cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3n5tb2rkp
title: Comparing genome-based estimates of relatedness for use in pedigree-based conservation management

description: Researchers have long debated which estimator of relatedness best captures
 the degree of relationship between two individuals. In the genomics era,
 this debate continues, with relatedness estimates being sensitive to the
 methods used to generate markers, marker quality, and levels of diversity
 in sampled individuals. Here, we compare six commonly used genome-based
 relatedness estimators (kinship genetic distance (KGD), Wang Maximum
 Likelihood (TrioML), Queller and Goodnight (Rxy), Kinship INference for
 Genome-wide association studies (KING-robust), and Pairwise Relatedness
 (RAB), allele-sharing co-ancestry (AS)) across five species bred in
 captivity–including three birds and two mammals–with varying degrees of
 reliable pedigree data, using reduced-representation and whole genome
 resequencing data. Genome-based relatedness estimates varied widely across
 estimators, sequencing methods, and species, yet the most consistent
 results for known first order relationships were found using Rxy, RAB, and
 AS. However, AS was found to be less consistently correlated with known
 pedigree relatedness than either Rxy or RAB. Our combined results indicate
 there is not a single genome-based estimator that is ideal across
 different species and data types. To determine the most appropriate
 genome-based relatedness estimator for each new dataset, we recommend
 assessing the relative: (1) correlation of candidate estimators with known
 relationships in the pedigree and (2) precision of candidate estimators
 with known first-order relationships. These recommendations are broadly
 applicable to conservation breeding programs, particularly where
 genome-based estimates of relatedness can complement and complete poorly
 pedigreed populations. Given a growing interest in the application of wild
 pedigrees, our results are also applicable to in-situ wildlife management.
DOI: 10.7280/d1v97t
title: A hierarchy of global ocean models coupled to CESM1

description: Data associated with the following publication: Hsu, T. Y., Primeau, F.
 W., & Magnusdottir, G. (2022). A Hierarchy of Global Ocean Models
 Coupled to CESM1. Paper Abstract: We develop a hierarchy of simplified
 ocean models for coupled ocean, atmosphere, and sea ice climate
 simulations using the Community Earth System Model version 1 (CESM1). The
 hierarchy has four members: a slab ocean model, a mixed-layer model with
 entrainment and detrainment, an Ekman mixed-layer model, and an ocean
 general circulation model (OGCM). Flux corrections of heat and salt are
 applied to the simplified models ensuring that all hierarchy members have
 the same climatology. We diagnose the needed flux corrections from
 auxiliary simulations in which we restore the temperature and salinity to
 the daily climatology obtained from a target CESM1 simulation. The
 resulting 3-dimensional corrections contain the interannual variability
 fluxes that maintain the correct vertical gradients of temperature and
 salinity in the tropics. We find that the inclusion of mixed-layer
 entrainment and Ekman flow produces sea surface temperature and surface
 air temperature fields whose means and variances are progressively more
 similar to those produced by the target CESM1 simulation. We illustrate
 the application of the hierarchy to the problem of understanding the
 response of the climate system to the loss of Arctic sea ice. We find that
 the shifts in the positions of the mid-latitude westerly jet and of the
 Inter-tropical Convergence Zone (ITCZ) in response to sea-ice loss depend
 critically on upper ocean processes. Specifically, heat uptake associated
 with the mixed-layer entrainment influences the shift in the westerly jet
 and ITCZ. Moreover, the shift of ITCZ is sensitive to the form of Ekman
 flow parameterization.
description: <strong>Description of methods used for generation of
 data: </strong><br>The data is generated with EMOM, a
 hierarchy of ocean models that are applied in CESM1. The detailed
 description of the model is in the paper the dataset is presented in (i.e.
 A Hierarchy of Global Ocean Models Coupled to
 CESM1).<br><br><strong>Methods for processing the
 data:</strong> This dataset consists of a set of
 atmospheric and oceanic fields produced by the NCAR CESM1 climate model.
 The data is in NETCDF format and has been post-processed and formatted
 using the NCO command language (see http://nco.sourceforge.net/ for more
 details). <strong>Software-specific information
 needed to interpret the data:</strong><br>The data is in
 NetCDF format.
DOI: 10.5061/dryad.wdbrv15r5
title: Extreme reproductive skew at the dawn of sociality is consistent with inclusive fitness theory but problematic for routes to eusociality

description: To understand the earliest stages of social evolution we need to identify
 species that are undergoing the initial steps into sociality. Amphylaeus
 morosus is the only unambiguously known social species in the bee family
 Colletidae and represents an independent origin of sociality within the
 Apoidea. This allows us to investigate the selective factors promoting the
 transition from solitary to social nesting. Using genome-wide SNP
 genotyping, we infer robust pedigree relationships to identify maternity
 of brood and intracolony relatedness for colonies at the end of the
 reproductive season. We show that A. morosus forms both
 matrifilial and full-sibling colonies, both involving complete or almost
 complete monopolization over reproduction. In social colonies, the
 reproductive primary was also the primary forager with the secondary
 female remaining in the nest, presumably as a guard. Social nesting
 provided significant protection against parasitism and increased brood
 survivorship in general. We show that secondary females gain large
 indirect fitness benefits from defensive outcomes, enough to satisfy the
 conditions of inclusive fitness theory, despite an over-production of
 males in social colonies. These results suggest an avenue to sociality
 that involves high relatedness and, very surprisingly, extreme
 reproductive skew in its earliest stages and raises important questions
 about the evolutionary steps in pathways to eusociality.
DOI: 10.5281/zenodo.18393247
title: Source data for: "Bimodal Dynamics of Viscous Pearls"
DOI: 10.5281/zenodo.18393248
title: Source data for: "Bimodal Dynamics of Viscous Pearls"
DOI: 10.5281/zenodo.18400022
title: TALE model training dataset
DOI: 10.5061/dryad.xsj3tx9hp
title: Alignments used for the phylogenetic analysis of sweet cucumber (Solanum muricatum, Solanaceae)

description: Sweet cucumber (Solanum muricatum) sect. Basarthrum, is a neglected native
 crop to the Andean region. It is naturally distributed very close to
 potatoes (Solanum sect. Petota) and tomatoes (Solanum sect. Lycopersicon),
 two groups with great economic importance. We obtained the first complete
 chloroplast (cp) genome of sweet cucumber and compared with seven
 Solanacea species. Pair-end clean reads were obtained by PE 150 library
 and the Illumina HiSeq 2500 platform. The complete cp genome of S.
 muricatum had a 155,681 bp with typical quadripartite structure,
 containing a large single copy (LSC) region (86,182 bp) and a small
 single-copy (SSC) region (18,360 bp), separated by two inverted repeat
 (IR) regions (25,568 bp). The annotation of chloroplast genome predicted
 88 protein-coding genes (CDS), 8 ribosomal RNA (rRNA) genes, 37 transfer
 RNA (tRNA) genes, and one pseudogene. A total of 48 perfect
 microsatellites were identified, divided in mononucleotide repeats (32),
 followed by tetranucleotide (6) and dinucleotides (5). SSRs with
 trinucleotides repeats (3), pentanucleotide (1) and hexanucleotide (1)
 repeats motifs in these genomes were identified in lower quantity. Most of
 these repeats were distributed in the noncoding regions. Whole chloroplast
 genome comparison with the other seven Solanaceae species revealed that
 the small single copy and large single copy regions showed more divergence
 than inverted regions. Finally, phylogenetic analyses resolved that S.
 muricatum is a sister species to members of sections Petota + Lycopersicum
 + Etuberosum. This study reports for the first time the genome
 organization, gene content, and structural features of the chloroplast
 genome of S. muricatum. Also, this study may provide the basis for
 evaluating genetic diversity within the Solanaceae species, and will be
 useful to examine the evolutionary processes in sweet cucumber landraces.
DOI: 10.5061/dryad.d51c5b05q
title: Data set for: Leaf trait association in relation to herbivore defense, drought resistance, and economics in a tropical invasive plant

description: Premsie: Exploring how functional traits vary and covary is important to
 understand plant responses to environmental change. However, we have
 limited understanding of the ways multiple functional traits vary and
 covary within invasive species. Methods: We measured 12 leaf traits of an
 invasive plant Chromolaena odorata, associated with plant or leaf
 economics, herbivore defense, and drought resistance on 10 introduced
 populations from Asia and 12 native populations from America, selected
 across a broad range of climatic conditions, and grown in a common garden.
 Results: Species’ range and climatic conditions influenced leaf traits,
 but trait variation across climate space differed between the introduced
 and native ranges. Traits that confer defense against herbivores and
 drought resistance were associated with economic strategy, but the
 patterns differed by range. Plants from introduced populations that were
 at the fast-return end of the spectrum (high photosynthetic capacity) had
 high physical defense traits (high trichome density), whereas plants from
 native populations that were at the fast-return end of the spectrum had
 high drought escape traits (early leaf senescence and high percentage of
 withered shoots). Conclusions: Our results indicate that invasive plants
 can rapidly adapt to novel environmental conditions. C. odorata showed
 multiple different functional trait covariation patterns and clines in the
 native and introduced ranges. Our results emphasize that interaction
 between multiple traits or functions should be considered when
 investigating the adaptive evolution of invasive plants.
description: See details in the paper: Leaf trait association in relation to
 herbivore defense, drought resistance, and economics in a tropical
 invasive plant.
description: <strong>Paper</strong>: Leaf trait association in relation to herbivore defense, drought resistance, and economics in a tropical invasive plant. <strong>Authors</strong>: Yang-Ping Li, Yu-Long Feng, Wei-Tao Li, Kyle Tomlinson, Zhi-Yong Liao, Yu-Long Zheng, and Jiao-Lin Zhang <strong>Description</strong>: This README file describes the data files accompanying the above publication. <strong>Files</strong>： 1.        <strong>Functional trait data file</strong>: Includes functional traits (mean) data of <em>Chromolaena odorata</em> from 12 native and 10 introduced populations. A<sub>mass</sub>, maximum photosynthesis rate per unit mass; N<sub>m</sub>, nitrogen content per mass; LMA, leaf mass per area; LDMC, leaf dry mass content; Trichome<sub>upper</sub>, trichome density on upper leaf surface; Trichome<sub>lower</sub>, trichome density on the lower leaf surface. 2.        <strong>Climatic data file</strong>: Includes climatic data of 22 population sampling sites 3.        <strong>Population level structure q-scores data file</strong>: Includes data to account for demographic history in patterns of trait divergence in the mixed models, as a random effect.
DOI: 10.5061/dryad.gqnk98sqd
title: Unexpected morphological diversity in ancient dogs compared to modern relatives

description: Dogs are among the most variable species today, but little is known about
 the morphological variability in the early phases of their history. The
 Neolithic transition to farming may have resulted in an early
 morphological diversification as a result of changes in the anthropic
 environment or intentional selection on specific morphologies. Here, we
 explore the variability and modularity in mandible form by comparing 525
 dog mandibles from European archaeological sites ranging from 8,100 to
 3,000 cal. BC to a reference sample of modern dogs, wolves, and dingoes.
 We use three-dimensional geometric morphometrics to quantify the form of
 complete and fragmented mandibles. We demonstrate that an important
 morphological variability already existed before the Bronze Age in Europe,
 yet the largest, smallest, most brachycephalic or dolichocephalic extant
 dogs have no equivalent in the archaeological sample, resulting in a lower
 variation compared to modern relatives. The covariation between the
 anterior and posterior parts of the mandible is lower in archaeological
 dogs, suggesting a low degree of intentional human selection in early
 periods. The mandible of modern and ancient dogs differs in functionally
 important areas, possibly reflecting differences in diet, competition, or
 the implication of ancient dogs in hunting or defense.
DOI: 10.5061/dryad.m37pvmd4d
title: Fatty acid oxidation: A neglected factor in understanding the adjustment of mitochondrial function to cold temperatures

description: For ectothermic species, adaptation to thermal changes is of critical
 importance. Mitochondrial oxidative phosphorylation (OXPHOS), which
 leverages multiple electron pathways to produce energy needed for
 survival, is among the crucial metabolic processes impacted by
 temperature. Our aim in this study was to identify how changes in
 temperature affect the less-studied electron transferring flavoprotein
 pathway, fed by fatty acid substrates. We used the planarian Dugesia
 tigrina, acclimated for 4 weeks at 10°C (cold acclimated) or 20°C
 (normothermic). Respirometry experiments were conducted at an assay
 temperature of either 10 or 20°C to study specific states of the OXPHOS
 process using the fatty acid substrates palmitoylcarnitine (long chain),
 octanoylcarnitine (medium chain) or acetylcarnitine (short chain).
 Following cold acclimation, octanoylcarnitine exhibited increases in both
 the OXPHOS and electron transfer (ET, non-coupled) states, indicating that
 the pathway involved in medium-chain length fatty acids adjusts to cold
 temperatures. Acetylcarnitine only showed an increase in the OXPHOS state
 as a result of cold acclimation, but not in the ET state, indicative of a
 change in phosphorylation system capacity rather than fatty acid
 β-oxidation. Palmitoylcarnitine oxidation was unaffected. Our results show
 that cold acclimation in D. tigrina caused a specific adjustment in the
 capacity to metabolize medium-chain fatty acids rather than an adjustment
 in the activity of the enzymes carnitineacylcarnitine translocase,
 carnitine acyltransferase and carnitine palmitoyltransferase-2. Here, we
 provide novel evidence of the alterations in fatty acid β-oxidation during
 cold acclimation in D. tigrina.
description: Using High Resolution Respirometry.
DOI: 10.5061/dryad.n02v6wx0d
title: Climate alters the movement ecology of a non-migratory bird - dataset

description: Global climate change is causing increased climate extremes threatening
 biodiversity and altering ecosystems. Climate is comprised of many
 variables including air temperature, barometric pressure, solar radiation,
 wind, relative humidity, and precipitation that interact with each other.
 As movement connects various aspects of an animal’s life, understanding
 how climate influences movement at a fine-temporal scale will be critical
 to the long-term conservation of species impacted by climate change. The
 sedentary nature of non-migratory species could increase some species risk
 of extirpation caused by climate change. We used Northern Bobwhite
 (Colinus virginianus; hereafter bobwhite) as a model to better understand
 the relationship between climate and the movement ecology of a
 non-migratory species at a fine-temporal scale. We collected movement data
 on bobwhite from across western Oklahoma during 2019–2020 and paired these
 data with meteorological data. We analyzed movement three different ways
 (probability of movement, hourly distance moved, and sinuosity) using two
 calculated movement metrics: hourly movement (displacement between two
 consecutive fixes an hour apart) and sinuosity (a form of tortuosity that
 determines the amount of curvature of a random search path). We used
 generalized linear-mixed models to analyze probability of movement and
 hourly distance moved, and used linear-mixed models o analyze sinuosity.
 The interaction between air temperature and solar radiation affected
 probability of movement and hourly distance moved. Bobwhite movement
 increased as air temperature increased beyond 10oC during low solar
 radiation. During medium and high solar radiation, bobwhite moved farther
 as air temperature increased until 25–30oC when hourly distance moved
 plateaued. Bobwhite sinuosity increased as solar radiation increased. Our
 results show that specific climate variables alter the fine-scale movement
 of a non-migratory species. Understanding the link between climate and
 movement is important to determining how climate change may impact a
 species’ space use and fitness now and in the future.
DOI: 10.5061/dryad.c2fqz61b5
title: Genotypic sex shapes maternal care in the African Pygmy mouse, Mus minutoides

description: Sexually dimorphic behaviours, such as parental care, have long been
 thought to be mainly driven by gonadal hormones. In the past two decades,
 a few studies have challenged this view, highlighting the direct influence
 of the sex chromosome complement (XX vs XY or ZZ vs ZW). The African pygmy
 mouse, Mus minutoides, is a wild mouse species with naturally occurring XY
 sex reversal induced by a third, feminizing X* chromosome, leading to
 three female genotypes: XX, XX* and X*Y. Here, we show that sex reversal
 in X*Y females shapes a divergent maternal care strategy (maternal
 aggression, pup retrieval and nesting behaviours) from both XX and XX*
 females. Although neuroanatomical investigations were inconclusive, we
 show that the dopaminergic system in the anteroventral periventricular
 nucleus of the hypothalamus is worth investigating further as it may
 support differences in pup retrieval behaviour between females. Combining
 behaviours and neurobiology in a rodent subject to natural selection, we
 evaluate potential candidates for the neural basis of maternal behaviours
 and strengthen the underestimated role of the sex chromosomes in shaping
 sex differences in brain and behaviours. All things considered, we further
 highlight the emergence of a third sexual phenotype, challenging the
 binary view of phenotypic sexes.
DOI: 10.5061/dryad.b2rbnzshz
title: Interacting host modifier systems control Wolbachia-induced cytoplasmic incompatibility in a haplodiploid mite

description: Reproductive parasites such as Wolbachia spread within host populations by
 inducing cytoplasmic incompatibility (CI). CI occurs when
 parasite-modified sperm fertilizes uninfected eggs and is typified by
 great variation in strength across biological systems. In haplodiploid
 hosts, CI has different phenotypic outcomes depending on whether the
 fertilized eggs die or develop into males. Genetic conflict theories
 predict the evolution of host modulation of CI, which in turn influences
 the stability of reproductive parasitism. Yet, despite the ubiquity of
 CI-inducing parasites in nature, there is scarce evidence for
 intraspecific host modulation of CI strength and phenotype. Here, we
 tested for intraspecific host modulation of Wolbachia-induced CI in
 haplodiploid Tetranychus urticae mites. Using a single CI-inducing
 Wolbachia variant and mitochondrion, a nuclear panel was created that
 consisted of infected and cured near-isogenic lines. We performed a highly
 replicated age-synchronized full diallel cross comprised of incompatible
 and compatible control crosses. We uncovered host modifier systems that
 cause striking variation in CI strength when carried by infected T.
 urticae males. We observed a continuum of CI phenotypes in our crosses and
 identified strong intraspecific female modulation of CI phenotype. Crosses
 established a recessive genetic basis for the maternal effect and were
 consistent with polygenic Mendelian inheritance. Both male and female
 modulation interacted with the genotype of the mating partner. Our
 findings identify spermatogenesis as an important target of selection for
 host modulation of CI strength and underscore the importance of maternal
 genetic effects for the CI phenotype. Our findings reveal that
 intraspecific host modulation of CI is underpinned by complex genetic
 architectures and confirm that the evolution of reproductive parasitism is
 contingent on host genetics.
DOI: 10.5061/dryad.vhhmgqnwf
title: Heat shock protein gene expression varies among tissues and populations in free living birds

description: Climate change is dramatically altering our planet, yet our understanding
 of mechanisms of thermal tolerance is limited in wild birds. We
 characterized natural variation in heat shock protein (HSP) gene
 expression among tissues and populations of free-living Tree Swallows
 (Tachycineta bicolor). We focused on HSPs because they prevent cellular
 damage and promote recovery from heat stress. We used quantitative PCR to
 measure gene expression of three HSPs, including those in the HSP70 and
 HSP90 families that have robust experimental connections to heat in past
 literature. First, to evaluate how tissues and, by extension, the
 functions that they mediate, may vary in their thermal protection, we
 compared HSP gene expression among neural and peripheral tissues. We
 hypothesized that tissues with particularly vital functions would be more
 protected from heat as indicated by higher HSP gene expression. We found
 that brain tissues had consistently higher HSP gene expression compared to
 the pectoral muscle. Next, we compared HSP gene expression across four
 distinct populations that span over 20 degrees of latitude (&gt;2300
 km). We hypothesized that the more southern populations would have higher
 HSP gene expression, suggesting greater tolerance of, or experience with,
 warmer local conditions. We observed largely higher HSP gene expression in
 more southern populations than northern populations, although this pattern
 was more striking at the extremes (southern Indiana vs. Alaska) and it was
 stronger in some brain areas than others (ventromedial telencephalon vs.
 hypothalamus). These results shed light on the potential mechanisms that
 may underlie thermal tolerance differences among populations or among
 tissues.