cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.480cf
title: Data from: High lability of sexual system over 250 million years of evolution in morphologically conservative tadpole shrimps

description: Background: Sexual system is a key factor affecting the genetic diversity,
 population structure, genome structure and the evolutionary potential of
 species. The sexual system androdioecy -- where males and hermaphrodites
 coexist in populations -- is extremely rare, yet is found in three
 crustacean groups, barnacles, a genus of clam shrimps Eulimnadia, and in
 the order Notostraca, the tadpole shrimps. In the ancient crustacean order
 Notostraca, high morphological conservatism contrasts with a wide
 diversity of sexual systems, including androdioecy. An understanding of
 the evolution of sexual systems in this group has been hampered by poor
 phylogenetic resolution and confounded by the widespread occurrence of
 cryptic species. Here we use a multigene supermatrix for 30 taxa to
 produce a comprehensive phylogenetic reconstruction of Notostraca. Based
 on this phylogenetic reconstruction we use character mapping techniques to
 investigate the evolution of sexual systems. We also tested the hypothesis
 that reproductive assurance has driven the evolution of androdioecy in
 Notostraca. Results: Character mapping analysis showed that sexual system
 is an extremely flexible trait within Notostraca, with repeated shifts
 between gonochorism and androdioecy, the latter having evolved a minimum
 of five times. In agreement with the reproductive assurance hypothesis
 androdioecious notostracans are found at significantly higher latitudes
 than gonochoric ones indicating that post glacial re-colonisation may have
 selected for the higher colonisation ability conferred by androdioecy.
 Conclusions: In contrast to their conserved morphology, sexual system in
 Notostraca is highly labile and the rare reproductive mode androdioecy has
 evolved repeatedly within the order. Furthermore, we conclude that this
 lability of sexual system has been maintained for at least 250 million
 years and may have contributed to the long term evolutionary persistence
 of Notostraca. Our results further our understanding of the evolution of
 androdioecy and indicate that reproductive assurance is a recurrent theme
 involved in the evolution of this sexual system.
description: All_loci_aligned_SM7 gene supermatrix alignment used for phylogenetic analysis in fasta format. See readme file for partition information.
DOI: 10.5061/dryad.115m1
title: Data from: Multilocus phylogeny and ecological differentiation of the “Eupelmus urozonus species group” (Hymenoptera, Eupelmidae) in the West-Palaearctic

description: Background: The ecological differentiation of insects with parasitic
 life-style is a complex process that may involve phylogenetic constraints
 as well as morphological and/or behavioural adaptations. In most cases,
 the relative importance of these driving forces remains unexplored. We
 investigate here this question for the “Eupelmus urozonus species group”
 which encompasses parasitoid wasps of potential interest in biological
 control. This was achieved using seven molecular markers, reliable records
 on 91 host species and a proxy of the ovipositor length. Results: After
 using an adequate partitioning scheme, Maximum likelihood and Bayesian
 approaches provide a well-resolved phylogeny supporting the monophyly of
 this species group and highlighting its subdivision into three sub-groups.
 Great variations of both the ovipositor length and the host range
 (specialist versus generalist) were observed at this scale, with these two
 features being not significantly constrained by the phylogeny. Ovipositor
 length was not shown as a significant predictor of the parasitoid host
 range. Conclusions: This study provides firstly the first evidence for the
 strong lability of both the ovipositor’s length and the realised host
 range in a set of phylogenetically related and sympatric species. In both
 cases, strong contrasts were observed between sister species. Moreover, no
 significant correlation was found between these two features. Alternative
 drivers of the ecological differentiation such as interspecific
 interactions are proposed and the consequences on the recruitment of these
 parasitoids on native and exotic pests are discussed.
description: Dryad_BMCThis file contains : (i) information about the host range of each investigated/Eupelmus/ species including new records with regard to Al Khatib et al. - Systematic Entomology - 2014 ; (ii) information about the relationships between some morphological measurements and their ratios (two independent datasets).Driyad_BMC.xlsx
DOI: 10.5061/dryad.3gq01
title: Data from: Genetic diversity, demographical history and conservation aspects of the endangered yew tree Taxus contorta (syn. Taxus fuana) in Pakistan

description: Western Himalayan yew (Taxus contorta Griffith, synonym T. fuana Nan Li
 & R.R. Mill), one of the highly prized tree species for its
 anticancer properties is experiencing severe reduction in populations
 across its range in Pakistan. We examined a chloroplast DNA region
 (trnL-F) and ten nuclear microsatellite loci variations among seven
 populations to investigate the levels of genetic diversity and
 demographical history of T. contorta in Pakistan. Low haplotype diversity
 (HT = 0.182), moderate level of microsatellite diversity (HE = 0.526 ±
 0.034), significant population differentiation (FST = 0.106) and high
 level of inbreeding (FIS = 0.222-0.418) was found in T. contorta compared
 with its congeners. Results of mismatch distribution analysis, neutrality
 tests and data on glacial chronologies of western Himalaya indicated that
 demographic expansion of T. contorta in Pakistan predates extensive
 glaciations that occurred during late Pleistocene (140.06 thousand years
 ago (kya), and the spatial expansion most likely happened very recently in
 the Holocene (6.71 kya). An unprecedented level of habitat disturbances
 since past few decades coupled with the severe historic climate may have
 played an important role on an extant population structure of T. contorta.
 We have discussed a range of sustainable management measures for the
 ecological restoration of remnant populations as well as to exploit high
 economic benefits that can be obtained from this species.
description: Conservation Genetics of
 Taxus contorta_Pakistan
DOI: 10.5061/dryad.bq340
title: Data from: Assessing the influence of temporal autocorrelations on the population dynamics of a disturbance specialist plant population in a random environment

description: Biological populations are strongly influenced by random variations in
 their environment, which are often autocorrelated in time. For disturbance
 specialist plant populations, the frequency and intensity of environmental
 stochasticity (via disturbances) can drive the qualitative nature of their
 population dynamics. In this article, we extended our earlier model to
 explore the effect of temporally autocorrelated disturbances on population
 persistence. In our earlier work, we only assumed disturbances were
 independent and identically distributed in time. We proved that the plant
 seed bank population converges in distribution, and we showed that the
 mean and variance in seed bank population size were both increasing
 functions of the autocorrelation coefficient for all parameter values
 considered, but the interplay between increasing population size and
 increasing variability caused interesting relationships between
 quasi-extinction probability and autocorrelation. For example, for
 populations with low seed survival, fecundity, and disturbance frequency,
 increasingly positive autocorrelated disturbances decreased
 quasi-extinction probability. Higher disturbance frequency coupled with
 low seed survival and fecundity caused a nonmontone relationship between
 autocorrelation and quasi-extinction, where increasingly positive
 autocorrelations eventually caused an increase in quasi-extinction
 probability. For higher seed survival, fecundity, and/or disturbance
 frequency, quasi-extinction probability was generally a monotonically
 increasing function of the autocorrelation coefficient.
description: KSandNEdata
DOI: 10.5061/dryad.7983
title: Data from: Sperm whale population structure in the eastern and central North Pacific inferred by the use of single nucleotide polymorphisms (SNPs), microsatellites and mitochondrial DNA

description: We use mitochondrial DNA (400bp), six microsatellites and 36 single
 nucleotide polymorphisms (SNPs), 20 of which were linked, to investigate
 population structure of sperm whales (Physeter macrocephalus) in the
 eastern and central North Pacific. SNP markers, reproducible across
 technologies and laboratories, are ideal for long-term studies of globally
 distributed species such as sperm whales, a species of conservation
 concern due to both historical and contemporary impacts. We estimate
 genetic differentiation among three strata in the temperate to tropical
 waters where females are found: California Current, Hawai‛i and the
 eastern tropical Pacific. We then consider how males on sub-Arctic
 foraging grounds assign to these strata. The California Current stratum
 was differentiated from both the other strata (p&lt;0.05) for mtDNA,
 microsatellites and SNPs, suggesting that the region supports a
 demographically independent population and providing the first indication
 that males may exhibit reproductive philopatry. Comparisons between the
 Hawai‛i stratum and the eastern tropical Pacific stratum are not
 conclusive at this time. Comparisons with Alaska males were statistically
 significant or nearly so from all three strata and individuals showed
 mixed assignment to, and few exclusions from, the three potential source
 strata, suggesting widespread origin of males on sub-Arctic feeding
 grounds. We show that SNPs have sufficient power to detect population
 structure even when genetic differentiation is low. There is a need for
 better analytical methods for SNPs, especially when linked SNPs are used,
 but SNPs appear to be a valuable marker for long-term studies of globally
 dispersed and highly mobile species.
description: Mesnick et al_Physeter
 genotypes_17 Nov 2010_n=287.xlsThe sample set consisted
 of 287 North Pacific sperm whale samples for which six hypervariable
 microsatellite loci and 36 SNP loci have been genotyped. Samples obtained
 between 1972 and 2007. Samples were collected from solitary or groups of
 free-ranging sperm whales by directed biopsy or the collection of sloughed
 skin during cetacean research surveys and also from dead animals stranded
 on beaches, floating dead at sea and from incidental fishery takes. Sample
 locations refer to the waters of the eastern and central North Pacific.
 See manuscript for additional details on samples.Mesnick et al_Physeter
 genotypes_17 Nov 2010_n287.xls
DOI: 10.5061/dryad.5g10870
title: Data from: Temporal variation in plant-pollinator networks from seasonal tropical environments: higher specialization when resources are scarce

description: The temporal dynamics of plant phenology and pollinator abundance across
 seasons should influence the structure of plant-pollinator interaction
 networks. Nevertheless, such dynamics are seldom considered, especially
 for diverse tropical networks. Here, we evaluated the temporal variation
 of four plant-pollinator networks in two seasonal ecosystems in Central
 Brazil (Cerrado and Pantanal). Data were gathered on a monthly basis over
 one year for each network. We characterized seasonal and temporal shifts
 in plant-pollinator interactions, using temporally discrete networks. We
 predicted that the greater floral availability in the rainy season would
 allow for finer partitioning of the floral niche by the pollinators, i.e.,
 higher specialization patterns as previously described across large
 spatial gradients. Contrary to these expectations, we found that dry
 season networks, although characterized by lower floral resource richness
 and abundance, showed higher levels of network-wide interaction
 partitioning (complementary specialization and modularity). For nestedness
 and species level indices, though, this between-seasons difference was not
 consistent. Reduced resource availability in the dry season may promote
 higher interspecific competition among pollinators leading to reduced
 niche overlap, thus explaining the increase in specialization.
 Importantly, we also show that targeted data collection during peak
 flowering generates higher estimates of network specialization. Hence,
 depending on the period of data collection, different structural values
 for the networks of interactions may be found. Synthesis: Our study
 suggests that networks of tropical environments have structural properties
 that vary according to seasons, which should be taken into account in the
 description of the complex systems of interactions between plants and
 their pollinators in these areas.
description: Souza_et_al.2018-Journal_of_Ecology_Suplementar_file_species_data_networksWe collected data on plants and potential pollinators in four communities with distinct vegetation types located in the Central region of Brazil, being all characterized by a marked seasonality: Cerrado woody grassland (Campo sujo), Chaco vegetation, Palm swamp (Vereda) and Pantanal Wetland.
DOI: 10.5061/dryad.pd383
title: Data from: Predation's role in life-history evolution of a livebearing fish and a test of the Trexler-DeAngelis model of maternal provisioning

description: Populations experiencing consistent differences in predation risk and
 resource availability are expected to follow divergent evolutionary
 trajectories. For example, live-history theory makes specific predictions
 for how predation should drive life-history evolution, and according to
 the Trexler-DeAngelis model for the evolution of matrotrophy,
 post-fertilization maternal provisioning is most likely to evolve in
 environments with consistent, high levels of resource availability. Using
 the model system of Bahamas mosquitofish (Gambusia hubbsi) inhabiting blue
 holes with and without the piscivorous bigmouth sleeper (Gobiomorus
 dormitor), we provide some of the strongest tests of these predictions to
 date, as resource availability does not co-vary with predation regime in
 this system, and we examine numerous (14) isolated natural populations. We
 found clear evidence for the expected life-history divergence between
 predation regimes, and empirical support of the Trexler-DeAngelis model.
 Moreover, based on molecular and lab-rearing data, our study offers strong
 evidence for convergent evolution of similar life histories in similar
 predation regimes, largely matching previous phenotypic patterns observed
 in other poeciliid lineages (Brachyrhaphis spp., Poecilia reticulata), and
 further supports the notion that matrotrophy is most likely to evolve in
 stable high-resource environments.
description: Dryad_BahamasFemalesWithin this file are two worksheets. The first lists all the life history variables for each individual female used in the published study including the number of aborted embryos. The second worksheet lists the embryonic dry weight per developmental stage per population, which were used for the Matrotrophy Index analyses.Dryad_BahamasMalesThe four life history variables used for males (SL, Lean Weight, Fat Content, and GSI).Dryad_EnvrionmentalVariablesThis file contains the environmental variables we measured for each site (phycocyanin, chlorophyll a, small phytoplankton, large phytoplankton, and zooplankton).
DOI: 10.5061/dryad.v75rj24
title: Data from: Genetic diversity maintained among fragmented populations of a tree undergoing range contraction

description: Dwarf birch (Betula nana) has a widespread boreal distribution but has
 declined significantly in Britain where populations are now highly
 fragmented. We analysed the genetic diversity of these fragmented
 populations using markers that differ in mutation rate: conventional
 microsatellites markers (PCR-SSRs), RADseq generated transition and
 transversion SNPs (RAD-SNPs), and microsatellite markers mined from RADseq
 reads (RAD-SSRs). We estimated the current population sizes by census and
 indirectly, from the linkage disequilibrium found in the genetic surveys.
 The two types of estimate were highly correlated. Overall we found genetic
 diversity to be only slightly lower in Britain than across a comparable
 area in Scandinavia where populations are large and continuous. Whilst the
 ensemble of British fragments maintain diversity levels close to
 Scandinavian populations, individually they have drifted apart and lost
 diversity; particularly the smaller populations. An ABC analysis, based on
 coalescent models, favours demographic scenarios in which Britain
 maintained high levels of genetic diversity through post-glacial
 recolonisation. This diversity has subsequently been partitioned into
 population fragments that have recently lost diversity at a rate
 corresponding to the current population-size estimates. We conclude that
 the British population fragments retain sufficient genetic resources to be
 the basis of conservation and re-planting programmes. Use of markers with
 different mutation rates gives us greater confidence and insight than one
 marker set could have alone, and we suggest that RAD-SSRs are particularly
 useful as high mutation rate marker set with a well-specified
 ascertainment bias, which are widely available yet often neglected in
 existing RAD datasets.
description: Betula_nana_PCR-SSR_markersMicrosatellite markers for 1066 Betula nana individuals from 39 populations in Great Britain and Scandinavia. Dataset is stored in genepop format, with each allele coded by three digits.Betula_nana_PCRSSR.txtBetula_nana_RAD-SSR_markersMicrosatellite markers identified in silico from raw RAD-seq reads for 187 Betula nana individuals, from 36 populations, in Great Britain and Scandinavia. These individuals are a subset of those covered by the Betula_nana_PCRSSR.txt dataset. Dataset is stored in genepop format, with each allele coded by three digits. For details of the scripts used to generate these data, see https://github.com/JamesBorrell/RAD-SSR_extraction_scriptsBetula_nana_RADSSR.txt
DOI: 10.5061/dryad.k987h
title: Data from: Convergence and non-convergence in ecological, phenotypic, and genetic divergence across replicate population pairs of lake and stream stickleback

description: Convergent (or parallel) evolution provides strong evidence for a
 deterministic role of natural selection: similar phenotypes evolve when
 independent populations colonize similar environments. In reality,
 however, independent populations in similar environments always show some
 differences: some non-convergent evolution is present. It is therefore
 important to explicitly quantify the convergent and non-convergent aspects
 of trait variation, and to investigate the ecological and genetic
 explanations for each. We performed such an analysis for threespine
 stickleback (Gasterosteus aculeatus) populations inhabiting lake and
 stream habitats in independent watersheds. Morphological traits differed
 in the degree to which lake-stream divergence was convergent across
 watersheds. Some aspects of this variation were correlated with ecological
 variables related to diet, presumably reflecting the strength and
 specifics of divergent selection. Furthermore, a genetic scan revealed
 some markers that diverged between lakes and streams in many of the
 watersheds and some that diverged in only a few watersheds. Moreover, some
 of the lake-stream divergence in genetic markers was associated within
 some of the lake-stream divergence in morphological traits. Our results
 suggest that convergent evolution, and deviations from it, are primarily
 the result of natural selection, which corresponds in only some respect to
 the dichotomous habitat classifications frequently used in such studies.
description: Ecological
 dataIsotopes and proportion
 of limnetic prey for each individualGenotypesGenotypes for all the individuals at the 12 loci used in the publicationMorphological dataMorphological measurements for all the individuals
DOI: 10.5061/dryad.vt68r
title: Data from: Habitat connectivity and in-stream vegetation control temporal variability of benthic invertebrate communities

description: One of the key challenges to understanding patterns of β diversity is to
 disentangle deterministic patterns from stochastic ones. Stochastic
 processes may mask the influence of deterministic factors on community
 dynamics, hindering identification of the mechanisms causing variation in
 community composition. We studied temporal β diversity (among-year
 dissimilarity) of macroinvertebrate communities in near-pristine boreal
 streams across 14 years. To assess whether the observed β diversity
 deviates from that expected by chance, and to identify processes
 (deterministic vs. stochastic) through which different explanatory factors
 affect community variability, we used a null model approach. We observed
 that at the majority of sites temporal β diversity was low indicating high
 community stability. When stochastic variation was unaccounted for,
 connectivity was the only variable explaining temporal β diversity, with
 weakly connected sites exhibiting higher community variability through
 time. After accounting for stochastic effects, connectivity lost
 importance, suggesting that it was related to temporal β diversity via
 random colonization processes. Instead, β diversity was best explained by
 in-stream vegetation, community variability decreasing with increasing
 bryophyte cover. These results highlight the potential of stochastic
 factors to dampen the influence of deterministic processes, affecting our
 ability to understand and predict changes in biological communities
 through time.
description: Long-term monitoring
 data of benthic stream invertebrate communitiesData includes annual
 monitoring data of benthic stream invertebrates collected from 23
 near-pristine streams in northern Finland. Sampling was conducted during
 14 consecutive years (2000 to 2013), always by the same field crew. A
 2-min kick-net sampling was used. Samples were preserved in the field and
 later processed in the laboratory. All individuals were sorted, counted
 and identified to the lowest feasible level. Data in repository presents
 original abundance data for observed taxa (in alphabetical order) in each
 year at each study site. Environmental data is presented in related
 Scientic Reports paper.Kuusamon data
 2000_2013_DRYAD.xlsx