cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mt78r
title: Data from: Assessing metabolic constraints on the maximum body size of actinopterygians: locomotion energetics of Leedsichthys problematicus (Actinopterygii, Pachycormiformes)

description: Maximum sizes attained by living actinopterygians are much smaller than
 those reached by chondrichthyans. Several factors, including the high
 metabolic requirements of bony fishes, have been proposed as possible
 body-size constraints but no empirical approaches exist. Remarkably,
 fossil evidence has rarely been considered despite some extinct
 actinopterygians reaching sizes comparable to those of the largest living
 sharks. Here, we have assessed the locomotion energetics of Leedsichthys
 problematicus, an extinct gigantic suspension-feeder and the largest
 actinopterygian ever known, shedding light on the metabolic limits of body
 size in actinopterygians and the possible underlying factors that drove
 the gigantism in pachycormiforms. For this, phylogenetic generalized least
 squares analyses and power performance curves established in living fishes
 were used to infer the metabolic budget and locomotion costs of L.
 problematicus in a wide range of scenarios. Our approach predicts that
 specimens weighing up to 44.9 tonnes would have been energetically viable
 and suggests that similar body sizes could also be possible among living
 taxa, discarding metabolic factors as likely body size constraints in
 actinopterygians. Other aspects, such as the high degree of endoskeletal
 ossification, oviparity, indirect development or the establishment of
 other large suspension-feeders, could have hindered the evolution of
 gigantism among post-Mesozoic ray-finned fish groups. From this
 perspective, the evolution of anatomical innovations that allowed the
 transition towards a suspension-feeding lifestyle in medium-sized
 pachycormiforms and the emergence of ecological opportunity during the
 Mesozoic are proposed as the most likely factors for promoting the
 acquisition of gigantism in this successful lineage of actinopterygians.
description: Appendix
 S1Routine metabolic rate
 (RMR) and body mass of living fishes compiled from Froese & Pauly
 (2017) and Ferrón (2017).
DOI: 10.5061/dryad.2247b
title: Data from: Sex-specific patterns of morphological diversification: evolution of reaction norms and static allometries in neriid flies

description: The consequences of sex-specific selection for patterns of diversification
 remain poorly known. Because male secondary sexual traits are typically
 costly to express, and both costs and benefits are likely to depend on
 ambient environment and individual condition, such traits may be expected
 to diversify via changes in reaction norms as well as the scaling of trait
 size with body size (static allometry). We investigated morphological
 diversification within two species of Australian neriid flies
 (Telostylinus angusticollis, T. lineolatus) by rearing larvae from several
 populations on larval diets varying six-fold in nutrient concentration.
 Mean body size varied among populations of T. angusticollis, but body size
 reaction norms did not vary in either species. However, we detected
 diversification of reaction norms for body shape in males and females of
 both species. Moreover, unlike females, males also diversified in static
 allometry slope and reaction norms for static allometry slope of sexual
 and nonsexual traits. Our findings reveal qualitative sex-differences in
 patterns of morphological diversification, whereby shape-size
 relationships diversify extensively in males, but remain conserved in
 females despite extensive evolution of trait means. Our results highlight
 the importance of incorporating plasticity and allometry in studies of
 adaptation and diversification.
description: Cassidy-et-al-dataTab-delimited text file containing individual morphometric data.
DOI: 10.5061/dryad.4298p
title: Data from: The benefits of interpopulation hybridization diminish with increasing divergence of small populations

description: Interpopulation hybridization can increase the viability of small
 populations suffering from inbreeding and genetic drift, but it can also
 result in outbreeding depression. The outcome of hybridization can depend
 on various factors, including the level of genetic divergence between the
 populations, and the number of source populations. Furthermore, the
 effects of hybridization can change between generations following the
 hybridization. We studied the effects of population divergence (low vs.
 high level of divergence) and the number of source populations (two vs.
 four source populations) on the viability of hybrid populations using
 experimental Drosophila littoralis populations. Population viability was
 measured for seven generations after hybridization as proportion of
 populations facing extinction and as per capita offspring production.
 Hybrid populations established at the low level of population divergence
 were more viable than the inbred source populations and had higher
 offspring production than the large control population. The positive
 effects of hybridization lasted for the seven generations. In contrast, at
 the high level of divergence the viability of the hybrid populations was
 not significantly different from the inbred source populations, and
 offspring production in the hybrid populations was lower than in the large
 control population. The number of source populations did not have a
 significant effect at either low or high level of population divergence.
 The study shows that the benefits of interpopulation hybridization may
 decrease with increasing divergence of the populations, even when the
 populations share identical environmental conditions. We discuss the
 possible genetic mechanisms explaining the results and address the
 implications for conservation of populations.
description: Offspring
 dataData for offspring
 production and extinction of the inbred and hybrid
 populations.Microsatellite
 dataGenetic data for the
 control and inbred populations.
DOI: 10.5061/dryad.13173
title: Data from: Mismatch between dietary requirements for lipid by a predator and availability of lipid in prey

description: Growth is an important factor in predicting an organism's overall
 success as an adult. Understanding how abiotic and biotic factors
 influence body size is key to predicting how environmental changes will
 impact organisms and predicting optimal behaviors under varying
 conditions. Food items can vary widely in nutrient content and this
 variation can affect growth. We tested how the quantity and macronutrient
 content of live prey affected the growth of juvenile jumping spiders,
 Phiddipus audax, using 420 spiderlings raised on one of 21 diets. In
 addition, we measured the nutrient content of prey from the field and
 compared average prey nutrient content with the diet at which spiders
 maximized growth. Our results show that the quantity and nutrient content
 of prey have significant and interacting effects on the growth of an
 actively hunting predator. In particular, spiders grew larger in body size
 (tibia/patella length and posterior lateral eye width) and were heavier on
 diets with higher lipid content. Yet, data on the nutrient content of prey
 from the field shows that most potential prey have high protein and low
 lipid content in their bodies. This apparent mismatch between spider
 nutritional requirements and prey nutrient availability likely presents a
 challenge to spiders seeking to maximize growth in the field. Several
 hypotheses for how these predators overcome this challenge to reach the
 large body sizes observed in the field are discussed.
description: oikos_dryad_wiggins_OIK-04766R1data associate with juvenile jumping spiders fed live prey that varied in nutrients alter growth rates and sizes over four months.
DOI: 10.5061/dryad.222b6
title: Data from: Environmental determinism, and not interspecific competition, drive morphological variability in Australasian warblers (Acanthizidae)

description: Interspecific competition is thought to play a key role in determining the
 coexistence of closely related species within adaptive radiations.
 Competition for ecological resources can lead to different outcomes from
 character displacement to, ultimately, competitive exclusion. Accordingly,
 divergent natural selection should disfavor those species that are the
 most similar to their competitor in resource use, thereby increasing
 morphological disparity. Here we examined ecomorphological variability
 within an Australo-Papuan bird radiation, the Acanthizidae, which include
 both allopatric and sympatric complexes. In addition, we investigated
 whether morphological similarities between species are related to
 environmental factors at fine- (foraging niche) and/or large-scale
 (climate). Contrary to that predicted by the competition hypothesis, we
 did not find a significant correlation between the morphological
 similarities found between species and their degree of range overlap.
 Comparative modelling based on both a priori and data-driven
 identification of selective regimes suggested that foraging niche is a
 poor predictor of morphological variability in acanthizids. By contrast,
 our results indicate that climatic conditions were an important factor in
 the formation of morphological variation. We found a significant negative
 correlation between species scores for PC1 (positively associated to
 tarsus length and tail length) and both temperature and precipitation,
 whereas PC2 (positively associated to bill length and wing length)
 correlated positively with precipitation. In addition, we found that
 species inhabiting the same region are closer to each other in morphospace
 than to species outside that region regardless of genus to which they
 belong or its foraging strategy. Our results indicate that the
 conservative body form of acanthizids is one that can work under a wide
 variety of environments (an all-purpose morphology) and the observed
 interspecific similarity is probably driven by the common response to
 environment.
description: Dataset including
 phenotypic and climatic traitsMorphological and
 ecological attributes of Acanthizid species included in the
 study.Data.xlsx
DOI: 10.5061/dryad.826h4
title: Data from: Social interactions elicit rapid shifts in functional connectivity in the social decision-making network of zebrafish

description: According to the social decision-making (SDM) network hypothesis, SDM is
 encoded in a network of forebrain and midbrain structures in a distributed
 and dynamic fashion, such that the expression of a given social behaviour
 is better reflected by the overall profile of activation across the
 different loci rather than by the activity of a single node. This proposal
 has the implicit assumption that SDM relies on integration across brain
 regions, rather than on regional specialization. Here we tested the
 occurrence of functional localization and of functional connectivity in
 the SDM network. For this purpose we used zebrafish to map different
 social behaviour states into patterns of neuronal activity, as indicated
 by the expression of the immediate early genes c-fos and egr-1, across the
 SDM network. The results did not support functional localization, as some
 loci had similar patterns of activity associated with different social
 behaviour states, and showed socially driven changes in functional
 connectivity. Thus, this study provides functional support to the SDM
 network hypothesis and suggests that the neural context in which a given
 node of the network is operating (i.e. the state of its interconnected
 areas) is central to its functional relevance.
description: Raw data QPCR
 revisedqPCR and behavioural
 data.
DOI: 10.5281/zenodo.18381024
title: EEF-modulated SHG-mediated Photodynamic Therapy Raw Data
DOI: 10.5281/zenodo.18381025
title: EEF-modulated SHG-mediated Photodynamic Therapy Raw Data
DOI: 10.5061/dryad.jh4dr
title: Data from: Stepwise colonization of the Andes by Ruddy Ducks and the evolution of novel β-globin variants

description: Andean uplift played a key role in Neotropical bird diversification, yet
 past dispersal and genetic adaptation to high-altitude environments remain
 little understood. Here we use multilocus population genetics to study
 population history and historical demographic processes in the ruddy duck
 (Oxyura jamaicensis), a stiff-tailed diving duck comprising three
 subspecies distributed from Canada to Tierra del Fuego and inhabiting
 wetlands from sea level to 4500 m in the Andes. We sequenced the
 mitochondrial DNA, four autosomal introns and three haemoglobin genes (αA,
 αD, βA) and used isolation-with-migration (IM) models to study gene flow
 between North America and South America, and between the tropical and
 southern Andes. Our analyses indicated that ruddy ducks dispersed first
 from North America to the tropical Andes, then from the tropical Andes to
 the southern Andes. While no nonsynonymous substitutions were found in
 either α globin gene, three amino acid substitutions were observed in the
 βA globin. Based on phylogenetic reconstruction and power analysis, the
 first βA substitution, found in all Andean individuals, was acquired when
 ruddy ducks dispersed from low altitude in North America to high altitude
 in the tropical Andes, whereas the two additional substitutions occurred
 more recently, when ruddy ducks dispersed from high altitude in the
 tropical Andes to low altitude in the southern Andes. This stepwise
 colonization pattern accompanied by polarized βA globin amino acid
 replacements suggest that ruddy ducks first acclimatized or adapted to the
 Andean highlands and then again to the lowlands. In addition, ruddy ducks
 colonized the Andean highlands via a less common route as compared to
 other waterbird species that colonized the Andes northwards from the
 southern cone of South America.
description: oxyura_jamaicensis_files.ziparlequin, IMa2, nexus, and structure infilesgenbank_accessions_seqidsGenbank accessions and sequence IDs
DOI: 10.5061/dryad.jp34d
title: Data from: Species interactions and the effects of climate variability on a wetland amphibian metacommunity

description: Disentangling the role that multiple interacting factors have on species
 responses to shifting climate poses a significant challenge. However, our
 ability to do so is of utmost importance to predict the effects of climate
 change on species distributions. We examined how populations of three
 species of wetland breeding amphibians, which varied in life history
 requirements, responded to a six-year period of extremely variable in
 precipitation. This interval was punctuated by both extensive drought and
 heavy precipitation and flooding, providing a natural experiment to
 measure community responses to environmental perturbations. We estimated
 occurrence dynamics using a discrete hidden Markov modeling approach that
 incorporated information regarding habitat state and predator-prey
 interactions. This approach allowed us to measure how metapopulation
 dynamics of each amphibian species was affected by interactions among
 weather, wetland hydroperiod, and co-occurrence with fish predators. The
 pig frog, a generalist, proved most resistant to perturbations, with both
 colonization and persistence being unaffected by seasonal variation in
 precipitation or co-occurrence with fishes. The ornate chorus frog, an
 ephemeral wetland specialist, responded positively to periods of drought
 owing to increased persistence and colonization rates during periods of
 low-rainfall. Low probabilities of occurrence of the ornate chorus frog in
 long-duration wetlands were driven by interactions with predators due to
 low colonization rates when fishes were present. The mole salamander was
 most sensitive to shifts in water availability. In our study area, this
 species never occurred in short-duration wetlands and persistence
 probabilities decreased during periods of drought. At the same time,
 negative effects occurred with extreme precipitation because flooding
 facilitated colonization of fishes to isolated wetlands and mole
 salamanders did not colonize wetlands once fishes were present. We
 demonstrate that the effects of changes in water availability depend on
 interactions with predators and wetland type and are influenced by the
 life history of each of our species. The dynamic species occurrence
 modeling approach we used offers promise for other systems when the goal
 is to disentangle the complex interactions that determine species
 responses to environmental variability.
description: St. Marks amphibian
 metacommunity encounter histories (2009-2014)Amphibian metacommunity
 encounter histories, collected on St. Marks National Wildlife Refuge, 2009
 to 2014. Fall and spring sampling occasions occurred each year during the
 months of September-October and March-April, respectively. Species codes
 are as follows: ATAL, Mole salamander (Ambystoma talpoideum); PORN, Ornate
 chorus frog (Pseudacris ornata); RGRY, Pig frog (Rana grylio); FISH, all
 fish species detected (see manuscript for further
 details).Davis et
 al._AmphbianMetacommunity.xlsx
DOI: 10.5061/dryad.rd37p
title: Data from: Disentangling the Pelomedusa complex using type specimens and historical DNA (Testudines: Pelomedusidae)

description: Recent research has shown that the helmeted terrapin (Pelomedusa subrufa),
 a species that occurs throughout sub-Saharan Africa, in Madagascar and the
 southwestern Arabian Peninsula, consists of several deeply divergent
 genetic lineages. Here we examine all nominal taxa currently synonymized
 with Pelomedusa subrufa (Bonnaterre, 1789) and provide mitochondrial DNA
 sequences of type specimens or topotypic material for most taxa.
 Lectotypes are designated for Testudo galeata Schoepff, 1792, Pentonyx
 capensis Duméril & Bibron, 1835, Pelomedusa nigra Gray, 1863,
 Pelomedusa galeata var. disjuncta Vaillant & Grandidier, 1910, and
 Pelomedusa galeata damarensis Hewitt, 1935. For Pelomedusa gasconi
 Rochebrune, 1884, a taxon without preserved type material, a neotype is
 designated. Type material of Pentonix americana Cornalia, 1849, a nominal
 species without credible type locality, is lost and its identity remains
 questionable. Also the holotype of Pelomedusa galeata orangensis Hewitt,
 1935 is lost, but its allocation to the only genetic lineage occurring in
 South Africa is unambiguous. Phylogenetic analyses of type sequences or
 topotypic material reveal that the remaining nominal taxa represent three
 of the nine previously identified lineages of Pelomedusa. Among these
 three lineages is the South African one. Type specimens of Pentonyx
 gehafie Rüppell, 1835 correspond to an additional distinct lineage. The
 present study provides a sound basis for a subsequent integrative
 taxonomic revision of the Pelomedusa complex.
description: Fritz_2014_Pelomedusa_Zootaxa_Supporting InformationSupporting Information TABLE S1. Used samples, GenBank sequences and their accession numbers. TABLE S2. Primer sequences for mtDNA fragments for fresh samples. Nucleotides in brackets represent variable positions. TABLE S3. Primer sequences and lengths of amplified PCR products of mtDNA fragments of the 12S, cyt b and ND4 genes for historical DNA samples. TABLE S4. PCR conditions for historical and fresh samples. TABLE S5. Degree of overlap for individual mtDNA fragments yielding 251–252 bp of the 12S rRNA gene. TABLE S6. Degree of overlap for individual mtDNA fragments yielding 319 bp of the cyt b gene. TABLE S7. Degree of overlap for individual mtDNA fragments yielding 437 bp of the ND4 gene. TABLE S8. Partitioning scheme and models selected by the Akaike Information Criterion in MrMODELTEST 2.3 (Nylander 2004).Fritz_2014_Pelomedusa_Zootaxa_Supporting_Information.pdf
DOI: 10.5061/dryad.4gd87
title: Data from: First insights into the nature and evolution of antisense transcription in nematodes

description: Background: The development of multicellular organisms is coordinated by
 various gene regulatory mechanisms that ensure correct spatio-temporal
 patterns of gene expression. Recently, the role of antisense transcription
 in gene regulation has moved into focus of research. To characterize
 genome-wide patterns of antisense transcription and to study their
 evolutionary conservation, we sequenced a strand-specific RNA-seq library
 of the nematode Pristionchus pacificus. Results: We identified 1112
 antisense configurations of which the largest group represents 465
 antisense transcripts (ASTs) that are fully embedded in introns of their
 host genes. We find that most ASTs show homology to protein-coding genes
 and are overrepresented in proteomic data. Together with the finding, that
 expression levels of ASTs and host genes are uncorrelated, this indicates
 that most ASTs in P. pacificus do not represent non-coding RNAs and do not
 exhibit regulatory functions on their host genes. We studied the evolution
 of antisense gene pairs across 20 nematode genomes, showing that the
 majority of pairs is lineage-specific and even the highly conserved vps-4,
 ddx-27, and sel-2 loci show abundant structural changes including
 duplications, deletions, intron gains and loss of antisense transcription.
 In contrast, host genes in general, are remarkably conserved and encode
 exceptionally long introns leading to unusually large blocks of conserved
 synteny. Conclusions: Our study has shown that in P. pacificus antisense
 transcription as such does not define non-coding RNAs but is rather a
 feature of highly conserved genes with long introns. We hypothesize that
 the presence of regulatory elements imposes evolutionary constraint on the
 intron length, but simultaneously, their large size makes them a likely
 target for translocation of genomic elements including protein-coding
 genes that eventually end up as ASTs.
description: phylogenetic analysis of
 antisense gene pairs in nematodesThis archived folder
 contains sequences, alignments and trees that were used for the
 publication "First insights into the nature and evolution of
 antisense transcription in nematodes" (Figure 3,4,5) by Rödelsperger,
 Menden, Serobyan, Witte, Baskaran (BMC Evolutionary Biology, 2016). The
 protein sequences (.fa files) were obtained by aligning C. elegans
 reference sequences against 19 other nematode genomes with the help of the
 Software exonerate. Multiple sequence alignments (*_alignment.fa) for
 homologous proteins were generated by the MUSCLE software and
 Maximum-likelihood trees were estimated by the phangorn R-package (.nexml
 files).2016-08-01_data_dyad.zip