cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zw3r2287m
title: The implications of incongruence between gene tree and species tree topologies for divergence time estimation

description: Phylogenetic analyses are increasingly being performed with datasets that
 incorporate hundreds of loci. Due to incomplete lineage sorting,
 hybridization, and horizontal gene transfer, the gene trees for these loci
 may often have topologies that differ from each other and from the species
 tree. The effect of these topological incongruences on divergence time
 estimation has not been fully investigated. Using a series of simulation
 experiments and empirical analyses, we demonstrate that when topological
 incongruence between gene trees and the species tree is not accounted for,
 the temporal duration of branches in regions of the species tree that are
 affected by incongruence is underestimated, whilst the duration of other
 branches is considerably overestimated. This effect becomes more
 pronounced with higher levels of topological incongruence. We show that
 this pattern results from erroneous estimation of the number of
 substitutions along branches in the species tree, although the effect is
 modulated by the assumptions inherent to divergence time estimation, such
 as those relating to the fossil record or among-branch-substitution-rate
 variation. By only analysing loci with gene trees that are topologically
 congruent with the species tree, or only taking into account the branches
 from each gene tree that are topologically congruent with species tree, we
 demonstrate that the effects of topological incongruence can be
 ameliorated. Nonetheless, even when topologically congruent gene trees or
 topologically congruent branches are selected, error in divergence time
 estimates remains. This stems from temporal incongruences between
 divergence times in species trees and divergence times in gene trees, and
 more importantly, the difficulty of incorporating necessary assumptions
 for divergence time estimation.
DOI: 10.5061/dryad.sf7m0cg5r
title: Environment driven changes in diversity of riparian plant communities along a mountain river

description: The study of changes in species richness and composition along rivers has
 focused on large spatial scales. It has been ignored that in different
 sections of the river (high mountain area, middle zone and river mouth)
 the specific environmental conditions can generate different longitudinal
 patterns of the species richness and composition. In this study we
 determine if species richness and composition of the riparian plant
 communities change along a mountain river and if these changes are related
 with environmental variables. We expect an increase in species richness
 and turnover along the river, that the upstream communities would be a
 subset of the downstream communities and that such would be related to
 edaphic and hydrologic conditions. To test this, we sampled three strata
 of the riparian vegetation (upper: individuals with &lt;1 cm of ND,
 middle: individuals with &gt;1 cm of ND, low: individuals with
 &gt;1 m tall) in a set 15 sites that we place along a mountain river.
 Additionally, we recorded topographic, hydrological, morphological, and
 soil variables. We performed correlation analyzes to determine if changes
 in species richness and turnover were related to increased distance to the
 origin of the river. Also, we obtained the nestedness and evaluated the
 importance of environmental variables with GLM, LASSO regression and CCA.
 With the increase in distance the species richness decreases in the upper
 stratum, but not in the middle and the low stratum (although the highest
 values were observed near the origin of the river), the turnover increase
 in all strata and the upstream communities were not a subset of the
 downstream communities. The changes in species richness and composition
 were related to topographic (altitude), hydrological (flow) and edaphic
 (conductivity and pH) variables. Our results indicate that at small
 spatial scales the patterns of richness and composition differ from what
 has been found at larger spatial scales and that these patterns are
 associated with environmental changes in the strong altitude gradients of
 mountain rivers.
DOI: 10.25338/b8334z
title: Project factors and conservation outcome data for SeaDoc Society-funded research projects

description: This dataset reflects project factors and conservation success of 20 years
 of research funded by the academically-based marine conservation group the
 Sea Doc Society (UC Davis School of Veterinary Medicine). These data
 were compiled through interviews with Principal investigators and
 co-investigators, and SeaDoc Society's records.
description: This dataset was collected through interviews conducted over the
 phone using a standardized interview questionnaire.
description: Two ReadMe files are included with this dataset submission. They
 include "SeaDoc_Policy_Rcode_ReadMe", which describes the
 "SeaDoc_Policy_Rcode.txt" file, and
 "SeaDoc_Policy_dataset_ReadMe" which describes the
 "SeaDoc_Policy_dataset.csv" file.
DOI: 10.5061/dryad.4f4qrfjbn
title: An island-hopping bird reveals how founder events shape genome-wide divergence

description: When populations colonise new areas, both strong selection and strong
 drift can be experienced due to novel environments and small founding
 populations, respectively. Empirical studies have predominantly focused on
 the phenotype when assessing the role of selection, and limited
 neutral-loci when assessing founder-induced loss of diversity.
 Consequently, the extent to which processes interact to influence
 evolutionary trajectories is difficult to assess. Genomic-level approaches
 provide the opportunity to simultaneously consider these processes. Here,
 we examine the roles of selection and drift in shaping genomic diversity
 and divergence in historically documented sequential island colonisations
 by the silvereye bird (Zosterops lateralis). We provide the first
 empirical demonstration of the rapid appearance of highly diverged genomic
 regions following population founding, the position of which are highly
 idiosyncratic. As these regions rarely contained loci putatively under
 selection, it is most likely that these differences arise via the
 stochastic nature of the founding process. However, selection is required
 to explain rapid evolution of larger body size in insular silvereyes.
 Reconciling our genomic data with these phenotypic patterns suggests there
 may be many genomic routes to the island phenotype, that vary across
 populations. Finally, we show that accelerated divergence associated with
 multiple founding steps is the product of genome-wide rather than
 localised differences, and that diversity erodes due to loss of rare
 alleles. However even multiple founder events do not result in divergence
 and diversity levels seen in evolutionary older subspecies, and therefore
 do not provide a shortcut to speciation as proposed by founder-effect
 speciation models.
description: This dataset contains VCF files and custom script required to
 assign SNPs chromosomal positions (based on zebra finch
 assembly).
DOI: 10.5061/dryad.tmpg4f4z3
title: Data from: Cardiorespiratory adjustments to chronic environmental warming improves hypoxia tolerance in European perch

description: Aquatic hypoxia will become increasingly prevalent in the future as a
 result of eutrophication combined with climate warming. While short-term
 warming typically constrains fish hypoxia tolerance, many fishes cope with
 warming by adjusting physiological traits through thermal acclimation.
 Yet, little is known about how such adjustments affect tolerance to
 hypoxia. We examined European perch (Perca fluviatilis) from the Biotest
 enclosure (23°C, Biotest population), a unique ∼1 km2 ecosystem
 artificially warmed by cooling water from a nuclear power plant, and an
 adjacent reference site (16–18°C, reference population). Specifically, we
 evaluated how acute and chronic warming affect routine oxygen consumption
 rate (Ṁ O2, routine) and cardiovascular performance in acute hypoxia,
 alongside assessment of the thermal acclimation of the aerobic
 contribution to hypoxia tolerance (critical O2 tension for Ṁ O2, routine:
 Pcrit) and absolute hypoxia tolerance (O2 tension at loss of equilibrium;
 PLOE). Chronic adjustments (possibly across lifetime or generations)
 alleviated energetic costs of warming in Biotest perch by depressing Ṁ
 O2, routine and cardiac output, and by increasing blood O2 carrying
 capacity relative to reference perch acutely warmed to 23°C. These
 adjustments were associated with improved maintenance of cardiovascular
 function and Ṁ O2, routine in hypoxia (i.e. reduced Pcrit). However,
 while Pcrit was only partially thermally compensated in Biotest perch,
 they had superior absolute hypoxia tolerance (i.e. lowest PLOE) relative
 to reference perch irrespective of temperature. We show that European
 perch can thermally adjust physiological traits to safeguard and even
 improve hypoxia tolerance during chronic environmental warming. This
 points to cautious optimism that eurythermal fish species may be resilient
 to the imposition of impaired hypoxia tolerance with climate warming.
DOI: 10.5061/dryad.mw6m905w9
title: A Likelihood-Ratio Test for Lumpability of Phylogenetic Data: Is the Markovian Property of an Evolutionary Process Retained in Recoded DNA?

description: Abstract In molecular phylogenetics, it is typically assumed that the
 evolutionary process for DNA can be approximated by independent and
 identically distributed Markovian processes at the variable sites and that
 these processes diverge over the edges of a rooted bifurcating tree.
 Sometimes the nucleotides are transformed from a 4-state alphabet to a 3-
 or 2-state alphabet by a procedure that is called recoding, lumping, or
 grouping of states. Here, we introduce a likelihood-ratio test for
 lumpability for DNA that has diverged under different Markovian
 conditions, which assesses the assumption that the Markovian property of
 the evolutionary process over each edge is retained after recoding of the
 nucleotides. The test is derived and validated numerically on simulated
 data. To demonstrate the insights that can be gained by using the test, we
 assessed two published data sets, one of mitochondrial DNA from a
 phylogenetic study of the ratites and the other of nuclear DNA from a
 phylogenetic study of yeast. Our analysis of these data sets revealed that
 recoding of the DNA eliminated some of the compositional heterogeneity
 detected over the sequences. However, the Markovian property of the
 original evolutionary process was not retained by the recoding, leading to
 some significant distortions of edge lengths in reconstructed
 trees.[Evolutionary processes; likelihood-ratio test; lumpability;
 Markovian processes; Markov models; phylogeny; recoding of nucleotides.]
description: The data were generated as described in:
 Phillips et al. (2010). Tinamous and moa flock together:
 mitochondrial genome sequence analysis reveals independent losses of
 flight among ratites. Syst. Biol. 59:90-107. or
 obtained from: Phillips et al. (2004). Genome-scale
 phylogeny and the detection of systematic biases. Mol. Biol. Evol.
 21:1455-1458. The data were subsequently used
 in: Vera-Ruiz et al. (2021). A likelihood-ratio test
 for lumpability of phylogenetic data: Is the Markovian property of an
 evolutionary process retained in recoded DNA? Syst. Biol. (doi:
 10.1093/sysbio/syab074).
description: The data files are presented in the Nexus format and are
 identical to that obtained from Matthew J. Philips, first author
 of : Phillips et al. (2010). Tinamous and moa flock
 together: mitochondrial genome sequence analysis reveals independent
 losses of flight among ratites. Syst. Biol. 59:90-107.
 Phillips et al. (2004). Genome-scale phylogeny and the detection
 of systematic biases. Mol. Biol. Evol. 21:1455-1458.
DOI: 10.5061/dryad.6hdr7sr0d
title: Bat activity under three lighting treatments

description: Artificial light at night (ALAN) is a rapidly intensifying form of
 environmental degradation that can impact wildlife by altering
 light-mediated physiological processes that control a broad range of
 behaviors. Although nocturnal animals are most vulnerable, ALAN’s effects
 on North American bats have been surprisingly understudied. Most of what
 is known is based on decades-old observations of bats around street lights
 with traditional lighting technologies that have been increasingly
 replaced by energy-efficient broad-spectrum lighting, rendering our
 understanding of the contemporary effects of ALAN on North American bats
 even less complete. We experimentally tested the effects of broad-spectrum
 ALAN on presence/absence, foraging activity, and species composition in a
 Connecticut, USA bat community by illuminating foraging habitat with
 light-emitting diode (LED) floodlights and comparing acoustic recordings
 between light and dark conditions. Lighting dramatically decreased
 presence and activity of little brown bats (Myotis lucifugus), which we
 detected on only 14% of light nights compared to 65% of dark (lights off)
 and 69% of control (lights removed) nights. Big brown bat (Eptesicus
 fuscus) activity on light nights averaged only half that of dark
 and control nights. Lighting did not affect presence/absence of
 silver-haired bats (Lasionycteris noctivagans), but decreased their
 activity. There were no effects on eastern red bats (Lasiurus borealis) or
 hoary bats (L. cinereus), which have been described previously as
 light-tolerant. Aversion to lighting by some species but not others caused
 a significant shift in community composition, thereby potentially
 altering competitive balances from natural conditions. Our
 results demonstrate that only a small degree of ALAN can represent a
 significant form of habitat degradation for some North American bats,
 including the endangered little brown bat. Research on the extent to which
 different lighting technologies, colors, and intensities affect these
 species is urgently needed and should be a priority in conservation
 planning for North America’s bats.
DOI: 10.5061/dryad.cfxpnvx4s
title: Pedigree-based assessment of recent population connectivity in a threatened rattlesnake

description: Managing endangered species in fragmented landscapes requires estimating
 dispersal rates between populations over contemporary timescales. Here we
 develop a new method for quantifying recent dispersal using genetic
 pedigree data for close and distant kin. Specifically, we describe an
 approach that infers missing shared ancestors between pairs of kin in
 habitat patches across a fragmented landscape. We then apply a
 stepping-stone model to assign unsampled individuals in the pedigree to
 probable locations based on minimizing the number of movements required to
 produce the observed locations in sampled kin pairs. Finally, we use all
 pairs of reconstructed parent-offspring sets to estimate dispersal rates
 between habitat patches under a Bayesian model. Our approach measures
 connectivity over the timescale represented by the small number of
 generations contained within the pedigree and so is appropriate for
 estimating the impacts of recent habitat changes due to human activity. We
 used our method to estimate recent movement between newly discovered
 populations of threatened Eastern Massasauga Rattlesnakes (Sistrurus
 catenatus) using data from 2996 RAD-based genetic loci. Our pedigree
 analyses found no evidence for contemporary connectivity between five
 genetic groups, but, as validation of our approach, showed high dispersal
 rates between sample sites within a single genetic cluster. We conclude
 that these five genetic clusters of Eastern Massasauga Rattlesnakes have
 small numbers of resident snakes and are demographically isolated
 conservation units. More broadly, our methodology can be widely applied to
 determine contemporary connectivity rates, independent of bias from shared
 genetic similarity due to ancestry that impacts other approaches.
description: Dataset is ddRADseq from 86 individual <i>Sistrurus
 catenatus </i>(Eastern Massasauga Rattlesnake). Individuals were
 sequenced on Illumina HiSeq2500 and HiSeq4000 platforms, using single-end
 reads size selected from 300-600bp using EcoR1 and Pst1 for our
 restriction enzymes. Reads were aligned against a reference genome using
 ipyrad, and filtering done in PLINK 2.0, with all 2996 loci called in
 every individual.
description: No missing values should be present in the data. All loci are
 bi-allelic, and anonymized survey sites linked to sample names have
 been uploaded in a separate document. Due to concerns over the sensitive
 nature of these sites, no GPS coordinates or morphometric data are
 reported. All <em>S. catenatus</em> in this dataset came from
 Ashtabula county, Ohio, USA. Rscripts have been uploaded as examples to
 follow, but due to removed location and morphology data, cannot be
 run.
DOI: 10.5061/dryad.1zcrjdfrf
title: Data for: Costs of reproduction under experimental climate change across elevations in the perennial forb Boechera stricta

description: Investment in current reproduction can reduce future fitness by depleting
 resources needed for maintenance, particularly under environmental stress,
 and such trade-offs influence life history evolution. We tested whether
 climate change alters the future-fitness costs of current reproduction in
 a large-scale field experiment of Boechera stricta (Brassicaceae). Over
 six years, we simulated climate change along an elevational gradient in
 the Rocky Mountains through snow removal, which accelerates snowmelt and
 reduces soil water availability. Costs of reproduction were greatest in
 arid, lower elevations, where high initial reproductive effort depressed
 future fitness. At mid-elevations, initial reproduction augmented
 subsequent fitness in benign conditions, but pronounced costs emerged
 under snow removal. At high elevation, snow removal dampened these costs
 by prolonging the growing season. In most scenarios, failed reproduction
 in response to resource limitation depressed lifetime fecundity, and fruit
 abortion only benefited high-fitness individuals under benign conditions.
 We propose that climate change could shift life history trade-offs in an
 environment-dependent fashion, possibly favoring early reproduction and
 short lifespans in stressful conditions.
description: We collected the data in a long-term field study.
description: We provide all data files and R scripts for analysis.
DOI: 10.5061/dryad.z08kprrc9
title: Data from: Systematic evaluation of horizontal gene transfer between eukaryotes and viruses

description: Gene exchange between viruses and their hosts acts as a key facilitator of
 horizontal gene transfer and is hypothesized to be a major driver of
 evolutionary change. Our understanding of this process comes primarily
 from bacteria and phage co-evolution, but the mode and functional
 importance of gene transfers between eukaryotes and their viruses remains
 anecdotal. Here we systematically characterized viral-eukaryotic gene
 exchange across eukaryotic and viral diversity, identifying thousands of
 transfers, and revealing their frequency, taxonomic distribution, and
 projected functions. Eukaryote-derived viral genes, abundant in the
 Nucleocytoviricota, highlighted common strategies for viral
 host-manipulation, including metabolic reprogramming, proteolytic
 degradation, and extracellular modification. Furthermore, viral-derived
 eukaryotic genes implicate genetic exchange in the early evolution and
 diversification of eukaryotes, particularly through viral-derived
 glycosyltransferases, which have impacted structures as diverse as algal
 cell walls, trypanosome mitochondria, and animal tissues. These findings
 illuminate the nature of viral-eukaryotic gene exchange and its impact on
 the evolution of viruses and their eukaryotic hosts.
description: See README.txt
DOI: 10.5061/dryad.6djh9w113
title: Adaptive and non-adaptive plasticity in changing environments: implications for sexual species with different life history strategies

description: Populations adapt to novel environmental conditions by genetic changes or
 phenotypic plasticity. Plastic responses are generally faster and can
 buffer fitness losses under variable conditions. Plasticity is typically
 modelled as random noise and linear reaction norms that assume simple
 one-to-one genotype-phenotype maps and no limits to the phenotypic
 response. Most studies on plasticity have focused on its effect on
 population viability. However, it is not clear, whether the advantage of
 plasticity depends solely on environmental fluctuations or also on the
 genetic and demographic properties (life histories) of populations. Here
 we present an individual-based model and study the relative importance of
 adaptive and non-adaptive plasticity for populations of sexual species
 with different life histories experiencing directional stochastic climate
 change. Environmental fluctuations were simulated using differentially
 autocorrelated climatic stochasticity or noise color, and scenarios of
 directional climate change. Non-adaptive plasticity was simulated as a
 random environmental effect on trait development, while adaptive
 plasticity as a linear, saturating, or sinusoidal reaction norm. The last
 two imposed limits to the plastic response and emphasized flexible
 interactions of the genotype with the environment. Interestingly, this
 assumption led to (i) smaller phenotypic than genotypic variance in the
 population (many-to-one genotype-phenotype map) and the coexistence of
 polymorphisms, and (ii) the maintenance of higher genetic variation –
 compared to linear reaction norms and genetic determinism – even when the
 population was exposed to a constant environment for several generations.
 Limits to plasticity led to genetic accommodation, when costs were
 negligible, and to the appearance of cryptic variation when limits were
 exceeded. We found that adaptive plasticity promoted population
 persistence under red environmental noise and was particularly important
 for life histories with low fecundity. Populations producing more
 offspring could cope with environmental fluctuations solely by genetic
 changes or random plasticity, unless environmental change was too fast.
description: The data was collected using a modified version (attached to this
 website) of the model PanModel33, download
 link: https://github.com/danielrm84/PanModel33 All the
 simulation scenarios, parameter values, and full method are described in
 the paper Romero-Mujalli et al. Ecol. Evol.
description: No missing values. Please contact Daniel Romero-Mujalli if you
 have any questions. Note that the Rscripts are also available for
 download.