cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.14sg2
title: Data from: Overwintering strategies of migratory birds: a novel approach for estimating seasonal movement patterns of residents and transients

description: 1. Our understanding of movement patterns in wildlife populations has
 played an important role in current ecological knowledge, and can inform
 landscape conservation decisions. Direct measures of movement can be
 obtained using marked individuals, but this requires tracking individuals
 across a landscape or multiple sites. 2. We demonstrate how movements can
 be estimated indirectly using single-site, capture–mark–recapture (CMR)
 data with a multistate open robust design with state uncertainty model
 (MSORD-SU). We treat residence and transience as two phenotypic states of
 overwintering migrants, and use time- and state-dependent probabilities of
 site entry and persistence as indirect measures of movement. We applied
 the MSORD-SU to data on eight species of overwintering Neotropical birds
 collected in 14 countries between 2002 and 2011. In addition to entry and
 persistence probabilities, we estimated proportions of residents at a
 study site, and mean residence times. 3. We identified overwintering
 movement patterns and residence times that contrasted with prior
 categorizations of territoriality. Most species showed evidence of
 residents entering sites at multiple time intervals, with transients
 tending to enter between peak resident movement times. Persistence and the
 proportion of residents varied by latitude, but were not always positively
 correlated for a given species. 4. Synthesis and applications: Our results
 suggest that migratory songbirds commonly move among habitats during the
 overwintering period. Substantial proportions of populations appear to be
 comprised of transient individuals, and residents tend to persist at
 specific sites for relatively short periods of time. This information on
 persistence and movement patterns should be explored for specific habitats
 to guide landscape management on the wintering grounds, such as
 determining which habitats are conserved or restored as part of
 certification programs of tropical agroforestry crops. We suggest that
 research and conservation efforts on Neotropical migrant songbirds focus
 on identifying landscape configurations and regional habitat networks that
 support these diverse overwintering strategies to secure full life cycle
 conservation.
description: Input files for capture
 histories of individualsThese are basic input
 files without station or covariate information, for each of the species in
 the manuscript.Input_files.zip
DOI: 10.5061/dryad.q4157
title: Data from: Specialized specialists and the narrow niche fallacy: a tale of scale-feeding fishes

description: Although rare within the context of 30,000 species of extant fishes,
 scale-feeding as an ecological strategy has evolved repeatedly across the
 teleost tree of life. Scale-feeding (lepidophagous) fishes are diverse in
 terms of their ecology, behavior, and specialized morphologies for grazing
 on scales and mucus of sympatric species. Despite this diversity, the
 underlying ontogenetic changes in functional and biomechanical properties
 of associated feeding morphologies in lepidophagous fishes are less
 understood. We examined the ontogeny of feeding mechanics in two
 evolutionary lineages of scale-feeding fishes: Roeboides, a characin, and
 Catoprion, a piranha. We compare these two scale-feeding taxa to their
 nearest, non-lepidophagous taxa to identify traits held in common among
 scale-feeding fishes. We use a combination of micro-computed tomography
 scanning and iodine staining to measure biomechanical predictors of
 feeding behavior such as tooth shape, jaw lever mechanics, and jaw
 musculature. We recover a stark contrast between the feeding morphology of
 scale-feeding and non-scale-feeding taxa, with lepidophagous fishes
 displaying some paedomorphic characters through to adulthood. Few traits
 are shared between lepidophagous characins and piranhas, except for their
 highly-modified, stout dentition. Given such variability in development,
 morphology, and behavior, ecological diversity within lepidophagous fishes
 has been underestimated.
description: LepidophagyPCAData including in the PCA section of our paperLepidophagyALL_CharaCharacin datasetLepidophagyALL_SerraSerrasalmid datasetLepidophageRCodeSample R-Code used in this manuscript
DOI: 10.5061/dryad.dg82p
title: Data from: Discriminating selection on lateral plate phenotype and its underlying gene, Ectodysplasin, in threespine stickleback

description: When a signature of natural selection is discovered on a gene that is
 pleiotropic or in tight linkage with other genes, it is challenging to
 determine which of the affected phenotypes is under selection. One way to
 make progress is to employ methods for analyzing natural selection on
 correlated traits, including both genotype and phenotype. We used this
 approach in threespine stickleback to estimate selection on a rapidly
 evolving trait, lateral armor plates, while controlling for variation at
 its major underlying gene, Ectodysplasin (Eda), and vice versa. This
 allowed for independent estimates of selection on lateral plates and on
 Eda via other traits. Previously, we demonstrated allele frequency changes
 at Eda in a pond experiment. Here we show that this resulted from
 selection on both plates and on Eda, implying additional selection on
 other phenotypic traits affected by the same gene. This represents the
 first evidence for direct selection on lateral plates independent of
 selection on the Eda locus and highlights the value of measuring selection
 on both phenotypes and genotypes in studies of adaptation.
description: Morphological
 measurements and Ectodysplasin genotype scoresThis file contains raw
 and size-adjusted (adj) length measurements and lateral plate counts as
 well as ectodysplasin genotypes.Rennison et al
 archive.csv
DOI: 10.5061/dryad.788
title: Data from: Evolution and Phylogeny of the Diptera: A Molecular Phylogenetic Analysis Using 28S rDNA Sequences

description: Portions of the large ribosomal subunit RNA gene (28S rDNA) encompassing
 the D1 and the D7 region were obtained from 16 dipteran species and
 families to reconstruct early phylogenetic events in the order Diptera.
 For outgroup comparison, the corresponding sequences were used from
 representative taxa of the Siphonaptera, Mecoptera, and Lepidoptera. A
 subset of 488 unambiguously alignable sites was analyzed with respect to
 important sequence evolution parameters. We found (1) sequence variability
 is significantly higher in double-stranded sites than in single-stranded
 sites, (2) transitions are close to saturation in most pairwise sequence
 comparisons, (3) significant substitution rate heterogeneity exists across
 sites, and (4) significant substitution rate heterogeneity exists among
 lineages. Tree reconstruction was carried out with the neighbor joining,
 maximum parsimony, and maximum likelihood methods. Four major subgroups
 are consistently and robustly supported: the Brachycera, the Culicomorpha,
 the Tipulomorpha sensu stricto, and the hitherto controversial
 Bibionomorpha sensu lato, which includes the families Sciaridae,
 Mycetophilidae, Cecidomyiidae, Bibionidae, Scatopsidae, and Anisopodidae.
 The phylogenetic relationships within or among these subclades and the
 positions of the families Psychodidae and Trichoceridae were not robustly
 resolved. These results support the view that the mouthparts of extant
 dipteran larvae evolved from a derived ground state characterized by
 subdivided and obliquely moving mandibles. Furthermore, sequence
 divergence and the paleontological record consistently indicate that a
 period of rapid cladogenesis gave rise to the major dipteran subgroups.
description: Friedrich Data
 Setfriedrich.paup
DOI: 10.5061/dryad.q1vf1
title: Data from: Habitat partitioning and morphological differentiation: the Southeast Asian Draco lizards and Caribbean Anolis lizards compared

description: Sympatric species that initially overlap in resource use are expected to
 partition the environment in ways that will minimize interspecific
 competition. This shift in resource use can in turn prompt evolutionary
 changes in morphology. A classic example of habitat partitioning and
 morphological differentiation are the Caribbean Anolis lizards. Less well
 studied, but nevertheless striking analogues to the Anolis are the
 Southeast Asian Draco lizards. Draco and Anolis have evolved independently
 of each other for at least 80 million years. Their comparison subsequently
 offers a special opportunity to examine mechanisms of phenotypic
 differentiation between two ecologically diverse, but phylogenetically
 distinct groups. We tested whether Draco shared ecological axes of
 differentiation with Anolis (e.g., habitat use), whether this
 differentiation reflected interspecific competition, and to what extent
 adaptive change in morphology has occurred along these ecological axes.
 Using existing data on Anolis, we compared the habitat use and morphology
 of Draco in a field study of allopatric and sympatric species on the Malay
 Peninsula, Borneo and in the Philippines. Sympatric Draco lizards
 partitioned the environment along common resource axes to the Anolis
 lizards, especially in perch use. Furthermore, the morphology of Draco was
 correlated with perch use in the same way as it was in Anolis: species
 that used wider perches exhibited longer limb lengths. These results
 provide an important illustration of how interspecific competition can
 occur along common ecological axes in different animal groups, and how
 natural selection along these axes can generate the same type of adaptive
 change in morphology.
description: ORD_OECO-D-13-00537R2_draco_ecomorphologyAll morphological and habitat use data on Draco used in study.
DOI: 10.5061/dryad.nr0kj16
title: Data from: Neural correlates of domain-specific cognitive decline: the ARIC-NCS study

description: Objective: To evaluate the association of cognitive declines in the
 domains of memory, language, and executive function with brain gray matter
 (GM) volume in old age. Methods: Prospective study of 1,846 participants
 in the Atherosclerosis Risk in Communities (ARIC) study who underwent 3T
 brain MRI scans in 2011-2013. Participants were categorized by cognitive
 domain performance trajectory over the prior 20 years (cut-point to define
 decline: 20th percentile). Associations between GM volume and cognitive
 declines were assessed at the voxel level using voxel-based morphometry
 and at the regional level using atlas-defined GM volumes of specific
 regions of interest. Results: Participants were an average age of 76
 years, 60% were female, and 28% were black. Participants in the top 20th
 percentile for decline in the memory domain had smaller GM volumes in the
 medial temporal lobe (-3.3%, 95% CI: -4.6% to -2.1%), amygdala (-2.7%, 95%
 CI: -4.1% to -1.3%), entorhinal cortex (-4.1%, 95% CI: -6.0% to -2.2%),
 and hippocampus (-3.8%, 95% CI: -5.2% to -2.4%) compared to participants
 who were in the lowest 80th percentile for decline in all domains. In
 contrast, among participants who were in the top 20th percentile for
 decline in the language or executive function domains, GM volumes were
 smaller in more brain regions. Conclusions: Declines in memory function
 were associated with brain volume loss in the medial temporal and
 hippocampal formations. Declines in language and executive function were
 associated with decreases in brain volumes across more non-contiguous
 brain regions.
description: VBM Appendix
 9.27.18
DOI: 10.5061/dryad.n2d15
title: Data from: Diet dichotomy between two migrant seabirds breeding near a high Arctic polynya

description: High Arctic polynyas are predictable areas of open water, which offer
 long-distance migrant seabirds a reliable source of food during a period
 when they have to replenish and accumulate energy for reproduction.
 Investigating the interaction between species nesting sympatrically in the
 vicinity of polynyas should provide insights into the role that such
 oceanographic features play for pre-breeding seabirds. We used stable
 isotopes (δ13C and δ15N) to compare the diet of two ground-nesting
 seabirds, Sabine's gull (Xema sabini) and Arctic tern (Sterna
 paradisaea), nesting on an island adjacent to a recurring polynya in the
 Canadian high Arctic in 2008 and 2009. We show that, unlike Arctic terns,
 the diet of Sabine's gulls appears to include a non-negligible amount
 of terrestrially derived prey during early incubation, and that overall
 both species segregate their dietary niche during pre-laying and early
 incubation.
description: SIA_adult
 plasmaStable isotope data in
 plasma of adult Sabine's gulls and Arctic terns collected at
 Nasaruvaalik Island in 2008 and 2009.DATAbirds_supp.csvSIA_prey itemStable isotopes data of food sources and prey items collected at Nasaruvaalik Island in 2008, 2009 and 2011DATAfood_supp.csv
DOI: 10.5061/dryad.m8t2k
title: Data from: Seasonal and annual differences in the foraging ecology of two gull species breeding in sympatry and their use of fishery discards

description: Niche segregation between similar species will result from an avoidance of
 competition but also from environmental variability, including nowadays
 anthropogenic activities. Gulls are among the seabirds with greater
 behavioural plasticity, being highly opportunistic and feeding on a wide
 range of prey, mostly from anthropogenic origin. Here, we analysed blood
 and feather stable isotopes combined with pellet analysis to investigate
 niche partitioning between Audouin’s gull Larus audouinii and
 yellow-legged gull Larus michahellis breeding in sympatry at Deserta
 Island, southern Portugal, during 2014 and 2015. During the breeding
 season there was considerable overlap in the adults’ diet, as their stable
 isotope values of blood and primary feather (P1) did not differ, and their
 pellets were comprised mainly by marine fish species. However, Audouin’s
 gulls presented higher occurrences of pelagic fish, while yellow-legged
 gulls fed more on demersal fish, insects, and refuse. SIAR mixing models
 also estimated a higher proportion of demersal fish in the diet of
 yellow-legged gulls. We also found differences between the two gull
 species in chicks’ feathers, suggesting that Audouin’s gull adults
 selected prey with lower carbon isotope values to feed their young.
 Secondary feather (S8) of Audouin’s gull presented higher isotope values
 compared to yellow-legged gulls, indicating different foraging areas
 (δ13C) and/ or trophic levels (δ15N) between the two species in the
 non-breeding season. During both the all-year and non-breeding periods the
 yellow-legged gull showed a broader isotopic niche width than Audouin’s
 gull in 2013, and in 2014 the two gull species exhibited different
 isotopic niche spaces. Our study suggests that both gull species foraged
 in association with fisheries during the breeding season. In this sense, a
 discard ban implemented under the new European Union Common Fisheries
 Policy may lead to a food shortage, therefore future research should
 closely monitor the population dynamics of Audouin’s and yellow-legged
 gulls.
description: Stable isotopic values
 of different tissues from two gull speciesStable isotopic values
 from two gull species breeding at South PortugalSIA_gulls.txt
DOI: 10.5061/dryad.gk661
title: Data from: Optimized modelling and application of exhaust gas recirculation performance evaluation of turbocharged diesel engine

description: Aimed at the problem of turbocharged diesel engine EGR (exhaust gas
 recirculation) performance evaluation and optimal EGR rate determination,
 especially in some cases with poor data because of the limit of
 conditions, an optimized multi-objective grey decision method based on
 grey theory and entropy weight is proposed. The internal combustion
 pressure ,fuel consumption rate, NOX ,CO and smoke degree were selected as
 the decision target, and the initial decision-making model was established
 based on traditional grey situation theory. According to the
 characteristics and optimization requirements of EGR, The optimal
 compromise between combustion and emission performance is proposed to
 transform into the decision-making target weight problem , then a
 subjective weight optimization method based on expert scoring and grey
 relational analysis is proposed. In addition, the entropy weight method
 was used to solve the subjective and objective weight vector and the
 optimized multi-objective grey situation decision making model was
 established, which can not weaken the human error of subjective
 empowerment, but also fully explore the intrinsic objective relationship
 of the evaluation index parameters. At last, an optimization simulation
 platform for EGR performance evaluation based MATLB/GUIDE is designed and
 established. The results show that the optimization simulation platform
 can effectively improve the efficiency of simulation calculation, which is
 more convenient for practical engineering applications; the optimized
 method can successfully solve the EGR performance evaluation and optimal
 EGR rate determination under different working conditions, the decision
 result is reasonable and consistent with the prevailing principle of the
 EGR determining, which provide a new research ideas for EGR performance
 optimization.
description: experiment
 data
DOI: 10.5061/dryad.bt760
title: Data from: A new species of marsupial frog (Anura: Hemiphractidae: Gastrotheca) from the Andes of southern Peru

description: Gastrotheca nebulanastes sp. nov. from cloud forests in the upper
 Kosñipata Valley, Manu National Park, in the Andes of southern Peru is
 similar to G. excubitor, which inhabits grasslands in higher elevations
 than the cloud forests. The two species differ in relative lengths of the
 fingers, skin texture, coloration, and advertisement call. Although the
 new species has an elevational range of 2000–3300 m, it is most abundant
 at 2400–2800 m. A phylogenetic analysis of a previously defined clade of
 Gastrotheca based on a fragment of 16S mitochondrial gene provides strong
 support that the sister taxon to the new species is G. atympana, a species
 from farther north in the Cordillera Oriental in Peru.
description: Multiple sequence
 alignmentMultiple sequence
 alignment of DNA sequence data for mitochondrial 16S ribosomal RNA
 gene.Duellman_et_al_Zootaxa_Gnebulanastes.nex
DOI: 10.5061/dryad.rq43r
title: Data from: A novel method to analyze social transmission in chronologically sequenced assemblages, implemented on cultural inheritance of the art of cooking

description: Here we present an analytical technique for the measurement and evaluation
 of changes in chronologically sequenced assemblages. To illustrate the
 method, we studied the cultural evolution of European cooking as revealed
 in seven cook books dispersed over the past 800 years. We investigated if
 changes in the set of commonly used ingredients were mainly gradual or
 subject to fashion fluctuations. Applying our method to the data from the
 cook books revealed that overall, there is a clear continuity in cooking
 over the ages – cooking is knowledge that is passed down through
 generations, not something (re-)invented by each generation on its own.
 Looking at three main categories of ingredients separately (spices, animal
 products and vegetables), however, disclosed that all ingredients do not
 change according to the same pattern. While choice of animal products was
 very conservative, changing completely sequentially, changes in the
 choices of spices, but also of vegetables, were more unbounded. We
 hypothesize that this may be due a combination of fashion fluctuations and
 changes in availability due to contact with the Americas during our study
 time period. The presented method is also usable on other assemblage type
 data, and can thus be of utility for analyzing sequential archaeological
 data from the same area or other similarly organized material.
description: IngredientsIngredients present in cookery books from different time periods
DOI: 10.5061/dryad.n17d2
title: Data from: Population structure and landscape genetics of two endangered frog species of Genus Odorrana: different scenarios on two islands

description: Isolation by distance and landscape connectivity are fundamental factors
 underlying speciation and evolution. To understand how landscapes affect
 gene flow and shape population structures, island species provide
 intrinsic study objects. We investigated the effects of landscapes on the
 population structure of the endangered frog species, Odorrana ishikawae
 and O. splendida, which each inhabit an island in southwest Japan. This
 was done by examining population structure, gene flow, and demographic
 history of each species by analyzing 12 microsatellite loci and exploring
 causal environmental factors through ecological niche modeling (ENM) and
 the cost-distance approach. Our results revealed that the limited gene
 flow and multiple population structure in O. splendida and the single
 population structure in O. ishikawae were maintained after divergence of
 the species through ancient vicariance between islands. We found that
 genetic distance correlated with geographic dist ance between populations
 of both species. Our landscape genetic analysis revealed that the
 connectivity of suitable habitats influences gene flow and leads to the
 formation of specific population structures. In particular, different
 degrees of topographical complexity between islands are the major
 determining factor for shaping contrasting population structures of two
 species. In conclusion, our results illustrate the diversification
 mechanism of organisms through the interaction with space and environment.
 Our results also present an ENM approach for identifying the key factors
 affecting demographic history and population structures of target species,
 especially endangered species.
description: individual_genotypesconvert format