cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cz8w9gj1f
title: Limited genetic parallelism underlies recent, repeated incipient speciation in geographically proximate populations of an Arctic fish (Salvelinus alpinus)

description: The genetic underpinnings of incipient speciation, including the genomic
 mechanisms which contribute to morphological and ecological
 differentiation and reproductive isolation, remain poorly understood. The
 repeated evolution of consistently, phenotypically distinct morphs of
 Arctic Charr (Salvelinus alpinus) within the Quaternary period offer an
 ideal model to study the repeatability of evolution at the genomic level.
 Sympatric morphs of Arctic Charr are found across this species'
 circumpolar distribution. However, the specific genetic mechanisms driving
 this morph differentiation are largely unknown despite the cultural and
 economic importance of the anadromous morph. We used a newly designed 87k
 SNP chip to investigate the character and consistency of the genomic
 differences among sympatric morphs within three recently deglaciated and
 geographically proximate lakes in Labrador, Canada. We found genetically
 distinct small and large morph Arctic Charr in all three lakes consistent
 with resident and anadromous morphs, respectively. A degree of
 reproductive isolation among sympatric morphs is likely given genome-wide
 distributions of outlier SNPs and high genome-wide FSTs. Across all lakes,
 outlier SNPs were largely non-overlapping suggesting a lack of genetic
 parallelism driving morph differentiation. Alternatively, several genes
 and paralogous copies of the same gene consistently differentiated morphs
 across multiple lakes suggesting their importance to the manifestation of
 morphs. Our results confirm the utility of Arctic Charr as a model for
 investigating the predictability of evolution and support the importance
 of both genetic parallelism and non-parallelism to the incipient
 speciation of Arctic Charr morphs.
description: Files consist of genepop files for SNP data.
DOI: 10.5061/dryad.5hqbzkh3m
title: Data from: Fine-scale habitat selection by sympatric Canada lynx and bobcat

description: The Canada lynx (Lynx canadensis) and the bobcat (Lynx rufus) are closely
 related species with overlap at their range peripheries, but the factors
 that limit each species and the interactions between them are not well
 understood. Habitat selection is a hierarchical process, in which
 selection at higher orders (geographic range, home range) may constrain
 selection at lower orders (within the home range). Habitat selection at a
 very fine scale within the home range has been less studied for both lynx
 and bobcat compared to selection at broader spatio-temporal scales. To
 compare this fourth-order habitat selection by the two species in an area
 of sympatry, we tracked lynx and bobcat during the winters of 2017 and
 2018 on the north shore of Lake Huron, Ontario. We found that both lynx
 and bobcat selected shallower snow, higher snowshoe hare abundance, and
 higher amounts of coniferous forest at the fourth order. However, the two
 species were spatially segregated at the second order, and lynx were found
 in areas with deeper snow, more snowshoe hare, and more coniferous forest.
 Taken together, our findings demonstrate that the lynx and bobcat select
 different resources at the second order, assorting along an environmental
 gradient in the study area, and that competition is unlikely to be
 occurring between the two species at finer scales.
DOI: 10.15468/dl.58qgfa
title: Occurrence Download

description: A dataset containing 2820 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bowdichia virgilioides",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2820 records from 145 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002450-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.d2547d815
title: Supplementary material for: the phylogeny and evolution of the flashiest of the armored harvestmen (Arachnida: Opiliones)

description: Gonyleptoidea, largely restricted to the Neotropics, constitutes the most
 diverse superfamily of Opiliones and includes the largest and flashiest
 representatives of this arachnid order. However, the relationships among
 its main lineages (families and superfamilies) and the timing of their
 origin are not sufficiently understood to explain how this tropical clade
 has been able to colonize the temperate zone. Here we used transcriptomics
 and divergence time dating to investigate the phylogeny of Gonyleptoidea.
 Our results support the monophyly of Gonyleptoidea and all of its families
 with more than one species represented. Resolution within Gonyleptidae
 s.s. is achieved for many clades, but some subfamilies are not
 monophyletic (Gonyleptinae, Mitobatinae, and Pachylinae), requiring
 taxonomic revision. Our data show evidence for one colonization of today’s
 temperate zone early in the history of Gonyleptidae, during the Paleogene,
 at a time when the Neotropical area extended poleward into regions now
 considered temperate. This provides a possible mechanism for the
 colonization of the extratropics by a tropical group following the
 Paleocene–Eocene Thermal Maximum, explaining how latitudinal diversity
 gradients (LDGs) can be established. Taxonomic acts: Ampycidae Kury 2003
 is newly ranked as family; Neosadocus Mello-Leitão is
 transferred to Progonyleptoidellinae (new subfamilial assignment).
DOI: 10.5061/dryad.ffbg79crv
title: Data for Nicola Chinook Ricker stock-recruit model with environmental covariates

description: Climate change and human activities are transforming river flows globally,
 with potentially large consequences for freshwater life. To help inform
 watershed and flow management, there is a need for empirical studies
 linking flows and fish productivity. We tested the effects of river
 conditions and other factors on 22 years of Chinook salmon productivity in
 a watershed in British Columbia, Canada. Freshwater conditions during
 adult salmon migration and spawning, as well as during juvenile rearing,
 explained a large amount of variation in productivity. August river flows
 while salmon fry reared had the strongest effect on productivity – our
 model predicted that cohorts that experience 50% below average flow in the
 August of rearing have 21% lower productivity. These contemporary
 relationships are set within long-term changes in climate, land use, and
 hydrology. Over the last century, average August river discharge decreased
 by 26%, air temperatures warmed, and water withdrawals increased. 17% of
 the watershed was logged in the last 20 years.  Our results
 suggest that, in order to remain stable, this Chinook salmon population
 being assessed for legal protection requires substantially higher August
 flow than previously recommended. Changing flow regimes – driven by
 watershed impacts and climate change – can threaten imperiled fish
 populations.
description: This dataset is a combination of several sources:
 -Spawner and recruitment data from Fisheries and Oceans Canada,
 corrected for unmarked hatchery returns and fishing mortality using
 Regional Mark Processing Centre and Pasific Salmon Commission Chinook
 Technical Committee data -Summarized hydrometric data
 from the Water Survey of Canada -Smolt-to-age 3
 survival data for Chinook released from Spius Creek hatchery
description: This dataset was used to fit Bayesian stock-recruit models.
 Before analysis, the hydrometric and smolt-to-age 3 survival variables
 were centered and scaled to mean=0 and SD=1. We also include an un-scaled
 data set here for reference. See
 https://github.com/lukewarkentin/nicola_chinook for complete analysis
 codes and raw data files. <strong>Important
 note:</strong> For any re-analysis, contact Chuck Parken
 (Chuck.Parken@dfo-mpo.gc.ca) for any data revisions/updates. CWT data can
 have minor changes and new analysis should include most up to date data.
 CWT data is used to estimate smolt-to-age 3 survival and explotiation
 rate.
DOI: 10.6078/d1nq59
title: Data for: Low predictability of energy balance traits and leaf temperature metrics in desert, montane, and alpine plant communities

description: Leaf energy balance may influence plant performance and community
 composition. While biophysical theory can link leaf energy balance to many
 traits and environment variables, predicting leaf temperature and key
 driver traits with incomplete parameterizations remains challenging.
 Predicting thermal offsets (δ, Tleaf – Tair difference) or thermal
 coupling strengths (β, Tleaf vs. Tair slope) is challenging. We ask: 1)
 whether environmental gradients predict variation in energy balance traits
 (absorptance, leaf angle, stomatal distribution, maximum stomatal
 conductance, leaf area, leaf height); 2) whether commonly-measured leaf
 functional traits (dry matter content, mass per area, nitrogen fraction,
 δ13C, height above ground) predict energy balance traits; and 3) how
 traits and environmental variables predict δ and β among species. We
 address these questions with diurnal measurements of 41 species
 co-occurring along an 1100 m elevation gradient spanning desert to alpine
 biomes. We show that 1) energy balance traits are only weakly associated
 with environmental gradients, and 2) are not well predicted by common
 functional traits. We also show that 3) δ and β can be partially
 approximated using interactions among site environment and traits, with a
 much larger role for environment than traits. The heterogeneity in leaf
 temperature metrics and energy balance traits challenges larger-scale
 predictive models of plant performance under environmental change.
DOI: 10.5061/dryad.jwstqjq6m
title: Body shape transformations by alternate anatomical adaptive peak shifts in blenniiform fishes

description: Extreme body elongation has occurred repeatedly in the evolutionary
 history of ray-finned fishes. Lengthening of the anterior-posterior body
 axis relative to depth and width can involve changes in the cranial
 skeleton and vertebral column, but to what extent is anatomical evolution
 determined by selective factors and intrinsic constraints that are shared
 broadly among closely related lineages? In this study, we fit adaptive
 (Ornstein-Uhlenbeck) evolutionary models to body shape and its anatomical
 determinants and identified two instances of extreme elongation by
 divergent anatomical peak shifts in the Blenniiformes, a radiation of
 small-bodied substrate-associated marine teleost fishes. Species in the
 genus Xiphasia (hairtail blennies) evolved toward a peak defined by a
 highly elongated caudal vertebral region but ancestral cranial and
 precaudal vertebral morphology. In contrast, a clade that includes the
 genera Chaenopsis and Lucayablennius (pike and arrow blennies) evolved
 toward a peak with a long slender skull but ancestral axial skeletal
 anatomy. Neither set of anatomical peak shifts aligns closely with the
 major axis of anatomical diversification in other blenniiform fishes.
 These results provide little evidence that ancestral constraints have
 affected body shape transformation, and instead suggest that extreme
 elongation arose with distinct shifts in selective factors and
 development.
DOI: 10.18739/a2gb1xk1m
title: Snow depths near Toolik Field Station, Alaska 2014-2025

description: The Toolik Field Station (TFS) snow depth program monitors the accumulation of snow monthly near the station in three frequently studied environmental microhabitats - in the dry heath, moist acidic tundra and on Toolik Lake. The TFS snow monitoring began in response to TFS research community requests to collect baseline environmental data that would be broadly applicable and provide context to research projects conducted near TFS. Very little snow depth data is collected year round on the north slope of Alaska and what is collected is done via remote automated gauges. This is the only dataset collected by hand throughout the winter on the North Slope of Alaska. This snow depth monitoring began in January 2014 and is adaptively measured every month of the winter season.
 The TFS snow depth data collection protocol is based on the United States Department of Agriculture snow survey sampling guide (https://www.nrcs.usda.gov/sites/default/files/2023-11/Snow%20Survey%20Sampling%20Guide%20Handout.pdf).
DOI: 10.5061/dryad.vdncjsxrk
title: An amplicon sequencing protocol for attacker identification from DNA traces left on artificial prey

description: Clay model studies are a popular tool to identify predator-prey
 interactions that are challenging to observe directly in the field. But
 despite its wide use, the method’s applicability is limited by its low
 taxonomic resolution. Attack marks on clay models are usually identified
 visually, which only allows classification into higher taxonomic levels of
 predators. Thus, the method is often biased, lacks proof and, above all,
 standardization. Here, we tested whether precise identification of
 attackers can be provided by amplification and sequencing of mitochondrial
 DNA left in bite marks on clay models. We validated our approach in a
 controlled laboratory study as well as in a field experiment using clay
 models of a common European amphibian, the European fire salamander
 (Salamandra salamandra). DNA based taxonomic assignments were additionally
 compared to visual assessments of bite marks. We show that trace DNA of
 attackers can be routinely isolated and sequenced from bite marks,
 providing accurate species level classification. In contrast, visual
 identification alone yielded a high number of unassigned predator taxa. We
 also highlight the sensitivity of the method and show likely sources of
 contamination as well as probable cases of secondary and indirect
 predation. Our standardized approach for species level attacker
 identification opens up new possibilities far beyond the standard use of
 clay models to date, including food web studies at unprecedented detail,
 invasive species monitoring as well as biodiversity inventories.
description: Amplicon sequencing data, collected from clay models of
 salamanders
DOI: 10.5061/dryad.95x69p8h5
title: The code used to simulate range expansion in "The effect of the recombination rate between adaptive loci on the capacity of a population to expand its range"

description: Previous theoretical work on range expansions over heterogeneous
 environments showed that there is a critical environmental gradient where
 range expansion stops. For populations with freely recombining loci
 underlying the trait under selection (hereafter adaptive loci), the
 critical gradient in one-dimensional habitats depends on the fitness cost
 of dispersal, and the strength of selection relative to genetic drift.
 Here, we extend the previous work in two directions and ask: What is the
 role of the recombination rate between the adaptive loci during range
 expansions? And what effect does the ability of selfing as opposed to
 obligate outcrossing have on range expansions? To answer these questions,
 we use computer simulations. We demonstrate that, while reduced
 recombination rates between adaptive loci slow down range expansions due
 to poor purging of locally deleterious alleles at the expansion front,
 they may also allow a species to occupy a greater range. In addition, we
 find that the allowance of selfing may improve the ability of populations
 to expand their ranges. We conclude that during range expansions
 there is a trade-off between positive and negative effects of
 recombination within and between individuals.
description: This is a custom-made code, written in Matlab. 
description: For the explanation of how to use the code, please see
 ReadMeFirst.txt.
DOI: 10.5061/dryad.n02v6wwv3
title: Acoustic and temporal birdsong measurements

description: In tropical birds, survival is dependent on the ability to effectively
 communicate with others against a background of high ambient noise. The
 Acoustic Niche Hypothesis proposes that the deterrent selective force of
 signal masking has caused animals sharing a habitat to partition their
 calling behaviour amongst the acoustic bandwidths available, so as to
 minimise interference between one another. Whether and why species share
 the so-called ‘acoustic space’ remains a gap in our understanding of
 animal ecosystems. The aim of this study was to investigate differences
 between the acoustic structure of avian communities in two spatially
 distinct habitats in the montane tropical forests of the Caparaó National
 Park in south-eastern Brazil, and to test whether the distribution of
 birdsong at each conformed to the ANH. Birdsong from nine hours of passive
 acoustic recordings at each study site were analysed using principal
 component analyses. The results contradicted the ANH, revealing strikingly
 similar patterns of synchronised vocal behaviour. No correlation was
 evident between the acoustic and temporal partitioning behaviour of
 songbirds. This study provides a novel comparative analysis of the
 acoustic dynamics in two separate and diverse avian communities and
 support for theories of synchronized vocal behaviour in such groups.
description: Sound recordings used for this study were recorded by MCK in
 January and March of 2017 using four autonomous recording units (ARU)
 (SongMeter SM3, Wildlife Acoustics Inc., Concord, MA, USA) deployed across
 a "listening post" in Aleixo Valley and another in Santa Marta
 Valley(20°28'46.49" S, 41°50'25.00" W and
 20°29'25.74"S, 41°44'21.55"W). Each listening post
 comprised of two SongMeters fixed 1.8 m above ground, each attached to two
 microphones, facing opposite directions and thus recording in the four
 cardinal directions (Figure 2). Recordings were sampled at 44.1 kHz and 16
 bits per second and recorded in 1-hour segments. A high-pass filter was
 set at 220 Hz to filter out wind and river noise. Recordings from the two
 SongMeters at each post were time-synchronized using Garmin GPS’s to
 triangulate the sound source. Three hours of recording from 0800 to 1100
 on three consecutive days were used from each site to investigate the
 singing avian communities. The nine hours of recording taken from each
 study site combined for a total of 18 hours of recording for this study.
 Analysis was carried out in Raven Pro and R Studio. 
description: Recordings from earlier in the morning during the dawn chorus
 were orginially intended for use but were omitted to dominant
 cicada noise. IMPORTANT: pathnames for csv files to be read must be filled
 in to run analysis R Scripts (see metadata README).
DOI: 10.5061/dryad.bg79cnp8j
title: Is drought tolerance a domestication trait in tepary bean?: Allelic diversity at abiotic stress responsive genes in cultivated Phaseolus acutifolius A. Gray and its wild relatives

description: Some of the major impacts of climate change are expected in the poorest
 regions of the world where drought stress and nutrient deficiency are
 already a main issue. Legumes are an essential food crop for the poorest
 because of their high dietary protein and micronutrient contents. However,
 they are generally drought susceptible. Therefore, our goal in this study
 was to explore allele diversity at abiotic stress responsive candidate
 genes in the only drought tolerant cultivated bean species of the genus
 Phaseolus, tepary bean (P. acutifolius A. Gray) and its related species P.
 parvifolius Freytag. Specifically, we estimated drought tolerance in 52
 tepary bean s.l. geo-referenced germplasm accessions from the P.
 acutifolius–parvifolius clade using climate information, and used this
 estimated drought stress index to examine allele correlations with Asr2,
 Dreb2B and ERECTA-encoding candidate genes for drought tolerance. Genetic
 clustering showed that cultivated and wild P. acutifolius were
 intermingled with P. acutifolius var. tenuifolius and P. parvifolius,
 signifying that allele diversity at candidate genes for drought tolerance
 was not scarce in tepary bean s.l. Dreb2B and ERECTA-encoding genes
 harbored signatures of directional/purifying selection, likely in favor of
 adaptive alleles selectively advantageous because each had two SNPs
 significantly correlated (p-value &lt; 0.05) with habitat drought
 stress at six and 12 months. These results suggest that tepary bean s.l.
 is a reservoir of novel alleles at candidate genes for drought tolerance,
 as expected for a drought-tolerant species that originated in warmer and
 arid environments. Abiotic stress responsive candidate genes also exhibit
 comparable patterns of selective signatures when comparing orthologous
 across species, which speaks for a predominant role of gene
 sub-functionalization likely due to ecological constrains. Our study
 therefore corroborates that the candidate gene approach is still an
 effective alternative for marker validation across a broader genetic basis
 of germplasm accessions. Further efforts to determine the genetic
 architecture of drought tolerance will unlock novel alleles hidden in a
 crop with limited modern relevance as tepary bean, but capable of acting
 as a donor in backcrossing and genome editing strategies with elite common
 bean lines aiming to meet the imminent demands of a drier world.
DOI: 10.15468/dl.mfcs4y
title: Occurrence Download

description: A dataset containing 54630 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Observation, Human Observation, Specimen)",
 "Geometry POLYGON((-74.18 43.34,-54.59 43.34,-54.59 48.25,-74.18 48.25,-74.18 43.34))",
 "HasCoordinate is true",
 "License is one of (CC-BY-NC 4.0, CC-BY 4.0, CC0 1.0)",
 "OccurrenceStatus is Present",
 "TaxonKey is Ochrophyta"
 ]
}

 The dataset includes 54630 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002393-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.m905qftzf
title: Loon Project Database

description: Data collected since 1993 in Oneida County, Wisconsin, on the breeding and
 territorial behavior of the common loon, Gavia immer. This study
 population is marked with USGS metal bands and colored leg bands for
 individual identification. It includes many individuals banded as chicks,
 whose life histories are known thoroughly. Data are collected from April
 through August of most years on this migratory species. Data are in the
 form of a MS-Access file, with many individual "tables"
 containing data on banding, breeding, dispersal and other life-history
 information. 
description: Field observations on marked breeding pairs of common loons from
 April through October from Oneida County, Wisconsin. Collected beginning
 in 1993. Data are entered daily by field observers or by the principal
 investigator. 
description: Data are self-explanatory, but queries may be directed to the
 principal investigator at wpiper@chapman.edu.