cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63xwv
title: Untangling the structural and molecular mechanisms underlying colour and rapid colour change in a lizard, Agama atra

description: With functions as diverse as communication, protection and
 thermoregulation, colouration is one of the most important traits in
 lizards. The ability to change colour as a function of varying social and
 environmental conditions is thus an important innovation. While colour
 change is present in animals ranging from squids, to fish and reptiles,
 not much is known about the mechanisms behind it. Traditionally, colour
 change was attributed to migration of pigments, in particular melanin.
 More recent work has shown that the changes in nanostructural
 configuration inside iridophores are able to produce a wide palette of
 colours. However, the genetic mechanisms underlying colour, and colour
 change in particular, remain unstudied. Here we use a combination of
 transcriptomic and microscopic data to show that melanin, iridophores and
 pteridines are the main colour producing mechanisms in Agama atra, and
 provide molecular and structural data that suggests that rapid colour
 change is achieved via melanin dispersal. This contrasts with recent
 research postulating that rapid colour changes are caused by changes in
 the spacing of guanine crystals in the iridophore layer. This work
 demonstrates the power of combining genotypic (gene expression) and
 phenotypic (microscopy) information for addressing physiological
 questions, providing a basis for future studies of colour change.
description: Files
 included are: Raw reflectance spectra
 transcriptome read
 counts Annotated transcriptome
DOI: 10.5061/dryad.7pvmcvdrs
title: A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution

description: Larger and larger molecular phylogenies based on ever more genes are
 becoming commonplace with the advent of cheaper and more streamlined
 sequencing and bioinformatics pipelines. However, many groups of
 inconspicuous but no less evolutionarily or ecologically important marine
 invertebrates are still neglected in the quest for understanding species-
 and higher-level phylogenetic relationships using high-throughput
 sequencing approaches. Here, we alleviate this issue by presenting a 17
 gene phylogeny of &gt;200 newly sequenced cheilostome bryozoan
 species, mainly from New Zealand waters. New Zealand is our geographic
 region of choice as its cheilostome fauna is taxonomically, functionally
 and ecologically diverse, and better characterized than many other such
 faunas in the world. Using this most taxonomically broadly-sampled and
 statistically-supported cheilostome phylogeny to date, we tested several
 existing systematic hypotheses based solely on morphological observations.
 We find that lower taxonomic level hypotheses (species and genera) are
 very robust while our inferred trees often did not reflect current
 higher-level systematics (family and above), illustrating a general need
 for the rethinking of current hypotheses. To illustrate the utility of our
 new phylogeny, we reconstructed the evolutionary history of frontal
 shields (i.e. a calcified body-wall layer in ascus-bearing cheilostomes)
 and asked if the presence of a calcified frontal shield has any bearing on
 the diversification rates of cheilostomes.
DOI: 10.5061/dryad.gxd2547jv
title: How competitive intransitivity and niche overlap affect spatial coexistence

description: Competitive intransitivity is mostly considered outside the main body of
 coexistence theories that rely primarily on the role of niche overlap and
 differentiation. How the interplay of competitive intransitivity and niche
 overlap jointly affects species coexistence has received little attention.
 Here, we consider a rock-paper-scissors competition system where
 interactions between species can represent the full spectra of
 transitive-intransitive continuum and niche overlap/differentiation under
 different levels of competition asymmetry. By comparing results from pair
 approximation that only considers interference competition between
 neighbouring cells in spatial lattices, with those under the mean-field
 assumption, we show that (1) species coexistence under transitive
 competition is only possible at high niche differentiation; (2) in
 communities with partial or pure intransitive interactions, high levels of
 niche overlap are not necessary to beget species extinction; and (3)
 strong spatial clustering can widen the condition for intransitive loops
 to facilitate species coexistence. The two mechanisms, competitive
 intransitivity and niche differentiation, can support species persistence
 and coexistence, either separately or in combination. Finally, the
 contribution of intransitive loops to species coexistence can be enhanced
 by strong local spatial correlations, modulated and maximised by moderate
 competition asymmetry. Our study, therefore, provides a bridge to link
 intransitive competition to other generic ecological theories of species
 coexistence.
description: This dataset contains the analyses of pair approximationthe
 (PA) model, codes of drawing Figure 3 and numerical solution datas. It is
 performed by Matlab R2014a. 
description: <strong>Code of
 calculating the change in invasion growth rate under pair approximation
 (PA) model</strong><br> The ZIP archive contains three kinds
 of files: (1) The numerical solution of the main program
 ("PAsimulation.m"). It is used to set parameter values and run
 all the sub codes. (2) Calculation of  <em>R<sub>i
 </sub></em>and
 <em>R<sub>i,-j</sub>,</em> where
 <em>i</em>=1,2,3,  <em>j</em>=1,2,3 and<em>
 j </em><em>≠</em><em>i</em>. They are files "PAr_i.m" and "PAr_iLj.m". (3) The nested functions used in calculation process of step (2). They are files "f_i.m" and "f_iLj.m".<br> <strong>Programs of drawing Figure 3</strong><br> Detail contents of how to draw Figure 3 in main text. It is the file "Critical_region_for_PA_model.m".<br> <strong>Numerical solution Data</strong><br> These are numerical data abstained from the process of step (1).
DOI: 10.5061/dryad.crjdfn332
title: Experimental tests of selection against heterospecific aggression as a driver of avian color pattern divergence

description: Signal divergence is thought to reduce the costs of co-occurrence for
 closely related species and may thereby be important in the generation and
 maintenance of new biodiversity. In birds, closely related, sympatric
 species are more divergent in their color patterns than those that live
 apart, but the selective pressures driving sympatric divergence in color
 pattern are not well understood. Here, we conducted field experiments on
 naïve birds using spectrometer-matched, painted 3D-printed models to test
 whether selection against heterospecific aggression might drive color
 pattern divergence in the genus Poecile. We found that territorial male
 black-capped chickadees (P. atricapillus) are equally likely to attack
 sympatric and allopatric congeners, and wintering flocks are equally
 likely to visit feeders occupied by sympatric and allopatric congeners,
 despite sympatric congeners being more divergent in color pattern. These
 results suggest that either the concerted evolution of additional traits
 (e.g., discrimination), or interactions in sympatry that promote learning,
 are required if color pattern divergence among sympatric species is to
 reduce heterospecific aggression. Alternatively, color pattern divergence
 among sympatric species may be caused by other selective pressures, such
 as selection against hybridization or habitat partitioning and secondary
 signal adaptation.
DOI: 10.5061/dryad.dncjsxkz1
title: Social learning by mate-choice copying increases dispersal and reduces local adaptation

description: 1. In heterogeneous environments, dispersal may be hampered not only by
 direct costs, but also because immigrants may be locally maladapted. While
 maladaptation affects both sexes, this cost may be modulated in females if
 they express mate preferences that are either adaptive or maladaptive in
 the new local population. 2. Dispersal costs under local adaptation may be
 mitigated if it is possible to switch to expressing traits of locally
 adapted residents. In a sexual selection context, immigrant females may
 learn to mate with locally favoured males. Mate-choice copying is a type
 of social learning, where individuals, usually females, update their
 mating preferences after observing others mate. If it allows immigrant
 females to switch from maladapted to locally adapted preferences, their
 dispersal costs are mitigated as mate choice helps them create locally
 adapted offspring. 3. To study if copying can promote the evolution of
 dispersal, we created an individual-based model to simulate the
 coevolution of four traits: copying, dispersal, a trait relevant for local
 adaptation, and female preference. We contrast two scenarios with copying
 — either unconditional, or conditional such that only dispersers copy —
 with a control scenario that lacks any copying. 4. We show copying to lead
 to higher dispersal, especially if copying is conditionally expressed.
 This leads to an increase in gene flow between patches and, consequently,
 a decrease in local adaptation and trait-preference correlations. 5. While
 our study is phrased with female preference as the learned trait, one may
 generally expect social learning to mitigate dispersal costs, with
 consequent feedback effects on the spatial dynamics of adaptation.
description: The compressed ZIP file includes the code used for the
 simulation, a folder with an example of an output, and a readme.txt
 file.
DOI: 10.5061/dryad.f7m0cfxtt
title: The prevalence, severity and chronicity of abuse towards older men: insights from a multinational European survey

description: Data come from: the main study “ABUEL” (ELder ABUse: A multinational
 prevalence survey), regarding on the whole a sample of 4,467 not demented
 randomly selected individuals aged 60-84 years (males and females). It was
 a multinational and cross-sectional prevalence survey on elder abuse,
 which in 2009 was conducted by face-to-face interviews to older people in
 seven urban European cities (Ancona, in Italy; Athens, in Greece; Granada,
 in Spain; Kaunas, in Lithuania; Stuttgart, in Germany; Porto, in Portugal,
 and Stockholm, in Sweden). The present dataset includes only older men
 (n=1908), who were interviewed to explore their abuse exposure during the
 past 12 months (last year). Measures include the following: Abuse
 (Psychological, Physical, Injury, Sexual, financial); Abuse chronicity
 (frequency of acts: 1, 2, 4, 8, 15, 25 times); Abuse severity (minor,
 severe acts); Depression and anxiety (HADS scale: high scores correspond
 to high depression/anxiety levels);  Somatic symptoms (GBB scale:
 the higher the scores, the more one is affected); Social support (MSPSS
 scale: from family, significant others, and friends; high scores
 correspond to high perceived social support); Alcohol use and smoking
 (yes/no format); Demographics/socio-economics (country, age, marital
 status, ethnic background; educational level; still on work; current or
 past main profession; main source of financial support; with whom the
 participants lived; and number of people at home including the
 respondent); Financial strain (concerns with how to make ends meet);
 Foreign (whether the participants were migrants or indigenous
 inhabitants). Finally, perpetrator variables were assessed in form of sex
 (women/men) and relation to the victim (e.g. spouse/cohabitant,
 children/grandchildren, other relatives, friends, neighbors) in a yes/no
 format. The dataset is provided in open format (xlsx) and includes 3
 sheets: “numeric” regarding the unlabelled dataset used for statistics
 elaboration; “labelled” regarding labelled dataset with variables and
 related labelled items; and “var. list” regarding the complete variables
 list and variables labels we used.
DOI: 10.5061/dryad.ghx3ffbmp
title: Data of: Myrcia longipetiolata (Myrtaceae), a new species from the Atlantic Forest of Bahia, Brazil

description: Myrcia longipetiolata, a new species of Myrcia is here described and
 illustrated. This species resembles M. unana due to its long leaves, acute
 or acuminate leaf apex, cuneate leaf base, long petioles, but differs by
 its larger leaves, lanceolate bracteoles, rounded or apiculate calyx lobes
 and floral disc of 3 mm diam. Besides, these two species share the area of
 occurrence (southern Bahia). We also provide the phylogenetic
 relationships of M. longipetiolata within the genus, morphological
 comparisons with related species, comments of its distribution, habitat
 and conservation status.
DOI: 10.5061/dryad.xd2547dfs
title: Cellular costs underpin micronutrient limitation in phytoplankton

description: Micronutrients control phytoplankton growth in the ocean, influencing
 carbon export and fisheries. It is currently unclear how micronutrient
 scarcity affects cellular processes, and how interdependence across
 micronutrients arises. We show that proximate causes of micronutrient
 growth limitation and interdependence are governed by cumulative cellular
 costs of acquiring and using micronutrients. Using a mechanistic proteomic
 allocation model of a polar diatom focused on iron and manganese, we
 demonstrate how cellular processes fundamentally underpin micronutrient
 limitation, and how they interact and compensate for each other to shape
 cellular elemental stoichiometry and resource interdependence. We coupled
 our model with metaproteomic and environmental data, yielding a novel
 approach for estimating biogeochemical metrics including taxon-specific
 growth rates. Our results show that cumulative cellular costs govern how
 environmental conditions modify phytoplankton growth.
description: Data generated using a diatom proteomic allocation model, as well
 as trace metal concentration data, data from GEOTRACES, and
 metaproteome-derived diatom proteomic observations.
description: Code for running analyses is found
 at: https://github.com/bertrand-lab/mn-fe-allocation.
DOI: 10.5061/dryad.2z34tmpk9
title: Darwin's finch foraging behaviour and naris size

description: The avian beak is a key morphological trait used for foraging. If
 parasites alter beak shape, we expect changes in host foraging behaviour.
 Nestling Darwin’s finches on the Galápagos Islands experience naris size
 enlargement caused by Philornis downsi larvae. We predict (1) altered
 foraging behaviour in birds with malformed beaks from P. downsi. To test
 the evolutionary implications of naris malformation, we predict (2)
 changes in foraging niche overlap between sympatric species, and (3) worse
 body condition in birds with malformed beaks. Our focal species are small
 tree finch (Camarhynchus parvulus), medium tree finch (C. pauper), hybrid
 tree finch (Camarhynchus spp.), and small ground finch (Geospiza
 fuliginosa) on Floreana Island. With the exception of hybrid finches,
 Darwin’s finch species with malformed beaks exhibited increased surface
 prey removal and decreased hidden prey extraction during foraging. Naris
 size enlargement, and different beak size traits per species, was
 associated with worse body condition in Camarhynchus finches. Divergence
 can be rapidly undone when introduced parasites alter functional
 morphological traits that create ecological distinctiveness in species.
description: Darwin's finches were mist-netted, banded for later field
 identification, and measured. Foraging data were collected as first
 foraging observations of Darwin's finches during transect sampling on
 Floreana Island, Galapagos. For a sub-set of foraging observations of
 color-banded birds, we have information on body size and naris size in
 relation to foraging behavior. 
description: Each row represents a unique foraging observation per bird
 collected from ad hoc observations during transect sampling. Sheet two
 provides explanations for the column headings.
DOI: 10.5061/dryad.tmpg4f4x7
title: Dataset from: Ardipithecus hand provides evidence that humans and chimpanzees evolved from an ancestor with suspensory adaptations

description: The morphology and positional behavior of the last common ancestor of
 humans and chimpanzees are critical for understanding the evolution of
 bipedalism. Early 20th century anatomical research supported the view that
 humans evolved from a suspensory ancestor bearing some resemblance to
 apes. However, the hand of the 4.4 million-year-old hominin Ardipithecus
 ramidus, purportedly provides evidence that the hominin hand was derived
 from a more generalized form. Here we use morphometric and phylogenetic
 comparative methods to show that Ardipithecus retains suspensory adapted
 hand morphologies shared with chimpanzees and bonobos. We identify an
 evolutionary shift in hand morphology between Ardipithecus and
 Australopithecus that renews questions about the coevolution of hominin
 manipulative capabilities and obligate bipedalism initially proposed by
 Darwin. Overall, our results suggest that early hominins evolved from an
 ancestor with a varied positional repertoire including suspension and
 vertical climbing, directly affecting the viable range of hypotheses for
 the origin of our lineage.
DOI: 10.5061/dryad.3tx95x6f2
title: Thermal constraints on energy balance, behavior, and spatial distribution of grizzly bears

description: 1. Heat dissipation limit theory posits that energy available for growth
 and reproduction in endotherms is limited by their ability to dissipate
 heat. In mammals, endogenous heat production increases markedly during
 gestation and lactation, and thus female mammals may be subject to greater
 thermal constraints on energy expenditure than males. Such constraints
 likely have important implications for behavior and population performance
 in a warming climate. 2. We used a mechanistic simulation model based on
 first principles of heat and mass transfer to study thermal constraints on
 activity (both timing and intensity) of captive female grizzly bears
 (Ursus arctos) in current and future climate scenarios. We then quantified
 the relative importance of regulatory behaviors for maintaining heat
 balance using GPS telemetry locations of lactating versus non-lactating
 female bears from Yellowstone National Park, and assessed the degree to
 which costs of thermoregulation constrained the distribution of sampled
 bears in space and time. 3. Lactating female bears benefitted considerably
 more from behavioral cooling mechanisms (e.g., partial submersion in cool
 water or bedding on cool substrate) than non-lactating females in our
 simulations; the availability of water for thermoregulation increased the
 number of hours during which lactating females could be active by up to
 60% under current climatic conditions and by up to 43% in the future
 climate scenario. Moreover, even in the future climate scenario lactating
 bears were able to achieve heat balance 24 hrs/day by thermoregulating
 behaviorally when water was available to facilitate cooling. 4. The most
 important predictor of female grizzly bear distribution in Yellowstone,
 regardless of reproductive status, was elevation. However, variables
 associated with the thermal environment occurred with greater frequency in
 rules for predicting the distribution of lactating than non-lactating
 female bears.  5. Our results suggest that the costs of
 heat dissipation, which are modulated by climate, may impose constraints
 on the behavior and energetics of large endotherms like grizzly bears, and
 that access to water for cooling will likely be an increasingly important
 driver of grizzly bear distribution in Yellowstone as the climate
 continues to warm.
DOI: 10.5061/dryad.z34tmpgbz
title: Portfolio simplification arising from a century of change in salmon population diversity and artificial production

description: 1. Population and life-history diversity can buffer species from
 environmental variability and contribute to long-term stability through
 differing responses to varying conditions akin to the stabilizing effect
 of asset diversity on financial portfolios. While it is well known that
 many salmon populations have declined in abundance over the last century,
 we understand less about how different dimensions of diversity may have
 shifted. Specifically, how has diminished wild abundance and increased
 artificial production (i.e., enhancement) changed portfolios of salmon
 populations, and how might such change influence fisheries and ecosystems?
 2. We apply modern genetic tools to century-old sockeye salmon
 (Oncorhynchus nerka) scales from Canada’s Skeena River watershed to (i)
 reconstruct historical abundance and age-trait data for 1913–1947 to
 compare with recent information, (ii) quantify changes in population and
 life-history diversity and the role of enhancement in population dynamics,
 and (iii) quantify the risk to fisheries and local ecosystems resulting
 from observed changes in diversity and enhancement. 3. The total number of
 wild sockeye returning to the Skeena River during the modern era is 69%
 lower than during the historical era; all wild populations have declined,
 several by more than 90%. However, enhancement of a single population has
 offset declines in wild populations such that aggregate abundances now are
 similar to historical levels. 4. Population diversity has declined by 70%,
 and life-history diversity has shifted: populations are migrating from
 freshwater at an earlier age, and spending more time in the ocean. There
 also has been a contraction in abundance throughout the watershed, which
 likely has decreased the spatial extent of salmon provisions to Indigenous
 fisheries and local ecosystems. Despite the erosion of portfolio strength
 that this salmon complex hosted a century ago, total returns now are no
 more variable than they were historically perhaps in part due to the
 stabilizing effect of artificial production. 5. Policy implications. Our
 study provides a rare example of the extent of erosion of within-species
 biodiversity over the last century of human influence. Rebuilding a
 diversity of abundant wild populations – that is, maintaining functioning
 portfolios - may help ensure that watershed complexes like the Skeena are
 robust to global change.   
description: Generated from fish scales collected in commercial fisheries
 during 1913–1947 and the skeena tyee test fishery 1973–2016, genetically
 assigned to population.