cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r6d4j
title: Data from: Niche width impacts vertebrate diversification

description: Aim: The size of the climatic niche of a species is a major factor
 determining its distribution and evolution. In particular, it has been
 proposed that niche width should be associated with the rate of species
 diversification. Here, we test whether species niche width affects the
 speciation and extinction rates of three main clades of vertebrates:
 amphibians, mammals and birds. Location: Global. Methods: We obtained the
 time-calibrated phylogenies, IUCN conservation status, species
 distribution maps and climatic data for 2340 species of amphibians, 4563
 species of mammals and 9823 species of birds. We computed the niche width
 for each species as the mean annual temperature across the species range.
 We estimated speciation, extinction and transition rates associated with
 lineages with either narrow (specialist) or wide (generalist) niches using
 phylogeny-based birth–death models. We also tested if current conservation
 status was correlated with the niche width of species. Results: We found
 higher net diversification rates in specialist species than in generalist
 species. This result was explained by both higher speciation rates (for
 the three taxonomic groups) and lower extinction rates (for mammals and
 birds only) in specialist than in generalist species. In contrast, current
 specialist species tended to be more threatened than generalist species.
 Main conclusions: Our diversification analysis shows that the width of the
 climatic niche is strongly associated with diversification rates and may
 thus be a crucial factor for understanding the emergence of diversity
 patterns in vertebrates. The striking difference between our
 diversification results and current conservation status suggests that the
 current extinction process may be different from extinction rates
 estimated from the whole history of the group.
description: amphibians_BIO1_min_maxMininum and maximum annual temperature (BIO1 from worldclim) compiled for all the distributions of amphibians species present in the IUCN red list websitebirds_BIO1_min_maxMininum and maximum annual temperature (BIO1 from worldclim) compiled for all the distributions of birds species present in the Birdlife websitemammals_BIO1_min_maxMininum and maximum annual temperature (BIO1 from worldclim) compiled for all the distributions of mammals species present in the IUCN red list website
DOI: 10.5061/dryad.60k13v2
title: Data from: Phylogeny and spatio-temporal diversification of Prunus subgenus Laurocerasus section Mesopygeum (Rosaceae) in the Malesian region

description: The goals of this study were to reconstruct the phylogeny of Prunus
 subgenus Laurocerasus section Mesopygeum and to provide a preliminary
 assessment of its spatio-temporal diversification in the Malesian region.
 We inferred the phylogeny using nuclear ITS and ETS and plastid psbA-trnH,
 rps16, rpl16, and trnC-petN sequences. Our analyses support the monophyly
 of sect. Mesopygeum. Within sect. Mesopygeum, we identified four main
 subclades: (1) Prunus lancilimba from continental Asia; (2) Prunus ruthii
 from Malay Peninsula; (3) a subclade comprising species from areas
 centered on the Sunda shelf and also a few species from continental Asia
 and Wallacea; and (4) a subclade composed of species from areas of the
 Sahul shelf, with a small number of taxa also from areas of the Sunda
 shelf, continental Asia, and the Philippines. We estimated that sect.
 Mesopygeum originated in continental Asia at c. 44.71 Mya (95% HPD:
 31.66–46.90). Nine dispersals between major geographic areas were
 inferred. From continental Asia, three and two dispersals were inferred to
 the Sunda shelf and the Sahul shelf in the mid-Oligocene, respectively.
 Two dispersals were inferred from the Sahul shelf region to the Sunda
 shelf in late Oligecene and early Miocene, respectively. There were also
 two dispersals inferred from the Sunda shelf region, one to the
 Philippines and one to Wallacea, in the middle and late Miocene,
 respectively. The diversification in sect. Mesopygeum was likely driven by
 active geologic events and orogenies in the Neogene in the Malesian
 region.
description: Mesopygeum_6seqs_Sep18
 (nuclear + chloroplast)Mesopygeum nuclear and
 chloroplast datasets, 77 samplesMesopygeum_6seqs_Sep18.nexMesopygeum chloroplast datasets, 77 samplesMesopygeum chloroplast datasets, 77 samplesMesopygeum_4cpALL.nexMesopygeum nuclear datasets, 77 samplesMesopygeum nuclear datasets, 77 samplesMesopygeum_2nuclearALL.nex
DOI: 10.5061/dryad.f8j00mn
title: Data from: Cryptic speciation yields remarkable mimics: A new genus of sea slugs that masquerade as toxic algae (Caulerpa spp.)

description: “Cryptic” can refer to species that match their background through
 camouflage or disruptive coloration, or in taxonomy to externally similar
 but unrecognized congeners. In adaptive resemblance, organisms resemble
 parts of a larger host animal or plant on which the mimic is highly
 cryptic. Mimetic lineages that radiate onto superficially similar hosts
 may contain cryptic species in both senses: taxa that are difficult to
 detect, and challenging for taxonomists to distinguish. Here, we describe
 a new genus and four species of herbivorous sea slugs (Gastropoda,
 Heterobranchia, Sacoglossa), including remarkable mimics of toxic green
 algae (Caulerpa spp.) on which the slugs feed. The long-recognized
 Stiliger smaragdinus Baba 1949 is highly mimetic of ‘sea grapes’ (C.
 racemosa-lentilifera), but phylogenetic analyses of four genes indicated
 Stiliger was polyphyletic: the name-bearing species grouped within
 Placida, whereas Caulerpa-mimetic lineages were phylogenetically distinct.
 We erect the genus Sacoproteus gen. n. for S. smaragdinus (Baba 1949), and
 describe four new species: S. nishae sp. n. from the Indo-Pacific, which
 mimics C. chemnitzia; S. yhiae sp. n. and S. browni sp. n. from southern
 Australia, which mimic C. cactoides and C. gemminata; and S. thomasleei
 sp. n., a non-mimetic west Pacific species that shared key features.
 Stiliger s.s. and Placida species show crypsis and aposematism but not
 host mimicry, although Stiliger spp. feeding on undefended algae may be
 Batesian mimics. Investigating the ecology and biogeography of Sacoproteus
 gen. n. will yield insight into how selection generates such extraordinary
 examples of adaptive resemblance in the marine realm.
description: input file 1 for ABGD,
 pairwise TrN-corrected COI distancesMatrix of pairwise
 TrN-corrected COI distances for all Placida and nominal Stiliger
 haplotypes, used as input for ABGD analysis.file1_ABGD_COI_distance_datainput file 2 for RaxML, mtDNA haplotypesRaxML input (nexus file type) of concatenated mtDNA (COI + 16S) haplotypes representing Sacoproteus gen. nov. (11 unique haplotypes representing 5 supported taxa) and Placida/Stiliger s.s. species (49 unique haplotypes representing 14 candidate taxa).file2_sacoprot_placida_mtDNA.nex.nexinput file 3 for RaxML, 4 gene regions concatenated for SacoglossaRaxML input file for the aligned and concatenated four-gene data matrix comprising 211 ingroup sacoglossan species and six outgroup species in Siphonarioidea (one exemplar per species).file3_sacoprot_placida_4genes_217taxa.nex.nex
DOI: 10.5061/dryad.6fb64
title: Data from: Climate-driven mitochondrial selection: a test in Australian songbirds

description: Diversifying selection between populations that inhabit different
 environments can promote lineage divergence within species and ultimately
 drive speciation. The mitochondrial genome (mitogenome) encodes essential
 proteins of the oxidative phosphorylation (OXPHOS) system and can be a
 strong target for climate-driven selection (i.e. associated with
 inhabiting different climates). We investigated whether Pleistocene
 climate changes drove mitochondrial selection and evolution within
 Australian birds. First, using phylogeographic analyses of the
 mitochondrial ND2 gene for 17 songbird species, we identified
 mitochondrial clades (mitolineages). Second, using distance-based
 redundancy analyses, we tested whether climate predicts variation in
 intraspecific genetic divergence beyond that explained by geographic
 distances and geographic position. Third, we analyzed 41 complete
 mitogenome sequences representing each mitolineage of 17 species using
 codon models in a phylogenetic framework and a biochemical approach to
 identify signals of selection on OXPHOS protein-coding genes and test for
 parallel selection in mitolineages of different species existing in
 similar climates. Of 17 species examined, 13 had multiple mitolineages
 (range 2-6). Climate was a significant predictor of mitochondrial
 variation in eight species. At least two amino acid replacements in OXPHOS
 complex I could have evolved under positive selection in specific
 mitolineages of two species. Protein homology modelling showed one of
 these to be in the loop region of the ND6 protein channel and the other in
 the functionally-critical helix HL region of ND5. These findings call for
 direct tests of the functional and evolutionary significance of
 mitochondrial protein candidates for climate-associated selection.
description: Zip file with 15 xml
 files used as input for 15 Beast analyses of ND2 dataBeast xml input files:
 ND2 alignments with models from Partition Finder for 15 species/species
 complexND2_Beast_xml_files.zipZip file with 4 tree files used as input for CODEML branch- and branch-and-site modelsInput trees for CODEML branch- and branch-and-site models for testing for signatures of parallel selection in mitolineages of different species co-occurring in four climate categories: regions that are least temperate, most temperate, least arid and most arid.CODEML_input_mitogenome_trees_4_climate_extremes.zipZip with 2 files: whole mitogenome alignment in nexus format and phylogenetic treeTwo files: (1) whole mitogenome alignment in nexus format used for MrBayes phylogenetic analysis (rooted with lyrebird and partitioned as per PartitionFinder results), and (2) the 50% majority rule tree resulting from MrBayes analysis.WholeMitogenome_Lyrebird_Partitioned.zipNexus alignment of 3796 codons for 13 mitochondrial coding genesCoding gene alignment (11,388 nucleotides, 41 individuals) used for selection analyses, in nexus formatBirds_MitogenomeAlignment_Coding_Concatenated_RootedTree.nex
DOI: 10.5061/dryad.ck52b
title: Data from: What explains patterns of diversification and richness among animal phyla?

description: Animal phyla vary dramatically in species richness (from one species to
 &gt;1.2 million), but the causes of this variation remain largely
 unknown. Animals have also evolved striking variation in morphology and
 ecology, including sessile marine taxa lacking heads, eyes, limbs, and
 complex organs (e.g., sponges), parasitic worms (e.g., nematodes,
 platyhelminths), and taxa with eyes, skeletons, limbs, and complex organs
 that dominate terrestrial ecosystems (arthropods, chordates). Relating
 this remarkable variation in traits to the diversification and richness of
 animal phyla is a fundamental yet unresolved problem in biology. Here, we
 test the impacts of 18 traits (including morphology, ecology,
 reproduction, and development) on diversification and richness of extant
 animal phyla. Using phylogenetic multiple regression, the best-fitting
 model includes five traits that explain ∼74% of the variation in
 diversification rates (dioecy, parasitism, eyes/photoreceptors, a
 skeleton, nonmarine habitat). However, a model including just three
 (skeleton, parasitism, habitat) explains nearly as much variation (∼67%).
 Diversification rates then largely explain richness patterns. Our results
 also identify many striking traits that have surprisingly little impact on
 diversification (e.g., head, limbs, and complex circulatory and digestive
 systems). Overall, our results reveal the key factors that shape
 large-scale patterns of diversification and richness across &gt;80% of
 all extant, described species.
description: Supp_File_S1Character data for 18 traits for 28 phyla and 49 higher-level subclades.Supp_File_S2Time-calibrated phylogenies used.Supp_File_S3Species richness, clade ages, and diversification rates for 28 phyla and 49 higher-level clades.Supp_File_S4Results of PGLS regression between traits and diversification rates of animal phyla.Supp_File_S5Results of PGLS regression between traits and diversification rates of animal phyla using projected species richness.Supp_File_S6Results of PGLS regression between traits and diversification rates for 49 higher-level clades.Supp_File_S7Results of PGLS regression between traits and diversification rates within Annelida, Arthropoda, Mollusca, Deuterostomia, and Ecdysozoa.Supp_File_S8Results of multiple regression analyses.Supp_File_S9Relationships between selected pairs of traits.Supp_File_S10Ancestral state reconstruction of vision and habitat.
DOI: 10.5061/dryad.p5k25
title: Data from: Supplementing non-target taxa: bird feeding alters the local distribution of mammals

description: Although the effects of bird feeding on avian species have been
 extensively examined, few studies evaluate the indirect effects of bird
 feeding on non-target taxa. Bird seed could provide direct nourishment to
 several mammalian species (e.g., Lagomorpha, Rodentia, and
 (Cetartiodactyla), potentially altering their distribution and behavior
 with possible unintended consequences for some avian populations,
 particularly those not directly benefiting from the resource. To examine
 how bird feeders may influence the presence and behavior of mammals, we
 used camera traps to quantify differences in the distribution and richness
 of mammal species frequenting sites with bird feeders and control sites
 (lacking feeders) in Ithaca, New York. We recorded 15,684 images capturing
 12 mammal species with gray squirrel (Sciurus carolinensis) and raccoon
 (Procyon lotor) detected significantly more often at feeder sites than at
 control sites. Detections of white-tailed deer (Odocoileus virginianus)
 marginally increased near feeders whereas detections of several
 carnivorous species were unrelated to the presence of bird feeders. We
 recorded larger gray squirrel and raccoon group sizes and greater mammal
 richness at feeder sites than at nearby control sites. We detected
 squirrels and raccoons less when snow covered the ground than on snow-free
 days. Ambient temperature was not a strong predictor of mammal detections.
 Camera trapping revealed strong, species-specific patterns in the timing
 of daily visitation to areas with feeders. Because many mammals depredate
 bird nests, the local increases in mammal richness and activity near bird
 feeders may create an ecological trap for avian species nesting in close
 proximity to supplemental feeding stations.
description: photo_dataData from the camera trapssunriseSunrise and sunset dataweather_dataWeather data used in analysis
DOI: 10.5061/dryad.18bv1
title: Data from: Resolving neutral and deterministic contributions to genomic structure in Syntrichia ruralis (Bryophyta, Pottiaceae) informs propagule sourcing for dryland restoration

description: Syntrichia ruralis is a cosmopolitan moss that occupies steep
 environmental gradients. In arid to semi-arid regions of the world it is a
 key component of biological soil crusts, which are fundamental to healthy
 dryland ecosystem processes. As such, S. ruralis has attracted the
 attention of conservationists seeking to restore degraded biological soil
 crust communities and their associated vascular flora. Here, we generate
 genomic data for S. ruralis populations that span climatic gradients
 across the Colorado Plateau of the southwestern USA to investigate the
 contributions of neutral and deterministic processes to the partitioning
 of genomic structure. Although S. ruralis appears to be highly
 dispersible, geographic proximity significantly predicts genomic
 similarity. In addition, even when taking into account apparently high
 migration rates among populations and spatial autocorrelation of allele
 frequencies, some genomic variation is explained by environmental
 gradients correlated with elevation and latitude. Consequently, efforts to
 restore dryland ecosystems by establishing S. ruralis as a foundation
 should include strategies to ensure that propagule sources of this moss
 are environmentally stratified and targeted to the current/future climates
 of restoration sites.
description: pyrad
 parametersThese are the parameters
 used to demultiplex and process the data in pyrad.params.txtR functions to filter a vcfThese functions can be used to filter a vcf file. They can remove loci that have a given amount missing data, remove individuals that have a given amount of missing data, remove individuals by name, and create histograms either of missing data per locus or individuals. Finally, once data are filtered, there is a function to write a structure output file.vcf_functions.RMoss dataThese are the data used is analyses, recorded in a structure formatted file. There are 81 individuals and 1678 loci, with up to 60% missing data per locus.moss.stru
DOI: 10.5061/dryad.472b9
title: Data from: Two species of Southeast Asian cats in the genus Catopuma with diverging histories: an island endemic forest specialist and a widespread habitat generalist

description: Background. The bay cat Catopuma badia is endemic to Borneo, whereas its
 sister species the Asian golden cat Catopuma temminckii is distributed
 from the Himalayas and southern China through Indochina, Peninsular
 Malaysia and Sumatra. Based on morphological data, up to five subspecies
 of the Asian golden cat have been recognized, but a taxonomic assessment,
 including molecular data and morphological characters, is still lacking.
 Results. We combined molecular data (whole mitochondrial genomes),
 morphological data (pelage) and species distribution projections (up to
 the Late Pleistocene) to infer how environmental changes may have
 influenced the distribution of these sister species over the past 120 000
 years. The molecular analysis was based on sequenced mitogenomes of 3 bay
 cats and 40 Asian golden cats derived mainly from archival samples. Our
 molecular data suggested a time of split between the two species
 approximately 3.16 Ma and revealed very low nucleotide diversity within
 the Asian golden cat population, which supports recent expansion of the
 population. Discussion. The low nucleotide diversity suggested a
 population bottleneck in the Asian golden cat, possibly caused by the
 eruption of the Toba volcano in Northern Sumatra (approx. 74 kya),
 followed by a continuous population expansion in the Late
 Pleistocene/Early Holocene. Species distribution projections, the
 reconstruction of the demographic history, a genetic isolation-by-distance
 pattern and a gradual variation of pelage pattern support the hypothesis
 of a post-Toba population expansion of the Asian golden cat from south
 China/Indochina to Peninsular Malaysia and Sumatra. Our findings reject
 the current classification of five subspecies for the Asian golden cat,
 but instead support either a monotypic species or one comprising two
 subspecies: (i) the Sunda golden cat, distributed south of the Isthmus of
 Kra: C. t. temminckii and (ii) Indochinese, Indian, Himalayan and Chinese
 golden cats, occurring north of the Isthmus: C. t. moormensis.
description: Mitogenome alignment for
 Asian golden catCTE.fastaMitogenome alignment for Bay catCBA.fasta
DOI: 10.5061/dryad.dg380p9q
title: Data from: Short-term effects of elevated precipitation and nitrogen on soil fertility and plant growth in a Neotropical savanna

description: Increasing nitrogen (N) deposition and changing precipitation patterns in
 Neotropical savannas could alter plant growth, reproduction, and nutrients
 by altering soil nutrient and water availability. We examined the
 potential for simulated N deposition and increased dry season
 precipitation to have interactive effects on reproduction and growth of
 two abundant native Cerrado (Brazilian savanna) grasses – Loudetiopsis
 chrysothrix and Tristachya leiostachya – via feedbacks with soil nutrient
 status. Plant growth and reproduction responses consistently varied by
 species. Water addition led to more consistent increases in both growth
 and reproduction than nitrogen addition and the two treatments did have
 significant interactive effects. We expected that both treatments would
 affect plant growth and reproduction via positive effects on soil and
 plant N. Instead, we found that plant responses were linked to
 species-specific treatment effects on soil and foliar phosphorus (P).
 Structural equation models (SEM) confirmed that changes in soil P - rather
 than changes in soil N or increasing soil acidity - explained plant
 response to treatments. Our results imply that N deposition and
 precipitation change could impact Cerrado plant growth and reproduction
 via subtle effects on plant and soil phosphorus.
description: Copeland_etal_EcospherePlant, soils, foliar chemistry, and soil moisture data for field experiment in the Brazilian Cerrado associated with manuscript (Copeland et al.) in Ecosphere
DOI: 10.5061/dryad.70vc6
title: Data from: Change and stability in a steep morph-frequency cline in the snail Cepaea nemoralis (L.) over 43 years.

description: Populations of the polymorphic land snail Cepaea nemoralis (L.) from
 Deepdale, Derbyshire, UK, sampled in 1965-67, showed a pattern of area
 effects, with steep clines among groups of populations differing in shell
 colour and banding morph frequencies. In 2010 most of these populations
 were resampled. In particular a continuous transect made in 1967 of 42
 18.34m x 18.34m quadrats across a steep cline in several morph frequencies
 was completely resampled. In the dale as a whole, yellow shells had
 increased in frequency. In the transect the frequencies of banding morphs
 showed no significant changes, but colour morphs showed some changes. Pink
 shells had increased in frequency in a section in which scrub had
 developed, and brown shells had increased in frequency in the area in
 which they had originally been at the highest frequency. In each case, the
 selection coefficients were of the order of 4%. Yellow had increased
 elsewhere. Nevertheless, both in the dale as a whole and in the transect,
 the pattern of geographical change in morph frequencies had remained
 essentially the same. Estimates of migration based on previous studies of
 marked snails and on modelling of the effect of drift and migration
 suggest that whether the cline is a product of differential selection or
 of the gradual merging of previously separate founding populations, it has
 been in existence for a long time, and that migration occurs over greater
 distances than estimated from direct observation on marked snails. While
 we can demonstrate that selection has occurred, the origin and maintenance
 of the cline and others like it remain in doubt; the development and
 maintenance of polymorphism in this species may require consideration of
 several processes operating on different time scales.
description: Appendix
 1Sample scores and
 locations from the general surveys of Deepdale in 1967 and
 2010.appendix
 2Details of samples from
 the transect in Deepdale made in 1967 and 2010, with precise landmarks to
 identify each quadrat