cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v1t86
title: Data from: Promiscuous mating in the harem-roosting fruit bat, Cynopterus sphinx

description: Observations on mating behaviours and strategies guide our understanding
 of mating systems and variance in reproductive success. However, the
 presence of cryptic strategies often results in situations where social
 mating system is not reflective of genetic mating system. We present such
 a study of the genetic mating system of a harem-forming bat Cynopterus
 sphinx where harems may not be true indicators of male reproductive
 success. This temporal study using data from six seasons on paternity
 reveals that social harem assemblages do not play a role in the mating
 system, and variance in male reproductive success is lower than expected
 assuming polygynous mating. Further, simulations reveal that the genetic
 mating system is statistically indistinguishable from promiscuity. Our
 results are in contrast to an earlier study that demonstrated high
 variance in male reproductive success. Although an outcome of behavioural
 mating patterns, standardized variance in male reproductive success (I_m)
 affects the opportunity for sexual selection. To gain a better
 understanding of the evolutionary implications of promiscuity for mammals
 in general, we compared our estimates of I_m and total opportunity for
 sexual selection (I_m/I_f, where I_f is standardized variance in female
 reproductive success) with those of other known promiscuous species. We
 observed a broad range of I_m/I_f values across known promiscuous species,
 indicating our poor understanding of the evolutionary implications of
 promiscuous mating.
description: Genotype
 fileThe file contains
 details on the age, sex, season of capture and the microsatellite
 genotypes used for the paternity analysis.data_dryad.xlsx
DOI: 10.5061/dryad.rg22r
title: Data from: Neutral genetic variation in adult Chinook salmon (Oncorhynchus tshawytscha) affects brain-to-body trade-off and brain laterality

description: Low levels of heterozygosity can have detrimental effects on life history
 and growth characteristics of organisms but more subtle effects such as
 those on trade-offs of expensive tissues and morphological laterality,
 especially of the brain, have not been explicitly tested. The objective of
 the current study was to investigate how estimated differences in
 heterozygosity may potentially affect brain-to-body trade-offs and to
 explore how these heterozygosity differences may affect differential brain
 growth, focusing on directional asymmetry in adult Chinook salmon
 (Oncorhynchus tshawytscha) using the laterality and absolute laterality
 indices. Level of inbreeding was estimated as mean microsatellite
 heterozygosity resulting in four ‘inbreeding level groups’ (Very High,
 High, Medium, Low). A higher inbreeding level corresponded with a
 decreased brain-to-body ratio, thus a decrease in investment in brain
 tissue, and also showed a decrease in the laterality index for the
 cerebellum, where the left hemisphere was larger than the right across all
 groups. These results begin to show the role that differences in
 heterozygosity may play in differential tissue investment and in
 morphological laterality, and may be useful in two ways. Firstly, the
 results may be valuable for restocking programmes that wish to emphasize
 brain or body growth when crossing adults to generate individuals for
 release, as we show that genetic variation does affect these trade-offs.
 Secondly, this study is one of the first examinations to test the
 hypothesized relationship between genetic variation and laterality,
 finding that in Chinook salmon there is potential for an effect of
 inbreeding on lateralized morphology, but not in the expected direction.
description: Wiper et al. - Data -
 HeterozygosityHerein contains the
 genotype information (allele sizes) for 10 polymorphic microsatellite
 markers used to obtain the heterozygosity estimates outlined in the
 manuscript.Wiper et al. - Data -
 Morphology and LateralityThe attached excel file
 contains all data used to calculate somatic trade-off and laterality
 differences of two brain regions (optic tectum and cerebellum) between our
 four inbreeding level groups, as outlined in the
 manuscript.
DOI: 10.5061/dryad.3ng5c
title: Data from: Phenotype-environment matching in sand fleas

description: Camouflage is perhaps the most widespread anti-predator strategy in
 nature, found in numerous animal groups. A long-standing prediction is
 that individuals should have camouflage tuned to the visual backgrounds
 where they live. However, while several studies have demonstrated
 phenotype–environment associations, few have directly shown that this
 confers an improvement in camouflage, particularly with respect to
 predator vision. Here, we show that an intertidal crustacean, the sand
 flea (Hippa testudinaria), has coloration tuned to the different
 substrates on which it occurs when viewed by potential avian predators.
 Individual sand fleas from a small, oceanic island (Ascension) matched the
 colour and luminance of their own beaches more closely than neighbouring
 beaches to a model of avian vision. Based on past work, this
 phenotype–environment matching is likely to be driven through ontogenetic
 changes rather than genetic adaptation. Our work provides some of the
 first direct evidence that animal coloration is tuned to provide
 camouflage to prospective predators against a range of visual backgrounds,
 in a population of animals occurring over a small geographical range.
description: sand flea
 dataData on sand fleas and
 substrate
DOI: 10.5061/dryad.d2f5b
title: Data from: Crater lake habitat predicts morphological diversity in adaptive radiations of cichlid fishes

description: Adaptive radiations provide an excellent opportunity for studying the
 correlates and causes for the origin of biodiversity. In these radiations,
 species diversity may be influenced by either the ecological and physical
 environment, intrinsic lineage effects, or both. Disentangling the
 relative contributions of these factors in generating biodiversity remains
 a major challenge in understanding why a lineage does or does not radiate.
 Here, we examined morphological variation in body shape for replicate
 flocks of Nicaraguan Midas cichlid fishes and tested its association with
 biological and physical characteristics of their crater lakes. We found
 that variability of body elongation, an adaptive trait in freshwater
 fishes, is mainly predicted by average lake depth (N = 6, P &lt;
 0.001, R2 = 0.96). Other factors considered, including lake age, surface
 area, littoral zone area, number of co-occurring fish species, and genetic
 diversity of the Midas flock, did not significantly predict morphological
 variability. We also showed that lakes with a larger littoral zone have on
 average higher bodied Midas cichlids, indicating that Midas cichlid flocks
 are locally adapted to their crater lake habitats. In conclusion, we found
 that a lake's habitat predicts the magnitude and the diversity of
 body elongation in repeated cichlid adaptive radiations.
description: Individual body
 elongation DataIndividual data includes
 the identification number (ID), lake of origin, species name and the
 measurements standard length (SL), body depth (BD), and the ratio of body
 depth and standard length (BD/SL).raw_data_for_Dryad.xlsx
DOI: 10.5061/dryad.k43k4
title: Data from: Hybridization between genetically modified Atlantic salmon and wild brown trout reveals novel ecological interactions

description: Interspecific hybridization is a route for transgenes from genetically
 modified (GM) animals to invade wild populations, yet the ecological
 effects and potential risks that may emerge from such hybridization are
 unknown. Through experimental crosses, we demonstrate transmission of a
 growth hormone transgene via hybridization between a candidate for
 commercial aquaculture production, GM Atlantic salmon (Salmo salar), and
 closely related wild brown trout (S. trutta). Transgenic hybrids were
 viable and grew more rapidly than transgenic salmon and other
 non-transgenic crosses in hatchery-like conditions. In stream mesocosms
 designed to more closely emulate natural conditions, transgenic hybrids
 appeared to express competitive dominance and suppressed the growth of
 transgenic and non-transgenic (wild-type) salmon by 82% and 54%,
 respectively. To the best of our knowledge, this is the first
 demonstration of environmental impacts of hybridization between a GM
 animal and a closely related species. These results provide empirical
 evidence of the first steps towards introgression of foreign transgenes
 into the genomes of new species and contribute to the growing evidence
 that transgenic animals have complex and context-specific interactions
 with wild populations. We suggest that interspecific hybridization be
 explicitly considered when assessing the environmental consequences should
 transgenic animals escape to nature.
description: Oke et al._dryad
 dataGrowth and survival data
 for Oke et al.
DOI: 10.5061/dryad.86fr4
title: Data from: DNA sequencing of fish eggs and larvae reveals high species diversity and seasonal changes in spawning activity in the southeastern Gulf of California

description: Ichthyoplankton studies can provide valuable information on the species
 richness and spawning activity of fishes, complementing estimations done
 using trawls and diver surveys. Zooplankton samples were collected weekly
 between January and December 2014 in Cabo Pulmo National Park, Gulf of
 California, Mexico (n=48). Fish larvae and particularly eggs are difficult
 to identify morphologically, therefore the DNA barcoding method was
 employed to identify 4,388 specimens, resulting in 158 Operational
 Taxonomic Units (OTUs) corresponding to species. Scarus sp., Halichoeres
 dispilus, Xyrichtys mundiceps, Euthynnus lineatus, Ammodytoides gilli,
 Synodus lacertinus, Etrumeus acuminatus, Chanos chanos, Haemulon
 flaviguttatum, and Vinciguerria lucetia were the most abundant and
 frequent species recorded. Noteworthy species identified include rare
 mesopelagic species such as the giant oarfish (Regalecus glesne) and
 highly migratory and commercially important species such as black skipjack
 (Euthynnus lineatus) and yellowfin tuna (Thunnus albacares). Spawning
 activities showed distinct seasonal patterns with the highest abundance of
 ichthyoplankton recorded during spring, highest species richness during
 summer (90 OTUs) and lowest species richness during winter (28 OTUs). A
 total of seven OTUs were recorded throughout the year (4%), 11 OTUs during
 three seasons (7%), 36 OTUs in two seasons (23%) and 106 OTUs were
 recorded in only one season (66%). The study found eggs and/or larvae of
 47 species that were not previously reported in Cabo Pulmo National Park.
 Results allow resource managers to compare shifting populations and
 spawning patterns of species that may be affected by both conservation
 efforts and broader oceanographic changes associated with climate change.
description: FASTA_CP_IchthyoplanktonRaw (unedited) Sanger sequences (COI and 16S) obtained from ichthyoplankton collected from Cabo Pulmo National Park (Jan 2014- Dec 2014). Organized in rows by sequence ID.
DOI: 10.5061/dryad.6c7p5
title: Data from: Historical environment is reflected in modern population genetics and biogeography of an island endemic lizard (Xantusia riversiana reticulata)

description: The restricted distribution and isolation of island endemics often
 produces unique genetic and phenotypic diversity of conservation interest
 to management agencies. However, these isolated species, especially those
 with sensitive life history traits, are at high risk for the adverse
 effects of genetic drift and habitat degradation by non-native wildlife.
 Here, we study the population genetic diversity, structure, and stability
 of a classic “island giant” (Xantusia riversiana, the Island Night Lizard)
 on San Clemente Island, California following the removal of feral goats.
 Using DNA microsatellites, we found that this population is reasonably
 genetically robust despite historical grazing, with similar effective
 population sizes and genetic diversity metrics across all sampling
 locations irrespective of habitat type and degree of degradation. However,
 we also found strong site-specific patterns of genetic variation and low
 genetic diversity compared to mainland congeners, warranting continued
 special management as an island endemic. We identify both high and low
 elevation areas that remain valuable repositories of genetic diversity and
 provide a case study for other low-dispersal coastal organisms in the face
 of future climate change.
description: X. riversiana
 microsatellite genotypesMicrosatellite genotypes
 for Xantusia riversiana for the publication "Historical environment
 is reflected in modern population genetics and biogeography of an island
 endemic lizard (Xantusia riversiana reticulata)"Xriv_usat_dryad.csv
DOI: 10.5061/dryad.k5k3n
title: Data from: The biogeography of sodium in Neotropical figs (Moraceae)

description: Sodium is essential for animals but not for most plants. Terrestrial
 sodium comes largely from marine aerosols, so inland ecosystems should
 have greater potential for sodium limitation than coastal ecosystems. We
 report a significant decrease of sodium in fruits of four Neotropical
 Ficus species with distance from presumed marine source.
description: Mineral content in four
 Neotropical Ficus species fruitsInformation on specimens
 of four Ficus species including herbarium, locality, collector and
 specimen number, year of collection, distance of collection locality to
 the nearest effective marine sodium source, nearest effective marine
 sodium source, georeferenced locality (lat. and long.), and concentration
 of twelve minerals (Na, Al, Bo, Ca, Cu, Fe, Mg, Mn, P, K, S, Zn) found in
 each Ficus fruit specimen.Tabla S1 Bravo & Harms
 2016.xlsx
DOI: 10.5061/dryad.j5240
title: Data from: Nuclear markers reveal a complex introgression pattern among marine turtle species on the Brazilian coast

description: A surprisingly high frequency of interspecific sea turtle hybrids have
 been previously recorded in a nesting site along a short stretch of the
 Brazilian coast. Mitochondrial DNA data indicated that as much as 43% of
 the females identified as E. imbricata are hybrids in this area (Bahia
 State of Brazil). It is a remarkable find, since most of the nesting sites
 surveyed worldwide, including some in northern Brazil, presents no
 hybrids, and rare Caribbean sites present no more than 2% of hybrids.
 Thus, a detailed understanding of the hybridization process is needed to
 evaluate natural or anthropogenic causes of this regional phenomenon in
 Brazil, which could be an important factor affecting the conservation of
 this population. We analyzed a set of 12 nuclear markers to investigate
 the pattern of hybridization involving three species of sea turtles:
 hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), and
 olive ridley (Lepidochelys olivacea). Our data indicate that most of the
 individuals in the crossings L. olivacea × E. imbricata and L. olivacea ×
 C. caretta are F1 hybrids, whereas C. caretta × E. imbricata crossings
 present F1 and backcrosses with both parental species. In addition, the C.
 caretta × E. imbricata hybridization seems to be gender and species
 biased, and we also found one individual with evidence of multispecies
 hybridization among C. caretta × E. imbricata × Chelonia mydas. The
 overall results also indicate that hybridization in this area is a recent
 phenomenon, spanning at least two generations or ~40 years.
description: BDNF fasta
 alignmentAlignments of BDNF gene.
 Sequences are identified as haplotype number (see article text for more
 details) and GenBank number.BDNF.fasCmos fasta alignmentAlignment of Cmos gene. Sequences are identified as haplotype number (see article text for more details) and GenBank number.Cmos.fasR35 fasta alignmentAlignment of R35 intron. Sequences are identified as haplotype number (see article text for more details) and GenBank number.R35.fasRag1 fasta alignmentAlignments of Rag1 gene. Sequences are identified as haplotype (see article text for more details) and GenBank number.Rag1.fasRag2 fasta alignmentAlignments of Rag2 gene. Sequences are identified as haplotype (see article text for more details) and GenBank number.Rag2.fasIndividual-by-individual sequence informationThe table describes which GenBank accessions numbers came from each individual (smaller database, see article's SI Tab3).individual-by-individual sequence information .xls
DOI: 10.5061/dryad.0g794
title: Data from: Sensitivity of the farmland bird community to crop diversification in Sweden: does the CAP fit?

description: Crop diversification has been introduced as an environmental strategy in
 the ‘Greening’ of the EU Common Agricultural Policy (CAP) for 2015–2020.
 The primary target of crop diversification is soil and ecosystem
 resilience, but claims for potential benefits for farmland biodiversity
 are also common. However, understanding of relationships between the
 number (compositional heterogeneity) and spatial arrangement
 (configurational heterogeneity) of crop fields and biodiversity is
 generally poor, making such claims relatively unfounded. In this study, we
 monitored crop and farmland bird diversity on 178 farms across
 Sweden's main agricultural areas. From a pre-implementation
 assessment, we show that &gt;97% of the assessed farms would not be
 required to change their management under the CAP crop diversification
 measure (minimum of three crops for farms with 30+ ha), suggesting that
 this measure has generated little change on Swedish farms. While
 accounting for non-crop elements and farming system (conventional or
 organic), we show that crop structural diversity (i.e. the management and
 vegetation structure of crops) rather than crop diversity senso lato
 positively affected richness of non-crop breeding bird species with
 stronger effects in arable, compared with forest-dominated landscapes. No
 such effects were observed among field-nesting farmland bird species.
 Organic farming had little influence on farmland birds with positive
 effects only in the most arable-dominated landscapes and for field-nesting
 species only. In forest-dominated landscapes, organic farms even held
 lower field-nester densities compared with conventional farms, possibly
 due to the dominance of grasslands on organic farms that in these
 landscapes support lower densities of field-nesting species compared with
 cereals. Policy implications. Our study illustrates the importance of a
 consideration of structural instead of species diversity of crops for
 biodiversity, in this case farmland birds. We also underline the absence
 of such a distinction in current EU Common Agricultural Policy Greening,
 while simultaneously setting levels on crop diversification too low
 resulting in little to no change in landscape-scale crop diversity on
 Swedish farmland. We recommend that future efforts to manage farmland
 biodiversity should include ways of increasing the structural diversity of
 crops at the scale of farms and landscapes.
description: Complete data
 setFarmland bird inventory
 data (species richness and abundance) was collected through the Swedish
 Volunteer & Farmer Alliance. A Read me, including explanations for
 each column, is found in the second tab of the
 xlsx-file.Josefssonetal_farmlandbird-data.xlsx
DOI: 10.5061/dryad.v7t4q
title: Data from: Plant, soil and microbial controls on grassland diversity restoration: a long-term, multi-site mesocosm experiment

description: The success of grassland biodiversity restoration schemes is determined by
 many factors; as such their outcomes can be unpredictable. There is a need
 for improved understanding of the relative importance of belowground
 factors to restoration success, such as contrasting soil type and
 management intensities, as well as plant community composition and order
 of assembly. We carried out an eight-year mesocosm experiment across three
 locations in the UK to explore the relative and interactive roles of
 various aboveground and belowground factors in the establishment of target
 species, to determine general constraints on grassland restoration. Each
 location had a series of mesocosms with contrasting soil types and
 management status, which were initially sown with six grasses typical of
 species-poor grasslands targeted for restoration. Over five years, sets of
 plant species were added, to test how different vegetation treatments,
 including early-coloniser species and the hemiparasite Rhinanthus minor,
 and soil type and management, influenced the establishment of target plant
 species and community diversity. The addition of early-coloniser species
 to model grasslands suppressed the establishment of target species,
 indicating a strong priority effect. Soil type was also an important
 factor, but effects varied considerably across locations. In the absence
 of early-coloniser species, low soil nutrient availability improved
 establishment of target species across locations, although R. minor had no
 beneficial effect. Synthesis and applications. Our long-term, multi-site
 study indicates that successful restoration of species rich grassland is
 dependent primarily on priority effects, especially in the form of
 early-coloniser species that suppress establishment of slow-growing target
 species. We also show that priority effects vary with soil conditions,
 being stronger in clay than sandy soils, and on soils of high nutrient
 availability. As such, our work emphasises the importance of considering
 priority effects and local soil conditions in developing management
 strategies for restoring plant species diversity in grassland.
description: 2005 all
 dataThis file contains all
 data used in the 2005 analyses for the paper. It lists pot and treatment
 details, and biomass, chemistry and microbial data.2011 all
 dataThis file contains all
 data from the 2011 analyses including pot and treatment ID, biomass,
 chemistry and microbial data. See Readme file attached to the 2005 data
 for more details.