cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3f765
title: Data from: Evolution of body shape in differently colored sympatric congeners and allopatric populations of Lake Malawi’s rock-dwelling cichlids

description: The cichlid fishes of Lake Malawi represent one of the most diverse
 adaptive radiations of vertebrates known. Among the rock-dwelling cichlids
 (mbuna), closely related sympatric congeners possess similar trophic
 morphologies (i.e. cranial and jaw structures), defend overlapping or
 adjacent territories, but can be easily distinguished based on male
 nuptial coloration. The apparent morphological similarity of congeners,
 however, leads to an ecological conundrum: theory predicts that ecological
 competition should lead to competitive exclusion. Hence, we hypothesized
 that slight, yet significant, ecological differences accompanied the
 divergence in sexual signals and that the divergence of ecological and
 sexual traits is correlated. To evaluate this hypothesis, we quantified
 body shape, a trait of known ecological importance, in populations of
 Maylandia zebra, a barred, widespread mbuna, and several sympatric
 non-barred congeners. We found that the barred populations differ in body
 shape from their non-barred sympatric congeners and that the direction of
 shape differences was consistent across all barred versus non-barred
 comparisons. Barred species are generally deeper-bodied which may be an
 adaptation to the structurally complex habitat they prefer, whereas the
 non-barred species have a more fusiform body shape, which may be adaptive
 in their more open micro-habitat. Furthermore, M. zebra populations
 sympatric with non-barred congeners differ from populations where the
 non-barred phenotype is absent and occupy less morphospace, indicating
 potential ecological character displacement. Mitochondrial DNA as well as
 published AFLP data indicated that the non-barred populations are not
 monophyletic and therefore may have evolved multiple times independently.
 Overall our data indicate that the evolution of coloration and body shape
 may be coupled as a result of correlational selection. We hypothesize that
 correlated evolution of sexually selected and ecological traits may have
 contributed to rapid speciation as well as the maintenance of diversity in
 one of the most diverse adaptive radiations known.
description: DLoop_alignmentalignment of DLoop sequences from 172 specimens for Bayes Factor analyses, PhiST calculation and construction of a haplotype network.Morphometric_DataLandmark data from 16 morphometric landmarks for 315 specimens
DOI: 10.5061/dryad.487mp
title: Data from: Disentangling endogenous versus exogenous pattern formation in spatial ecology: a case study of the ant Azteca sericeasur in southern Mexico

description: Spatial patterns in ecology can be described as reflective of
 environmental heterogeneity (exogenous), or emergent from dynamic
 relationships between interacting species (endogenous), but few empirical
 studies focus on the combination. The spatial distribution of the nests of
 Azteca sericeasur, a keystone tropical arboreal ant, is thought to form
 endogenous spatial patterns among the shade trees of a coffee plantation
 through self-regulating interactions with controlling agents (i.e. natural
 enemies). Using inhomogeneous point process models, we found evidence for
 both types of processes in the spatial distribution of A. sericeasur. Each
 year's nest distribution was determined mainly by a density-dependent
 relationship with the previous year's lagged nest density; but using
 a novel application of a Thomas cluster process to account for the effects
 of nest clustering, we found that nest distribution also correlated
 significantly with tree density in the later years of the study. This
 coincided with the initiation of agricultural intensification and tree
 felling on the coffee farm. The emergence of this significant exogenous
 effect, along with the changing character of the density-dependent effect
 of lagged nest density, provides clues to the mechanism behind a unique
 phenomenon observed in the plot, that of an increase in nest population
 despite resource limitation in nest sites. Our results have implications
 in coffee agroecological management, as this system provides important
 biocontrol ecosystem services. Further research is needed, however, to
 understand the effective scales at which these relationships occur.
description: Azteca_dataThe associated data of the manuscript "Disentangling endogenous versus exogenous pattern formation in spatial ecology: A case study of the ant Azteca sericeasur in southern Mexico". Data is contained within a .zip file and is described by the readme, also within.
DOI: 10.5061/dryad.n99n3
title: Data from: No effect of elevated carbon dioxide on reproductive behaviors in the three-spined stickleback

description: Ocean acidification, the reduction in ocean pH resulting from
 anthropogenic emissions of carbon dioxide (CO2), has been predicted to
 alter the behavior of fishes. During experimental exposure to CO2
 concentrations projected for the year 2100 (~1000 µatm), fish have been
 reported to display disturbances in activity, learning, behavioral
 lateralization, and even attraction to predator cues. Reproductive
 behaviors have received far less attention, despite an intensive research
 effort on ocean acidification and its ecological importance. Here, we
 investigate whether elevated levels of CO2 affect reproduction in breeding
 pairs of the three-spined stickleback, Gasterosteus aculeatus, a model
 species in behavioral, evolutionary ecology, and environmental toxicology.
 We found that males under both present day levels (400 µatm) and future
 levels (1000 µatm) of CO2 developed normal sexual ornaments, pursued
 normal nest building activities, exhibited similar levels of courtship
 behaviors and displacement fanning, and had the same mating probability.
 Moreover, fanning behavior during the paternal care period followed what
 is expected for the species for males from both treatments, and there was
 no effect of treatment on the numbers of offspring produced. This study is
 the first to investigate the effect of elevated CO2 on the complete
 breeding cycle in detail, studying an array of highly fitness-relevant
 traits. Our study showing surprising resilience of fish reproduction is an
 important contribution in order to realistically predict the impacts of
 future ocean acidification.
description: Sundin et al. 2017 Behav
 Ecol Suppl dataRaw-data
DOI: 10.5061/dryad.cv46n
title: Data from: Range expansion and population dynamics of an invasive species: the Eurasian Collared-Dove (Streptopelia decaocto)

description: Invasive species offer ecologists the opportunity to study the factors
 governing species distributions and population growth. The Eurasian
 Collared-Dove (Streptopelia decaocto) serves as a model organism for
 invasive spread because of the wealth of abundance records and the recent
 development of the invasion. We tested whether a set of environmental
 variables were related to the carrying capacities and growth rates of
 individual populations by modeling the growth trajectories of individual
 populations of the Collared-Dove using Breeding Bird Survey (BBS) and
 Christmas Bird Count (CBC) data. Depending on the fit of our growth
 models, carrying capacity and growth rate parameters were extracted and
 modeled using historical, geographical, land cover and climatic
 predictors. Model averaging and individual variable importance weights
 were used to assess the strength of these predictors. The specific
 variables with the greatest support in our models differed between data
 sets, which may be the result of temporal and spatial differences between
 the BBS and CBC. However, our results indicate that both carrying capacity
 and population growth rates are related to developed land cover and
 temperature, while growth rates may also be influenced by dispersal
 patterns along the invasion front. Model averaged multivariate models
 explained 35–48% and 41–46% of the variation in carrying capacities and
 population growth rates, respectively. Our results suggest that widespread
 species invasions can be evaluated within a predictable population ecology
 framework. Land cover and climate both have important effects on
 population growth rates and carrying capacities of Collared-Dove
 populations. Efforts to model aspects of population growth of this
 invasive species were more successful than attempts to model static
 abundance patterns, pointing to a potentially fruitful avenue for the
 development of improved invasive distribution models.
description: cbc.growthcbc.abundcbc.2010.abundbbs.growthbbs.abund
DOI: 10.5061/dryad.25tf0
title: Data from: Population genetic structure in hyacinth macaws (Anodorhynchus hyacinthinus) and identification of the probable origin of confiscated individuals

description: Understanding the intraspecific genetic composition of populations in
 different geographic locations is important for the conservation of
 species. If genetic variability is structured, conservation strategies
 should seek to preserve the diversity of units. Also, origin of
 individuals can be determined, which is important for guiding actions
 against animal trafficking. The hyacinth macaw (Anodorhynchus
 hyacinthinus) is located in allopatric regions, vulnerable to extinction
 and suffering animal trafficking pressure. Therefore, we characterized its
 population genetic structure based on 10 microsatellites from 98
 individuals and 2123bp of mitochondrial sequence (ND5, cytochrome b, and
 ND2) from 80 individuals. Moderate to high levels of differentiation were
 observed among 3 geographic regions of Brazil: the north/northeast of the
 country, the north Pantanal, and the south Pantanal. Differentiation
 between the 2 regions within the Pantanal was not expected, as they are
 relatively close and there is no known barrier to macaw movement between
 these regions. These genetically differentiated groups were estimated to
 have diverged 16000 to 42000 years ago. The low genetic variability
 observed seems not to be the result of past bottlenecks, although a
 star-shaped haplotype network and the mismatch distribution suggest that
 there was recent demographic expansion in the north and northeast.
 Environmental changes in the Holocene could have caused this expansion.
 Given the genetic structure observed, the most probable regions of origin
 of 24 confiscated individuals were identified. Thus, these data helped to
 trace illegal traffic routes and identify natural populations that are
 being illegally harvested.
description: Microsatellite
 genotypingMicrosatellite
 genotyping of Hyacinth Macaw by population.Cytochrome b sequences
 of mitochondrial DNASequencing of the
 cytochrome b of mitochondrial DNA of Hyacinth MacawsND2 Sequences of
 mitochondrial DNANADH dehydrogenase 2
 (ND2) sequencing of the mitochondrial DNA of Hyacinth
 macaws.
DOI: 10.5061/dryad.sq816
title: Data from: Rapid evolution of ant thermal tolerance across an urban-rural temperature cline

description: Rates of urbanization are accelerating worldwide. The increases in
 temperature associated with ‘urban heat island’ effects provide both an
 ecological imperative and a unique opportunity to explore the ecological
 and evolutionary mechanisms that underlie organismal responses to rapid
 environmental change. We used the acorn ant, Temnothorax curvispinosus
 (Mayr 1866), to compare shifts in thermal tolerance of ants from rural and
 urban habitats throughout Cleveland, USA. Urban warming in the region has
 been ongoing for the past century which translates to 20 or fewer acorn
 ant generations. Using a common garden experiment, we found gains in the
 ability to withstand high temperatures and losses in the ability to
 withstand cool temperatures among ants in urban habitats. Owing to the
 greater magnitude of phenotypic change in lower compared with upper
 tolerances, tolerance breadth decreased in urban habitats.
 Mechanistically, these shifts in thermal tolerance under urbanization
 reflected both evolutionary change and phenotypic plasticity, as ants from
 urban areas exhibited higher thermal tolerances compared with ants from
 rural areas regardless of rearing temperature, and ants reared in the
 warmer temperature treatment exhibited higher tolerances than ants reared
 in the cooler temperature treatment. We also found evidence of evolved
 plasticity as the slope of the response to warmer and colder rearing
 environments differed significantly among rural and urban populations.
 While much of the ecological forecasting literature focuses on plastic
 responses to environmental change, our study provides evidence of rapid
 evolution of thermal tolerances, and suggests the importance of including
 evolutionary responses in forecasts of organismal responses to climatic
 change.
description: AcornAntThermalToleranceAcorn ant thermal tolerances (upper and lower) from urban and rural sites in Cleveland Ohio USA. Column header descriptions: ColonyID = unique identifier for each ant colony; latitude = decimal degrees latitude for collection site; longitude = decimal degrees longitude for collection site; ISA = percent developed impervious surface of collection site; UR = whether the habitat is considered urban or rural; Individual = unique identifier for each individual; Genus/Species = latin binomial for study organism; Caste = whether the individual is a worker, alate or queen; WhenTol = when the tolerances were assessed, post.cg is post-common garden; Treatment = temperature treatment, daytime_nighttime; DateIn = date put in temperature treatment; DateTol = date thermal tolerance assessed; TrtDays = number of days in the temperature treatment; Tolerance = thermal tolerance estimate; TolType = maximum or minimum tolerance assessed; TolRamp = rate of temperature increase degreesC_per number of minutes
DOI: 10.5061/dryad.8vr04
title: Data from: Waiving the extinction debt: can shade from coffee prevent extinctions of epiphytic plants from isolated trees?

description: Aim: Local extinction after habitat modifications is often delayed,
 leading to an extinction debt. Our first aim was to develop a conceptual
 model for natural and human-mediated habitat improvements after a
 disturbance that may waive part of the predicted extinction debt. Second,
 we wanted to test this model on the distribution of epiphytic plants on
 trees that had been isolated in the agricultural matrix after forest
 clearing, around which coffee subsequently had been planted with a
 possible improvement of the microclimate. Location: Bonga, Southern
 Nations, Nationalities and Peoples Region (SNNPR), Ethiopia. Methods: We
 studied 50 trees that had been isolated for periods ranging from a few
 years to half a century after clearing. The trees were now located in the
 agricultural landscape at different distances from intact Afromontane
 forests. Fourteen trees in the forests were used as references. Each tree
 was inventoried for all vascular epiphytic plants, mosses and liverworts.
 Results: Time since clearance had a direct negative effect on number of
 forest specialist species via delayed extinctions and the detected large
 extinction debt of both bryophytes and vascular plants continued to be
 paid over several decades. However, time since clearance had an indirect
 positive effect on number of forest indicator species via the reappearance
 of shade from coffee planted surrounding the trees, even if the waiving
 effect on the extinction debt was rather small. Additionally, trees at
 further distances from the forest edge had fewer forest-associated
 species. Main conclusions: Our results show that the ability of
 agroecological landscapes to foster forest biodiversity may be
 overestimated if meta-community processes over time and space are not
 taken into account. However, the possibility of initiating counteracting
 processes that modify the level of expected local extinctions should be
 evaluated more often to find ways of improving conditions for biodiversity
 in human-modified landscapes.
description: Data_Hylander_NemomissaEnvironmental data and species occurrence data from all sites. See the ReadMe file for more explanations.
DOI: 10.5061/dryad.29560
title: Data from: Evidence for the adaptive significance of secondary compounds in vertebrate-dispersed fruits

description: Although the primary function of fleshy fruits is to attract seed
 dispersers, many ripe fruits contain toxic secondary compounds. A number
 of hypotheses have been proposed to explain this evolutionary paradox,
 most of which describe the potential adaptive role secondary compounds may
 play in seed dispersal. However, some authors have argued that fruit
 secondary compounds may be non-adaptive, and instead explain their
 occurrence as a pleiotropic consequence of selection for defense of leaves
 and other tissues. We address these alternative evolutionary hypotheses
 through a comparative examination of iridoid glycosides in leaves, unripe
 fruits, and ripe fruits of Lonicera x bella (Belle's bush
 honeysuckle), combined with an examination of fruit damage and removal in
 natural populations. We provide several lines of evidence that fruit
 secondary compounds cannot be explained solely as a consequence of foliar
 defense, including higher concentrations and more individual compounds in
 fruits compared to leaves and a negative relationship between iridoid
 glycoside concentration and fruit damage. However, we also show that the
 composition and concentrations of secondary compounds in leaves and fruits
 are not entirely independent, emphasizing that selection in different
 plant parts is intrinsically linked. We conclude that the adaptive
 significance of chemical traits is best considered in a whole-plant
 context that includes fruit-frugivore interactions.
description: 12 iridoid glycosides in
 different plant parts of Lonicera x bellaIndividual IGs in plant
 parts_for NMDS.csvTotal iridoid glycosides
 in different plant parts of Lonicera x bellaTotal IGs in plant parts_for
 GLMM.csvCorrelations among
 iridoid glycosides in different plant parts of Lonicera x
 bellaIndividual IGs in plant
 parts_for correlations.csvFruit Damage and Removal
 Rates to Lonicera x bella in 2007Field Data_2007_for
 GLMM.csvFruit Damage and Removal
 Rates to Lonicera x bella in 2008Field Data_2008_for
 GLMM.csvEffects of fruit iridoid
 glycosides on insect damage in Lonicera x bellaIG Effects on Insect Damage_for
 PC regression.csvEffects of fruit iridoid
 glycosides on microbe damage in Lonicera x bellaIG Effects on Microbe
 Damage_for PC regression.csvEffects of fruit iridoid
 glycosides on fruit removal in Lonicera x bellaIG Effects on Removal_for PC
 regression.csv
DOI: 10.5061/dryad.2kp7q7vb
title: Data from: A second species of the family Allophrynidae (Amphibia: Anura)

description: We describe Allophryne resplendens, a new species from two localities in
 the Amazon rainforest of Loreto, Peru, of the family Allophrynidae, which
 was monotypic until this discovery. The new species can be readily
 differentiated from Allophryne ruthveni on the basis of dorsal and ventral
 coloration both in life and in preservative, transverse processes of
 presacral II oriented anterolaterally (oriented laterally in A. ruthveni),
 and 19 nucleotide autapomorphies for 761 base pairs (bp) of the
 mitochondrial gene 16S and 16 for 923 bp of 12S. Maximum parsimony
 analysis of the mitochondrial gene 12S and a fragment of up to 1060 bp of
 16S supports the new species as sister to A. ruthveni.
description: Alloprhyne_resplendens_TotalAlloprhyne_distances_12SAllophryne_distances_16S
DOI: 10.5061/dryad.s1t53
title: Data from: Evidence for an association between post-fledging dispersal and microsatellite multilocus heterozygosity in a large population of greater flamingos

description: Dispersal can be divided into three stages: departure, transience and
 settlement. Despite the fact that theoretical studies have emphasized the
 importance of heterozygosity on dispersal strategies, empirical evidence
 of its effect on different stages of dispersal is lacking. Here, using
 multi-event capture-mark-recapture models, we show a negative association
 between microsatellite multilocus heterozygosity (MLH; 10 loci; n = 1023)
 and post-fledging dispersal propensity for greater flamingos,
 Phoenicopterus roseus, born in southern France. We propose that the
 negative effects of inbreeding depression affects competitive ability and
 therefore more homozygous individuals are more likely to disperse because
 they are less able to compete within the highly saturated natal site.
 Finally, a model with the effect of MLH on propensity of post-fledgling
 dispersers to disperse to the long-distance sites of Africa was equivalent
 to the null model, suggesting that MLH had low to no effect on dispersal
 distance. Variations in individual genetic quality thus result in
 context-dependent heterogeneity in dispersal strategies at each stage of
 dispersal. Our results have important implications on fitness since sites
 visited early in life are known to influence site selection later on in
 life and future survival.
description: DataPlosOneCapture mark recapture data (from summer 1995 to winter 2010) for greater flamingos captured as fledglings and ringed between 1995 and 1998 which were genotyped for microsatellite multi-locus heterozygosity. Body condition of fledgling also provided.
DOI: 10.5061/dryad.4r910
title: Data from: Integrating sequence evolution into probabilistic orthology analysis

description: Orthology analysis, that is, finding out whether a pair of homologous
 genes are orthologs — stemming from a speciation — or paralogs — stemming
 from a gene duplication - is of central importance in computational
 biology, genome annotation, and phylogenetic inference. In particular, an
 orthologous relationship makes functional equivalence of the two genes
 highly likely. A major approach to orthology analysis is to reconcile a
 gene tree to the corresponding species tree, (most commonly performed
 using the most parsimonious reconciliation, MPR). However, most such
 phylogenetic orthology methods infer the gene tree without considering the
 constraints implied by the species tree and, perhaps even more
 importantly, only allow the gene sequences to influence the orthology
 analysis through the a priori reconstructed gene tree. We propose a sound,
 comprehensive Bayesian Markov chain Monte Carlo-based method,
 DLRSOrthology, to compute orthology probabilities. It efficiently sums
 over the possible gene trees and jointly takes into account the current
 gene tree, all possible reconciliations to the species tree, and the,
 typically strong, signal conveyed by the sequences. We compare our method
 with PrIME-GEM, a probabilistic orthology approach built on a
 probabilistic duplication-loss model, and MRBAYESMPR, a probabilistic
 orthology approach that is based on conventional Bayesian inference
 coupled with MPR. We find that DLRSOrthology outperforms these competing
 approaches on synthetic data as well as on biological data sets and is
 robust to incomplete taxon sampling artifacts.
description: Supplementary Material
 for “Integrating Sequence Evolution into Probabilistic Orthology
 Analysis”This document contains
 the supplementary information including synthetic data parameters,
 figures, and tables for the paper “Integrating Sequence Evolution into
 Probabilistic Orthology Analysis”Supplementary_Material.pdf