamster pairs: 47 with
 51, 45 with 53, 42 with 50, 41 with 52, 49 with 44, 46 with 43, 54 with
 48, 124 with 98, 75 with 127, 118 with 102, 89 with 116, 113 with 108, 76
 with 122, 101 with 81, 117 with 74, 94 with 99, 111 with 84, 93 with 86,
 91 with 82. Virtually-paired hamsters: 112 with 73, 126 with 106, 78 with
 104, 110 with 103, 114 with 128, 105 with 100, 129 with 96, 80 with 107,
 87 with 95, 88 with 123, 90 with 83, 77 with 92.