cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.537
title: Data from: Molecular phylogeny of the marmots (Rodentia: Sciuridae): tests of evolutionary and biogeographic hypotheses

description: There are 14 species of marmots distributed across the Holarctic, and
 despite extensive systematic study, their phylogenetic relationships
 remain largely unresolved. In particular, comprehensive studies have been
 lacking. A well-supported phylogeny is needed to place the numerous
 ecological and behavioral studies on marmots in an evolutionary context.
 To address this situation, we obtained complete cytochrome (cyt) b
 sequences for 13 of the species and partial sequence for the 14th. We
 employed a statistical approach to both phylogeny estimation and
 hypothesis testing using parsimony and maximum likelihood based methods.
 We conducted statistical tests on a suite of previously proposed
 hypotheses of phylogenetic relationships and biogeographic histories. The
 cyt b data strongly support the monophyly of Marmota and a western montane
 clade in the Nearctic. The results are consistent with an initial
 diversification in North America followed by an invasion and subsequent
 rapid diversification in the Palearctic. These analyses reject the two
 major competing hypotheses of M. broweri's phylogenetic
 relationships: namely, that it is the sister species to camtschatica of
 eastern Siberia and that it is related closely to caligata of the
 Nearctic. The Alaskan distribution of M. broweri is best explained as a
 reinvasion from the Palearctic but a Nearctic origin can not be rejected.
 Several other conventionally recognized species groups can also be
 rejected. Social evolution has been homoplastic, with large colonial
 systems evolving in two groups convergently. The cyt b data do not provide
 unambiguous resolution of several basal nodes in the Palearctic radiation,
 leaving some aspects of pelage and karyotypic evolution equivocal.
description: Steppan et al Data
 SetSteppan.txt
DOI: 10.5061/dryad.m4v48
title: Data from: Geographic variation in chin shape challenges the universal facial attractiveness hypothesis

description: The universal facial attractiveness (UFA) hypothesis proposes that some
 facial features are universally preferred because they are reliable
 signals of mate quality. The primary evidence for this hypothesis comes
 from cross-cultural studies of perceived attractiveness. However, these
 studies do not directly address patterns of morphological variation at the
 population level. An unanswered question is therefore: Are universally
 preferred facial phenotypes geographically invariant, as the UFA
 hypothesis implies? The purpose of our study is to evaluate this often
 overlooked aspect of the UFA hypothesis by examining patterns of
 geographic variation in chin shape. We collected symphyseal outlines from
 180 recent human mandibles (90 male, 90 female) representing nine
 geographic regions. Elliptical Fourier functions analysis was used to
 quantify chin shape, and principle components analysis was used to compute
 shape descriptors. In contrast to the expectations of the UFA hypothesis,
 we found significant geographic differences in male and female chin shape.
 These findings are consistent with region-specific sexual selection and/or
 random genetic drift, but not universal sexual selection. We recommend
 that future studies of facial attractiveness take into consideration
 patterns of morphological variation within and between diverse human
 populations.
description: Principal Components
 valuesThe universal facial
 attractiveness (UFA) hypothesis proposes that some facial features are
 universally preferred because they are reliable signals of mate quality.
 The primary evidence for this hypothesis comes from cross-cultural studies
 of perceived attractiveness. However, these studies do not directly
 address patterns of morphological variation at the population level. An
 unanswered question is therefore: Are universally preferred facial
 phenotypes geographically invariant, as the UFA hypothesis implies? The
 purpose of our study is to evaluate this often overlooked aspect of the
 UFA hypothesis by examining patterns of geographic variation in chin
 shape. We collected symphyseal outlines from 180 recent human mandibles
 (90 male, 90 female) representing nine geographic regions. Elliptical
 Fourier functions analysis was used to quantify chin shape, and principle
 components analysis was used to compute shape descriptors. In contrast to
 the expectations of the UFA hypothesis, we found significant geographic
 differences in male and female chin shape. These findings are consistent
 with region-specific sexual selection and/or random genetic drift, but not
 universal sexual selection. We recommend that future studies of facial
 attractiveness take into consideration patterns of morphological variation
 within and between diverse human populations.Thayer Dryad
 data.xlsx
DOI: 10.25919/qb6p-x416
title: Collation of published data on cotton lint yield response to nitrogen fertiliser

description: Cotton yield responses to N collated from publications and other data sources. These data were used in the publication: "Uncertainty in nitrogen fertiliser management of cotton crops: Implications for sustainable production from a meta-analysis."

Most data come from publications on Australian experiments. However, there are data from three studies in USA (Tennessee, Mississippi and Georgia) and one in China. 

The location information only relates to the Australia data.
DOI: 10.5061/dryad.mq8fn
title: Data from: Forest trees in human modified landscapes: ecological and genetic drivers of recruitment failure in Dysoxylum malabaricum (Meliaceae)

description: Tropical agro-forest landscapes are global priority areas for biodiversity
 conservation. Little is known about the ability of these landscapes to
 sustain large late successional forest trees upon which much forest
 biodiversity depends. These landscapes are subject to fragmentation and
 additional habitat degradation which may limit tree recruitment and thus
 compromise numerous ecosystem services including carbon storage and timber
 production. Dysoxylum malabaricum is a large canopy tree species in the
 Meliaceae, a family including many important tropical timber trees. This
 species is found in highly fragmented forest patches within a complex
 agro-forest landscape of the Western Ghats biodiversity hot spot, South
 India. In this paper we combined a molecular assessment of inbreeding with
 ecological and demographic data to explore the multiple threats to
 recruitment of this tree species. An evaluation of inbreeding, using
 eleven microsatellite loci in 297 nursery-reared seedlings collected form
 low and high density forest patches embedded in an agro-forest matrix,
 shows that mating between related individuals in low density patches leads
 to reduced seedling performance. By quantifying habitat degradation and
 tree recruitment within these forest patches we show that increasing
 canopy openness and the increased abundance of pioneer tree species lead
 to a general decline in the suitability of forest patches for the
 recruitment of D. malabaricum. We conclude that elevated inbreeding due to
 reduced adult tree density coupled with increased degradation of forest
 patches, limit the recruitment of this rare late successional tree
 species. Management strategies which maintain canopy cover and enhance
 local densities of adult trees in agro-forest mosaics will be required to
 ensure D. malabaricum persists in these landscapes. Our study highlights
 the need for a holistic understanding of the incipient processes that
 threaten populations of many important and rare tropical tree species in
 human dominated agro-forest landscapes.
description: DysoxylumMalabaricumNurseryGenotypesThe data file contains allelic information of 297 DNA samples of Dysoxylum malabaricum on 11 microsatellite markers.DryadRawDataIsmailDysmalNursery.xlsx
DOI: 10.5061/dryad.4k7c5
title: Data from: Multiple reversals of bill length over 1.7 million years in a Hawaiian bird lineage

description: Evolutionary change has been documented over geological time, but
 reversals in morphology, from an ancestral state to a derived state and
 back again, tend to be rare. Multiple reversals along the same lineage are
 even rarer. We use the chronology of the Hawaiian Islands and an avian
 example, the Hawaiian honeycreeper ‘amakihi (Hemignathus spp.) lineage,
 which originated on the oldest main island of Kaua‘i 1.7 million years
 ago, to examine the process of sequential reversals in bill length. We
 document three single and two multiple reversals of bill length on six
 main islands from oldest to youngest, consistent with the phylogeny of the
 lineage. Longer bills occur on islands with endemic species, including
 phylogenetically relevant outgroups, that may compete with or dominate the
 ‘amakihi. On islands without those species, the ‘amakihi had shorter bills
 of similar length. Both types of reversals in morphology in this lineage
 integrate microevolutionary processes with macroevolution in the adaptive
 radiation of Hawaiian honeycreepers.
description: Eight files for eight
 analysesThere are 8 sheets in
 this excel file, one for each analysis performed. The ReadMe file details
 the variables.Dryad
 files.xls
DOI: 10.5061/dryad.jg43t
title: Data from: Resource allocation during ontogeny is influenced by genetic, developmental, and ecological factors in the horned beetle, Onthophagus taurus

description: Resource allocation trade-offs arise when developing organs are in
 competition for a limited pool of resources to sustain growth and
 differentiation. Such competition may constrain the maximal size to which
 structures can grow and may force a situation in which the evolutionary
 elaboration of one structure may only be possible at the expense of
 another. However, recent studies have called into question both the
 consistency and evolutionary importance of resource allocation trade-offs.
 This study focuses on a well-described trade-off between the horns and
 eyes of Onthophagus beetles and assesses the degree to which it is
 influenced by genetic, developmental and ecological conditions. Contrary
 to expectations, we observed that trade-off signatures (i) were mostly
 absent within natural populations, (ii) mostly failed to match naturally
 evolved divergences in horn investment among populations, (iii) were
 subject to differential changes in F1 populations derived from divergent
 field populations and (iv) remained largely unaffected by developmental
 genetic manipulations of horn investment. Collectively, our results
 demonstrate that populations subject to different ecological conditions
 exhibit different patterns of, and differential plasticity in, resource
 allocation. Further, variation in ecological conditions, rather than
 canalized developmental mechanisms, may determine whether and to what
 degree morphological structures engage in resource allocation trade-offs.
description: Schwab and Moczek All
 DataContains data used in
 all analyses, sorted (see tabs) by the corresponding
 figure.
DOI: 10.5061/dryad.5b1cc
title: Data from: Isotopic niche partitioning between two apex predators over time

description: 1. Stable isotope analyses have become an important tool in reconstructing
 diets, analyzing resource use patterns, elucidating trophic relations
 among predators and understanding the structure of food webs. 2. Here, we
 use stable carbon and nitrogen isotope ratios in bone collagen to
 reconstruct and compare the isotopic niches of adult South American fur
 seals (Arctocephalus australis); n = 86) and sea lions (Otaria
 flavescens); n = 49) –two otariid species with marked morphological
 differences– in the Río de la Plata estuary (Argentina - Uruguay) and the
 adjacent Atlantic Ocean during the second half of the 20th century and the
 beginning of the 21st century. Samples from the middle Holocene (n = 7 fur
 seals and n = 5 sea lions) are also included in order to provide a
 reference point for characterizing resource partitioning before major
 anthropogenic modifications of the environment. 3. We found that the South
 American fur seals and South American sea lions had distinct isotopic
 niches during the middle Holocene. Isotopic niche segregation was similar
 at the beginning of the second half of the 20th century, but has
 diminished over time. 4. The progressive convergence of the isotopic
 niches of these two otariids during the second half of the 20th century
 and the beginning of the 21st century is most likely due to the increased
 reliance of South American fur seals on demersal prey. 5. This recent
 dietary change of South American fur seals can be explained by at least
 two non-mutually exclusive mechanisms: (i) the decrease in the abundance
 of sympatric South American sea lions as a consequence of small colony
 size and high pup mortality resulting from commercial sealing; and (ii)
 the decrease in the average size of demersal fishes due to intense fishing
 of the larger class sizes, which may have increased their accessibility to
 those eared seals with a smaller mouth gape, i.e., South American fur
 seals of both sexes and female South American sea lions.
description: Isotopic data of eared
 seals and musselsStable isotope values
 (δ13C and δ15N) of modern blue mussel (Mytilus edulis) shells, and stable
 isotope values (δ13C and δ15N) and condylobasal length of ancient and
 modern South American sea lion (Otaria flavescens) and fur seal
 (Arctocephalus australis) skulls. δ13C and δ15N: values not corrected for
 isotopic baseline shifts; δ13Ccor and δ15Ncor: values corrected for
 isotopic baseline shifts.Drago Masimiliano et al 2017 (J
 Anim Ecol) .xls
DOI: 10.5061/dryad.mf103
title: Data from: Porosity and water vapor conductance of two Troodon formosus eggs an assessment of incubation strategy in a maniraptoran dinosaur

description: Using tangential thin sections, we examined variation in porosity and
 water vapor conductance across two eggs of Troodon formosus, a small (∼50
 kg) theropod dinosaur from the North American Upper Cretaceous, testing
 two hypotheses of egg incubation: (1) full burial within sediments or
 vegetation and (2) partial burial with exposed upper egg portions. We
 divided and sampled the eggs in five zones, 1 through 5 from blunt top to
 more pointed bottom. A geometric model composed of a hemisphere, cone, and
 paraboloid was used to estimate total and zonal volumes and surface areas.
 The 138 × 67 mm idealized Troodon egg has a volume, surface area, and mass
 of 296.4 cm3, 239.23 cm2, and 314.2 g, respectively. Zonal surface areas
 and volumes highlight the strongly asymmetric and elongate form of the
 Troodon egg. Geometric modeling provides better estimates of volume and
 surface area where egg shape diverges markedly from that of a typical bird
 egg. Porosity varies significantly across both Troodon eggs, with zones 2
 and 3 having the largest pores and a majority (70–78%) of total
 conductance, whereas zone 5 has very low conductance. Total water vapor
 conductance in the two eggs are 31.85 and 40.62 mg H2O day− Torr−, values
 76% and 97% of those predicted for an avian egg of similar size. Low total
 conductance compares favorably to values in extant birds and non-avian
 reptiles that incubate in open nests, arguing against full burial
 incubation. Together with nesting site evidence, low conductance values
 favor partial burial and incubation by a Troodon adult. Asymmetric egg
 shape concentrates volume, surface area, and conductance near or at the
 point of subaerial exposure. Among non-avian dinosaurs, the eggs of
 Troodon and troodontids are most similar to those of modern birds in
 having an asymmetric shape, low porosity, no ornamentation, and three
 structural eggshell layers.
description: Varricchio-Suppl
 MatFive tables on: 1) the
 gas conductance of an average Troodon egg from MOR 299 and 750, 2) the gas
 conductance of a weighted (by sample size) average Troodon egg from MOR
 299 ad 750, 3) chi-square test results for for uniform pore distributions
 in MOR 299 and 750, 4) chi-square test results for pore distribution
 comparison of Troodon eggs MOR 750 and 299, and 5) chi-square test for
 uniform distribution for average Troodon egg.
DOI: 10.5061/dryad.g00qr
title: Data from: Foraging mode of spiders affects risk of predation by birds

description: Avian insectivores are top predators of arboreal arthropods in different
 forest ecosystems. The selective effects of bird predation in relation to
 foraging behaviour in canopy-living spiders were studied in a 2-year field
 experiment using exclosures in a spruce forest in southern Sweden. Three
 different hunting strategies – free-hunting, two-dimensional web,
 three-dimensional web – were included in the analysis. Comparisons of bird
 predation rate (ratio ln (abundance net-enclosed branch/abundance
 control)) showed considerable variation between spider groups.
 Free-hunting spiders suffered most from avian insectivores and predation
 rate was significantly higher than in spiders with two-dimensional webs.
 Spiders with three-dimensional webs were exposed to a predation rate in
 between those of the two other hunting strategies. Generally, the
 experimental effect was significantly higher in spring samples than in
 autumn, suggesting a stronger predation pressure in winter. The high
 variation in susceptibility to predation by insectivores implies that
 selection on behaviour of spider individuals is strong. Web building in
 itself is probably part of the protective mechanism, suggesting that webs
 have dual functions. We conclude that the risk of bird predation is a
 selective force on foraging behaviour of spiders in a forest canopy
 system.
description: BJLS Predation risk in
 spidersNumber of spider
 individuals in relation to hunting strategy on spruce branches (bird
 predation-free and control)
DOI: 10.5061/dryad.42nk23k
title: Data from: The influence of selection on MHC DQA and DQB haplotypes in the endemic New Zealand Hector’s and Māui dolphins

description: Strong balancing selection on the Major Histocompatibility Complex (MHC)
 can lead to different patterns in gene frequencies and neutral genomic
 variation within species. We investigated diversity and geographic
 structure of MHC genes DQA and DQB, as well as their inferred functional
 haplotypes, from two regional populations (East and West Coast) of the
 endangered Hector’s dolphin (Cephalorhynchus hectori hectori) and the
 critically endangered Māui dolphin (Cephalorhynchus hectori maui) (West
 Coast, North Island), and contrasted these results with patterns from
 neutral microsatellites. The Māui had the lowest number of alleles for DQA
 (2) and DQB (3), consistent with strong genetic drift acting on this
 remnant population. However, the two retained DQA alleles are amongst the
 most divergent combinations of all four alleles found across the Hector’s
 metapopulation, potentially reflecting the retention of divergent alleles
 due to balancing selection. The high frequency of the divergent DQB04
 allele also gave this population the highest nucleotide diversity for DQB.
 Strong differentiation was evident for DQA, DQB, and DQA-DQB haplotypes
 between the regional populations of Hector’s dolphins (FST&gt;0.213)
 and both subspecies (FST&gt;0.311). Differentiation was generally
 greater than observed at neutral microsatellite loci, suggesting the
 influence of selection between geographically proximate East and West
 Coast populations. This might be the result of spatial differences in
 directional selection on those opposite coastlines. Additionally, measures
 of the ratio of non-synonymous to synonymous substitutions (dN/dS) were
 consistent with balancing selection over evolutionary time. Together,
 these results suggest a complex interplay of balancing selection,
 directional selection, local fidelity, and genetic drift.
description: Hector's and
 Maui's dolphin MHC and microsatellite genotyping
 dataThe file contains MHC
 genotyping data from SSCP and microsatellite data for 162 individual
 Hector's and Maui's dolphins from New Zealand. The individuals
 are from two subspecies and two populations of the Hector's
 dolphins.Hector's and Maui's
 MHC and microsatellite genotyping
 data_Sep18.xlsx
DOI: 10.5061/dryad.k871qr2
title: Data from: Environmental drivers of varying selective optima in a small passerine: a multivariate, multiepisodic approach

description: In changing environments, phenotypic traits are shaped by numerous agents
 of selection. The optimal phenotypic value maximizing the fitness of an
 individual thus varies through time and space with various environmental
 covariates. Selection may differ between different life cycle stages and
 act on correlated traits inducing changes in the distribution of several
 traits simultaneously. Despite increasing interests in environmental
 sensitivity of phenotypic selection, estimating varying selective optima
 on various traits throughout the life cycle, while considering (a)biotic
 factors as potential selective agents has remained challenging. Here, we
 provide a statistical model to measure varying selective optima from
 longitudinal data. We apply our approach to analyse environmental
 sensitivity of phenotypic selection on egg-laying date and clutch size
 throughout the life cycle of a white-throated dipper population. We show
 the presence of a joint optimal phenotype that varies over the 35-yr
 period, being dependent on altitude and temperature. We also find that
 optimal laying date is density-dependent, with high population density
 favoring earlier laying dates. By providing a flexible approach, widely
 applicable to free-ranging populations for which long-term data on
 individual phenotypes, fitness and environmental factors are available,
 our study improves the understanding of phenotypic selection in varying
 environments.
description: Dipper
 dataData
 Dryad with embargo.zipCodes to run the
 analysesData
 Dryad without embargo.zip
DOI: 10.5061/dryad.mm7kk
title: Data from: Phylogeography of Primula allionii (Primulaceae), a narrow endemic of the Maritime Alps

description: Primula allionii is endemic to a tiny area of the Maritime Alps and has
 one of the narrowest distribution ranges in this hotspot of biodiversity.
 Phylogeographical patterns in P. allionii were studied using plastid DNA
 markers and dominantly inherited markers (AFLP and ISSR) to verify any
 admixture between P. allionii and the sympatric P. marginata and to detect
 the phylogeographical history of the species. Morphometric measurements of
 flowers and admixture analysis support the hypothesis that hybridization
 occurs in nature. Species distribution models using two climate models
 (CCSM and MIROC) suggested a reduction in habitat suitability during cold
 periods. Phylogeographical analysis suggested an old allopatric divergence
 during the mid-Pleistocene transition (about 0.8 Mya) without
 recolonization/contraction cycles. The Alps watershed does not act as a
 strong barrier between the two main areas of the distribution range, and
 moderate gene flow by pollen seems to create the admixture recorded among
 the stands. According to our results, the persistence of P. allionii
 throughout the Ice Age appears to be linked to the capacity of the
 Maritime Alps to provide a wide diversity of microhabitats consistent with
 the recent biogeographical pattern proposed for the Mediterranean Basin.
description: MatrixesM1: Matrix of stigma height and anther height of flowers of Primula marginata and Primula allionii. The morph types was reported L = long-styled flower (pin); S = shorth-styled flowers (thrum). Flowers are reported in rows. Species, morph, stigma height and anther height are reported in columns. M2: ISSR and AFLP combined matrix. Individuals are reported in rows. IssR and AFLP bands are reported in columns. M3: trnL intron and psbA-trnH intregenic spacer sequences concatenated to form a single matrix. The code of each individuals is reported.