cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3h5kv
title: Data from: Different evolutionary paths to complexity for small and large populations of digital organisms

description: A major aim of evolutionary biology is to explain the respective roles of
 adaptive versus non-adaptive changes in the evolution of complexity. While
 selection is certainly responsible for the spread and maintenance of
 complex phenotypes, this does not automatically imply that strong
 selection enhances the chance for the emergence of novel traits, that is,
 the origination of complexity. Population size is one parameter that
 alters the relative importance of adaptive and non-adaptive processes: as
 population size decreases, selection weakens and genetic drift grows in
 importance. Because of this relationship, many theories invoke a role for
 population size in the evolution of complexity. Such theories are
 difficult to test empirically because of the time required for the
 evolution of complexity in biological populations. Here, we used digital
 experimental evolution to test whether large or small asexual populations
 tend to evolve greater complexity. We find that both small and large—but
 not intermediate-sized—populations are favored to evolve larger genomes,
 which provides the opportunity for subsequent increases in phenotypic
 complexity. However, small and large populations followed different
 evolutionary paths towards these novel traits. Small populations evolved
 larger genomes by fixing slightly deleterious insertions, while large
 populations fixed rare beneficial insertions that increased genome size.
 These results demonstrate that genetic drift can lead to the evolution of
 complexity in small populations and that purifying selection is not
 powerful enough to prevent the evolution of complexity in large
 populations.
description: ReadMe
 FileThis file is a guide to
 the rest of the files associated with this manuscript.Avida Configuration
 FilesThis folder contains the
 Avida configuration files needed to replicate all but one of the
 experimental treatments in the paper.config_files.zipAvida nopX Configuration FilesThis file contains the Avida configuration files needed to run the "non-functional insertion" treatment experiments. "nopX" refers to the nop-X instruction added in this configuration.config_files_nopx.zipSubmission FilesThis folder contains the scripts used to submit the Avida experiments to a computing cluster.sub_files.zipFigures ScriptThis python script creates all of the figures in the paper.create_figures.pyCSV ScriptThis python script created the final csv used to create the figures for the paper.create_final_csv.pyRename Detail Files ScriptThis python script renamed the detail files from the Avida experiments in order to better use them in Avida's Analyze mode.rename_detail_files.pyData CSVThis csv file contains all of the data from the experiments used in the paper.data_final.csv
DOI: 10.5061/dryad.70628
title: Data from: Independent origins of parasitism in Animalia

description: Nearly half of all animals may have a parasitic lifestyle, yet the number
 of transitions to parasitism and their potential for species
 diversification remain unresolved. Based on a comprehensive survey of the
 animal kingdom, we find that parasitism has independently evolved at least
 223 times in just 15 phyla, with the majority of identified independent
 parasitic groups occurring in the Arthropoda, at or below the level of
 Family. Metazoan parasitology is dominated by the study of helminthes;
 however, only 20% of independently derived parasite taxa belong to those
 groups, with numerous transitions also seen in Mollusca, Rotifera,
 Annelida and Cnidaria. Parasitism is almost entirely absent from
 deuterostomes, and although worm-like morphology and host associations are
 widespread across Animalia, the dual symbiotic and trophic interactions
 required for parasitism may constrain its evolution from antecedent
 consumer strategies such as generalist predators and filter feeders. In
 general, parasitic groups do not differ from their free-living relatives
 in their potential for speciation. However, the 10 largest parasitic
 clades contain 90% of described parasitic species, or perhaps 40% of all
 animal species. Hence, a substantial fraction of animal diversity on the
 Earth arose following these few transitions to a parasitic trophic
 strategy.
description: Supplementary data and
 figuresThis file contains an
 annotated list of independent origins of parasitism in Animalia, derived
 from an extensive search of available literature. Monophyletic parasite
 groups for which the closest free-living relatives are known are listed in
 an additional table, including species and genera counts and estimated age
 of divergence for each pair. The file also contains the approximately 300
 references used to identify parasite clades and compare species diversity
 between parasite and free-living sister groups.supp
 mat6.11.docx
DOI: 10.5061/dryad.g792f
title: Data from: Pleiotropy in the wild: the dormancy gene DOG1 exerts cascading control on life-cycles

description: In the wild, organismal life cycles occur within seasonal cycles, so
 shifts in the timing of developmental transitions can alter the seasonal
 environment experienced subsequently. Effects of genes that control the
 timing of prior developmental events can therefore be magnified in the
 wild because they determine seasonal conditions experienced by subsequent
 life stages, which can influence subsequent phenotypic expression. We
 examined such environmentally-induced pleiotropy of developmental-timing
 genes in a field experiment with Arabidopsis thaliana. When studied in the
 field under natural seasonal variation, an A. thaliana seed-dormancy gene,
 Delay Of Germination 1 (DOG1), was found to influence not only
 germination, but also flowering time, overall life history, and fitness.
 Flowering time of the previous generation, in turn, imposed maternal
 effects that altered germination, the effects of DOG1 alleles, and the
 direction of natural selection on these alleles. Thus under natural
 conditions, germination genes act as flowering genes and potentially vice
 versa. These results illustrate how seasonal environmental variation can
 alter pleiotropic effects of developmental-timing genes, such that effects
 of genes that regulate prior life stages ramify to influence subsequent
 life stages. In this case, one gene acting at the seed stage impacted the
 entire life cycle.
description: Data for DRYAD
 "Pleiotropy in the wild"Phenological data
 collected in the field in Massachusetts. Replicates of ifferent
 genotypes--near isogenic lines carryign contrasting alleles at DOG1, FLC,
 and CRY2--were matured under three conditions and dispersed during three
 seasons. date of dispersal, date of germination, date of flowering, and
 total silique production (a measure of fitness) was
 recordedData for DRYAD NILs in
 field.xls
DOI: 10.5061/dryad.h237q
title: Data from: Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici

description: Understanding the mode of temporal maintenance of plant pathogens is an
 important domain of microbial ecology research. Due to the inconspicuous
 nature of microbes, their temporal maintenance cannot be studied directly
 through tracking individuals and their progeny. Here, we suggest a series
 of population genetic analyses on molecular marker variation in
 temporally-spaced samples to infer about the relative contribution of
 sexual reproduction, off-season survival and migration in the temporal
 maintenance of pathogen populations. We used the proposed approach to
 investigate the temporal maintenance of wheat yellow rust pathogen,
 Puccinia striiformis f.sp. tritici (PST), in the Himalayan region of
 Pakistan. Multilocus microsatellite genotyping of PST isolates revealed
 high genotypic diversity and recombinant population structure across all
 locations, confirming the existence of sexual reproduction in this region.
 The genotypes were assigned to four genetic groups, revealing a clear
 differentiation between zones with and without Berberis spp., the
 alternate host of PST, with an additional subdivision within the Berberis
 zone. The lack of any differentiation between samples across two sampling
 years, and the very few re-sampling of multilocus genotypes over-years at
 a given location was consistent with limited over-year clonal survival,
 and a limited genetic drift. The off-season over-summering population in
 the Berberis zone, likely to be maintained locally, served as a source of
 migrants contributing to the temporal maintenance in the non-Berberis
 zone. Our study hence demonstrated the contribution of both sexual
 recombination and off-season over-summering survival to the temporal
 maintenance of the pathogen. These new insights into the population
 biology of PST highlight the general usefulness of the analytical approach
 proposed.
description: SSR_Profile_Data_Pk-SASampling year, country, location (GPS), host and the SSR profile for the PST isolates studied in the articel Ali et al., Mol Ecol.
DOI: 10.5061/dryad.503kg
title: Data from: Evidence for mega-landslides as drivers of island colonization

description: Aim: How non-dispersive taxa colonize islands is generalized as being by
 wind, or rafting, with the implicit assumption that such events involve
 one (wind) or a few (rafting) individuals. However, because of the
 evolutionary time-scale for colonization events, the fit of individual
 species to a conceptual model of wind or rafting is difficult to assess.
 Here, we describe an alternative testable geological model for
 inter-island colonization that can result in larger effective founding
 population sizes than traditionally accepted colonization mechanisms. We
 then test for the fit of genetic data to this model using weevils from the
 Laparocerus tessellatus species complex. Location: Canary Islands.
 Methods: Using a combination of geological data for the Canary Islands,
 and mtDNA data from a weevil radiation within the Canary Islands, we test
 three species-level predictions for mega-landslides as drivers of oceanic
 rafting between islands and subsequent speciation: (1) colonization should
 involve multiple female lineages, (2) founding lineages should have a
 common geographical origin, consistent with a mega-landslide event, and
 (3) colonization direction should be consistent with ocean currents.
 Results: Both individual-level and population-level analyses support a
 mega-landslide event as the driver of colonization from the island of
 Tenerife to La Palma. At least four female lineages colonized La Palma
 from Tenerife, with the geographical range of ancestral sequences to these
 four lineages describing the limits of the La Orotava mega-landslide in
 Tenerife. Main conclusions: In the context of island biogeographical
 theory, mega-landslides may be an important driver of colonization, and
 subsequent lineage diversification. They provide a framework for
 hypothesis testing using genetic data from species, or closely related
 species, with ranges that encompass landslides and potential areas of
 colonization.
description: Landslides_alignmentThis files contains all sequences from the manuscript. The Excel file README contains additional data for each sequence
DOI: 10.5281/zenodo.18381823
title: Natural history specimens collected and/or identified and deposited.

description: Natural history specimen data collected and/or identified by Robert L. Minckley, https://orcid.org/0000-0002-1217-7693. Claims or attributions were made on Bionomia, https://bionomia.net using specimen data from the Global Biodiversity Information Facility, https://gbif.org.
DOI: 10.5061/dryad.r19c2
title: Data from: Differentiating founder and chronic HIV envelope sequences

description: Significant progress has been made in characterizing broadly neutralizing
 antibodies against the HIV envelope glycoprotein Env, but an effective
 vaccine has proven elusive. Vaccine development would be facilitated if
 common features of early founder virus required for transmission could be
 identified. Here we employ a combination of bioinformatic and operations
 research methods to determine the most prevalent features that distinguish
 78 subtype B and 55 subtype C founder Env sequences from an equal number
 of chronic sequences. There were a number of equivalent optimal networks
 (based on the fewest covarying amino acid (AA) pairs or a measure of
 maximal covariance) that separated founders from chronics: 13 pairs for
 subtype B and 75 for subtype C. Every subtype B optimal solution contained
 the founder pairs 178–346 Asn-Val, 232–236 Thr-Ser, 240–340 Lys-Lys,
 279–315 Asp-Lys, 291–792 Ala-Ile, 322–347 Asp-Thr, 535–620 Leu-Asp,
 742–837 Arg-Phe, and 750–836 Asp-Ile; the most common optimal pairs for
 subtype C were 644–781 Lys-Ala (74 of 75 networks), 133–287 Ala-Gln
 (73/75) and 307–337 Ile-Gln (73/75). No pair was present in all optimal
 subtype C solutions highlighting the difficulty in targeting transmission
 with a single vaccine strain. Relative to the size of its domain (0.35% of
 Env), the α4β7 binding site occurred most frequently among optimal pairs,
 especially for subtype C: 4.2% of optimal pairs (1.2% for subtype B).
 Early sequences from 5 subtype B pre-seroconverters each exhibited at
 least one clone containing an optimal feature 553–624 (Ser-Asn), 724–747
 (Arg-Arg), or 46–293 (Arg-Glu).
description: HIV envelope
 sequencesAligned HIV subtype B
 and C envelope sequences for early transmission (Founders) and chronically
 infected individuals (Chronics). Founders are denoted by FR, Chronics by
 CR, with B and C in the sequence name denoting the subtype. The reference
 sequence HXB2 is included.Main_sequences.txtSeroconverter HIV subtype B envelope sequencesPre-seroconverter subtype B envelope sequences for 5 individuals. Separate clones are listed for most individuals.Seroconverter_sequences.txt
DOI: 10.5061/dryad.td12f
title: Data from: Extensive hybridization and associated geographic trends between two rockfishes Sebastes vulpes and S. zonatus (Teleostei: Scorpaeniformes: Sebastidae)

description: Interspecific hybridization is an important evolutionary process which has
 significant influence on the diversity within and between participating
 taxa. Although interspecific hybridization in terrestrial and freshwater
 organisms have been subjected to many detailed studies, studies in marine
 realm have been limited in terms of both numbers and detail. In this
 study, the potential for interspecific hybridization between two
 rockfishes, Sebastes vulpes and S. zonatus, occurring in the western North
 Pacific, was assessed on the basis of 177 specimens collected from three
 sampling localities within the main geographic distribution of both
 species, and analyzed using a combination of amplified fragment length
 polymorphisms (AFLP), mitochondrial DNA (mtDNA) markers and morphometric
 characters. Bayesian-based individual genetic assignment based on 364 AFLP
 loci detected a total of 63 (35.6%) hybrid specimens in the dataset, the
 presence of interspecific hybrids also being rigorously supported by mtDNA
 analysis using partial sequences from the control region and morphological
 analysis based on 31 morphometric characters. Hybrids from all three
 localities were found, showing a common pattern of biased introgression
 across the localities whereby hybrids were more closely related to S.
 zonatus than to S. vulpes. Apart from this common pattern, rates of
 hybridization varied considerably among the localities, being greater in
 the northern localities. Variations in the local rates of hybridization
 were associated with variations in habitat segregation and thermal regime,
 implying that vertical water temperature regimes determined the extent of
 habitat segregation of the two species and, accordingly, the opportunity
 for hybridization.
description: AFLPscoreAFLP scores for the specimens examined.morphologyMorphometric characters and body coloration of the specimens examined.
DOI: 10.5061/dryad.5qk4s
title: Data from: Resolving biological impacts of multiple heat waves: interaction of hot and recovery days

description: Heat waves are increasing with global warming and have more dramatic
 biological effects on organisms in natural and agricultural ecosystems
 than mean temperature increase. However, predicting the impact of future
 heat waves on organisms and ecosystems is challenging because we still
 have a limited understanding of how the different components that
 characterize heat waves interact. Here we take an experimental approach to
 examine the individual and combine consequences of two important features
 that characterize heat waves: duration of successive hot days and recovery
 days between two hot spells. Specifically we exposed individuals of a
 global agricultural pest, the aphid Sitobion avenae to different heat wave
 scenarios by factorially manipulating the number of extreme hot days vs.
 normal days and altered which period individuals experienced first in
 their life cycle. We found that effects of heat waves were driven by a
 delicate balance of damage during hot periods vs. repair during normal
 periods. Increasing the duration of hot days in heat waves had a negative
 effect on various demographic rates and life-time fitness of individuals,
 but magnitude of this effect was typically contingent on the temporal
 clustering of hot periods. Importantly, this interaction effect indicates
 that changes in the temporal distribution of extreme hot vs. normal days
 can strongly alter the performance of organisms and dynamics of
 populations even when the total number of hot days during a given period
 remains unchanged. Together, these results emphasize the importance of
 accounting for the temporal distribution and quantitative patterns of
 extreme temperature events for predicting their consequences of natural
 and agricultural ecosystems.
description: Development
 traitDevelopment.csvReproduction traitReproduction.csvother traitsTraits.csv
DOI: 10.5061/dryad.17fj8
title: Data from: Defense mutualisms enhance plant diversification

description: The ability of plants to form mutualistic relationships with animal
 defenders has long been suspected to influence their evolutionary success,
 both by decreasing extinction risk and by increasing opportunity for
 speciation through an expanded realized niche. Nonetheless, the hypothesis
 that defense mutualisms consistently enhance plant diversification across
 lineages has not been well tested due to a lack of phenotypic and
 phylogenetic information. Using a global analysis, we show that the
 &gt;100 vascular plant families in which species have evolved
 extrafloral nectaries (EFNs), sugar-secreting organs that recruit
 arthropod mutualists, have twofold higher diversification rates than
 families that lack species with EFNs. Zooming in on six distantly related
 plant clades, trait-dependent diversification models confirmed the
 tendency for lineages with EFNs to display increased rates of
 diversification. These results were consistent across methodological
 approaches. Inference using reversible-jump Markov chain Monte Carlo
 (MCMC) to model the placement and number of rate shifts revealed that high
 net diversification rates in EFN clades were driven by an increased number
 of positive rate shifts following EFN evolution compared with sister
 clades, suggesting that EFNs may be indirect facilitators of
 diversification. Our replicated analysis indicates that defense mutualisms
 put lineages on a path toward increased diversification rates within and
 between clades, and is concordant with the hypothesis that mutualistic
 interactions with animals can have an impact on deep macroevolutionary
 patterns and enhance plant diversity.
description: Genbank Accession
 NumbersThe taxa included in the
 phylogenetic analyses for each of the six clades with Genbank accession
 numbers for all loci. Outgroup taxa are marked with an
 asterisk.genbank_accessions.docxEFN Character MatrixPresence or absence character matrix of extrafloral nectaries for the six clades used in the studycharacter_matrix.docxMCC_Tree_FilesTrees.zipR_Scripts
DOI: 10.5061/dryad.20234
title: Data from: Costs of resistance and infection by a generalist pathogen

description: Pathogen infection is typically costly to hosts, resulting in reduced
 fitness. However, pathogen exposure may also come at a cost even if the
 host does not become infected. These fitness reductions, referred to as
 “resistance costs”, are inducible physiological costs expressed as a
 result of a trade-off between resistance to a pathogen and aspects of host
 fitness (e.g., reproduction). Here, we examine resistance and infection
 costs of a generalist fungal pathogen (Metschnikowia bicuspidata) capable
 of infecting a number of host species. Costs were quantified as reductions
 in host lifespan, total reproduction, and mean clutch size as a function
 of pathogen exposure (resistance cost) or infection (infection cost). We
 provide empirical support for infection costs and modest support for
 resistance costs for five Daphnia host species. Specifically, only one
 host species examined incurred a significant cost of resistance. This
 species was the least susceptible to infection, suggesting the possibility
 that host susceptibility to infection is associated with the detectability
 and size of resistance cost. Host age at the time of pathogen exposure did
 not influence the magnitude of resistance or infection cost. Lastly,
 resistant hosts had fitness values intermediate between unexposed control
 hosts and infected hosts. Although not statistically significant, this
 could suggest that pathogen exposure does come at some marginal cost.
 Taken together, our findings suggest that infection is costly, resistance
 costs may simply be difficult to detect, and the magnitude of resistance
 cost may vary among host species as a result of host life history or
 susceptibility.
description: costDataData from experiment examining host responses (reductions in fitness) as a function of pathogen exposure and/or infection.costCode pdfR markdown code to reproduce all the analyses from the manuscript. The associated ReadMe file is the compiled pdf containing the code.costCode.Rmd
DOI: 10.5061/dryad.5p1tg
title: Data from: Soldiers in a stingless bee: work rate and task repertoire suggest they are an elite force

description: The differentiation of workers into different morphological sub-castes
 (e.g. soldiers) represents an important evolutionary transition and is
 thought to improve division of labor in social insects. Soldiers occur in
 many ant and termite species where they make up a small proportion of the
 workforce. A common assumption of worker caste evolution is that soldiers
 are behavioral specialists. Here, we report the first test of the “rare
 specialist” hypothesis in a eusocial bee. Colonies of the stingless bee
 Tetragonisca angustula are defended by a small group of morphologically
 differentiated soldiers. Contrary to the “rare-specialist” hypothesis, we
 found that soldiers worked more (+34-41%) and performed a greater variety
 of tasks (+23-34%) than other workers, particularly early in life. Our
 results suggest a “rare elite” function of soldiers in T. angustula, i.e.
 they perform a disproportionately large amount of the work. Division of
 labor was based on a combination of temporal and physical castes, but
 soldiers transitioned faster from one task to the next. We discuss why the
 “rare specialist” assumption might not hold in species with a moderate
 degree of worker differentiation.
description: RawDataContains the raw data of the observations