cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1204
title: Data from: Inbreeding depression and drift load in small populations at demographic disequilibrium

description: Inbreeding depression is a major driver of mating system evolution and has
 critical implications for population viability. Theoretical and empirical
 attention has been paid to predicting how inbreeding depression varies
 with population size. Lower inbreeding depression is predicted in small
 populations at equilibrium, primarily due to higher inbreeding rates
 facilitating purging and/or fixation of deleterious alleles (drift load),
 but predictions at demographic and genetic disequilibrium are less clear.
 In this study, we experimentally evaluate how lifetime inbreeding
 depression and drift load, estimated by heterosis, vary with census (Nc)
 and effective (estimated as genetic diversity, He) population size across
 six populations of the biennial Sabatia angularis as well as present novel
 models of inbreeding depression and heterosis under varying demographic
 scenarios at disequilibrium (fragmentation, bottlenecks, disturbances).
 Our experimental study reveals high average inbreeding depression and
 heterosis across populations. Across our small sample, heterosis declined
 with He, as predicted, whereas inbreeding depression did not vary with He
 and actually decreased with Nc. Our theoretical results demonstrate that
 inbreeding depression and heterosis levels can vary widely across
 populations at disequilibrium despite similar He and highlight that joint
 demographic and genetic dynamics are key to predicting patterns of genetic
 load in nonequilibrium systems.
description: FruitSet_InitialCrossesFruit set data: whether or not a fruit resulted from the pollination treatments. Data are at the flower level.SeedSet_InitialCrosses.Seed set data: Mass of fruits is used as surrogate for seeds per fruit. Data are at the flower level.GerminationEarlySurvivalSizeSurvivalReproductionLifetimeFitnessPerMomdemogenetCode for simulationsID&Heterosis vs Nc&HeSimulated dataHe vs N simSimulated datafixed.and.seg.lociSimulated datar effect on bottleneckSimulated data
DOI: 10.5061/dryad.53g73
title: Data from: Socially segregated, sympatric sperm whale clans in the Atlantic Ocean

description: Sperm whales (Physeter macrocephalus) are unusual in that there is good
 evidence for sympatric populations with distinct culturally determined
 behaviour, including potential acoustic markers of the population
 division. In the Pacific, socially segregated, vocal clans with distinct
 dialects coexist; by contrast, geographical variation in vocal repertoire
 in the Atlantic has been attributed to drift. We examine networks of
 acoustic repertoire similarity and social interactions for 11 social units
 in the Eastern Caribbean. We find the presence of two socially segregated,
 sympatric vocal clans whose dialects differ significantly both in terms of
 categorical coda types produced by each clan (Mantel test between clans:
 matrix correlation = 0.256; p ≤ 0.001) and when using classification-free
 similarity which ignores defined types (Mantel test between clans: matrix
 correlation = 0.180; p ≤ 0.001). The more common of the two clans makes a
 characteristic 1 + 1 + 3 coda, while the other less often sighted clan
 makes predominantly regular codas. Units were only observed associating
 with other units within their vocal clan. This study demonstrates that
 sympatric vocal clans do exist in the Atlantic, that they define a higher
 order level of social organization as they do in the Pacific, and suggests
 that cultural identity at the clan level is probably important in this
 species worldwide.
description: ICI data from Gero et al
 2016 Socially segregated sympatric sperm whales clans in
 RSOSICI data from analysis
 in Gero et al (2016) Socially Segregated, Sympatric Sperm Whale Clans in
 the Atlantic Ocean in RSOS
DOI: 10.5061/dryad.gt74m
title: Data from: Molecular phylogeny and revised classification of the haplotilapiine cichlid fishes formerly referred to as “Tilapia”

description: African cichlids formerly referred to as ”Tilapia” represent a
 paraphyletic species assemblage belonging to the so called haplotilapiine
 lineage which gave rise to the spectacular East African cichlid radiations
 (EARs) as well as to globally important aquaculture species. We present a
 comprehensive molecular phylogeny of representative haplotilapiine
 cichlids, combining in one data set four mitochondrial and five nuclear
 loci for 76 species, and compare it with phylogenetic information of a
 second data set of 378 mitochondrial ND2 haplotypes representing almost
 all important “Tilapia” or Tilapia-related lineages as well as most EAR
 lineages. The monophyly of haplotilapiines is supported, as is the nested
 sister group relationship of Etia and mouthbrooding tilapiines with the
 remaining haplotilapiines. The latter are consistently placed in eight
 monophyletic clades over all datasets and analyses, but several
 dichotomous phylogenetic relationships appear compromised by cytonuclear
 discordant phylogenetic signal. Based on these results as well as on
 extensive morphological evidence we propose a novel generic and
 suprageneric classification including a (re-)diagnosis of 20
 haplotilapiine cichlid genera and nine tribes. New tribes are provided for
 the former subgenera Coptodon Gervais, 1853, HeterotilapiaRegan, 1920 and
 PelmatolapiaThys van den Audenaerde, 1969, in addition for “Tilapia” joka,
 Tilapia sensu stricto and Chilochromis, Etia, Steatocranus sensu stricto,
 the mouthbrooding tilapiines and for a clade of West African tilapiines.
description: final “dataset A” with
 6122 bpThe final “dataset A”
 contained five nuclear loci (ENC1: 698 bp, Ptr: 691 bp, SH3PX3: 681 bp,
 Tmo4c4: 425 bp, S7 intron: 508 bp) and four partial mitochondrial
 fragments (12S: 350 bp, 16S: 522 bp, 12S/16S: 1239 bp (originally 1295 bp,
 56 bp were excluded due to alignment ambiguities), ND2: 1008
 bp).Final
 dataset A.fasta
DOI: 10.5061/dryad.v2j1r
title: Data from: Implications of the circumpolar genetic structure of polar bears for their conservation in a rapidly warming Arctic

description: We provide an expansive analysis of polar bear (Ursus maritimus)
 circumpolar genetic variation during the last two decades of decline in
 their sea-ice habitat. We sought to evaluate whether their genetic
 diversity and structure have changed over this period of habitat decline,
 how their current genetic patterns compare with past patterns, and how
 genetic demography changed with ancient fluctuations in climate.
 Characterizing their circumpolar genetic structure using microsatellite
 data, we defined four clusters that largely correspond to current
 ecological and oceanographic factors: Eastern Polar Basin, Western Polar
 Basin, Canadian Archipelago and Southern Canada. We document evidence for
 recent (ca. last 1–3 generations) directional gene flow from Southern
 Canada and the Eastern Polar Basin towards the Canadian Archipelago, an
 area hypothesized to be a future refugium for polar bears as
 climate-induced habitat decline continues. Our data provide empirical
 evidence in support of this hypothesis. The direction of current gene flow
 differs from earlier patterns of gene flow in the Holocene. From analyses
 of mitochondrial DNA, the Canadian Archipelago cluster and the Barents Sea
 subpopulation within the Eastern Polar Basin cluster did not show signals
 of population expansion, suggesting these areas may have served also as
 past interglacial refugia. Mismatch analyses of mitochondrial DNA data
 from polar and the paraphyletic brown bear (U. arctos) uncovered offset
 signals in timing of population expansion between the two species, that
 are attributed to differential demographic responses to past climate
 cycling. Mitogenomic structure of polar bears was shallow and developed
 recently, in contrast to the multiple clades of brown bears. We found no
 genetic signatures of recent hybridization between the species in our
 large, circumpolar sample, suggesting that recently observed hybrids
 represent localized events. Documenting changes in subpopulation
 connectivity will allow polar nations to proactively adjust conservation
 actions to continuing decline in sea-ice habitat.
description: Circumpolar polar bear
 microsatellite datasetPeacock_et_al_2014.xlsx
DOI: 10.5061/dryad.sk64k
title: Data from: Revaccination of cattle with Bacille Calmette-Guérin two years after first vaccination when immunity has waned, boosted protection against challenge with Mycobacterium bovis

description: In both humans and animals, controversy exists concerning the duration of
 protection induced by BCG vaccine against tuberculosis (TB) and whether
 revaccination enhances protection. A long-term study was undertaken to
 determine whether BCG-vaccinated calves would be protected against
 challenge with Mycobacterium bovis 2½ years after vaccination and to
 determine the effect of revaccination after 2 years. Seventy–nine calves
 were divided into five groups (n = 15–17 calves/group) with four of the
 groups vaccinated subcutaneously with 105 CFU of BCG Danish at 2–4 weeks
 of age and the fifth group serving as non-vaccinated controls. Three of
 the four BCG-vaccinated groups were revaccinated 2 years after the initial
 vaccination. One BCG-vaccinated group was revaccinated with BCG. A second
 group was vaccinated subcutaneously with a TB protein vaccine consisting
 of biopolyester particles (Biobeads) displaying two mycobacterial
 proteins, ESAT-6 and Antigen 85A, mixed with an adjuvant. A third group
 was vaccinated with TB proteins from M. bovis culture filtrate, mixed with
 an adjuvant. Twenty-three weeks after the BCG revaccination, all animals
 were challenged endotracheally with virulent M. bovis and a further 13
 weeks later, animals were killed and necropsied to determine protection
 against TB. The BCG-vaccinated animals produced positive tuberculin caudal
 fold intradermal (15 of 62 animals) and IFN-γ TB test responses (six of 62
 animals) at 6 months after vaccination, but not at subsequent time-points
 compared to the non-vaccinated animals. Calves receiving a single
 vaccination with BCG vaccine 2½ years prior to challenge were not
 protected against TB, while those revaccinated with BCG 2 years after the
 initial vaccination displayed significant reductions in lung and pulmonary
 lymph node lesion scores compared to the non-vaccinated animals. In
 contrast, no reduction in lesion scores was observed in the animals
 revaccinated with the TB protein vaccines with their immune responses
 biased towards induction of antibody.
description: Ag 85A serology
 DryadAntibody responses of
 cattle to mycobacterial antigen 85A (Ag85A). Excel file from ELISA plate
 reader using Softmax-pro.CFP Serology
 DryadAntibody responses to
 mycobacterial culture filtrate protein. Excel file from ELISA plate reader
 using Softmax-pro.ESAT Serology
 DryadAntibody responses to
 ESAT6. Excel file from ELISA plate reader using
 Softmax-pro.Histo lesion scores 3.14
 DryadHistology lesion scores.
 Data collected in field at post-mortem. Excel fileIFN pgml results
 dryadInterferon-gamma
 cytokine responses. Excel file from ELISA plate reader using
 Softmax-pro.Lesion table for bacto
 DryadLesion table from histo
 scores. Samples collected at post-mortem. Excel fileWallaceville IFN and CFT
 results DryadSkin test results
 collected in the field. Excel file. CFT= caudal fold
 test.
DOI: 10.5061/dryad.m24n2
title: Data from: Vocalisation repertoire of female bluefin gurnard (Chelidonichthys kumu) in captivity: Sound structure, context and vocal activity

description: Fish vocalisation is often a major component of underwater soundscapes.
 Therefore, interpretation of these soundscapes requires an understanding
 of the vocalisation characteristics of common soniferous fish species.
 This study of captive female bluefin gurnard, Chelidonichthys kumu, aims
 to formally characterise their vocalisation sounds and daily pattern of
 sound production. Four types of sound were produced and characterised,
 twice as many as previously reported in this species. These sounds fit two
 aural categories; grunt and growl, the mean peak frequencies for which
 ranged between 129 to 215 Hz. This species vocalized throughout the 24
 hour period at an average rate of (18.5 ± 2.0 sounds fish-1 h-1) with an
 increase in vocalization rate at dawn and dusk. Competitive feeding did
 not elevate vocalisation as has been found in other gurnard species.
 Bluefin gurnard are common in coastal waters of New Zealand, Australia and
 Japan and given their vocalization rate, are likely to be significant
 contributors to ambient underwater soundscape in these areas.
description: craigsgrowl-gurnardcraigsgrunt-gurnard
DOI: 10.5061/dryad.8jv30
title: Data from: The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno

description: Gene duplications can facilitate adaptation and may lead to
 inter-population divergence, causing reproductive isolation. We used
 whole-genome re-sequencing data from 34 butterflies to detect duplications
 in two Heliconius species, H. cydno and H. melpomene. Taking advantage of
 three distinctive signals of duplication in short-read sequencing data, we
 identified 744 duplicated loci in H. cydno and H. melpomene, 96% of which
 were validated with single molecule sequencing. We have found that
 duplications overlap genes significantly less than expected at random in
 H. melpomene, consistent with the action of background selection against
 duplicates in functional regions of the genome. Duplicate loci that are
 highly differentiated between H. melpomene and H. cydno map to four
 different chromosomes. Four duplications were identified with a strong
 signal of divergent selection, including an odorant binding protein and
 another in close proximity with a known wing colour pattern locus that
 differs between the two species.
description: merge_within_each_toolMerge within each tool: delly, cnvnator, pindelmerged_by_tool_trio_cydnochromosome 2 duplication calls merged by tool for the H. cydno (trio)merged_by_tool_trio_melpomenechromosome 2 merged by tool on the trio H. melpomene samplesheliconius_set.vcfHeliconius set from population data (H. cydno + H. melpomene)discovery_set_cydnoH. cydno discovery setdiscovery_set_melpH. melpomene discovery set
DOI: 10.5061/dryad.5t5s1
title: Data from: Metabarcoding and mitochondrial metagenomics of endogean arthropods to unveil the mesofauna of the soil

description: Biological communities inhabiting the soil are among the most diversified,
 complex and yet most poorly studied terrestrial ecosystems. The greatest
 knowledge gaps apply to the arthropod mesofauna (0·1–2 mm body size)
 because conventional morphological and molecular approaches are in many
 cases insufficient for the characterisation of these complex communities.
 The development of high-throughput sequencing (HTS) methodologies is
 required to solve current impediments and to further advance our
 understanding of below-ground biodiversity. We propose a
 flotation–Berlese–flotation (FBF) protocol for sampling and specimen
 processing to obtain ‘clean’ DNA extractions of arthropod mesofauna from
 the soil. In addition, we developed and tested HTS protocols for the
 characterisation of arthropod communities from these bulk DNA extractions
 using cox1 metabarcoding and shotgun metagenomic sequencing on the MiSeq
 Illumina platform. The FBF protocol provided DNA of soil arthropods from
 sufficiently large volumes of soil and free from contaminating bacteria
 and inhibitors. Metabarcoding and metagenomic sequencing on two deep soil
 samples from Iberian grasslands revealed &gt;100 species of Acari and
 Collembola from 28 families. Genome assembly straight from shotgun
 sequencing of bulk specimens produced partial and full mitogenomes for 54
 species with average length of &gt;6000 bp. Metabarcoding and
 metagenomic sequencing resulted in closely congruent OTUs, but species
 numbers were highest with metabarcoding, while ∼73% of species were
 confirmed by matching shotgun sequence reads and ∼48% by contig assembly
 from those shotgun reads. In combination, the FBF protocol together with
 the PCR-based and shotgun sequencing pipelines addressed most of the
 challenges of studying soil arthropod mesofauna on the MiSeq Illumina
 platform. They are powerful, cost-efficient tools for characterising soil
 diversity in a phylogenetic and community ecology context. These
 methodological developments of HTS approaches for the study of mesofauna
 will accelerate ecological and evolutionary studies, biomonitoring of soil
 arthropods, and progress in both theoretical and applied soil science.
description: Combined full-length
 OTUsCombined
 OTUsmetagenomic-cox1
DOI: 10.5061/dryad.7sq67
title: Data from: Genetic dissection of a genomic region with pleiotropic effects on domestication traits in maize reveals multiple linked QTL

description: The domesticated crop maize and its wild progenitor, teosinte, have been
 used in numerous experiments to investigate the nature of divergent
 morphologies. This study examines a poorly understood region on the fifth
 chromosome of maize associated with a number of traits under selection
 during domestication using a QTL mapping population specific to the fifth
 chromosome. In contrast with other major domestication loci in maize where
 large effect, highly pleiotropic, single genes are responsible for
 phenotypic effects, our study found the region on chromosome five
 fractionates into multiple QTL regions, none with singularly large
 effects. The smallest 1.5 LOD support interval for a QTL contained 54
 genes, one of which was a MADS MIKCC transcription factor, a family of
 proteins implicated in many developmental programs. We also used simulated
 trait datasets to investigate the power of our mapping population to
 identify QTL for which there is a single underlying causal gene. This
 analysis showed that while QTL for traits controlled by single genes can
 be accurately mapped, our population design can detect no more than ~4.5
 QTL per trait even when there are 100 causal genes. Thus when a trait is
 controlled by 5 or more genes in the simulated data, the number of
 detected QTL can represent a simplification of the underlying causative
 factors. Our results show how a QTL region with effects on several
 domestication traits may be due to multiple linked QTL of small effect as
 opposed to a single gene with large and pleiotropic effects.
description: T5SAllTraitDataFull phenotype data collected for the NIRIL mapping population.Genotypes and LSMeansGenotypes and LSMeans for the NIRIL populationT5S.csv
DOI: 10.6084/m9.figshare.31151752
title: Temperature preferences of Athabasca Rainbow Trout (Oncorhynchus mykiss) across a gradient of thermal landscapes.

description: Streamside thermal physiology experiments were conducted on Athabasca Rainbow Trout in July and August 2022 near Hinton, Alberta, Canada. Fish were collected from three streams using electrofishing and transferred to instream flow through holding bags. The following morning, fish were transferred into the shuttlebox system to begin the experiment during which the preferred temperature (T<sub>pref</sub>) and avoidance temperature (T<sub>avoid</sub>) were measured. After the experiment had concluded, a fin clip, length, and weight measurements were recorded, and the fish were released back into their respective streams once they had fully recovered.
DOI: 10.6084/m9.figshare.31151752.v1
title: Temperature preferences of Athabasca Rainbow Trout (Oncorhynchus mykiss) across a gradient of thermal landscapes.

description: Streamside thermal physiology experiments were conducted on Athabasca Rainbow Trout in July and August 2022 near Hinton, Alberta, Canada. Fish were collected from three streams using electrofishing and transferred to instream flow through holding bags. The following morning, fish were transferred into the shuttlebox system to begin the experiment during which the preferred temperature (T<sub>pref</sub>) and avoidance temperature (T<sub>avoid</sub>) were measured. After the experiment had concluded, a fin clip, length, and weight measurements were recorded, and the fish were released back into their respective streams once they had fully recovered.
DOI: 10.5061/dryad.3r3q4
title: Data from: How to calculate the non­-synonymous to synonymous rate ratio of protein-coding genes under the Fisher­-Wright mutation­-selection framework

description: First principles of population genetics are used to obtain formulae
 relating the non-synonymous to synonymous substitution rate ratio to the
 selection coefficients acting at codon sites in protein-coding genes. Two
 theoretical cases are discussed and two examples from real data (a
 chloroplast gene and a virus polymerase) are given. The formulae give much
 insight into the dynamics of non-synonymous substitutions and may inform
 the development of methods to detect adaptive evolution.
description: Accompanying data for
 the paperThis zip file contains
 sequence alignments (*.phyl) and phylogenetic trees (*.tree) for the PB2
 and RBCL protein-coding genes analysed in the paper. It also contains
 estimates of fitness values at codon sites for the two proteins. The
 fitness estimates can be used to calculate the relative non-synonymous
 substitution rate as explained in the paper (e.g. Eq
 3.1).data.zip
DOI: 10.5061/dryad.97d83g0
title: Data from: Incongruence in molecular species delimitation schemes: what to do when adding more data is difficult.

description: Using multiple, independent approaches in molecular species delimitation
 is advocated to accommodate limitations and assumptions of a single
 approach. Incongruence in delimitation schemes is a potential byproduct of
 employing multiple methods on the same data, and little attention has been
 paid to its reconciliation. Instead, a particular scheme is prioritized
 and/or molecular delimitations are coupled with additional, independent
 lines of evidence that mitigate incongruence. We advocate that
 incongruence within a line of evidence should be accounted for before
 comparing across lines of evidence, that can themselves be incongruent.
 Additionally, it is not uncommon for empiricists working in non-model
 systems to be data-limited, generating some concern for the adequacy of
 available data to address the question of interest. With conservation and
 management decisions often hinging on the status of species, it seems
 prudent to understand the capabilities of approaches we use given the data
 we have. Here we apply two molecular species delimitation approaches,
 spedeSTEM and BPP, to the Castilleja ambigua (Orobanchaceae) species
 complex, a relatively young plant lineage in western North America. Upon
 finding incongruence in our delimitation, we employed a post-hoc
 simulation study to examine the power of these approaches to delimit
 species. Given the data we collected, we find that spedeSTEM lacks the
 power to delimit while BPP is capable, thus allowing us to address
 incongruence before proceeding in delimitation. We suggest post-hoc
 simulation studies like this compliment empirical delimitation, and serve
 as a means of exploring conflict within a line of evidence and dealing
 with it appropriately.
description: cp.ambigua.final.nexchloroplast alignmentnuc.ambigua.final.nexnuclear alignmentcp.ambigua.mb.con.trethe bayesian reconstruction of the chloroplast phylogeny - the chloroplast bayesian gene treenuc.ambigua.mb.con.trethe bayesian reconstruction of the nuclear phylogeny - the nuclear bayesian gene treechl.ML.boot.trethe maximum likelihood reconstruction of chloroplast phylogeny - the chloroplast ML treenuc.ML.boot.trethe maximum likelihood reconstruction of nuclear phylogeny - the nuclear ML treeamb.starbeast.species.trespecies tree based from *BEAST using cp and nuclear datapost.hoc.simulation.Rused to perform post-hoc simulations and species delimitation with spedeSTEM.