cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.57kg0
title: Data from: Sex-chromosome recombination in common frogs brings water to the fountain-of-youth

description: According to the canonical model of sex-chromosome evolution, the
 degeneration of Y or W chromosomes (as observed in mammals and birds
 respectively) results from an arrest of recombination in the heterogametic
 sex, driven by the fixation of sexually antagonistic mutations. However,
 sex chromosomes have remained homomorphic in many lineages of fishes,
 amphibians, and non-avian reptiles. According to the ‘fountain-of-youth’
 model, this homomorphy results from occasional events of sex reversal. If
 recombination arrest in males is controlled by maleness per se (and not by
 genotype), then Y chromosomes are expected to recombine in XY females,
 preventing their long-term degeneration. Here we provide field support for
 the fountain-of-youth, by showing that sex-chromosome recombination in
 Rana temporaria only depends on phenotypic sex: naturally-occurring XX
 males show the same restriction of recombination as XY males (average map
 length ~2 cM), while XY females recombine as much as XX females (average
 map length ~150 cM). Our results challenge several common assumptions
 regarding the evolution of sex chromosomes, including the role of sexually
 antagonistic genes as drivers of recombination arrest, and that of
 chromosomal inversions as underlying mechanisms.
description: Table
 S1Raw
 genotypes of 15 families, including parents and offspring, at 12 anonymous
 microsatellite loci and 4 length polymorphisms at
 Dmrt1.
DOI: 10.5061/dryad.658433g
title: Data from: Controlled feeding experiments with diets of different abrasiveness reveal slow development of mesowear signal in goats (Capra aegagrus hircus)

description: Dental mesowear is applied as a proxy to determine the general diet of
 mammalian herbivores based on tooth-cusp shape and occlusal relief. Low,
 blunt cusps are considered typical for grazers and high, sharp cusps
 typical for browsers. However, how internal or external abrasives impact
 mesowear, and the time frame the wear signature takes to develop, still
 need to be explored. Four different pelleted diets of increasing
 abrasiveness (lucerne, grass, grass and rice husks, grass, rice husks and
 sand) were fed to four groups of a total of 28 adult goats in a controlled
 feeding experiment over a six-month period. Tooth morphology was captured
 by medical CT scans at the beginning and end of the experiment. These
 scans, as well as the crania obtained postmortem, were scored using the
 mesowear method. Comparisons between diet groups only showed few
 significant differences after six months, irrespective of whether CT scans
 or the real teeth were scored. Only when assessing the difference in
 signal between start and end did relevant, significant diet-specific
 effects emerge. Diets containing lower phytolith content caused a more
 pronounced change in mesowear towards sharper cusps/higher reliefs, while
 the feed containing sand did not result in more extreme changes in
 mesowear when compared to the same feed without sand. Our experiment
 suggests that the formation of a stable and hence reliable mesowear signal
 requires more time to develop than six months.
description: Original data
 supplementExcel file containing
 the original data for all individualsMC_SupplementOriginalData_180831_na.xlsx
DOI: 10.5061/dryad.5fr85
title: Data from: Do differences in food web structure between organic and conventional farms affect the ecosystem service of pest control?

description: While many studies have demonstrated that organic farms support greater
 levels of biodiversity, it is not known whether this translates into
 better provision of ecosystem services. Here we use a food-web approach to
 analyse the community structure and function at the whole-farm scale.
 Quantitative food webs from 10 replicate pairs of organic and conventional
 farms showed that organic farms have significantly more species at three
 trophic levels (plant, herbivore and parasitoid) and significantly
 different network structure. Herbivores on organic farms were attacked by
 more parasitoid species on organic farms than on conventional farms.
 However, differences in network structure did not translate into
 differences in robustness to simulated species loss and we found no
 difference in percentage parasitism (natural pest control) across a
 variety of host species. Furthermore, a manipulative field experiment
 demonstrated that the higher species richness of parasitoids on the
 organic farms did not increase mortality of a novel herbivore used to
 bioassay ecosystem service. The explanation for these differences is
 likely to include inherent differences in management strategies and
 landscape structure between the two farming systems.
description: Plant_20farms_0506Plant species recorded on 20 farmsPlant_Herb_Int_20farms_0506Interactions between plants and insect herbivores on 20 farmsHerb_Para_Int_20farms_0506Data on insect herbivore and parasitoid interactions on 20 farms.
DOI: 10.5061/dryad.r1538
title: Data from: Multilocus genetic diversity and historical biogeography of the endemic wall lizard from Ibiza and Formentera, Podarcis pityusensis (Squamata: Lacertidae)

description: Two monophyletic sister species of wall lizards inhabit the two main
 groups of Balearic Islands: Podarcis lilfordi from islets and small
 islands around Mallorca and Menorca and Podarcis pityusensis from Ibiza,
 Formentera and associated islets. Genetic diversity within the endangered
 P. lilfordi has been well characterized, but P. pityusensis has not been
 studied in depth. Here, 2430 bp of mtDNA and 15 microsatellite loci were
 analysed from P. pityusensis populations from across its natural range.
 Two main genetic groupings were identified, although geographical
 structuring differed slightly between the mtDNA and the nuclear loci. In
 general, individuals from islets/islands adjacent to the main island of
 Ibiza were genetically distinct from those from Formentera and the
 associated Freus islands for both mtDNA and the nuclear loci. However,
 most individuals from the island of Ibiza were grouped with neighbouring
 islets/islands for nuclear loci, but with Formentera and Freus islands for
 the mitochondrial locus. A time-calibrated Bayesian tree was constructed
 for the principal mitochondrial lineages within the Balearics, using the
 multispecies coalescent model, and provided statistical support for
 divergence of the two main P. pityusensis lineages 0.111–0.295 Ma. This
 suggests a mid-late Pleistocene intraspecific divergence, compared with an
 early Pleistocene divergence in P. lilfordi, and postdates some major
 increases in sea level between 0.4 and 0.6 Ma, which may have flooded
 Formentera. The program IMa2 provided a posterior divergence time of
 0.089–0.221 Ma, which was similar to the multispecies coalescent tree
 estimate. More significantly, it indicated low but asymmetric effective
 gene copy migration rates, with higher migration from Formentera to Ibiza
 populations. Our findings suggest that much of the present-day diversity
 may have originated from a late Pleistocene colonization of one island
 group from the other, followed by allopatric divergence of these
 populations. Subsequent gene flow between these insular groups seems
 likely to be explained by recent human introductions. Two evolutionary
 significant units can be defined for P. pityusensis but these units would
 need to exclude the populations that have been the subjects of recent
 admixture.
description: IMa2 input file (mtDNA
 and STRs)Sample input file for
 IMa2 analysis of two geographical populations from P. pityusensis with 16
 loci (2430 bp mtDNA sequence and 15 STRs).IMa2 input
 file.u
DOI: 10.5061/dryad.3p4v855
title: Data from: Estimating the number of sexual events per generation in a facultatively sexual haploid population

description: In populations of facultatively sexual organisms the proportion of
 sexually produced offspring contributed each generation is a critical
 determinant of their evolutionary potential. However, estimating this
 parameter in natural populations has proved difficult. Here we develop a
 population genetic model for estimating the number of sexual events
 occurring per generation for facultatively sexual haploids possessing a
 biallelic mating type locus (e.g. Chlamydomonas, ascomycete fungi). Our
 model treats the population as two subpopulations possessing opposite
 mating type alleles which exchange genes only when a sexual event takes
 place. Where mating types are equally abundant we show that, for a neutral
 genetic marker, genetic differentiation between mating type subpopulations
 is a simple function of the effective population size, the frequency of
 sexual reproduction and the recombination fraction between the genetic
 marker and the mating type locus. We employ simulations to examine the
 effects of linkage of markers to the mating type locus, inequality of
 mating type frequencies, mutation rate and selection on this relationship.
 Finally we apply our model to estimate the number of sexual reproduction
 events per generation in populations of four species of facultatively
 sexual ascomycete fungi which have been jointly scored for mating type and
 a range of polymorphic molecular markers. Relative estimates of are in
 line with expectations based on the known reproductive biology of these
 species.
description: C script used in
 simulationsFile contains the C
 scripts for three models used to simulated the behaviour of Fst between
 mating type subpopulations and LD between marker and mating type loci in
 haploid populations where there is 1. No selection, 2. Constant selection
 and 3. Stochastic selection on marker loci.Oregon early 1990
 Zymoseptoria tritici RFLP dataFile contains joint
 mating type and RFLP genotypes for Zymoseptoria tritici samples collected
 in Oregon early in 1990Oregon late 1990
 Zymoseptoria tritici RFLP dataContains joint mating
 type and RFLP genotypes of Zymoseptoria tritici isolates collected late in
 1990 in Oregon.VA 2009 Erisiphe necator
 microsatellite dataContains joint mating
 type and microsatellite genotypes of Erisiphe necator isolates collected
 late in 2009 in Virginia.VA 2010 Erisiphe necator
 microsatellite dataContains joint mating
 type and microsatellite genotypes of Erisiphe necator isolates collected
 early in 2010 in Virginia.Australia Rhyncosporium
 secalis microsatellite dataContains joint mating
 type and microsatelite genotypes of Rhyncosporium secalis isolates
 collected in Australia.Norway Rhyncosporium
 secalis microsatellite dataContains joint mating
 type and microsatelite genotypes of Rhyncosporium secalis isolates
 collected in Norway.Dothistroma septosporum
 microsatellite dataContains joint mating
 type and microsatelite genotypes of Dothistroma septosporum isolates
 collected in Scotland.
DOI: 10.5061/dryad.q7nf0
title: Data from: Fluctuating asymmetry in Menidia beryllina before and after the 2010 DeepWater Horizon oil spill

description: Assessing the impacts of the Deepwater Horizon oil spill with a dependable
 baseline comparison can provide reliable insight into environmental
 stressors on organisms that were potentially affected by the spill.
 Fluctuating asymmetry (small, non-random deviations from perfect bilateral
 symmetry) is an informative metric sensitive to contaminants that can be
 used to assess environmental stress levels. For this study, the
 well-studied and common Gulf of Mexico estuarine fish, Menidia beryllina,
 was used with pre and post-oil spill collections. Comparisons of
 fluctuating asymmetry in three traits (eye diameter, pectoral fin length,
 and pelvic fin length) were made pre and post-oil spill across two sites
 (Old Fort Bayou and the Pascagoula River), as well as between years of
 collection (2011, 2012)-one and two years, respectfully, after the spill
 in 2010. We hypothesized that fluctuating asymmetry would be higher in
 post-Deepwater Horizon samples, and that this will be replicated in both
 study areas along the Mississippi Gulf coast. We also predicted that
 fluctuating asymmetry would decrease through time after the oil spill as
 the oil decomposed and/or was removed. Analyses performed on 1135 fish
 (220 pre and 915 post Deepwater Horizon) showed significantly higher post
 spill fluctuating asymmetry in the eye but no difference for the pectoral
 or pelvic fins. There was also higher fluctuating asymmetry in one of the
 two sites both pre and post-spill, indicating observed asymmetry may be
 the product of multiple stressors. Fluctuating asymmetry decreased in 2012
 compared to 2011. Fluctuating asymmetry is a sensitive measure of sub
 lethal stress, and the observed variability in this study (pre vs.
 post-spill or between sites) could be due to a combination of oil,
 dispersants, or other unknown stressors.
description: M. beryllina data for FA
 analysisMorphological
 measurements for fluctuating asymmetry analysis of Menidia beryllina
 before and after the Deepwater Horizon Oil spill.Michaelsen_et_al_FA.csv
DOI: 10.5061/dryad.7g902
title: Data from: The ichnogenus Tubotomaculum: an enigmatic pellet-filled structure from Upper Cretaceous to Miocene deep-marine deposits of southern Spain

description: The trace-fossil name Tubotomaculum has been extensively used to refer to
 spindle-shaped pellet-filled tubes present in Upper Cretaceous to Miocene
 deep-marine deposits of the western Mediterranean region. However, it has
 never been formally diagnosed, and accordingly it was regarded as a nomen
 nudum. In this paper, we formally introduce the ichnogenus Tubotomaculum,
 including the new ichnospecies Tubotomaculum mediterranensis. Bioglyphs,
 represented by scratch traces that may be present on the basal and lateral
 surfaces of the structure, suggesting production by crustaceans. The
 functional meaning of these structures challenges the simple model of a
 mining strategy. Instead, the storing of pellets to use them as a
 bacteria-enriched resource during times when organic detritus was scarce
 is suggested. The association with chemoautothrophic bacteria in modern
 analogs of Tubotomaculum provides a crucial piece of evidence to support
 the cache model. Integration of information from modern environments and
 the fossil record points to a connection between Tubotomaculum, mud
 volcanism, fluid venting, and hydrocarbon seeps. The presence of bioglyphs
 suggests firmgrounds that may have resulted from bottom current scouring
 of the sea sediment, leading to erosional exhumation of previously buried
 compacted sediment, which was therefore available for colonization by the
 infauna. However, an alternative scenario involves enriched fluids related
 to mud-volcanism resulting in reducing conditions that favored carbonate
 precipitation and nodule formation just a few centimeters below the
 sediment-water interface.
description: 2250_1_supp_0_my0clfMangano Supplemental Data1Mangano Supplemental Data2
DOI: 10.5061/dryad.6gj58
title: Data from: Predation on feather stars by regular echinoids as evidenced by laboratory and field observations and its paleobiological implications

description: Among extant crinoids, the feather stars are the most diverse and occupy
 the greatest bathymetric range, being especially common in reef
 environments. Feather stars possess a variety of morphological, behavioral
 and physiological traits that have been hypothesized to be critical to
 their success, especially in their ability to cope with predation.
 However, knowledge of their predators is exceptionally scant, consisting
 primarily of circumstantial evidence of attacks by fishes. In this study
 the question whether regular echinoids, recently shown to consume stalked
 crinoids, also consume feather stars is explored. Aquarium observations
 indicate that regular echinoids find feather stars palatable, including
 feather stars known to be distasteful to fish, and that regular echinoids
 can capture and eat live feather stars, including those known to swim.
 Gut-content analyses of the echinoid Araeosoma fenestratum (Thomson,
 1872), which is commonly observed with large populations of the feather
 star Koehlermetra porrecta (Carpenter, 1888) in video transects from
 marine canyons off the coast of France, revealed elements of feather stars
 in the guts of 6 of 13 individuals. The high proportion of crinoid
 material (up to 90%), and the presence of articulated crinoid skeletal
 elements in the gut of A. fenestratum, suggest that these echinoids
 consumed at least some live crinoids, although they may have also ingested
 some postmortem remains found in the sediment. Additionally, photographic
 evidence from the northeast Atlantic suggests that another regular
 echinoid, Cidaris cidaris (Linnaeus, 1758), preys on feather stars. Thus
 in spite of the broad suite of antipredatory adaptations, feather stars
 are today subject to predation by regular echinoids and may have been
 since the Mesozoic, when this group of crinoids first appeared.
description: Supplementary Table
 1Summary of echinoids
 collected during sampling campaign.Supplementary Table
 2Gut
 content of all specimens (excluding A. fenestratum) collected in Ireland
 and France. NA – Not applicable; guts absent due to damage upon
 ascent.
DOI: 10.5061/dryad.p2d8h
title: Data from: Broad-scale genetic diversity of Cannabis for forensic applications

description: Cannabis (hemp and marijuana) is an iconic yet controversial crop. On the
 one hand, it represents a growing market for pharmaceutical and
 agricultural sectors. On the other hand, plants synthesizing the
 psychoactive THC produce the most widespread illicit drug in the world.
 Yet, the difficulty to reliably distinguish between Cannabis varieties
 based on morphological or biochemical criteria impedes the development of
 promising industrial programs and hinders the fight against
 narcotrafficking. Genetics offers an appropriate alternative to
 characterize drug vs. non-drug Cannabis. However, forensic applications
 require rapid and affordable genotyping of informative and reliable
 molecular markers for which a broad-scale reference database, representing
 both intra- and inter-variety variation, is available. Here we provide
 such a resource for Cannabis, by genotyping 13 microsatellite loci (STRs)
 in 1 324 samples selected specifically for fibre (24 hemp varieties) and
 drug (15 marijuana varieties) production. We showed that these loci are
 sufficient to capture most of the genome-wide diversity patterns recently
 revealed by NGS data. We recovered strong genetic structure between
 marijuana and hemp and demonstrated that anonymous samples can be
 confidently assigned to either plant types. Fibres appear genetically
 homogeneous whereas drugs show low (often clonal) diversity within
 varieties, but very high genetic differentiation between them, likely
 resulting from breeding practices. Based on an additional test dataset
 including samples from 41 local police seizures, we showed that the
 genetic signature of marijuana cultivars could be used to trace crime
 scene evidence. To date, our study provides the most comprehensive genetic
 resource for Cannabis forensics worldwide.
description: Cannabis
 GenotypesReference (N=1324) and
 test (340) genotypes of Cannabis sativa for 13 microsatellite
 lociCannabisGenotypes.xlsx
DOI: 10.5061/dryad.3bn62
title: Data from: Forest cover mediates genetic connectivity of northwestern cougars

description: Population structure, connectivity, and dispersal success of individuals
 can be challenging to demonstrate for solitary carnivores with low
 population densities. Though the cougar (Puma concolor) is widely
 distributed throughout North America and is capable of dispersing long
 distances, populations can be geographically structured and genetic
 isolation has been documented in some small populations. We described
 genetic structure and explored the relationship between landscape
 resistance and genetic variation in cougars in Washington and southern
 British Columbia using allele frequencies of 17 microsatellite loci for
 felids. We evaluated population structure of cougars using the Geneland
 clustering algorithm and spatial principal components analysis. We then
 used Circuitscape to estimate the landscape resistance between pairs of
 individuals based on rescaled GIS layers for forest canopy cover,
 elevation, human population density and highways. We quantified the effect
 of landscape resistance on genetic distance using multiple regression on
 distance matrices and boosted regression tree analysis. Cluster analysis
 identified four populations in the study area. Multiple regression on
 distance matrices and boosted regression tree models indicated that only
 forest canopy cover and geographic distance between individuals had an
 effect on genetic distance. The boundaries between genetic clusters
 largely corresponded with breaks in forest cover, showing agreement
 between population structure and genetic gradient analyses. Our data
 indicate that forest cover promotes gene flow for cougars in the Pacific
 Northwest, which provides insight managers can use to preserve or enhance
 genetic connectivity.
description: Warren_ConservGenet_2016_genotypes_Dryad_kw160315Excel file with N = 667 samples and 18 microsatellite loci, two column format. File also includes sample location data, life stage, and sex information. Missing genotype data is coded as -999
DOI: 10.5061/dryad.t2k1b
title: Data from: Pleistocene survival on central Alpine nunataks: genetic evidence from the jumping bristletail Machilis pallida

description: Mechanisms of survival during the Pleistocene glaciation periods have been
 studied for more than a century. Until now, molecular studies that
 confirmed animal survival on Alpine nunataks, i.e., ice-free summits
 surrounded by glaciers, were restricted to peripheral areas. Here, we
 search for molecular signatures of inner-Alpine survival of the
 narrow-endemic and putatively parthenogenetic Alpine jumping bristletail
 Machilis pallida combining mitochondrial and AFLP data from its three
 known populations. The mitochondrial data indicate survival on both
 peripheral and central nunataks, the latter suggesting that refugia in the
 centre of the Alpine main ridge were more widespread than previously
 recognised. Incongruences between mitochondrial and AFLP patterns suggest
 a complex evolutionary history of the species and may be explained via
 parallel fixation of parthenogenesis of different origins during the Last
 Glacial Maximum. We suggest that the inferred parthenogenesis may have
 been essential for central-nunatak survival, but may pose a serious threat
 for M. pallida in consideration of the present climatic changes.
description: AFLPdata and GenBank
 accession numbersThis Excel file provides
 AFLP genotype data and genbank accession numbers from individuals of a
 Alpine endemic jumping bristletail. The file shows individual numbers, the
 corresponding mtDNA haplotypes , and the AFLP genotypes (72 loci).
 Fragment analysis was done on an ABI 3130 sequencer (Applied Biosystems,
 USA), data were analysed with Peakscanner v1.0, and the binary matrix was
 created with tinyFLP.AFLP_mtDNA.xlsmtDNA AlignmentThis sequence file provides the final 840 bp Alignment of 144 individuals from three populations. Sequences were edited manually and aligned by Clustal W.M.pallida_mtDNA.fas