cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.125gd
title: Data from: The interplay between local ecology, divergent selection and genetic drift in population divergence of a sexually antagonistic female trait

description: Genetically polymorphic species offer the possibility to study maintenance
 of genetic variation and the potential role for genetic drift in
 population divergence. Indirect inference of the selection regimes
 operating on polymorphic traits can be achieved by comparing population
 divergence in neutral genetic markers with population divergence in trait
 frequencies. Such an approach could further be combined with ecological
 data to better understand agents of selection. Here, we infer the
 selective regimes acting on a polymorphic mating trait in an insect group;
 the dorsal structures (either rough or smooth) of female diving beetles.
 Our recent work suggests that the rough structures have a sexually
 antagonistic function in reducing male mating attempts. For two species
 (Dytiscus lapponicus and Graphoderus zonatus), we could not reject genetic
 drift as an explanation for population divergence in morph frequencies,
 while for the third (Hygrotus impressopunctatus) we found that divergent
 selection pulls morph frequencies apart across populations. Furthermore,
 population morph frequencies in H. impressopunctatus were significantly
 related to local bioclimatic factors, providing an additional line of
 evidence for local adaptation in this species. These data therefore
 suggest that local ecological factors and sexual conflict interact over
 larger spatial scales to shape population divergence in the polymorphism.
description: AFLP
 LociThe file contains one
 sheet for each species, containing the loci used in the
 studyBioClimDataMorphFreqThis excel file has one sheet for each species, containing the bioclimatic data and the morph frequencies for each sampled population
DOI: 10.5061/dryad.j8h41
title: Data from: Analytical modeling of the feto-placental vasculature system of the placenta: consideration of oxygen transport

description: The placenta is a transient vascular organ that enables nutrients and
 blood gases to be exchanged between fetal and maternal circulations.
 Herein, the structure and oxygen diffusion across the trophoblast membrane
 between the fetal and maternal red blood cells in the feto-placental
 vasculature system in both human and mouse placentas are present together
 as a functional unit. Previous models have claimed that the most efficient
 fetal blood flow relies upon structures containing a number of
 ‘conductive’ symmetrical branches, offering a path of minimal resistance
 that maximizes blood flow to the terminal villi, where oxygen diffusion
 occurs. However, most of these models have disregarded the actual
 descriptions of the exchange at the level of the intermediate and terminal
 villi. We are proposing a ‘mixed model’ whereby both ‘conductive’ and
 ‘terminal’ villi are presumed to be present at the end of single (in
 human) or multiple (in mouse) pregnancies. We predict an optimal number of
 18 and 22 bifurcation levels in the human and the mouse placentas,
 respectively. Wherever possible, we have compared our model’s predictions
 with experimental results reported in the literature and found close
 agreement between them.
description: Manuscript data and
 calculations
DOI: 10.5061/dryad.v80q9
title: Data from: Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish

description: Vertical divergence in marine organisms is being increasingly documented,
 yet much remains to be carried out to understand the role of depth in the
 context of phylogeographic reconstruction and the identification of
 management units. An ideal study system to address this issue is the
 beaked redfish, Sebastes mentella – one of four species of ‘redfish’
 occurring in the North Atlantic – which is known for a widely distributed
 ‘shallow-pelagic’ oceanic type inhabiting waters between 250 and 550 m,
 and a more localized ‘deep-pelagic’ population dwelling between 550 and
 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate
 the extent of population structure in relation to both depth and
 geographic spread of oceanic beaked redfish throughout most of its
 distribution range. By sequencing the mitochondrial control region of 261
 redfish collected over a decadal interval, and combining 160 rhodopsin
 coding nuclear sequences and previously genotyped microsatellite data, we
 map the existence of two strongly divergent evolutionary lineages with
 significantly different distribution patterns and historical demography,
 and whose genetic variance is mostly explained by depth. Combined genetic
 data, analysed via independent approaches, are consistent with a Late
 Pleistocene lineage split, where segregation by depth probably resulted
 from the interplay of climatic and oceanographic processes with life
 history and behavioural traits. The ongoing process of diversification in
 North Atlantic S. mentella may serve as an ‘hourglass’ to understand
 speciation and adaptive radiation in Sebastes and in other marine taxa
 distributed across a depth gradient.
description: Shum et al 3D usat
 genotypesMicrosatellite data
 previously genotyped by Stefansson et al Heredity (2009) 102,
 514–524.Dryad_mtDNA_Sebastes_Peter_Shum_Genbank_KP988027–KP988288Mitochondrial control region of North Atlantic Sebastes (S. viviparus, S. fasciatus, S. norvegicus, S. mentella)Dryad_Rhodopsin_Sebastes_mentella_Peter_Shum_Genbank_KR818563–KR818700Rhodopsin sequences of North Atlantic Sebastes mentella
DOI: 10.5061/dryad.h468f
title: Data from: Crimson spotted rainbowfish (Melanotaenia duboulayi) change their spatial position according to nutritional requirement

description: Decision making in moving animal groups has been shown to be
 disproportionately influenced by individuals at the front of groups.
 Therefore, an explanation of state-dependent positioning of individuals
 within animal groups may provide a mechanism for group movement decisions.
 Nutritional state is dynamic and can differ between members of the same
 group. It is also known to drive animal movement decisions. Therefore, we
 assayed 6 groups of 8 rainbowfish foraging in a flow tank. Half of the
 fish had been starved for 24h and half had been fed 1h prior to
 experimental start. Groups were assayed again one week later but
 individuals were allocated to the opposite nutritional treatment. During
 the assay the positions of individually identified fish were recorded as
 were the number of food items they each ate and the position within the
 group they acquired them from. Food-deprived fish were more often found
 towards the front of the shoal; the mean weighted positional score of
 food-deprived fish was significantly larger than that of well-fed fish.
 Individuals were not consistent in their position within a shoal between
 treatments. There was a significant positive correlation between mean
 weighted positional score and number of food items acquired which displays
 an obvious benefit to front positions. These results suggest that
 positional preferences are based on nutritional state and provide a
 mechanism for state-dependent influence on group decision-making as well
 as increasing our understanding of what factors are important for group
 functioning.
description: Rainbowfish positional
 and feeding data and Matlab scriptsRainbowfish positional
 and feeding data and Matlab scriptsDRYAD_Revised.zip
DOI: 10.5061/dryad.4ph00
title: Data from: Microsites of seed arrival: spatio-temporal variations in complex seed-disperser networks

description: Microsites where seeds arrive during the dispersal process determine plant
 reproductive success, affecting the quality of dispersal. Despite their
 crucial role for plant recruitment, very few studies have addressed
 spatio-temporal variations in microsites of seed arrival in complex
 seed-disperser networks. Using an endozoochorous dispersal system, we
 characterized the microsites of seed arrival of eight fleshy-fruited plant
 species dispersed by five mammal species during two consecutive seasons
 across three sites in a Mediterranean environment (n = 383 feces with
 seeds; 261,453 seeds). We evaluated spatial and temporal variations in the
 probability of a seed to arrive at open microsites or at microsites with
 varying plant cover, considering selection by frugivores and assessing the
 extent to which seeds of particular species arrived under conspecifics or
 heterospecifics. We found strong spatio-temporal variations in the amounts
 of seeds of the eight target species arriving at different microsites.
 These variations were strongly driven by frugivores’ selection of
 different landscape elements (i.e. open areas and microsites dominated by
 different plant species), which differed from expectations based on their
 local availability. In general, more seeds than expected arrived at vacant
 (open) microsites. Using bipartite network graphs to connect seeds with
 their arrival microsites, we found that the proportion of seeds of
 fleshy-fruited species arriving near conspecifics or heterospecifics, or
 at vacant microsites, varied depending on the target plant species, but
 also on the frugivore species dispersing it, on the study site and on the
 dispersal season. Our study revealed marked spatio-temporal variations in
 the microsites of seed arrival, which will potentially have implications
 for the quality of dispersal effectiveness, ultimately affecting plant
 population dynamics and community structure. Such a strong
 context-dependence in the microsites of seed arrival is likely to confer
 resilience against unpredictable environmental conditions, like those
 typical of Mediterranean ecosystems.
description: Microsites_of_seed_arrivalmicrosites_of_seed_arrival.xlsx
DOI: 10.5061/dryad.pg4c0
title: Data from: Integrating incomplete fossils by isolating conflictive signal in saturated and non-independent morphological characters

description: Morphological characters are indispensable in phylogenetic analyses for
 understanding the pattern, process, and tempo of evolution. If characters
 are independent and free of systematic errors, then combining as many
 different kinds of characters as are available will result in the
 best-supported phylogenetic hypotheses. But since morphological characters
 are subject to natural selection for function and arise from the
 expression of developmental pathways, they may not be independent, a
 situation that may amplify any underlying homoplasy. Here, we use new
 dental and multi-locus genetic data from bats (Mammalia: Chiroptera) to
 quantify saturation and similarity in morphological characters and
 introduce two likelihood-based approaches to identify strongly conflicting
 characters and integrate morphological and molecular data. We implement
 these methods to analyze the phylogeny of incomplete Miocene fossils in
 the radiation of Phyllostomidae (New World Leaf-nosed Bats), perhaps the
 most ecologically diverse family of living mammals. Morphological
 characters produced trees incongruent with molecular phylogenies, were
 saturated, and showed rates of change higher than most molecular
 substitution rates. Dental characters encoded variation similar to that in
 other morphological characters, while molecular characters encoded highly
 dissimilar variation in comparison. Saturation and high rates of change
 indicate randomization of phylogenetic signal in the morphological data,
 and extensive similarity suggests characters are non-independent and
 errors are amplified. To integrate the morphological data into tree
 building while accounting for homoplasy, we used statistical molecular
 scaffolds and combined phylogenetic analyses excluding a small subset of
 strongly conflicting dental characters. The phylogenies revealed the
 Miocene nectar-feeding †Palynephyllum nests within the crown
 nectar-feeding South American subfamily Lonchophyllinae, while the Miocene
 genus †Notonycteris is sister to the extant carnivorous Vampyrum. These
 relationships imply new calibration points for timing of radiation of the
 ecologically diverse Phyllostomidae.
description: Supplementary Tables and
 Figure Legendssupplementary_noctilionoid270213.docxSupplementary Figuressuppfigs270713.pdf
DOI: 10.5061/dryad.7908
title: Data from: Species delimitation of common reef corals in the genus Pocillopora using nucleotide sequence phylogenies, population genetics, and symbiosis ecology

description: Stony corals in the genus Pocillopora are among the most common and widely
 distributed of Indo-Pacific corals and, as such, are often the subject of
 research. In the far Tropical Eastern Pacific (TEP), they are major
 constituents of shallow coral communities, exhibiting considerable
 variability in colony shape and branch morphology and marked differences
 in response to thermal stress. Numerous intermediates occur between
 morphospecies that may relate to extensive hybridization. The diversity of
 the Pocillopora genus in the TEP was analyzed genetically using nuclear
 ribosomal (ITS2) and mitochondrial (ORF) sequences, and population genetic
 markers (7 microsatellite loci). The resident dinoflagellate endosymbiont
 (Symbiodinium sp.) in each sample was also characterized using sequences
 of the internal transcribed spacer 2 (ITS2) rDNA and the non-coding region
 of the chloroplast psbA minicircle. From these analyses, three
 symbiotically distinct, reproductively isolated, non-hybridizing,
 evolutionarily divergent animal lineages were identified. Designated types
 1, 2, and 3, these groupings were incongruent with traditional
 morphospecies' classification. Type 1 was abundant and widespread
 throughout the TEP; type 2 was restricted to the Clipperton Atoll; and
 type 3 was found only in Panama and the Galapagos Islands. Each type
 harboured a different Symbiodinium 'species lineage' in Clade C,
 and only type 1 associated with the 'stress-tolerant'
 Symbiodinium glynni (D1). The accurate delineation of species and
 implementation of a proper taxonomy may profoundly improve our assessment
 of Pocillopora's reproductive biology, biogeographic distributions,
 and resilience to climate warming, information that must be considered
 when planning for the conservation of reef corals.
description: DATA MOL ECOLOGY
 JOURNAL** This file contains
 errors. A corrected version can be found at
 http://dx.doi.org/10.5061/dryad.7908/5 ** This file contains the
 multilocus genotypes (7 microsatellite loci) of Pocillopora from the
 Eastern Pacific. In addition, ORF. and ITS types as well as identity of
 the symbiont and information on each sampleITSNexus file with the
 alignment of the unique rDNA (ITS2) sequences of Pocillopora found in the
 Eastern Pacific.ORFNexus file with the
 alignment of the unique mt DNA (ORF) sequences of Pocillopora found in the
 Eastern Pacific.psbA_miniCircle_Pocillopora_SymNexus file with the alignment of the psbA minicircle sequences from Symbiodinium found in association with Pocillopora corals in the Eastern Pacific.DATA MOL ECOLOGY JOURNAL (CORRECTED)** Please use this corrected version of the file. ** This file contains the multilocus genotypes (7 microsatellite loci) of Pocillopora from the Eastern Pacific. In addition, ORF. and ITS types as well as identity of the symbiont and information on each sample.
DOI: 10.5061/dryad.c1b4h
title: Data from: Climate change and body size shift in Mediterranean bivalve assemblages: unexpected role of biological invasions

description: Body size is a synthetic functional trait determining many key ecosystem
 properties. Reduction in average body size has been suggested as one of
 the universal responses to global warming in aquatic ecosystems. Climate
 change, however, coincides with human-enhanced dispersal of alien species
 and can facilitate their establishment. We address effects of species
 introductions on the size structure of recipient communities using data on
 Red Sea bivalves entering the Mediterranean Sea through the Suez Canal. We
 show that the invasion leads to increase in median body size of the
 Mediterranean assemblage. Alien species are significantly larger than
 native Mediterranean bivalves, even though they represent a random subset
 of the Red Sea species with respect to body size. The observed patterns
 result primarily from the differences in the taxonomic composition and
 body-size distributions of the source and recipient species pools. In
 contrast to the expectations based on the general temperature–size
 relationships in marine ectotherms, continued warming of the Mediterranean
 Sea indirectly leads to an increase in the proportion of large-bodied
 species in bivalve assemblages by accelerating the entry and spread of
 tropical aliens. These results underscore complex interactions between
 changing climate and species invasions in driving functional shifts in
 marine ecosystems.
description: Dataset S1. List of Red
 Sea and Mediterranean bivalve species used in the
 analyses.List of bivalve species
 reported from shelf depths in the Mediterranean Sea and the Red Sea, their
 alien status in the Mediterranean, body size, and taxonomic and functional
 affiliation.Nawrot_DatasetS1_ESM.xlsDataset S2. Body size of Lessepsian bivalves in their native and invaded range.Body size data for Brachidontes pharaonis and Pinctada imbricata radiata from multiple sites across their native (Red Sea and NW Indian Ocean) and invaded range (Mediterranean Sea and Suez Canal).Nawrot_DatasetS2_ESM.xls
DOI: 10.5061/dryad.7nk1nc63
title: Data from: The biogeography of Sulawesi revisited: is there evidence for a vicariant origin of taxa on Wallace’s “anomalous island”?

description: Sulawesi, the largest island in the Indonesian biodiversity hotspot region
 Wallacea, hosts a diverse endemic fauna whose origin has been debated for
 more than 150 years. We use a comparative approach based on dated
 phylogenies and geological constraints to test the role of vicariance
 versus dispersal in the origin of Sulawesi taxa. Most divergence time
 estimates for the split of Sulawesi lineages from their sister groups
 postdate relevant tectonic vicariant events, suggesting that the island
 was predominantly colonized by dispersal. Vicariance cannot be refuted for
 20 % of the analyzed taxa, though. While vicariance across Wallace’s Line
 was only supported for one arthropod taxon, divergence time estimates were
 consistent with a “tectonic dispersal” vicariance hypothesis from the East
 in three (invertebrate and vertebrate) taxa. Speciation on Sulawesi did
 not occur before the Miocene, which is consistent with geological evidence
 for more extensive land on the island from that time. The Pliocene onset
 of periodic sea-level changes may have played a role in increasing the
 potential for dispersal to Sulawesi. A more extensive taxon sampling in
 Wallacea will be crucial for refining our understanding of the region’s
 biogeography and for testing hypotheses on the origin of taxa on its most
 important island.
description: BEAST nex
 filesThe ZIP folder contains
 all nex files used for the single gene BEAST analyses according to dataset
 numbers in the publication
DOI: 10.5061/dryad.k71q8
title: Data from: An explicit model for the inbreeding load in the evolutionary analysis of selfing

description: I present analytical predictions for the equilibrium inbreeding load
 expected in a population under mutation, selection and a regular mating
 system, for any population size and for any magnitude and recessivity of
 the deleterious effects. Using this prediction, I deduce the relative
 fitness of mutant alleles with small effect on selfing, to explore the
 situations where selfing or outcrossing are expected to evolve. The
 results obtained are in agreement with previous literature, showing that
 natural selection is expected to lead to stable equilibria where
 populations show either complete outcrossing or complete selfing, and that
 selfing is promoted by large deleterious mutation rates. I find that the
 evolution of selfing is favoured by a large recessivity of deleterious
 effects, while the magnitude of homozygous deleterious effects only
 becomes relevant in relatively small populations. This result contradicts
 the standard assumption that purging in large populations will only
 promote selfing when homozygous deleterious effects are large, and implies
 that previously published results obtained assuming lethal mutations in
 large populations can be extrapolated to non-lethal alleles of similar
 recessivity. This conclusion and the general approach used in this
 analysis can be useful in the study of the evolution of mating systems.
description: Simulation of the
 evolution of inbreeding load under partial selfingStarting with allele
 frequencies corresponding to the mutation-selection balance, this program
 simulates the evolution of independent loci under mutation and selection
 in populations with N monoecious individuals. These populations are run
 for t generations (generaciones) assuming a given selfing rate. The
 inbreeding load is computed as B=Σ2dpq (the addition is over loci; see
 article), and its value at the Mutation-Selection-Drift-Inbreeding balance
 must be obtained by averaging B over a number of generations well after it
 reached a plateau. Values were averaged over a number of simulation
 replicates (repeticiones).Simul_InbreedLoad-Selfing.nb
DOI: 10.5061/dryad.v1pr721v
title: Data from: Divergence estimates and early evolutionary history of Figitidae (Hymenoptera: Cynipoidea)

description: [No abstract entered]
description: matrix08REDUCEDBayes04The combined molecular and morphological dataset analyzed using MrBayes.cynipoid_dating_all_calibrationsThe molecular dataset analyzed using BEAST.
DOI: 10.5061/dryad.d7q6564
title: Data from: Replicated latitudinal clines in reproductive traits of European and North American yellow dung flies

description: Geographic variation in phenotypic traits is commonly correlated with
 spatial variation in the environment, e.g., seasonality and mean
 temperature, providing evidence that natural selection generates such
 patterns. In particular, both body size and egg size of ectothermic
 animals are commonly larger in northern climates, and temperature induces
 plastic responses in both traits. Size-independent egg quality can also
 vary with latitude, though this is rarely investigated. For the widespread
 yellow dung fly (Scathophaga stercoraria; Diptera: Scathophagidae), we
 investigated whether there are latitudinal clines in reproductive traits
 (clutch size, egg size and egg composition), whether these clines are due
 to variation in body and/or egg size, and whether such clines replicate
 across independent experiments performed on different continents (North
 America and Europe). Egg size generally increased with latitude
 (especially in Europe), an effect largely explained by body size of the
 mother, while clutch size did not; overall reproductive effort thus
 increased with latitude. Both the absolute and relative (correcting for
 egg size) amount of egg protein increased with latitude, egg glycogen
 decreased with latitude, while latitudinal trends for egg lipids and total
 egg energy content were complex and non-linear. Altitude sometimes showed
 relationships analogous to those of latitude (egg proteins and glycogen)
 but occasionally opposite (egg size), possibly because latitude and
 altitude are negatively related among populations of this cold-adapted
 species. There was no evidence of a trade-off between egg size and number
 across latitudinal populations; if anything, the relationship was
 positive. All traits, including body and egg size, varied with rearing
 temperature (12°C, 18°C, 24°C), generally following the
 temperature-size-rule. Clines based on common garden rearing, thus
 reflecting genetic differentiation, were qualitatively but not always
 quantitatively consistent between continents, and were similar across
 rearing temperatures, suggesting they evolved due to natural selection,
 although the concrete selective mechanisms involved require further study.
description: Dung fly data for
 DryadReproductive trait data
 for dung flies