cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kd51c5b5z
title: Lack of neophobic responses to color in a jumping spider that uses color cues when foraging (Habronattus pyrrithrix)

description: Chemically defended prey often advertise their toxins with bright and
 conspicuous colors. To understand why such colors are effective at
 reducing predation, we need to understand the psychology of key predators.
 In bird predators, there is evidence that individuals avoid novelty -
 including prey of novel colors (with which they have had no prior
 experience). Moreover, the effect of novelty is strongest for colors that
 are typically associated with aposematic prey (e.g., red, orange, yellow).
 Given these findings in the bird literature, color neophobia has been
 argued to be a driving force in the evolution of aposematism. However, no
 studies have yet asked whether invertebrate predators respond similarly to
 novel colors. Here, we tested whether naive lab-raised jumping spiders
 (Habronattus pyrrithrix) exhibit similar patterns of color neophobia to
 birds. Using color-manipulated living prey, we first color-exposed spiders
 to prey of two out of three colors (blue, green, or red), with the third
 color remaining novel. After this color exposure phase, we gave the
 spiders tests where they could choose between all three colors (two
 familiar, one novel). We found that H. pyrrithrix attacked novel and
 familiar-colored prey at equal rates with no evidence that the degree of
 neophobia varied by color. Moreover, we found no evidence that either prey
 novelty or color (nor their interaction) had an effect on which color
 first caught the spiders’ attention. We discuss these findings in the
 context of what is known about color neophobia in other animals and how
 this contributes to our understanding of aposematic signals.
description: The attached excel file provides data for "Lack of neophobic
 responses to color in a jumping spider that uses color cues when foraging
 (<i>Habronattus pyrrithrix</i>)". The attached excel file
 has two separate worksheets labeled for all tests described in the
 manuscript. On the first worksheet tab, we recorded the following data
 points: trial ID, the color termites (blue, green, or red), was the color
 considered to be novel (yes or no), and whether that color was attacked
 (yes or no). On the second worksheet tab, we recorded the following data
 points: spider ID, the color assigned to be novel, whether the
 attacked color was novel (yes or no), and latency to attack (time from
 trial start to attack measured in seconds).
DOI: 10.5061/dryad.rr4xgxd8d
title: Genetics of quantitative traits with dominance under stabilizing and directional selection in partially selfing species

description: Recurrent self-fertilization is thought to lead to reduced adaptive
 potential by decreasing the genetic diversity of populations, thus leading
 selfing lineages down an evolutionary ‘blind alley’. Though well supported
 theoretically, empirical support for reduced adaptability in selfing
 species is limited. One limitation of classical theoretical models is that
 they assume pure additivity of the fitness-related traits that are under
 stabilizing selection, despite ample evidence that quantitative traits are
 subject to dominance. Here we relax this assumption and explore the effect
 of dominance on a fitness-related trait under stabilizing selection for
 populations that differ in selfing rates. By decomposing the genetic
 variance into additional components specific to inbred populations, we
 show that dominance components can explain a substantial part of the
 genetic variance of inbred populations. We also show that ignoring these
 components leads to an upward bias in the predicted response to selection.
 Finally, we show that when considering the effect of dominance, the
 short-term evolutionary potential of populations remains comparable across
 the entire gradient in outcrossing rates, and genetic associations can
 even make selfing populations more evolvable on the longer term,
 reconciling theoretical and empirical results.
DOI: 10.5061/dryad.gtht76hmk
title: Functional assembly of tropical montane tree islands in the Atlantic Forest is shaped by stress-tolerance, bamboo-presence and facilitation

description: Aims: Amidst the Campos de Altitude (Highland Grasslands) in the Brazilian
 Atlantic Forest, woody communities grow either clustered in tree islands
 or interspersed within the herbaceous matrix. The functional ecology,
 diversity and biotic processes shaping these plant communities are largely
 unstudied. We characterised the functional assembly and diversity of these
 tropical montane woody communities and investigated how they fit within
 Grime’s CSR (C – competitor, S – stress-tolerant, R – ruderal) scheme,
 what functional trade-offs they exhibit and how traits and functional
 diversity vary in response to bamboo presence/absence. Methods: To
 characterize the functional composition of the community, we sampled five
 leaf traits and wood density along transects covering the woody
 communities both inside tree islands and outside (i.e. isolated woody
 plants in the grasslands community) . Then, we used Mann Whitney test,
 t-test and variation partitioning to determine the effects of inside vs
 outside tree island and bamboo presence on community weighted means, woody
 species diversity and functional diversity. Results: We found a general
 SC/S strategy with drought-related functional trade-offs. Woody plants in
 tree islands had more acquisitive traits than those within the grasslands.
 Trait variation was mostly taxonomically than spatially driven, and
 species composition varied between inside and outside tree islands. Leaf
 thickness, wood density and foliar water uptake were unrelated to
 CSR-strategies, suggesting independent trait dimensions and multiple
 drought-coping strategies within the predominant S-strategy. Islands with
 bamboo presence showed lower Simpson diversity, lower functional
 dispersion, lower foliar water uptake and greater leaf thickness than in
 tree islands without bamboo. Conclusions: The observed functional assembly
 hints towards large-scale environmental abiotic filtering shaping
 stress-tolerant community strategy, and small-scale biotic interactions
 driving small-scale trait variation. We recommend experimental studies
 with fire, facilitation treatments, eco-physiological and recruitment
 traits to elucidate on tree island expansion and communities response to
 climate change.
description: Data was collected according to a Point-Quarter method in a
 transect design along the ecotones of 10 tree islands within the Campos de
 Altitude. We collected data on vegetation structure, species composition
 and functional traits. Detailed information on data
 collection and processing can be found in the manuscript and supplementary
 material of Christmann et al 2021 Ecology & Evolution.
DOI: 10.5061/dryad.r2280gbd8
title: Embryonic muscle splitting patterns reveal homologies of amniote forelimb muscles

description: Limb muscles are remarkably complex and evolutionarily labile; although
 their anatomy is of great interest for studies of the evolution of form
 and function, their homologies among major amniote clades have remained
 obscure. Studies of adult musculature are inconclusive owing to the highly
 derived morphology of modern amniote limbs, but correspondences become
 increasingly evident earlier in ontogeny. Amniote forelimb muscles derive
 from early embryonic muscle masses of somitic origin, which grow and
 cleave into recognizable divisions that split into the individualized
 muscles. We followed the embryonic development of forelimb musculature in
 representatives of six major amniote clades and found, contrary to current
 consensus, that these early splitting patterns are highly conserved across
 Amniota. Muscle mass cleavage patterns and topology are highly conserved
 in reptiles including birds, irrespective of their skeletal modifications:
 the avian flight apparatus results from slight early topological
 modifications that are exaggerated during ontogeny. Therian mammals, while
 conservative in their cleavage patterns, depart drastically from the
 ancestral amniote musculoskeletal organization in terms of topology. These
 topological changes occur through extension, translocation, and
 displacement of muscle groups later in development. Overall, the
 simplicity underlying the apparent complexity of forelimb muscle
 development allows us to resolve conflicting hypotheses about homology and
 to trace the history of each individual forelimb muscle throughout the
 amniote radiations. 
description: .czi images can be viewed in Fiji (ImageJ).
DOI: 10.5061/dryad.4f4qrfjc7
title: Comparing the clinical utility and diagnostic performance of cerebrospinal fluid P-tau181, P-tau217 and P-tau231 assays

description: Background and Objectives: Phosphorylated tau (P-tau) in
 cerebrospinal fluid (CSF) is considered an important biomarker in
 Alzheimer’s disease (AD) and has been incorporated in recent
 diagnostic criteria. Several variants exist, including P-tau
 at threonines 181 (P-tau181), 217 (P-tau217) and 231
 (P-tau231). However, no studies have compared their diagnostic
 performance or association to amyloid-β (Aβ) and
 Tau positron emission tomography (PET). Understanding which P-tau
 variant to use remains an important yet answered question. We
 aimed to compare the diagnostic accuracy of P-tau181, P-tau217 and
 P-tau231 in CSF for AD and their association with Aβ and Tau-PET.
 Methods: 629 subjects from the Swedish BioFINDER-2 study were
 included (cognitively unimpaired, n=334; Aβ-positive mild cognitive
 impairment, n=84; AD dementia, n=119; and non-AD disorders, n=92). In
 addition to P-tau181 and P-tau217 measured using assays with the
 same detector antibodies from Eli Lilly (P-tau181Lilly,
 P-tau217Lilly) and P-tau231, we also included
 P-tau181 measurements from two commonly used assays (Innotest and
 Elecsys).  Results: Though all P-tau variants increased
 across the AD continuum, P-tau217Lilly showed the greatest
 dynamic range (13-fold-increase vs 1.9-5.4-fold-increase for other P-tau
 variants for AD dementia vs non-AD). P-tau217Lilly showed
 stronger correlations with Aβ- and Tau-PET (P&lt;0.0001).
 P-tau217Lilly exhibited higher accuracy than other P-tau variants
 for separating AD dementia from non-AD (AUC, 0.991vs
 0.906-0.982, P&lt;0.0001) and for identifying Aβ- (AUC, 0.951
 vs 0.816-0.924, P&lt;0.0001) and Tau-PET positivity (AUC,
 0.957 vs 0.836-0.938, P&lt;0.0001).
 Finally, P-tau181Lillygenerally performed better than the other
 P-tau181 assays, (e.g., AD dementia vs non-AD, AUC, 0.976 vs
 0.923, P&lt;0.0001).  Discussion:
 CSF P-tau217Lilly seem to be more useful than other
 included P-tau assays in the work-up of AD. Varied results across P-tau181
 assays also highlights the importance of anti-tau antibodies for biomarker
 performance. Classification of evidence: This study provides
 class II evidence that phosphorylated tau at threonine 217 provides higher
 diagnostic accuracy for diagnosis of AD dementia than P-tau at threonine
 181 or 231.
DOI: 10.5061/dryad.08kprr52s
title: Phylogenomics and biogeography of Torreya (Taxaceae) – Integrating data from three organelle genomes, morphology, and fossils and a practical method for reducing missing data from RAD-seq

description: Restriction site-associated DNA sequencing (RAD-seq) enables obtaining
 thousands of genetic markers for phylogenomic studies. However, RAD-seq
 data are subject to allele dropout (ADO) due to polymorphisms at enzyme
 cutting sites. We developed a new pipeline, RADADOR, to mitigate the ADO
 in outgroups by recovering missing loci from previously published
 transcriptomes in our study of a gymnosperm genus Torreya. Using
 the supplemented RAD-seq data in combination with plastome and
 mitochondrial gene sequences, morphology, and fossil records, we
 reconstructed the phylogenetic and biogeographic histories of the genus
 and test hypotheses on diversity anomaly in eastern Asian-North American
 floristic disjunction. Our results showed that our pipeline recovered many
 loci missing from the outgroup, and the improved data yielded a more
 robust phylogeny for Torreya. Using the fossilized-birth-death
 model and divergence-extinction-cladogenesis method we resolved detailed
 biogeographic history of Torreya that suggested a
 Jurassic origin in the Laurasia and differential speciation and extinction
 among continents accounting for the modern diversity anomaly biased toward
 Eastern Asia (EA). The history also supported a vicariance origin of the
 modern Torreya from a widespread ancestor in EA and NA
 in the mid-Eocene, cross-Beringia exchange in the early Paleogene before
 the vicariant isolation, in contrast to the “Out of NA” pattern common to
 gymnosperms and in contrast to the “Out of EA” hypothesis previously
 proposed for the genus. Furthermore, we observed phylogenetic discordance
 between the nuclear and plastid phylogenies on T. jackii,
 suggesting differential lineage sorting of plastid genomes
 among Torreya species or plastid genome capture
 in T. jackii.
DOI: 10.5061/dryad.02v6wwq39
title: FGF gene sequence of Carnivora animals

description: This is a dataset of Carnivora FGF genes for studying their evolutionary
 characteristics. The dataset is in the format of fasta, and
 contains 1186 FGF gene sequence.
description: The sequences were partial downloaded from GenBank and 660
 sequences were annotated through the method of local blast.
description: There are no missing values for this dataset.
DOI: 10.5061/dryad.j9kd51ccm
title: Immigration dynamics of tropical and subtropical Southeast Asian limestone karst floras

description: Ex situ origins and dispersal of taxa have played
 important roles in the assembly of island-like biodiversity
 hotspots. Insular limestone karsts in Southeast
 Asia are hotspots of biodiversity and endemism, but the
 immigration processes of their unique floras are still
 poorly
 known. Here, we used Gesneriaceae as a proxy to investigate immigration dynamics of tropical and subtropical Southeast Asian karst floras. We show that immigration into subtropical Southeast Asian karst floras first occurred in the early Miocene, with two peaks in the early to middle Miocene and the Pliocene to early Pleistocene, whereas immigration into tropical Southeast Asian karsts initiated in the late Eocene, with two peaks in the late Oligocene and the late Miocene. The rich geological and ecological diversities of different regions, together with habitat isolation due to climatic changes, might be responsible for the different immigration patterns. We also discover that Southeast Asian karst biodiversity comprises a mix of immigrant pre-adapted lineages and descendants from local acid soil ancestors, although niche shift from acid soil to karst in tropical Southeast Asian islands was lacking. These findings provide insights into how Southeast Asian karsts respond to ongoing climate change and are of particular importance for their conservation planning.
DOI: 10.5061/dryad.j3tx95xdp
title: Deep ancestral introgression shapes evolutionary history of dragonflies and damselflies

description: Introgression is arguably one of the most important biological processes
 in the evolution of groups of related species, affecting at least 10% of
 the extant species in the animal kingdom. Introgression reduces genetic
 divergence between species, and in some cases can be highly beneficial,
 facilitating rapid adaptation to ever-changing environmental pressures.
 Introgression also significantly impacts inference of phylogenetic species
 relationships where a strictly binary tree model cannot adequately explain
 reticulate net-like species relationships. Here we use phylogenomic
 approaches to understand patterns of introgression along the evolutionary
 history of a unique, non-model insect system: dragonflies and damselflies
 (Odonata). We demonstrate that introgression is a pervasive evolutionary
 force across various taxonomic levels within Odonata. In particular, we
 show that the morphologically “intermediate” species of Anisozygoptera
 (one of the three primary suborders within Odonata besides Zygoptera and
 Anisoptera), which retain phenotypic characteristics of the other two
 suborders, experienced high levels of introgression likely coming from
 zygopteran genomes. Additionally, we find evidence for multiple cases of
 deep inter-superfamilial ancestral introgression.
DOI: 10.5061/dryad.gtht76hmm
title: Life-cycle complexity in helminths: What are the benefits?

description: Parasitic worms (i.e. helminths) commonly infect multiple hosts in
 succession. With every transmission step, they risk not infecting the next
 host and thus dying before reproducing. Given this risk, what are the
 benefits of complex life cycles? Using a dataset for 973 species of
 trophically transmitted acanthocephalans, cestodes, and nematodes, we
 tested whether hosts at the start of a life cycle increase transmission
 and whether hosts at the end of a life cycle enable growth to larger, more
 fecund sizes. Helminths with longer life cycles, i.e. more successive
 hosts, infected conspicuously smaller first hosts, slightly larger final
 hosts, and exploited trophic links with lower predator-prey mass ratios.
 Smaller first hosts likely facilitate transmission because of their higher
 abundance and because parasite propagules were the size of their normal
 food. Bigger definitive hosts likely increase fecundity because parasites
 grew larger in big hosts, particularly endotherms. Helminths with long
 life cycles attained larger adult sizes through later maturation, not
 faster growth. Our results indicate that complex helminth life cycles are
 ubiquitous because growth and reproduction are highest in large,
 endothermic hosts that are typically only accessible via small
 intermediate hosts, i.e. the best hosts for growth and transmission are
 not the same.
description: We assessed the presumed
 benefits of complex life cycles in parasitic worms (acanthocephalans,
 cestodes, and nematodes) by combining a life cycle dataset (see Benesh et al. 2017. Ecology 98: 882) with host traits, specifically host body masses and trophic levels. Host traits were compiled from literature sources and databases. More details on how data were compiled, processed, and analyzed can be found in our manuscript (Benesh et al. 2021. Life-cycle complexity in helminths: what are the benefits? Evolution), in the metadata associated with the data files, and in this GitHub repository: https://github.com/dbenesh82/benefits_of_life_cycle_complexity.
description: The data are divided into
 two zip archives. The first (“<b>host_traits.zip</b>”)
 contains all the species-level host body size and trophic level data. The
 second archive (“<b>parasite_stage_level.zip</b>”) combines
 host traits with parasite life-cycle and life-history traits at the level
 of parasite life stages. Parasite stage refers to the ‘host in the cycle’.
 For example, a parasite with a three-host life cycle has three stages:
 first intermediate host, second intermediate host, and third, definitive
 host. Each archive contains a
 "<strong>METADA.txt</strong>" describing the
 contents of the data files. Finally, we used multiple imputation to
 address missing data in our analyses, so each archive also contains a zip
 file with 100 imputed datasets.
DOI: 10.5061/dryad.r2280gbd9
title: Metapopulation structure modulates sexual antagonism

description: Despite the far-reaching evolutionary implications of sexual conflict, the
 effects of metapopulation structure, when populations are subdivided into
 several demes connected to some degree by migration, on sexual conflict
 dynamics are unknown. Here, we used experimental evolution in an insect
 model system, the seed beetle Callosobruchus maculatus, to assess the
 independent and interacting effects of selection histories associated with
 mating system (monogamy vs. polygamy) and population subdivision on sexual
 conflict evolution. We confirm traditional predictions from sexual
 conflict theory by revealing increased resistance to male harm in females
 from populations with a history of intense sexual selection (polygamous
 populations) compared to females from populations with a history of
 relaxed sexual selection (monogamous populations). However, selection
 arising from metapopulation structure reversed the classic pattern of
 sexually antagonistic coevolution and led to reduced resistance in females
 from polygamous populations. These results underscore that population
 spatial structure moderates sexual selection and sexual conflict, and more
 broadly, that the evolution of sexual conflict is contingent on ecological
 context. The findings also have implications for population dynamics,
 conservation biology and biological control.
description: Explanations are given in the files and further information is
 provided in the Appendix of the study (available online together with the
 article), and in the article.
DOI: 10.5061/dryad.j0zpc86f4
title: Genomic and common garden approaches yield complementary results for quantifying environmental drivers of local adaptation in rubber rabbitbrush, a foundational Great Basin shrub

description: The spatial structure of genomic and phenotypic variation across
 populations reflects historical and demographic processes as well
 as evolution via natural selection. Characterizing such variation
 can provide an important perspective for understanding the evolutionary
 consequences of changing climate and for guiding ecological
 restoration. While evidence for local adaptation has been
 traditionally evaluated using phenotypic data, modern methods for
 generating and analyzing landscape genomic data can directly
 quantify local adaptation by associating allelic variation with
 environmental variation. Here, we analyze both genomic and phenotypic
 variation of rubber rabbitbrush (Ericameria nauseosa), a
 foundational shrub species of western North America. To quantify
 landscape genomic structure and provide perspective on patterns of
 local adaptation, we generated reduced representation sequencing
 data for 17 wild populations (222 individuals; 38,616 loci)
 spanning a range of environmental conditions. Population
 genetic analyses illustrated pronounced landscape genomic
 structure jointly shaped by geography and environment.
 Genetic-environment association (GEA) analyses using both redundancy
 analysis (RDA) and a machine-learning approach (Gradient Forests)
 indicated environmental variables (precipitation seasonality,
 slope, aspect, elevation, and annual precipitation) influenced
 spatial genomic structure, and were correlated with allele
 frequency shifts indicative of local adaptation at a consistent
 set of genomic regions. We compared our GEA based inference of
 local adaptation with phenotypic data collected by growing seeds
 from each population in a greenhouse common garden. Population
 differentiation in seed weight, emergence, and seedling traits was
 associated with environmental variables (e.g., precipitation seasonality)
 that were also implicated in GEA analyses, suggesting complementary
 conclusions about the drivers of local adaptation across different methods
 and data sources. Our results provide a baseline understanding of spatial
 genomic structure for E. nauseosa across the western Great Basin and
 illustrate the utility of GEA analyses for detecting the environmental
 causes and genetic signatures of local adaptation in a widely distributed
 plant species of restoration significance.