cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.36c10
title: Data from: Long-term stasis and short-term divergence in the phenotypes of microsnails on oceanic islands

description: Phenotypic divergence is often unrelated to genotypic divergence. An
 extreme example is rapid phenotypic differentiation despite genetic
 similarity. Another extreme is morphological stasis despite substantial
 genetic divergence. These opposite patterns have been viewed as reflecting
 opposite properties of the lineages. In this study, phenotypic radiation
 accompanied by both rapid divergence and long-term conservatism is
 documented in the inferred molecular phylogeny of the micro land snails
 Cavernacmella (Assimineidae) on the Ogasawara Islands. The populations of
 Cavernacmella on the Sekimon limestone outcrop of Hahajima Island showed
 marked divergence in shell morphology. Within this area, one lineage
 diversified into types with elongated turret shells, conical shells and
 flat disc-like shells without substantial genetic differentiation.
 Additionally, a co-occurring species with these types developed a much
 larger shell size. Moreover, a lineage adapted to live inside caves in
 this area. In contrast, populations in the other areas exhibited no
 morphological differences despite high genetic divergence among
 populations. Accordingly, the phenotypic evolution of Cavernacmella in
 Ogasawara is characterized by a pattern of long-term stasis and periodic
 bursts of change. This pattern suggests that even lineages with phenotypic
 conservatism could shift to an alternative state allowing rapid phenotypic
 divergence.
description: DNA seq alignments for
 BEASTDNA sequence alignments
 for divergence time analysis; COI, 16S and 28S. Including the sequences of
 Cavernacmella spp. and outgroup species.seq_alignments_for_divergence_time_analysis.zipDNA seq alignments for phylogenetic treeDNA sequence alignments for phylogenetic trees; COI, 16S, 28S and ITS. Including the sequences of Cavernacmella spp.seq_alignments_for_phylogenetic_tree.zipMorphological measurements of Cavernacmella spp. in Ogasawara.Raw data of morphological measurements of Cavernacmella spp. in Ogasawara. Site nos. and abbreviation for each measurements refer to manuscript.DA_morphological_data.xls
DOI: 10.5061/dryad.6b16k45
title: Data from: Contrasting effects of habitat discontinuity on three closely related fungivorous beetle species with diverging host-use patterns and dispersal ability

description: Understanding how landscape structure influences biodiversity patterns and
 ecological processes is essential in ecological research and conservation
 practices. Forest discontinuity is a primary driver affecting the
 population persistence and genetic structure of forest-dwelling species.
 However, the actual impacts on populations are highly species-specific. In
 this study, we tested whether dispersal capability and host specialization
 are associated with susceptibility to forest discontinuity using three
 closely related, sympatric fungivorous ciid beetle species (two host
 specialists, Octotemnus assimilis and O. crassus; one host generalist, O.
 kawanabei). Landscape genetic analyses and the estimation of effective
 migration surfaces (EEMS) method consistently demonstrated contrasting
 differences in the relationships between genetic structure and
 configuration of forest land cover. Octotemnus assimilis, one of the
 specialists with a presumably higher dispersal capability due to lower
 wing loading, lacked a definite spatial genetic structure in our study
 landscape. The remaining two species showed clear spatial genetic
 structure, but the results of landscape genetic analyses differed between
 the two species: while landscape resistance appeared to describe the
 spatial genetic structure of the specialist O. crassus, genetic
 differentiation of the generalist O. kawanabei was explained by geographic
 distance alone. This finding is consistent with the prediction that
 non-forest areas act more strongly as barriers between specialist
 populations. Our results suggest that differences in host range can
 influence the species-specific resistance to habitat discontinuity among
 closely related species inhabiting the same landscape.
description: Microsat_Genotypes_DryadMicrosatellite genotypes of studied species.Morphology_DryadBody and wing measurement data of studied species.
DOI: 10.15468/dl.wwn4jp
title: Occurrence Download

description: A dataset containing 4279 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "GadmGid is CHN.15.6_1",
 "OccurrenceStatus is Present",
 "Year 2000-2024"
 ]
}

 The dataset includes 4279 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000984-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.sj168561
title: Data from: Invasion facilitates hybridization with introgression in the Rattus rattus species complex

description: Biological invasions result in novel species interactions, which can have
 significant evolutionary impacts on both native and invading taxa. One
 evolutionary concern with invasions is hybridization among lineages that
 were previously isolated, but make secondary contact in their invaded
 range(s). Black rats, consisting of several morphologically very similar
 but genetically distinct taxa that collectively have invaded six
 continents, are arguably the most successful mammalian invaders on the
 planet. We used mitochondrial cytochrome b sequences, two nuclear gene
 sequences (Atp5a1 and DHFR), and nine microsatellite loci to examine the
 distribution of three invasive black rat lineages (R. tanezumi, R. rattus
 I, and R. rattus IV) in the U.S. and Asia, and determine the extent of
 hybridization among these taxa. Our analyses revealed two mitochondrial
 lineages that have spread to multiple continents, including a previously
 undiscovered population of R. tanezumi in the southeastern U.S., whereas
 the third lineage (R. rattus IV) appears to be confined to Southeast Asia.
 Analyses of nuclear DNA (both sequences and microsatellites) suggested
 significant hybridization is occurring among R. tanezumi and R. rattus I
 in the U.S., and also suggest hybridization between R. tanezumi and R.
 rattus IV in Asia, although further sampling of the latter species pair in
 Asia is required. Furthermore, microsatellite analyses suggest
 unidirectional introgression from both R. rattus I and R. rattus IV into
 R. tanezumi. Within the U.S., introgression appears to be occurring to
 such a pronounced extent that we were unable to detect any nuclear genetic
 signal for R. tanezumi, and a similar pattern was detected in Asia.
description: MicrosatellitesMicrosatellite data included in this study, formatted for input into GenAlex
DOI: 10.5061/dryad.65vs3
title: Data from: Greater root phosphatase activity in nitrogen-fixing rhizobial but not actinorhizal plants with declining phosphorus availability

description: 1. The abundance of nitrogen (N)-fixing plants in ecosystems where
 phosphorus (P) limits plant productivity poses a paradox because N
 fixation entails a high P cost. One explanation for this paradox is that
 the N-fixing strategy allows greater root phosphatase activity to enhance
 P acquisition from organic sources, but evidence to support this
 contention is limited. 2. We measured root phosphomonoesterase (PME)
 activity of 10 N-fixing species, including rhizobial legumes and
 actinorhizal Allocasuarina species, and eight non-N-fixing species across
 a retrogressive soil chronosequence showing a clear shift from N to P
 limitation of plant growth and representing a strong natural gradient in P
 availability. 3. Legumes showed greater root PME activity than
 non-legumes, with the difference between these two groups increasing
 markedly as soil P availability declined. By contrast, root PME activity
 of actinorhizal species was always lower than that of co-occurring legumes
 and not different from non-N-fixing plants. 4. The difference in root PME
 activity between legumes and actinorhizal plants was not reflected in a
 greater or similar reliance on N fixation for N acquisition by
 actinorhizal species compared to co-occurring legumes. 5. Synthesis. Our
 results support the idea that N-fixing legumes show high root phosphatase
 activity, especially at low soil P availability, but suggest that this is
 a phylogenetically conserved trait rather than one directly linked to
 their N-fixation capacity.
description: PME_JEcol_myco_dataRoot mycorrhizal colonisation data. Root materials were field-collected along the Jurien Bay dune chronosequence in Western Australia in 2013. Arbuscular mycorrhizal fungi root colonisation were determined using gridline-intersect method at 200× magnification, while all viable root tips were scored for ectomycorrhizal fungi root colonisation or non-mycorrhizal colonisation. This PME_JEcol_myco_data.csv file was created using Microsoft Excel 2013. See readme file for descriptions of (abbreviated) column headings.PME_JEcol_main_dataAll data, except mycorrhizal colonisation data, collected for the analyses presented in this paper. All plant materials were field-collected along the Jurien Bay dune chronosequence in Western Australia in 2013. Data in this file include: root phosphomonoesterase (PME) activity (dry and fresh weight basis), leaf [N], leaf [P], leaf N:P, leaf δ15N and %Ndfa. This PME_JEcol_main_data.csv file was created using Microsoft Excel 2013. See readme file for descriptions of (abbreviated) column headings.
DOI: 10.5061/dryad.1s53q
title: Data from: Nutritional imbalance suppresses migratory phenotypes of the Mongolian locust (Oedaleus asiaticus)

description: For many species, migration evolves to allow organisms to access better
 resources. However, the proximate factors that trigger these developmental
 changes, and how and why these vary across species, remain poorly
 understood. One prominent hypothesis is that poor-quality food promotes
 development of migratory phenotypes and this has been clearly shown for
 some polyphenic insects. In other animals, particularly long-distance bird
 migrants, it is clear that high-quality food is required to prepare
 animals for a successful migration. We tested the effect of diet quality
 on the flight behaviour and morphology of the Mongolian locust, Oedaleus
 asiaticus. Locusts reared at high population density and fed low-N grass
 (performance-enhancing for this species) had enhanced migratory morphology
 relative to locusts fed high-N grass. Furthermore, locusts fed synthetic
 diets with an optimal 1 : 2 protein : carbohydrate ratio flew for longer
 times than locusts fed diets with lower or higher protein : carbohydrate
 ratios. In contrast to the hypothesis that performance-degrading food
 should enhance migration, our results support the more nuanced hypothesis
 that high-quality diets promote development of migratory characteristics
 when migration is physiologically challenging.
description: Cease-et-al-Data_RoySocOpen_v03
DOI: 10.5061/dryad.j4h5c
title: Data from: The effect of nitrogen availability and water conditions on competition between a facultative CAM plant and an invasive grass

description: Abstract Plants with crassulacean acid metabolism (CAM) are increasing
 their abundance in drylands worldwide. The drivers and mechanisms
 underlying the increased dominance of CAM plants and CAM expression (i.e.,
 nocturnal carboxylation) in facultative CAM plants, however, remain poorly
 understood. We investigated how nutrient and water availability affected
 competition between Mesembryanthemum crystallinum (a model facultative CAM
 species) and the invasive C3 grass Bromus mollis that co-occur in
 California's coastal grasslands. Specifically we investigated the
 extent to which water stress, nutrients, and competition affect nocturnal
 carboxylation in M. crystallinum. High nutrient and low water conditions
 favored M. crystallinum over B. mollis, in contrast to high water
 conditions. While low water conditions induced nocturnal carboxylation in
 9-week-old individuals of M. crystallinum, in these low water treatments,
 a 66% reduction in nutrient applied over the entire experiment did not
 further enhance nocturnal carboxylation. In high water conditions M.
 crystallinum both alone and in association with B. mollis did not perform
 nocturnal carboxylation, regardless of the nutrient levels. Thus,
 nocturnal carboxylation in M. crystallinum was restricted by strong
 competition with B. mollis in high water conditions. This study provides
 empirical evidence of the competitive advantage of facultative CAM plants
 over grasses in drought conditions and of the restricted ability of M.
 crystallinum to use their photosynthetic plasticity (i.e., ability to
 switch to CAM behavior) to compete with grasses in well-watered
 conditions. We suggest that a high drought tolerance could explain the
 increased dominance of facultative CAM plants in a future environment with
 increased drought and nitrogen deposition, while the potential of
 facultative CAM plants such as M. crystallinum to expand to wet
 environments is expected to be limited.
description: Nitrogen experiment
 data
DOI: 10.5061/dryad.9c31c
title: Data from: Molecular and morphological evidence of hybridization between native Ruditapes philippinarum and the introduced Ruditapes form in Japan

description: Marine aquaculture and stock enhancement are major causes of the
 introduction of alien species. A good example of such an introduction is
 the Japanese shortneck clam Ruditapes philippinarum, one of the most
 important fishery resources in the world. To meet the domestic shortage of
 R. philippinarum caused by depleted catches, clams were imported to Japan
 from China and the Korean peninsula. The imported clam is an alien species
 that has a very similar morphology, and was misidentified as R.
 philippinarum (hereafter, Ruditapes form). We genotyped 1,186 clams of R.
 philippinarum and R. form at four microsatellite loci, sequenced
 mitochondrial DNA (COI gene fragment) of 485 clams, 34 of which were R.
 variegatus, and measured morphometric and meristic characters of 754 clams
 from 12 populations in Japan and China, including the Ariake Sea and Tokyo
 Bay, where large numbers of R. form were released. Our analyses confirmed
 that R. form was from the genus Ruditapes, and the genetic differentiation
 between R. philippinarum and R. form was distinct, but small, compared
 with five bivalve outgroups. However, R. form had distinct shell
 morphology, especially larger numbers of radial ribs on the shell surface,
 suggesting that R. form might be a new Ruditapes species or a variation of
 R. philippinarum that originated from southern China. A genetic affinity
 of the sample from the Ariake Sea to R. form was found with the
 intermediate shell morphology and number of radial ribs, and the hybrid
 proportion was estimated at 51.3 ± 4.6 % in the Ariake Sea.
description: Genotypes_shell
 measurements_Manila clamThis .zip includes six
 files: genotypes and shell measurements in Excel, sequences of mtDNA COI
 for Figs. 2 and 3, and individual sequences in fast files. Haplotypes for
 R. philippinarum and R. variegatus in text files.Genotypes_and
 _molphometrics_Manila clam.zip
DOI: 10.5061/dryad.hc6bv
title: Data from: Maintenance of species boundaries in a Neotropical radiation of Begonia

description: A major goal of evolutionary biology is to determine the mechanisms
 generating biodiversity. In Begonia, one of the largest plant genera
 (1900+ species), it has been postulated that the high number of endemic
 species is a by-product of low gene flow among populations, which
 predisposes the group to speciation. However, this model of divergence
 requires that reproductive barriers accumulate rapidly among diverging
 species that overlap in their geographic ranges, otherwise speciation will
 be opposed by homogenizing gene flow in zones of secondary contact. Here,
 we test the outcomes of secondary contact in Begonia by genotyping
 multiple sympatric sites with 12 nuclear and seven plastid loci. We show
 that three sites of secondary contact between B. heracleifolia and B.
 nelumbiifolia are highly structured, mostly containing parental genotypes,
 with few F1 hybrids. A sympatric site between B. heracleifolia and B.
 sericoneura contains a higher proportion of F1s, but little evidence of
 introgression. The lack of later-generation hybrids contrasts with that
 documented in many other plant taxa, where introgression is extensive. Our
 results, in conjunction with previous genetic work, show that Begonia
 demonstrate properties making them exceptionally prone to speciation, at
 multiple stages along the divergence continuum. Not only are populations
 weakly connected by gene flow, promoting allopatric speciation, but
 species often show strong reproductive barriers in secondary contact.
 Whether similar mechanisms contribute to diversification in other large
 genera remains to be tested.
description: Raw genotype data for
 hybridization in BegoniaMicrosatellite genotypes
 in 2-column format. Missing data denoted with
 '-1'.Twyford et al (2015)
 Microsatellite raw genotypes for
 Dryad.csvSimulated genotypes for
 an artificial Begonia heracleifolia x B. nelumbiifolia hybrid
 swarmGenotypic data in
 GenePop file format. Missing data denoted by
 '000'.FileS2_Simulated_B_heracleifolia_x_B_nelumbiifolia.txtSimulated genotypes for an artificial Begonia heracleifolia x B. sericoneura hybrid swarmGenotypic data in GenePop file format. Missing data denoted by '000'.FileS3_Simulated_B_heracleifolia_x_B_sericoneura.txt
DOI: 10.5061/dryad.6f5kh38
title: Data from: Hybrid chickadees are deficient in learning and memory

description: Identifying the phenotypes underlying postzygotic reproductive isolation
 is crucial for fully understanding the evolution and maintenance of
 species. One potential postzygotic isolating barrier that has rarely been
 examined is learning and memory ability in hybrids. Learning and memory
 are important fitness-related traits, especially in scatter-hoarding
 species, where accurate retrieval of hoarded food is vital for winter
 survival. Here, we test the hypothesis that learning and memory ability
 can act as a postzygotic isolating barrier by comparing these traits among
 two scatter-hoarding songbird species, black-capped (Poecile
 atricapillus), Carolina chickadees (Poecile carolinensis), and their
 naturally occurring hybrids. In an outdoor aviary setting, we find that
 hybrid chickadees perform significantly worse on an associative learning
 spatial task and are worse at solving a novel problem compared to both
 parental species. Deficiencies in learning and memory abilities could
 therefore contribute to postzygotic reproductive isolation between
 chickadee species. Given the importance of learning and memory for
 fitness, our results suggest that these traits may play an important, but
 as yet overlooked, role in postzygotic reproductive isolation.
description: ProblemSolvingContains behavioral data for the novel problem-solving task.AssociativeLearningSpatialTaskContains behavioral data for the associative learning spatial task.BodyConditionContains morphological data used to calculate and compare the scaled mass index (a measure of body condition).R.ScriptsThis file contains representative R scripts used to analyze behavioral and morphological data.Dryad.Scripts.RRead_MeThis read-me file contains detailed descriptions of all data and script files accompanying this manuscript.Structure_InputThis is an input file for the program STRUCTURE, and contains multi-locus genotypes for chickadees collected across the hybrid zone in Pennsylvania.
DOI: 10.5061/dryad.56f4160
title: Data from: Multiple anthropogenic interventions drive puma survival following wolf recovery in the Greater Yellowstone Ecosystem

description: Humans are primary drivers of declining abundances and extirpation of
 large carnivores worldwide. Management interventions to restore
 biodiversity patterns, however, include carnivore reintroductions, despite
 the many unresolved ecological consequences associated with such efforts.
 Using multistate capture-mark-recapture models, we explored age-specific
 survival and cause-specific mortality rates for 134 pumas (Puma concolor)
 monitored in the Greater Yellowstone Ecosystem during gray wolf (Canis
 lupus) recovery. We identified two top models explaining differences in
 puma survivorship, and our results suggested three management
 interventions (unsustainable puma hunting, reduction of a primary prey,
 reintroduction of a dominant competitor) have unintentionally impacted
 puma survival. Specifically, puma survival across age classes was lower in
 the 6-month hunting season than the 6-month non-hunting season;
 human-caused mortality rates for juveniles and adults, and predation rates
 on puma kittens, were higher in the hunting season. Predation on puma
 kittens, and starvation rates for all pumas, also increased as managers
 reduced elk (Cervus elaphus) abundance in the system, highlighting direct
 and indirect effects of competition between recovering wolves and pumas
 over prey. Our results emphasize the importance of understanding the
 synergistic effects of existing management strategies and the recovery of
 large, dominant carnivores to effectively conserve subordinate, hunted
 carnivores in human-dominated landscapes.
description: Elbrochetal_PumaData_forCMRPuma binary data--detected or not, and cause specific mortality codes. Kitten/litter codes. All data at 3-month intervals.