cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kj3km
title: Data from: Tree-to-tree competition in mixed European beech-Scots pine forests has different impacts on growth and water-use efficiency depending on site conditions

description: 1. Mixed conifer-hardwood forests can be more productive than pure forests
 and they are increasingly considered as ecosystems that could provide
 adaptation strategies in the face of global change. However, the combined
 effects of tree-to-tree competition, rising atmospheric CO2 concentrations
 and climate on such mixtures remain poorly characterized and understood.
 2. To fill this research gap, we reconstructed 34-year series (1980-2013)
 of growth (basal area increment, BAI) and intrinsic water-use efficiency
 (iWUE) of Scots pine (Pinus sylvestris L.) – European beech (Fagus
 sylvatica L.) mixed stands at two climatically contrasting sites located
 in the southwestern Pyrenees. We also gathered data on tree-to-tree
 competition and climate variables in order to test the hypotheses that (i)
 radial growth will be greater when inter-specific competition exceeds
 intra-specific competition, i.e. when species complementarity occurs, and
 (ii) enhanced iWUE could be linked to improved stem radial growth. 3.
 Growth of both species was reduced when intra-specific competition
 increased. Species complementarity was linked to improved growth of Scots
 pine at the continental site, whilst competition overrode any
 complementarity advantage at the drought-prone Mediterranean site. Beech
 growth did not show any significant response to pine admixture likely due
 to shade tolerance and the highly competitive nature of this species.
 Increasing inter-specific competition drove recent iWUE changes, which
 increased in Scots pine but decreased in European beech. The iWUE
 enhancement did not involve any growth improvement in Scots pine. However,
 the positive BAI-iWUE relationship found for beech suggests an enhanced
 beech growth in drought-prone sites due to improved water use. 4.
 Synthesis. Complementarity may enhance growth in mixed forests. However,
 water scarcity can constrict light-related complementarity for shade
 intolerant species (Scots pine) in drought-prone sites. BAI-iWUE
 relationships were negative for Scots pine and positive for European
 beech. These contrasting behaviours have got implications for coping with
 the expected increasing drought events in Scots pine-European beech
 mixtures located near the ecological limit of the two species.
 Complementarity effects between tree species should be considered to avoid
 overestimating the degree of future carbon uptake by mixed
 conifer-broadleaf forests.
description: Scots pine and European
 beech BAI and iWUE 1980-2013These data series
 describe the values for BAI and iWUE for Scots pine and European beech
 trees in the period 1980-2013 growing in the southwestern
 Pyrenees.Gonzalez de Andres et al JEcol
 2017-0231 Dataset.xlsx
DOI: 10.5061/dryad.v26gh
title: Data from: Facultative asexual reproduction and genetic diversity of populations in the humivorous termite Cavitermes tuberosus

description: Termite colonies are typically founded by a pair of sexually reproducing
 dispersers, which can sometimes be replaced by some of their offspring.
 Some Reticulitermes and Embiratermes species routinely practice asexual
 queen succession (AQS): the queen is replaced by neotenic daughters
 produced by parthenogenesis, which mate with the primary king. Here, to
 cast light on the evolution of AQS, we investigated another candidate
 species, Cavitermes tuberosus (Termitinae). Of 95 nests, 39 contained a
 primary queen and 28 contained neotenic females (2–667 individuals),
 usually with the primary king. Microsatellite analyses confirmed that
 colonies were initiated by single pairs after large dispersal flights.
 More than 80% of the neotenic females were of exclusively maternal origin
 and completely homozygous, suggesting automictic parthenogenesis with
 gamete duplication. Conversely, workers, soldiers, and most alates and
 primary reproductives were produced sexually. AQS often occurs late, after
 colonies have reached maturity, whereas early AQS in other species may
 boost the young colony's growth rate. We suggest additional benefits
 of AQS in C. tuberosus, related with a smaller size, lesser stability and
 higher mobility of colonies. Our data add to the phylogenetical dispersion
 and diversity of modalities of AQS in termites, supporting a multiple
 evolutionary origin of this process.
description: Microsatellite genotype
 data for queens, kings, neotenics, workers, soldiers, alates and nymphs of
 the termite Cavitermes tuberosusMicrosatellite genotype
 data for queens, kings, neotenics, workers, soldiers, alates and nymphs.
 Qi (and respectively Ki) indicate that the genotype of the primary queen
 (respectively primary king) was inferred from nestmate individuals and the
 collected primary king (respectively primary queen). Qii and Kii indicate
 that genotypes of both primary reproductives were inferred from nestmate
 individuals. Inferences were obtained using the maximum likelihood method
 implemented in the program Colony 2.0.5. f and m indicate female and male
 individuals, respectively.Fournier C. tuberosus microsat
 data Dryad.txt
DOI: 10.5061/dryad.8832
title: Data from: Separated by sand, fused by dropping water: habitat barriers and fluctuating water levels steer the evolution of rock-dwelling cichlid populations in Lake Tanganyika

description: The conditions of phenotypic and genetic population differentiation allow
 inferences about the evolution, preservation and loss of biological
 diversity. In Lake Tanganyika, water level fluctuations are assumed to
 have had a major impact on the evolution of stenotopic littoral species,
 though this hypothesis has not been specifically examined so far. The
 present study investigates whether subtly differentiated color patterns of
 adjacent Tropheus moorii populations are maintained in isolation or in the
 face of continuous gene flow, and whether the presumed influence of water
 level fluctuations on lacustrine cichlids can be demonstrated in the
 small-scale population structure of the strictly stenotopic, littoral
 Tropheus. Distinct population differentiation was found even across short
 geographic distances and minor habitat barriers. Population splitting
 chronology and demographic histories comply with our expectation of old
 and rather stable populations on steeper sloping shore, and more recently
 established populations in a shallower region. Moreover, population
 expansions seem to coincide with lake level rises in the wake of Late
 Pleistocene megadroughts ~100 KYA. The imprint of hydrologic events on
 current population structure in the absence of ongoing gene flow suggests
 that phenotypic differentiation among proximate Tropheus populations
 evolves and persists in genetic isolation. Sporadic gene flow is effected
 by lake level fluctuations following climate changes and controlled by the
 persistence of habitat barriers during lake level changes. Since similar
 demographic patterns were previously reported for Lake Malawi cichlids,
 our data furthermore strengthen the hypothesis that major climatic events
 synchronized facets of cichlid evolution across the East African Great
 Lakes.
description: Tropheus_yellow_blotch_SSRTropheus_yellow_blotch_DLPalignment
DOI: 10.5061/dryad.2q3n104v
title: Data from: Maternal lineages in native Canadian equine populations and their relationship to the Nordic and Mountain and Moorland pony breeds

description: A 378-bp section of the mitochondrial displacement loop was used to
 estimate genetic diversity in the native Canadian equine populations. The
 inclusion of 10 Mountain and Moorland, 3 Nordic pony breeds, 2 feral
 populations, and 5 horse breeds were also investigated as they may have
 influenced the development (or rejuvenation) of the native Canadian
 populations. A total of 281 samples were sequenced, which produced 75
 haplotypes derived from 54 informative sites. On further investigation, 36
 of these 75 haplotypes were found to be previously unreported. Overall,
 total diversity was lowest in the feral Sable Island population with a
 haplotype diversity (0.27 ± 0.12), nucleotide diversity (0.0007 ± 0.0004),
 and pairwise difference of 0.286 ± 0.317. This is not surprising due to
 the geographic isolation of this population. Haplotype diversity was
 highest (1.00 ± 0.13) in the New Forest population, pairwise difference
 was highest (8.061 ± 4.028) in the Icelandic breed, whereas nucleotide
 diversity was highest in the Exmoor breed (0.0209 ± 0.0025). Within the
 Canadian populations, haplotype diversity was highest in the Newfoundland
 pony (0.96 ± 0.08), whereas pairwise difference and nucleotide diversity
 was highest in the Canadian horse (7.090 ± 3.581 and 0.0188 ± 0.0042,
 respectively). Three different estimates of genetic distances were used to
 examine the phylogenetic relationships amongst these populations. All 3
 estimates produced similar topologies. In general, the native Canadian
 populations were highly represented in the D clade, with particular
 emphasis in the D1 and D2 clades. This is an important factor when
 considering the phylogenetic conservation of these Canadian equine
 populations.
description: JOH sequence
 dataAll the sequence data
 that was used in this studySupplementaryTable1 Dec
 14 referencesAll accession numbers
 for the sequences used in this study.
DOI: 10.5061/dryad.sp521
title: Data from: Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution

description: A central prediction of much theory on adaptive radiations is that traits
 should evolve rapidly during the early stages of a clade's history
 and subsequently slowdown in rate as niches become saturated – a so-called
 “Early Burst”. Although a common pattern in the fossil record, evidence
 for early bursts of trait evolution in phylogenetic comparative data has
 been equivocal at best. We show here that this may not necessarily be due
 to the absence of this pattern in nature. Rather, commonly used methods to
 infer its presence perform poorly when when the strength of the burst -
 the rate at which phenotypic evolution declines - is small, and when some
 morphological convergence is present within the clade. We present two
 modifications to existing comparative methods that allow greater power to
 detect early bursts in simulated datasets. First, we develop posterior
 predictive simulation approaches and show that they outperform maximum
 likelihood approaches at identifying early bursts at moderate strength.
 Second, we use a robust regression procedure that allows for the
 identification and down-weighting of convergent taxa, leading to moderate
 increases in method performance. We demonstrate the utility and power of
 these approach by investigating the evolution of body size in cetaceans.
 Model fitting using maximum likelihood is equivocal with regards the mode
 of cetacean body size evolution. However, posterior predictive simulation
 combined with a robust node height test return low support for Brownian
 motion or rate shift models, but not the early burst model. While the jury
 is still out on whether early bursts are actually common in nature, our
 approach will hopefully facilitate more robust testing of this hypothesis.
 We advocate the adoption of similar posterior predictive approaches to
 improve the fit and to assess the adequacy of macroevolutionary models in
 general.
description: Functions to perform
 posterior predictive model fittingA series of functions
 written in the R language for performing posterior predictive simulation
 under Brownian motion and Early burst models of trait
 evolution.Slater_Pennell_Post.Pred_functions.Rcetacean analysesR code to perform posterior predictive and maximum likelihood model fitting to a cetacean body length datasetfitContinuous_modified_cetaceansA modified version of the fitContinuous function from the geiger library that allows a model to be fitted to a comparative dataset wherein the Brownian rate is permitted to vary along one, pre-specified internal edge of the phylogenyCetacean phylogenytime calibrated phylogeny of cetaceans from Slater et al (Proc Roy Soc B 2010) and used for posterior predictive model fittingwhales_final.phycetacean body length datacetacean body length data from Slater et al (Proc Roy Soc B 2010) and used for posterior predictive model fittingCetlengthdata.csvSlater_Pennel_supplementSupplementary results for posterior predictive tests performed on simulated data.
DOI: 10.5061/dryad.9nj6s
title: Data from: Social genetic and social environment effects on parental and helper care in a cooperatively breeding bird

description: Phenotypes expressed in a social context are not only a function of the
 individual, but can also be shaped by the phenotypes of social partners.
 These social effects may play a major role in the evolution of cooperative
 breeding if social partners differ in the quality of care they provide and
 if individual carers adjust their effort in relation to that of other
 carers. When applying social effects models to wild study systems, it is
 also important to explore sources of individual plasticity that could
 masquerade as social effects. We studied offspring provisioning rates of
 parents and helpers in a wild population of long-tailed tits Aegithalos
 caudatus using a quantitative genetic framework to identify these social
 effects and partition them into genetic, permanent environment and current
 environment components. Controlling for other effects, individuals were
 consistent in their provisioning effort at a given nest, but adjusted
 their effort based on who was in their social group, indicating the
 presence of social effects. However, these social effects differed between
 years and social contexts, indicating a current environment effect, rather
 than indicating a genetic or permanent environment effect. While this
 study reveals the importance of examining environmental and genetic
 sources of social effects, the framework we present is entirely general,
 enabling a greater understanding of potentially important social effects
 within any ecological population.
description: Long-tailed tit feeding
 ratesObservations of
 provisioning rates (visits/hour) with focal and social partner identities
 and time-varying covariates.lotti_feeding_rates.csv
DOI: 10.5061/dryad.nq3s6
title: Data from: Susceptibility to ecological traps is similar among closely related taxa but sensitive to spatial isolation

description: Ecological traps are maladaptive behavioural scenarios in which animals
 prefer to settle in habitats with the lowest survival and/or reproductive
 success. Aquatic insect species, for example, are attracted to sources of
 horizontally polarized light associated with natural water bodies, but
 today they commonly prefer to lay their eggs upon asphalt roads and
 buildings that reflect an unnaturally high percentage of polarized light.
 Ecological traps are a rapidly emerging threat to the persistence of
 animal populations, but the degree to which species vary in their
 susceptibility to them remains uninvestigated. We designed a field
 experiment to (1) assess the relative susceptibility of aquatic flies
 (Diptera) to a single maladaptive behavioural cue: variation in degree of
 horizontally polarized light (d), and (2) quantify how the isolation of an
 ecological trap from a high-quality habitat affects its relative
 attractiveness. We exposed wild dipterans to experimental test surfaces
 varying in d at three distances from natural streams and mapped
 behavioural reaction norms of habitat preference as a function of d and
 distance from high-quality habitat. All seven of the dipteran families
 were captured most in traps with progressively higher d values, especially
 those (d = 90–100%) that exceeded that of natural water bodies (30–80%).
 In most taxa, the height and slope of numerical responses to d were
 influenced by the distance of an ecological trap from a natural water
 body. Our results illustrate that dipterans have broadly evolved the use
 of a habitat selection behaviour that treats more strongly polarized light
 sources as indicative higher-quality habitats, making them broadly
 susceptible to ecological traps driven by polarized light pollution. We
 also found that the spatial isolation of ecological traps from
 higher-quality, but less attractive, habitats can either increase or
 reduce species' susceptibility to them.
description: Captures of aquatic
 insects in polarized light traps at three distances from rivers in New
 York StateWe created traps
 consisting of illumated oil-filled trays of 5 different colors that
 variously horizontally polarized light from ~20% to ~100%. These were
 placed in a row 5, 10 and 15 meters from 5 different rivers in southern
 New York State. They were exposed for 2 hours before sunset and their
 location randomized every 20 minutes. The goal of the study was to map the
 behavioral reaction norms of a diversity of aquatic insects to variation
 in the degree of polarized light and to understand how those reaction
 norms shifted as a function of the distance between a high quality natural
 habitat and the ecological trap habitat the test surfaces represented.
 Metadata for the variables is provided.PLP distance
 captures_dryad.xlsx
DOI: 10.5061/dryad.vt298
title: Data from: Influence of Pleistocene glacial/interglacial cycles on the genetic structure of the mistletoe cactus Rhipsalis baccifera (Cactaceae) in Mesoamerica

description: Phylogeographical work on cloud forest-adapted species provides
 inconsistent evidence on cloud forest dynamics during glacial cycles. A
 study of Rhipsalis baccifera (Cactaceae), a bird-dispersed epiphytic
 mistletoe cactus, was conducted to investigate genetic variation at
 sequence data from nuclear [internal transcribed spacer (ITS), 677 bp] and
 chloroplast (rpl32-trnL, 1092bp) DNA for 154 individuals across the
 species range in Mesoamerica to determine if such patterns are consistent
 with the expansion/contraction model of cloud forest during glacial
 cycles. We conducted population and spatial genetic analyses as well as
 gene flow and divergence time estimates between 24 populations comprising
 the distribution of R. baccifera in Mexico and Guatemala to gain insight
 of the evolutionary history of these populations, and a complementary
 species distribution modeling approach to frame information derived from
 the genetic analyses into an explicit paleoecological context. The results
 revealed a phylogeographical break at the Isthmus of Tehuantepec, and high
 levels of genetic diversity among populations and cloud forest areas.
 Despite the genetic differentiation of some R. baccifera populations, the
 widespread ITS ribotypes suggest effective nuclear gene flow via pollen
 and population differentiation shown by the rpl32-trnL suggests more
 restricted seed flow. Predictions of species distribution models under
 past last glacial maximum (LGM) climatic conditions and a significant
 signal of demographic expansion suggest that R. baccifera populations
 experienced a range expansion tracking the conditions of the cloud forest
 distribution and shifted to the lowlands with population connectivity
 during the LGM.
description: IMa (nuclear and
 chloroplast) comparing populations separated by the Isthmus of
 TehuantepecIMa_West populations
 from Isthmus of Tehuantepec versus East populations from Isthmus of
 Tehuantepec of Rhipsalis baccifera, combining chloroplast and nuclear
 markers.Ornelas&Rodríguez-Gómez_IMa_WESTvsEAST_comb.doc
DOI: 10.5061/dryad.j2d6v
title: Data from: Basilotritus uheni, a new cetacean (Cetacea, Basilosauridae) from the late Middle Eocene of Eastern Europe

description: A new basal basilosaurid cetacean, Basilotritus uheni n. gen. n. sp.,
 comes from the late middle Eocene (Bartonian) of Ukraine. It is the
 earliest dated record of a cetacean from Eastern Europe. The tympanic
 bulla of Basilotritus uheni shares basilosaurid synapomorphies but
 possesses unusual traits inherited from protocetids. Cetaceans related to
 Basilotritus uheni and referred to as Eocetus or “Eocetus” have been
 recorded from Africa, Europe, North America and South America. “Eocetus”
 wardii from North America is recombined as Basilotritus wardii.
 Platyosphys paulsonii and Platyosphys einori from Ukraine are considered
 as nomina dubia; specimens prior referred to as Platyosphys sp. are
 similar or related to Basilotritus. Other records of the Eocene cetaceans
 from Ukraine and south Russia are identified as Basilotritus or related
 genera. Early basilosaurids are demonstrated to be a paraphyletic,
 morphologically and geographically diverse group of the genera that
 colonized the world ocean as late as in Bartonian age and were probably
 the ancestors of Neoceti, as well as of more derived basilosaurids.
description: Goldin Zvonok Ukraine
 Supplemental Data File 1 Character list 20120913Goldin_Zvonok_Ukraine_Supplemental_Data_File_1_Character_list_20120913.docGoldin_Zvonok_Ukraine_Supplemental_Data_File_2_Character_codings_20120913Goldin_Zvonok_Ukraine_Supplemental_Data_File_3_list_of_taxonomical_identifications_20120913Goldin_Zvonok_Ukraine_Supplemental_Data_File_4_age_data_for_phylogeny_20120913
DOI: 10.5061/dryad.41hc4
title: Data from: Quantifying and comparing phylogenetic evolutionary rates for shape and other high-dimensional phenotypic data

description: Many questions in evolutionary biology require the quantification and
 comparison of rates of phenotypic evolution. Recently, phylogenetic
 comparative methods have been developed for comparing evolutionary rates
 on a phylogeny for single, univariate traits (σ2), and evolutionary rate
 matrices (R) for sets of traits treated simultaneously. However,
 high-dimensional traits like shape remain under-examined with this
 framework, because methods suited for such data have not been fully
 developed. In this article, I describe a method to quantify phylogenetic
 evolutionary rates for high-dimensional multivariate data (σ2mult), found
 from the equivalency between statistical methods based on covariance
 matrices and those based on distance matrices (R-mode and Q-mode methods).
 I then use simulations to evaluate the statistical performance of
 hypothesis testing procedures that compare σ2mult for two or more groups
 of species on a phylogeny. Under both isotropic and non-isotropic
 conditions, and for differing numbers of trait dimensions, the proposed
 method displays appropriate Type I error and high statistical power for
 detecting known differences in σ2mult among groups. By contrast, the Type
 I error rate of likelihood tests based on the evolutionary rate matrix (R)
 increases as the number of trait dimensions (p) increases, and becomes
 unacceptably large when only a few trait dimensions are considered.
 Further, likelihood tests based on R cannot be computed when the number of
 trait dimensions equals or exceeds the number of taxa in the phylogeny
 (i.e., when p ≥ N). These results demonstrate that tests based on σ2mult
 provide a useful means of comparing evolutionary rates for
 high-dimensional data that are otherwise not analytically accessible to
 methods based on the evolutionary rate matrix. This advance thus expands
 the phylogenetic comparative toolkit for high-dimensional phenotypic
 traits like shape. Finally, I illustrate the utility of the new approach
 by evaluating rates of head shape evolution in a lineage of Plethodon
 salamanders.
description: 2013-SystBiol-Adams-SuppMaterialSupplementary material containing additional simulation resultsHeadShapeMeansMean head shape data for nine Plethodon salamander species used in empirical example