cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p5hqbzkqn
title: Data for: Eco-evolutionary consequences of dispersal syndromes during colonization in a passerine bird

description: In most animal species, dispersing individuals possess phenotypic
 attributes that mitigate the costs of colonization and/or increase
 settlement success in new areas (‘dispersal syndromes’). This phenotypic
 integration likely affects population dynamics and the direction of
 selection, but data are lacking for natural populations. Using an approach
 that combines population dynamics, quantitative genetics and phenotypic
 selection analyses, we reveal the existence of dispersal syndromes in a
 pied flycatcher (Ficedula hypoleuca) population in The Netherlands:
 immigrants were larger, tended to have darker plumage, bred earlier and
 produced larger clutches than local recruits, and some of these traits
 were genetically correlated. Over time, the phenotypic profile of the
 population gradually changed: each generation advanced arrival and
 breeding and exhibited longer wings as the result of direct and indirect
 selection on these correlated traits. Although phenotypic attributes of
 immigrants were favored by selection during the early phase of
 colonization, observed phenotypic changes were similar for immigrants and
 local recruits. We propose that immigrants facilitated initial population
 establishment but that temporal changes likely resulted from climate
 change-induced large-scale selection. This study highlights that newly
 established populations are of non-random composition and that phenotypic
 architecture affects evolutionary population trajectories.  
description: Data sets were collected in a wild pied flycatcher population in
 Drenthe in the Netherlands from 2007 until 2018. Three datasets have been
 used in this manuscript: 1. phenotypic data on
 population change (life-history and morphological traits measured in each
 year) = "data population change" 2.
 phenotypic selection dataset (relative fitness measurements and
 standardized phenotypic traits measured in each year) = "data
 phenotypic selection 3. quantitative genetics dataset
 (data + pedigree file) = "pedigree" & "data
 quantitative genetics"
description: Missing values are indicated as NA, and explanations of headings
 are provided in the tab 'codes' of the Excel files and in the
 "read me first" file. The data file can be
 opened with excel and/or R software (R codes are also provided).
DOI: 10.5061/dryad.xd2547dhq
title: DNA methylation as a tool to explore ageing in wild roe deer populations

description: DNA methylation-based biomarkers of aging (epigenetic clocks) promise to
 lead to new insights into evolutionary biology of ageing. Relatively
 little is known about how the natural environment affects epigenetic aging
 effects in wild species. In this study, we took advantage of a unique
 long-term (&gt;40 years) longitudinal monitoring of individual roe
 deer (Capreolus capreolus) living in two wild populations (Chizé and
 Trois-Fontaines, France) facing different ecological contexts, to
 investigate the relationship between chronological age and levels of DNA
 methylation (DNAm). We generated novel DNA methylation data from n = 94
 blood samples, from which we extracted leucocyte DNA, using a custom
 methylation array (HorvathMammalMethylChip40). We present three DNA
 methylation-based estimators of age (DNAm or epigenetic age), which were
 trained in males, females, and both sexes combined. We investigated how
 sex differences influenced the relationship between DNAm age and
 chronological age using sex-specific epigenetic clocks. Our results
 highlight that old females may display a lower degree of biological aging
 than males. Further, we identify the main sites of epigenetic alteration
 that have distinct aging patterns between the two sexes. These findings
 open the door to promising avenues of research at the crossroads of
 evolutionary biology and biogerontology.
DOI: 10.5061/dryad.51c59zw93
title: Data from: Resource heterogeneity but not inbreeding affects growth and grouping behaviour in socially foraging juvenile cichlid fish

description: 1. Spatial food distribution determines resource profitability,
 defensibility and encounter rate of foragers. Clumped food distribution
 can promote aggressiveness and resource monopolisation, in turn increasing
 within-group variation in food intake and growth. However, the effects of
 food distribution may depend on foraging strategies. Little is known about
 the impact of spatial food heterogeneity on growth and grouping behaviour
 in social foragers in the absence of monopolisation. 2. Social foraging is
 present in many fishes, particularly at early juvenile life stages when
 fish are especially sensitive to environmental variation. Here, a
 heterogeneous food distribution may impair foraging success and growth and
 juveniles may increase sociability to attain social information about food
 resources. 3. We examined the impact of the spatial distribution of food
 as well as inbreeding on growth and social behaviour in juveniles of the
 cichlid fish Pelvicachromis pulcher. Inbred individuals often show poorer
 performance than outbred individuals (inbreeding depression), but
 inbreeding effects can be environment-dependent. In the experiment, in-
 and outbred fish were reared in a split-clutch design either under
 homogeneously distributed or spatially clumped food conditions for eight
 weeks starting one week after juveniles could actively feed. We documented
 growth and performed a shoaling assay and a sociality test (choice between
 a large vs. a small shoal) after six weeks. 4. Spatial food distribution
 did not affect within-group body length variation, but individuals reared
 under clumped food conditions were smaller. Shoals of the different
 feeding conditions differed in social behaviour. Shoals of the clumped
 treatment group showed higher variation in inter-individual distances
 compared to shoals of the homogeneous treatment group. Furthermore, focal
 fish of the clumped treatment adjusted their association preference to the
 position of the groups’ largest individual. We did not find significant
 inbreeding or environment-dependent inbreeding effects regarding growth or
 social behaviour. 5. Our study suggests that a clumped food distribution
 can impede localisation of food resources and thus growth in juvenile
 social foragers. Accordingly, in heterogeneous environments, the use of
 social information may be highly relevant to increase individuals’
 foraging success potentially explaining orientation on successful
 foragers, i.e. large individuals. Inter-individual variation in juvenile
 social behaviour may precede variation in food monopolisation capability
 and in growth emerging at later life stages.
DOI: 10.5061/dryad.v41ns1rx9
title: Testosterone amplifies the negative valence of an agonistic gestural display by exploiting receiver perceptual bias

description: Many animals communicate by performing elaborate displays that are
 incredibly extravagant and wildly bizarre. So, how do these displays
 evolve? One idea is that innate sensory biases arbitrarily favor the
 emergence of certain display traits over others, leading to the design of
 an unusual display. Here, we study how physiological factors associated
 with signal production influence this process, a topic that has received
 almost no attention. We focus on a tropical frog, whose males compete for
 access to females by performing an elaborate waving display. Our results
 show that sex hormones like testosterone regulate specific display
 gestures that exploit a highly conserved perceptual system, evolved
 originally to detect “dangerous” stimuli in the environment. Accordingly,
 testosterone makes certain gestures likely appear more perilous to rivals
 during combat. This suggests that hormone action can interact with effects
 of sensory bias to create an evolutionary optimum that guides how display
 exaggeration unfolds.
DOI: 10.5061/dryad.1g1jwstxp
title: Investigating the utility of Anchored Hybrid Enrichment data to resolve the relationships among the Killifishes (Actinopterygii: Cyprinodontiformes), a globally distributed group of fishes

description: The Killifishes (Blenniiformes: Cyprinodontoidea) are a diverse and
 well-known group of fishes that contains sixteen families inclusive of
 Anablepidae, Aphaniidae Aplocheilidae, Cubanichthyidae, Cyprinodontidae,
 Fluviphylacidae, Fundulidae, Goodeidae, Nothobranchiidae, Orestiidae,
 Pantanodontidae, Poeciliidae, Procatopodidae, Profundulidae, Rivulidae,
 and Valenciidae and more than 1,200 species that are globally distributed
 in tropical and temperate, freshwater and estuarine habitats. The
 evolutionary relationships among the families within the group, based on
 different molecular and morphological data sets, have remained uncertain.
 Therefore, the objective of this study was to use a targeted approach,
 anchored hybrid enrichment, to resolve the phylogenetic relationships
 among the families within the Superfamily Cyprinodontoidea (formerly the
 Cyprindontiformes). This study included more than 100 individuals,
 representing all sixteen families within Cyprinodontoidea, including many
 recently diagnosed families. We recovered an average of 244 loci per
 individual. These data were submitted to phylogenetic analyses (RaxML and
 ASTRAL) and although we recovered many of the same relationships as in
 previous studies of the group, several novel sets of relationships for
 other families also were recovered. In addition, two well-established
 clades were recovered as monophyletic and are in agreement with most
 previous studies. We also assessed the degree of gene tree discordance in
 our dataset to evaluate support for alternative topological hypotheses for
 interfamilial relationships within the Cyprinodontoidea using a variety of
 different analyses. The results from this study will provide a robust,
 historical framework needed to investigate a plethora of biogeographic,
 taxonomic, ecological, and physiological questions for this group of
 fishes.
DOI: 10.5061/dryad.nzs7h44sm
title: Data from: Spatial variation in bidirectional pollinator-mediated interactions between two co-flowering species in serpentine plant communities

description: Pollinator-mediated competition and facilitation are two important
 mechanisms mediating co-flowering community assembly. Experimental
 studies, however, have mostly focused on evaluating outcomes for a single
 interacting partner at a single location. Studies that evaluate spatial
 variation in the bidirectional effects between co-flowering species are
 necessary if we aim to advance our understanding of the processes that
 mediate species coexistence in diverse co-flowering communities. Here, we
 examine geographic variation (i.e., at landscape level) in bidirectional
 pollinator-mediated effects between co-flowering Mimulus guttatus and
 Delphinium uliginosum. We evaluated effects on pollen transfer dynamics
 (conspecific and heterospecific pollen deposition) and plant reproductive
 success. We found evidence of asymmetrical effects (one species is
 disrupted and the other one is facilitated) but the effects were highly
 dependent on geographical location. Furthermore, effects on pollen
 transfer dynamics did not always translate to effects on overall plant
 reproductive success (i.e., pollen tube growth) highlighting the
 importance of evaluating effects at multiple stages of the pollination
 process. Overall, our results provide evidence of a spatial mosaic of
 pollinator-mediated interactions between co-flowering species and suggest
 that community assembly processes could result from competition and
 facilitation acting simultaneously. Our study highlights the importance of
 experimental studies that evaluate the prevalence of competitive and
 facilitative interactions in the field, and that expand across a wide
 geographical context, in order to more fully understand the mechanisms
 that shape plant communities in nature.
DOI: 10.5061/dryad.931zcrjm4
title: Sexually antagonistic selection maintains genetic variance when sexual dimorphism evolves

description: Breeding design data for body size in seed beetles (a sexually
 antagonistic trait) after 10 generations under different artificial
 selection conditions to test the effects of selection on the genetic
 variance of body size. The breeding design and sample size of the study
 allow us to partition genetic variances into additive autosomal, additive
 sex-linked, autosomal dominance and X-linked dominance variance.See
 related dataset for body size data of the ancestral population before
 selection.
description: Individual body weight measurements [mg] for
 <em>Callosobruchus</em> <em>maculatus</em> beetles
 of grandparental (GP), parental (P) and F1 offspring (F1) generation.
 Beetles belong to three different selection regimes (sexually antagonistic
 (SA), male limited (ML) and random selection (RS)), within each selection
 regime there are two replicate lines (A and B), see  Usage Notes and
 related articles for more details.
DOI: 10.5061/dryad.rv15dv48m
title: The Bayesian trees of the nuclear gene DMC1 and the chloroplast gene rps16 sequences

description: Some plants with low fertility are morphologically intermediate between
 Roegneria stricta and Roegneria turczaninovii, and were suspected to be
 natural hybrids between these species. In this study, karyotype analysis
 showed that natural hybrids and its putative parents were tetraploids (2n
 = 4x = 28). Meiotic pairing in natural hybrids is more irregular than its
 putative parents. Results of genomic in situ hybridization and
 fluorescence in situ hybridization indicate that natural hybrids contain
 the same genome as its putative parents. The nuclear gene DNA meiotic
 recombinase 1 (DMC1) and the chloroplast gene rps16 of natural hybrids and
 its putative parents were analyzed for evidence of hybridization. The
 results from molecular data supported by morphology and cytology
 demonstrated that the plants represent natural hybrids between R. stricta
 and R. turczaninovii. The study is important understanding species
 evolution in the genus since it demonstrates for the first time the
 existence of populations of natural homoploid hybrids in Roegneria. The
 study also reports for the first time that the composition of the genomic
 formula of R. turczaninovii is StY, confirming that the current taxonomic
 status is correct.
DOI: 10.5061/dryad.2z34tmpnh
title: Data from: European common frog (Rana temporaria) recolonised Switzerland from multiple glacial refugia in northern Italy via trans- and circum-Alpine routes

description: The high mountain ranges of western Europe had a profound effect on the
 biotic recolonisation of Europe from glacial refugia. The Alps present a
 particularly interesting case because they form an absolute barrier to
 dispersal for most taxa, obstructing recolonisation from multiple refugia
 in northern Italy. Here we investigate the effect of the European Alps on
 the phylogeographic history of the European common frog Rana temporaria.
 Based on partial cytochrome b and COXI sequences from Switzerland, we find
 two mitochondrial lineages roughly north and south of the alpine ridge,
 with contact zones between them in eastern and western Switzerland. The
 northern haplogroup falls within the previously identified western
 European haplogroup, while the southern haplogroup is unique to
 Switzerland. We find that the lineages diverged ~110 kya, at approximately
 the onset of the last glacial glaciation; this indicates that they are
 from different glacial refugia. Phylogenetic analyses suggest that the
 northern and southern haplogroups colonised Switzerland via trans- and
 circum-alpine routes from at least two separate refugia in northern Italy.
 Our results illustrate how a complex recolonisation history of the central
 European Alps can arise from the semi-permeable barrier created by high
 mountains.
DOI: 10.5061/dryad.k3j9kd58b
title: Brown-throated parakeet vocalization data

description: Learned vocalizations play a key role in parrot social dynamics and vocal
 dialects have been documented for several mainland species, but to date no
 studies of geographically structured call variation in parrot species have
 examined the role of isolation on islands. In a study of the
 Brown-throated Parakeet (Eupsittula pertinax), which inhabits five small
 Caribbean islands as well as the adjacent mainland, we found that the
 contact calls of island and mainland parakeets show divergence in vocal
 characters as well as in call variability. We assessed call variation
 using three approaches: frequency measurements, spectrogram
 cross-correlation (SPCC) analyses, and call duration
 measurements. Island parakeets’ calls were longer and had lower
 mean frequencies, and calls from different islands were distinguishable
 from each other as well as from mainland calls using measures derived from
 the SPCCs. In addition we measured call variability at two
 different levels—within-location and within-individual. We found
 calls to be more variable for island parakeets for SPCC and duration
 measures, but less variable for frequency measures. The observed
 call differentiation among locations may be due to drift, while the lower
 frequency of island calls could either be a response to the very windy
 environment on the islands or a consequence of the island subspecies’
 larger body sizes. We also hypothesize that the isolation of
 parakeet populations on very small islands may have resulted in reduced
 selection for local call convergence, allowing island parakeets to produce
 more variable calls. We suggest that due to poor signal
 transmission in the windy island environment, selective pressures may
 favor variability in more easily perceived call features (like call
 duration) rather than more subtle features, like frequency
 shifts. Experimental tests are required to determine whether
 observed call patterns translate into similarly structured patterns in the
 responses to vocal variants.
description: For information/notes on the archived files,
 see: Eberhard_etal_data_README.txt
DOI: 10.5061/dryad.jdfn2z3c2
title: Data from: String phase in an artificial spin ice

description: The appearance of one-dimensional strings of local excitations represents
 an interesting feature of the physical behavior of strongly correlated
 topological quantum matter. Here we demonstrate that strings of local
 excitations can also describe the physics of a classical thermal system of
 interacting nanomagnets, the Santa Fe Ice geometry of artificial spin ice.
 We measure the moment configuration of the nanomagnets, both after
 annealing near the ferromagnetic Curie point and in a thermally dynamic
 state. While the Santa Fe Ice lattice structure is complex, we demonstrate
 that its disordered magnetic state is naturally described within a
 framework of emergent strings. We show experimentally that the string
 length follows a simple Boltzmann distribution with an energy scale that
 is associated with the system’s magnetic interactions and that is
 consistent with theoretical predictions. The results demonstrate that
 string descriptions and associated topological characteristics are not
 unique to quantum models, but that they also provide a simplifying
 description of complex classical systems with non-trivial frustration.
DOI: 10.5061/dryad.4xgxd25b3
title: Shift in competitive ability mediated by soil biota in an invasive plant

description: This dataset contains data from a greenhouse experiment described in the
 paper: Huang F, Huang Q, Gan X, Zhang W, Guo Y and Huang Y. (2021) Shift
 in competitive ability mediated by soil biota in an invasive plant.
 Ecology and Evolution, DOI: 10.1002/ece3.8287. This experiment
 investigated the interactive effects of competition environment and soil
 biota on competitive ability of an invasive plant Mikania micrantha. The
 experimental design contained a combination of three factors: soil
 treatment (live soil vs. sterilized soil), competition treatment (grown in
 isolation, with intraspecific competitors and interspecific competitors)
 and soil source (from three invaded sites), on the growth and competitive
 performance of seven M. micrantha populations varying in their field
 conspecific and heterospecific abundance. The main results of this
 experiment are that, with increasing conspecific abundance and decreasing
 heterospecific abundance, (1) M. micrantha increased intraspecific
 competition tolerance and intra- vs. interspecific competitive ability,
 but decreased interspecific competition tolerance; (2) M. micrantha
 increased tolerance of negative soil biota effect; (3) interspecific
 competition tolerance of M. micrantha was increasingly suppressed by the
 presence of soil biota, but intraspecific competition tolerance was less
 affected.
description: This dataset was collected
 during a greenhouse study at Guangdong Academy of Forestry, China and has
 been processed with a series of linear mixed models to produce a
 manuscript accepted for publication in Ecology and Evolution.
description: The readme file contains an
 explanation of each the variables in the dataset and its measurement
 unit. Information on how the measurements were done can be found in the
 associated manuscript referenced above.
DOI: 10.5061/dryad.547d7wm92
title: Combining metabolomics and experimental evolution reveals key mechanisms underlying longevity differences in laboratory evolved Drosophila melanogaster populations

description: Experimental evolution with Drosophila melanogaster has
 been used extensively for decades to study aging and longevity. In recent
 years, the addition of DNA and RNA sequencing to this framework has
 allowed researchers to leverage the statistical power inherent to
 experimental evolution to study the genetic basis of longevity itself.
 Here, we incorporated metabolomic data into to this framework to generate
 even deeper insights into the physiological and genetic mechanisms
 underlying longevity differences in three groups of experimentally
 evolved D. melanogaster populations with different aging
 and longevity patterns. Our metabolomic analysis found that aging alters
 mitochondrial metabolism through increased consumption of
 NAD+ and increased usage of the TCA cycle. Combining our genomic
 and metabolomic data produced a list of biologically relevant candidate
 genes. Among these candidates, we found significant enrichment for genes
 and pathways associated with neurological development and function, and
 carbohydrate metabolism. While we do not explicitly find enrichment for
 aging canonical genes, neurological dysregulation and carbohydrate
 metabolism are both known to be associated with accelerated aging and
 reduced longevity. Taken together, our results provide plausible genetic
 mechanisms for what might be driving longevity differences in this
 experimental system. More broadly, our findings demonstrate the value of
 combining multiple types of omic data with experimental evolution when
 attempting to dissect mechanisms underlying complex and highly polygenic
 traits such as aging.