cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.116n6
title: Data from: Between spines and molecules: a total evidence phylogeny of the Brazilian endemic genus Encholirium (Pitcairnioideae, Bromeliaceae)

description: We performed a phylogenetic study of Encholirium (Bromeliaceae,
 Pitcairnioideae) to test if this Brazilian endemic genus is monophyletic
 when including additional species and morphological characters compared to
 previous studies. Extensive fieldwork to increase the sampling of
 Encholirium and evolutionary analyses were conducted. Species of
 Fosterella, the sister group of the xeric clade of Pitcairnioideae, were
 used as outgroups. We analyzed two chloroplast DNA sequence markers (matK
 and ndhF) and 49 morphological characters with maximum parsimony analyses
 (MP), Bayesian inference (BI), and maximum likelihood (ML) with different
 sampling in the molecular analyses than the morphological. The
 phylogenetic analyses of the datasets, both independently and combined,
 did not recover Encholirium as monophyletic. We found few variable sites
 in the sequences used. This result is evidence of low nucleotide
 divergence and corroborates the hypothesis of the recent evolutionary
 history of these plants. The morphological differences between Dyckia and
 Encholirium, which are demonstrably associated with distinct pollination
 syndromes, ant-plant interactions, and single-multiple reproductive
 episodes, likely emerged in a short period of diversification in species
 assigned to these two genera.
description: Concat_genesData Matrix of molecular analysis.
DOI: 10.5061/dryad.6756p3cv
title: Data from: Experimental evidence of early costs of reproduction in conspecific viviparous and oviparous lizards

description: Reproduction entails costs, and disentangling the relative importance of
 each stage of the reproductive cycle may be important to assess the costs
 and benefits of different reproductive strategies. We studied the early
 costs of reproduction in oviparous and viviparous lizard females of the
 bimodal reproductive species Zootoca vivipara. Egg-retention time in
 oviparous females is approximately one third of the time in viviparous
 females. We compared the vitellogenesis and egg-retention stages which are
 common to both reproductive modes. Precisely, we monitored the
 thermoregulatory behaviour, the weight gain and the immunocompetence of
 the females. Moreover, we injected an antigen in half of the females
 (immune challenge) to study the trade-offs between reproductive mode and
 immune performance, and between different components of the immune system.
 Finally, we experimentally induced parturition in viviparous females at
 the time of egg-laying in oviparous females. Oviparous and viviparous
 females did not show strong differences in response to the immune
 challenge. However, viviparous females spent more time thermoregulating
 while partially hidden and gained more weight than oviparous females. The
 greater weight gain indicates that the initial period of egg-retention is
 less costly for viviparous than for oviparous females or that viviparous
 females are able to save and accumulate energy at this period. This energy
 may be used by viviparous females to cope with the subsequent costs of the
 last two thirds of the gestation. Such an ability to compensate the higher
 costs of a longer egg-retention period may account for the frequent
 evolution of viviparity in squamate reptiles.
description: data_Bleuetal_2012_JEB
DOI: 10.5061/dryad.st1s3
title: Data from: Ecological incumbency impedes stochastic community assembly in Holocene foraminifera from the Huon Peninsula, Papua New Guinea

description: Persistence in the structure of ecological communities can be predicted
 both by deterministic and by stochastic theory. Evaluating ecological
 patterns against the neutral theory of biodiversity provides an
 appropriate methodology for differentiating between these alternatives. We
 traced the history of benthic foraminiferal communities from the Huon
 Peninsula, Papua New Guinea. From the well-preserved uplifted reef terrace
 at Bonah River we reconstructed the benthic foraminiferal communities
 during a 2200-year period (9000–6800 yr B.P.) of reef building during the
 Holocene transgressive sea-level rise. We found that the similarity of
 foraminiferal communities was consistently above 60%, even when comparing
 communities on either side of a massive volcanic eruption that smothered
 the existing reef system with ash. Similarly, species diversity and rank
 dominance were unchanged through time. However, similarity dropped
 dramatically in the final stages of reef growth, when accommodation space
 was reduced as sea-level rise slowed. We compared the community inertia
 index (CII) computed from the observed species abundances with that
 predicted from neutral theory. Despite the differences in foraminiferal
 community composition in the younger part of the reef sequence, we found
 an overall greater degree of community inertia with less variance in
 observed communities than was predicted from neutral theory, regardless of
 foraminiferal community size or species migration rate. Thus, persistent
 species assemblages could not be ascribed to neutral predictions.
 Ecological incumbency of established foraminiferal species likely
 prevented stochastic increases in both migrant and rare taxa at the Bonah
 River site. Regardless of the structuring mechanisms, our reconstruction
 of Holocene foraminiferal assemblages provides historical context for the
 management and potential restoration of degraded species assemblages.
description: 09087
 Suppl_MatPooled abundance of the
 Holocene foraminifera identified from eight temporal horizons at Bonah
 River in the Huon Peninsula, Papua New Guinea. The species identified in
 this study are listed in alphabetical order. Included are the authors and
 the plate reference.
DOI: 10.5061/dryad.8478
title: Data from: Evolutionary novelties and losses in geometric morphometrics: a practical approach through hominin molar morphology

description: Geometric morphometric techniques may offer a promising methodological
 approach to analyse evolutionary novelties in a quantitative framework.
 Nevertheless, and despite continuous improvements to this methodology, the
 inclusion of novel features in these studies presents some difficulties.
 In the present study, different methods to explicitly include novel traits
 in geometric morphometric analyses are compared, including homology-free
 approaches, landmark-based approaches, and combinations of both
 techniques. The 2D occlusal morphology of the lower second molar in
 multiple hominin species was chosen to evaluate these methods, as an
 example of an anatomical structure including one novelty: a distal fifth
 cusp is present in earlier hominins, and notably absent in many later Homo
 species. Results reveal that different approaches provide different
 results, highlighting that the design of the conformations of landmarks
 has a high impact on the inferred conclusions. Among diverse methods, a
 combined approach including landmarks, sliding semilandmarks, and only one
 landmark related to the studied novelty, was able to directly discern
 structures with and without the novel feature, circumventing some of the
 methodological difficulties associated with these traits. This study
 demonstrates the ability of geometric morphometric techniques to
 investigate evolutionary novelties and explores the implications of
 different methods, providing a reference context for future studies.
description: Gómez-Robles et al
 homininsGómez-Robles et al
 chimps
DOI: 10.5061/dryad.sp74b
title: Data from: Assessing niche partitioning of co-occurring sibling bat species by DNA metabarcoding

description: Niche partitioning through foraging is a mechanism likely involved in
 facilitating the coexistence of ecologically similar and co-occurring
 animal species by separating their use of resources. Yet, this mechanism
 is not well understood in flying insectivorous animals. This is
 particularly true of bats, where many ecologically similar or cryptic
 species coexist. The detailed analysis of the foraging niche in sympatric,
 cryptic sibling species provides an excellent framework to disentangle the
 role of specific niche factors likely involved in facilitating
 coexistence. We used DNA metabarcoding to determine the prey species
 consumed by a population of sympatric sibling Rhinolophus euryale and R.
 mehelyi whose use of habitat in both sympatric and allopatric ranges has
 been well established through radio tracking. Although some subtle dietary
 differences exist in prey species composition, the diet of both bats
 greatly overlapped (Ojk = 0.83) due to the consumption of the same common
 and widespread moths. Those dietary differences we did detect might be
 related to divergences in prey availabilities among foraging habitats,
 which prior radio tracking on the same population showed are
 differentially used and selected when both species co-occur. This minor
 dietary segregation in sympatry may be the result of foraging on the same
 prey-types and could contribute to reduce potential competitive
 interactions (e.g. for prey, acoustic space). Our results highlight the
 need to evaluate the spatial niche dimension in mediating the
 co-occurrence of similar insectivorous bat species, a niche factor likely
 involved in processes of bat species coexistence.
description: Diet sequences data
 processedRepresentative sequences
 for each MOTUMOTU_representative_sequences_diet_Arrizabalaga_Escudero_etal.fastaDiet data matrixPresence/absence data matrix of bat individuals x MOTUsBat_MOTU_diet_matrix.xlsxBat individuals' dataData about the traits of each bat individual.bat_individuals_data.xlsx
DOI: 10.5061/dryad.2cq7r
title: Data from: Genetic load, inbreeding depression and hybrid vigor covary with population size: an empirical evaluation of theoretical predictions

description: Reduced population size is thought to have strong consequences for
 evolutionary processes as it enhances the strength of genetic drift. In
 its interaction with selection, this is predicted to increase the genetic
 load, reduce inbreeding depression, and increase hybrid vigour, and in
 turn affect phenotypic evolution. Several of these predictions have been
 tested, but comprehensive studies controlling for confounding factors are
 scarce. Here we show that populations of Daphnia magna, which vary
 strongly in genetic diversity, also differ in genetic load, inbreeding
 depression, and hybrid vigor in a way that strongly supports theoretical
 predictions: Inbreeding depression is positively correlated with genetic
 diversity (a proxy for Ne), and genetic load and hybrid vigour are
 negatively correlated with genetic diversity. These patterns remain
 significant after accounting for potential confounding factors and
 indicate that, in small populations, a large proportion of the segregation
 load is converted into fixed load. Overall, the results suggest that the
 nature of genetic variation for fitness-related traits differs strongly
 between large and small populations. This has large consequences for
 evolutionary processes in natural populations, such as selection on
 dispersal, breeding systems, ageing, and local adaptation.
description: life_historyCSV file with raw data of life history trait valuesloadCSV file with output values of genetic load, inbreeding depression and hybrid vigour. Methods for calculating the values are in the methods section of the paper.
DOI: 10.5061/dryad.4tj56
title: Data from: Genetic effects of landscape, habitat preference, and demography on three co-occurring turtle species

description: Expanding the scope of landscape genetics beyond the level of single
 species can help to reveal how species traits influence responses to
 environmental change. Multispecies studies are particularly valuable in
 highly threatened taxa, such as turtles, in which the impacts of
 anthropogenic change are strongly influenced by interspecific differences
 in life-history strategies, habitat preferences, and mobility. We sampled
 approximately 1500 individuals of three co-occurring turtle species across
 a gradient of habitat change (including varying loss of wetlands and
 agricultural conversion of upland habitats) in the Midwestern USA. We used
 genetic clustering and multiple regression methods to identify
 associations between genetic structure and permanent landscape features,
 past landscape composition, and landscape change in each species. Two
 aquatic generalists (the painted turtle, Chrysemys picta, and the snapping
 turtle Chelydra serpentina) both exhibited population genetic structure
 consistent with isolation-by-distance, modulated by aquatic landscape
 features. Genetic divergence for the more terrestrial Blanding's
 turtle (Emydoidea blandingii), on the other hand, was not strongly
 associated with geographic distance or aquatic features, and Bayesian
 clustering analysis indicated that many Emydoidea populations were
 genetically isolated. Despite long generation times, all three species
 exhibited associations between genetic structure and post-settlement
 habitat change, indicating that long generation times may not be
 sufficient to delay genetic drift resulting from recent habitat
 fragmentation. The concordances in genetic structure observed between
 aquatic species, as well as isolation in the endangered, long-lived
 Emydoidea, reinforce the need to consider both landscape composition and
 demographic factors in assessing differential responses to habitat change
 in co-occurring species.
description: Emydoideadata_MEC-16-0834Microsatellite data for Blanding's turtles.Emydoidea_metadata_MEC-16-0834_v2.txtChelydradata_MEC-16-0834Microsatellite data for snapping turtles.Chrysemysdata_MEC-16-0834Microsatellite data for painted turtles.
DOI: 10.34740/kaggle/dsv/14053583
title: WayangKulit2025
DOI: 10.5061/dryad.k60kb
title: Data from: Strong population structure and shallow mitochondrial phylogeny in the banded guitarfish, Zapteryx exasperata (Jordan y Gilbert, 1880) from the northern Mexican Pacific

description: The northern Mexican Pacific (NMP), the Gulf of California (GC), and Baja
 California have been recognized as an ecological and evolutionarily
 dynamic region having experienced significant tectonic and climatic
 changes leading to the diversification of terrestrial and marine biotas.
 Zapteryx exasperata is a predominant ray caught in the artisanal fisheries
 of the NMP. Morphometric and reproductive differences between rays from
 the GC and the Pacific Coast of Baja California (PCBC) regions suggest the
 presence of distinct populations. We investigate whether this distinction
 correlates with differences in genetic diversity and differentiation using
 sequences of the mitochondrial ND2 gene and the non-coding control region
 (CR) in 63 specimens. Contrary to our expectations, ND2 bore significantly
 more diversity (h = 0.76) than CR (h = 0.39). Geographic patterns of
 diversity of CR were opposite to those of ND2, with GC being significantly
 less (ND2) and more (CR) diverse than PCBC. The diversity of concatenated
 haplotypes was high (h = 0.84). Low nucleotide diversity suggests the
 recent coancestry of haplotypes. Marked genetic structure (Φst = 0.23 p
 &lt; 0.0001) revealed the existence of reproductive isolation and
 limited matrilineal gene flow between GC and PCBC, which correlates with
 their phenotypic distinction. These results suggest the influence of
 factors such as female reproductive philopatry, and ecological or
 historical vicariant barriers to gene flow. Our results point to the
 existence a distinct management unit of banded guitarfish in each region,
 and add to the increasing evidence attesting to the diversifying nature of
 this evolutionarily dynamic region.
description: Concatenated
 sequencesConcatenated sequences
 of 63 individuals of two genes mitochondrial ND2 and RCInd
 CAT.fastaArlequin plus
 matrixInfile for software
 Arlequin, contain sequences of haplotype, Distance Matrix generated in
 PAUP
DOI: 10.5061/dryad.51883
title: Data from: Tree species diversity promotes aboveground carbon storage through functional diversity and functional dominance

description: The relationship between biodiversity and ecosystem function has
 increasingly been debated as the cornerstone of the processes behind
 ecosystem services delivery. Experimental and natural field-based studies
 have come up with nonconsistent patterns of biodiversity–ecosystem
 function, supporting either niche complementarity or selection effects
 hypothesis. Here, we used aboveground carbon (AGC) storage as proxy for
 ecosystem function in a South African mistbelt forest, and analyzed its
 relationship with species diversity, through functional diversity and
 functional dominance. We hypothesized that (1) diversity influences AGC
 through functional diversity and functional dominance effects; and (2)
 effects of diversity on AGC would be greater for functional dominance than
 for functional diversity. Community weight mean (CWM) of functional traits
 (wood density, specific leaf area, and maximum plant height) were
 calculated to assess functional dominance (selection effects). As for
 functional diversity (complementarity effects), multitrait functional
 diversity indices were computed. The first hypothesis was tested using
 structural equation modeling. For the second hypothesis, effects of
 environmental variables such as slope and altitude were tested first, and
 separate linear mixed-effects models were fitted afterward for functional
 diversity, functional dominance, and both. Results showed that AGC varied
 significantly along the slope gradient, with lower values at steeper
 sites. Species diversity (richness) had positive relationship with AGC,
 even when slope effects were considered. As predicted, diversity effects
 on AGC were mediated through functional diversity and functional
 dominance, suggesting that both the niche complementarity and the
 selection effects are not exclusively affecting carbon storage. However,
 the effects were greater for functional diversity than for functional
 dominance. Furthermore, functional dominance effects were strongly
 transmitted by CWM of maximum plant height, reflecting the importance of
 forest vertical stratification for diversity–carbon relationship. We
 therefore argue for stronger complementary effects that would be induced
 also by complementary light-use efficiency of tree and species growing in
 the understory layer.
description: Data
DOI: 10.5061/dryad.rk13d
title: Data from: Unravelling the effects of contemporary and historical range expansion on the distribution of genetic diversity in the damselfly Coenagrion scitulum

description: Although genetic diversity provides the basic substrate for evolution,
 there are a limited number of studies that assess the impact of recent
 climate change on intraspecific genetic variation. This study aims to
 unravel the degree to which historical and contemporary factors shape
 genetic diversity and structure across a large part of the range of the
 range-expanding damselfly Coenagrion scitulum (Rambur, 1842). A total of
 525 individuals from 31 populations were genotyped at nine
 microsatellites, and a subset was sequenced at two mitochondrial genes. We
 inferred the importance of geography, environmental factors, and recent
 range expansion on genetic diversity and structure. Genetic diversity
 decreased going westwards, suggesting a signature of historical
 post-glacial expansion from east to west and the presence of eastern
 refugia. Although genetic differentiation decreased going northwards, it
 increased in the northern edge populations, suggesting a role of
 contemporary range expansion on the genetic make-up of populations. The
 phylogeographical context was proven to be essential in understanding and
 identifying the genetic signatures of local contemporary processes. Within
 this framework, our results highlight that recent range expansion of a
 good disperser can decrease genetic diversity and increase genetic
 differentiation which should be considered when devising suitable
 conservation strategies.
description: alignment_CO2_CO1_coenagrion_scitulumAlignment in fasta format of CO2 and CO1 sequences of Coenagrion scitulumalignment_CO2_CO1.fastaCscitulum_range_microsatellite_dryadMicrosatellite genotypes of populations across the range of Coenagrion scitulum. Details of locations can be found in supplementary file S2.
DOI: 10.5061/dryad.08v2c
title: Data from: The adsorption features between insecticidal crystal protein and Nano-Mg(OH)2

description: Nano-Mg(OH)2, with low biological toxicity, is an ideal nano-carrier for
 insecticidal protein to improve the bioactivity. In this work, the
 adsorption features of insecticidal protein by nano-Mg(OH)2 have been
 studied. The adsorption capacity could achieve as high as 136 mg/g, and
 the adsorption isotherm had been fitted with Freundlich model. Moreover,
 the adsorption kinetics followed pseudo-first or -second order rate model,
 and the adsorption was spontaneous and exothermic process. However, the
 high temperatures are not suitable to adsorption, which implies that the
 temperature would be a critical factor during the adsorption process. In
 addition, FT-IR confirmed that the protein was adsorbed on the
 nano-Mg(OH)2, the Zeta potential analysis suggested that insecticidal
 protein was loaded onto the nano-Mg(OH)2 not by electrostatic adsorption
 but might by intermolecular forces, and the circular dichroism (CD)
 spectroscopy of Cry11Aa protein before and after loading with nano-Mg(OH)2
 was changed. The study applied the adsorption information between Cry11Aa
 and nano-Mg(OH)2, which would be useful in the real appilation of
 nano-Mg(OH)2 as a nano-carrier.
description: data
DOI: 10.5061/dryad.1779
title: Data from: Geographic variation in phenotypic plasticity in response to dissolved oxygen in an African cichlid fish

description: Genetic adaptation and phenotypic plasticity are two ways in which
 organisms can adapt to local environmental conditions. We examined genetic
 and plastic variation in gill and brain size among swamp (low oxygen;
 hypoxic) and river (normal oxygen; normoxic) populations of an African
 cichlid fish, Pseudocrenilabrus multicolor victoriae. Larger gills and
 smaller brains should be advantageous when oxygen is low, and we
 hypothesized that the relative contribution of local genetic adaptation
 versus phenotypic plasticity should be related to potential for dispersal
 between environments (due to gene flow's constraint on local genetic
 adaptation). We conducted a laboratory-rearing experiment, with broods
 from multiple populations raised under high- and low-oxygen conditions. We
 found that most of the variation in gill size was due to plasticity.
 However, both plastic and genetic effects on brain mass were detected, as
 were genetic effects on brain mass plasticity. F1 offspring from
 populations with the highest potential for dispersal between environments
 had characteristically smaller and more plastic brains. This phenotypic
 pattern might be adaptive in the face of gene flow, if smaller brains and
 increased plasticity confer higher average fitness across environment
 types.
description: CrispoChapman-JEB-Dryad.xlsThe measurements of the gill metrics are described in detail in the manuscript. The size standardized values are also included in the spreadsheet, with the formulas for calculation. The data is for fish raised in a split-brood rearing experiment, with F1 offspring raised under high (normoxia) or low (hypoxia) oxygen conditions.