cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.jh9w0vt6z
title: Data from: Impacts of climate variability and adaptation strategies on crop yields and soil organic carbon in the US Midwest

description: Climate change is likely to increase the frequency of drought and more
 extreme precipitation events. The objectives of this study were i) to
 assess the impact of extended drought followed by heavy precipitation
 events on yield and soil organic carbon (SOC) under historical and future
 climate, and ii) to evaluate the effectiveness of climate adaptation
 strategies (no-tillage and new cultivars) in mitigating impacts of
 increased frequencies of extreme events and warming. We used the validated
 SALUS crop model to simulate long-term maize and wheat yield and SOC
 changes of maize-soybean-wheat rotation cropping systems in the northern
 Midwest USA under conventional tillage and no-till for three
 climate change scenarios (one historical and two projected climates under
 the Representative Concentration Path (RCP) 4.5 and RCP6) and two
 precipitation changes (extreme precipitation occurring early or late
 season). Extended drought events caused additional yield reduction when
 they occurred later in the season (10-22% for maize and 5-13% for wheat)
 rather than in early season (5-17% for maize and 2-18% for wheat). We
 found maize grain yield declined under the projected climates, whereas
 wheat grain yield increased. No-tillage is able to reduce yield loss
 compared to conventional tillage and increased SOC levels (1.4-2.0 t/ha
 under the three climates), but could not reverse the adverse impact of
 climate change, unless early and new improved maize cultivars are
 introduced to increase yield and SOC under climate change. This study
 demonstrated the need to consider extreme weather events, particularly
 drought and extreme precipitation events, in climate impact assessment on
 crop yield and adaptation through no-tillage and new genetics reduces
 yield losses. 
description: The “ValidationResults.xlsx” contain SALUS-model validation
 results for simulating maize-soybean-wheat rotation systems in Kellogg
 Biological Station. There are two sheets in this file. The “metadata”
 sheet explains the sources of field observations and each column in the
 data sheet “GWAD_ob_si_byTreat”.
 ClimateAdaptationInputs.zip contains (i) a readme file
 “ReadMe_Input.docx”, which explains each of the input files in the
 zipfile, and (ii) the input files to run SALUS model.
 ClimateAdaptationResults.zip contains (i) a readme file
 “ReadMe_Results.docx”, which explains the naming convention of the SALUS
 output files in the zipfile, and (ii) SALUS output files. The SALUS output
 files were generated by running SALUS model using input files in the
 “ClimateAdaptationInputs.zip”.
DOI: 10.5061/dryad.fj6q573qg
title: Data from: Complementary strengths of spatially-explicit and multi-species distribution models

description:          Species distribution models (SDMs) project the outcome of community assembly processes - dispersal, the abiotic environment, and biotic interactions - onto geographic space. Recent advances in SDMs account for these processes by simultaneously modeling the species that comprise a community in a multivariate statistical framework or by incorporating residual spatial autocorrelation in SDMs. However, the effects of combining both multivariate and spatially-explicit model structures on the ecological inferences and the predictive abilities of a model are largely unknown. We used data on eastern hemlock  (Tsuga canadensisL.) and five additional co-occurring overstory tree species in 35,569 forest stands across Michigan, USA to evaluate how the choice of model structure, including spatial and non-spatial forms of univariate and multivariate models, affects ecological inference about the processes that shape community composition as well as model predictive ability.             Incorporating residual spatial autocorrelation via spatial random effects did not improve out-of-sample prediction for the six tree species, although in-sample model fit was higher in the spatial models. Spatial models attributed less variation in occurrence probability to environmental covariates than the non-spatial models for all six tree species, and estimated higher (more positive) residual co-occurrence values for most species pairs. The non-spatial multivariate model was better suited for evaluating habitat suitability and hypotheses about the processes that shape community composition.  Environmental correlations and residual correlations among species pairs were positively related, perhaps indicating that residual correlations were due to shared responses to unmeasured environmental covariates. This work highlights the importance of choosing a non-spatial model formulation to address research questions about the species-environment relationship or residual co-occurrence patterns, and a spatial model formulation when within-sample prediction accuracy is the main goal.
description: Please see README.txt in the data package.
DOI: 10.5061/dryad.5mkkwh71v
title: Assessing changes in genomic divergence following a century of human mediated secondary contact among wild and captive-bred ducks

description: Along with manipulating habitat, the direct release of domesticated
 individuals into the wild is a practice used world-wide to augment
 wildlife populations. We test between possible outcomes of human-mediated
 secondary contact using genomic techniques at both historical and
 contemporary time scales for two iconic duck species. First, we sequence
 several thousand ddRAD-seq loci for contemporary mallards (Anas
 platyrhynchos) throughout North America, and two domestic mallard-types
 (i.e., known game-farm mallards and feral Khaki Campbell’s). We show that
 North American mallards may well be becoming a hybrid swarm due to
 interbreeding with domesticated game-farm mallards released for hunting.
 Next, to attain a historical perspective, we applied a bait-capture array
 targeting thousands of loci in century-old (1842-1915) and contemporary
 (2009-2010) mallard and American black duck (A. rubripes) specimens. We
 conclude that American black ducks and mallards have always been closely
 related, with a divergence time of ~600,000 years before present, and
 likely evolved through prolonged isolation followed by limited bouts of
 gene flow (i.e., secondary contact). They continue to maintain genetic
 separation, a finding that overturns decades of prior research and
 speculation suggesting the genetic extinction of the American black duck
 due to contemporary interbreeding with mallards. Thus, despite having high
 rates of hybridization, actual gene flow is limited between mallards and
 American black ducks. Conversely, our historical and contemporary data
 confirm that the intensive stocking of game-farm mallards during the last
 ~100 years has fundamentally changed the genetic integrity of North
 America’s wild mallard population, especially in the east. It thus becomes
 of great interest to ask whether the iconic North American mallard is
 declining in the wild due to introgression of maladaptive traits from
 domesticated forms. Moreover, we hypothesize that differential gene flow
 from domestic game-farm mallards into the wild mallard population may
 explain the overall temporal increase in differentiation between wild
 black ducks and mallards, as well as the uncoupling of genetic diversity
 and effective population size estimates across time in our results.
 Finally, our findings highlight how genomic methods can recover complex
 population histories by capturing DNA preserved in traditional museum
 specimens.
DOI: 10.5061/dryad.1zcrjdfnr
title: The mark of captivity: plastic responses in the ankle bone of a wild ungulate (Sus scrofa)

description: Deciphering the plastic (non-heritable) changes induced by human control
 over wild animals in the archaeological record is challenging. We
 hypothesized that changes in locomotor behaviour in a wild ungulate due to
 mobility control could be quantified in the bone anatomy. To test this, we
 experimented the effect of mobility reduction on the skeleton of wild boar
 (Sus scrofa), using the calcaneus shape as a possible phenotypic marker.
 We first assessed differences in shape variation and covariation in
 captive reared and wild caught wild boars, taking into account differences
 in sex, body mass, available space for movement, and muscle force. This
 plastic signal was then con-trasted with the phenotypic changes induced by
 selective breeding in domestic pigs. We found that mobility reduction
 induces a plastic response beyond the shape variation of wild boars in
 their natural habitat, associated with a reduction in the range of
 locomotor behaviors and muscle loads. This plastic signal of captivity in
 the calcaneus shape differ from the main changes induced by selective
 breeding for larger muscle and earlier development that impacted the pigs’
 calcaneus shape in a much greater extent than the mobility reduction
 during the domestication process of their wild ancestors.
DOI: 10.5061/dryad.vt4b8gtnd
title: On age-specific selection and extensive lifespan beyond menopause

description: Standard evolutionary theory of ageing predicts weaker purifying selection
 on genes critical to later life stages. Prolonged post reproductive
 lifespan (PPRLS), observed only in a few species like humans, is likely a
 result of disparate relaxation of purifying selection on survival and
 reproduction in late life stages. While the exact origin of PPRLS is under
 debate, many researchers agree on hypotheses like mother-care and
 grandmother-care, which ascribe PPRLS to investment into future
 generations---provision to one's descendants to enhance their overall
 reproductive success. Here we simulate an agent based model, which
 properly accounts for age-specific selection, to examine how different
 investment strategies affect the strength of purifying selection on
 survival and reproduction. We observed in the simulations that, investment
 strategies that allow a female individual to remain contributive to its
 own descendants at late life stages may lead to PPRLS. In sum, we showed
 that differential relaxation of selection on survival and reproduction,
 induced by appropriate investment strategies, can lead to adaptive
 evolution of PPRLS.
DOI: 10.5061/dryad.cnp5hqc1k
title: Natal origin of Pacific bluefin tuna from the California current large marine ecosystem

description: Natal origin of subadult (age-1) Pacific bluefin tuna (PBT, Thunnus
 orientalis) from the California Current Large Marine Ecosystem (CCLME) was
 determined using natural tracers in ear stones (otoliths). Age-0 PBT
 collected from the two known spawning areas in the western Pacific Ocean
 (East China Sea, Sea of Japan) were used to establish baseline signatures
 from otolith cores over four years (2014-2017) based on a suite of trace
 elements (Li, Mg, Mn, Sr, Zn, and Ba). Distinct chemical signatures
 existed in the otolith cores of age-0 PBT collected from the two spawning
 areas, with overall classification accuracy ranging from 73-93% by year.
 Subadult PBT collected in the CCLME over the following four years
 (2015-2018) were then age-class matched to baselines using mixed-stock
 analysis. Natal origin of trans-Pacific migrants in the CCLME ranged from
 43-78% from the East China Sea and 22-57% from the Sea of Japan,
 highlighting the importance of both spawning areas for PBT in the CCLME.
 This study provides the first estimates on the natal origin of subadult
 PBT in this ecosystem using otolith chemistry and expands upon the
 application of these natural tracers for population connectivity studies
 for this species.
description: Otolith chemistry data for age-0 and age-1 samples
DOI: 10.5061/dryad.kwh70rz09
title: Data from: Exploratory research on transportation related issues with manufacturers in small urban, rural and tribal areas

description: The Small Urban, Rural, and Tribal Center on Mobility (SURTCOM) at Montana
 State University focuses on research that improves the mobility of people
 and goods in small urban, rural, and tribal areas. In response to the
 challenges identified during the 2017 workshop, SURTCOM, in partnership
 with MMEC, began exploratory research. The goal of this project was to
 better understand specific challenges manufacturers face when receiving
 raw materials into their facilities or transporting finished products to
 the next facility. The research explored production in rural communities
 and how current transportation issues will likely increase as populations
 and demands continue to grow in rural and mega regions. Following a
 literature review, the research team reached out to the MEP National
 Network Centers in fourteen peer states (large, rural, western states) for
 help distributing a survey to manufacturers to quantify to what extent
 transportation issues affect them. For this study, when reaching out to
 tribal manufacturers, only federally recognized tribal communities were
 considered, omitting tribes that are state-recognized but not federally
 recognized (Oklahoma Tribal Statistical Areas were not used to measure
 tribal population).
description: Data was collected using the Qualtrics online survey tool.
 Respondents were able to skip any question that they wanted.
description: # Dataset: Exploratory research on transportation related issues with
 manufacturers in small urban, rural and tribal areas
 [https://doi.org/10.5061/dryad.kwh70rz09](https://doi.org/10.5061/dryad.kwh70rz09) ## Description of the data and file structure This dataset contains responses from manufacturers to a Qualtrics survey seeking information on transportation issues faced by manufacturers in small urban, rural and tribal regions. Respondents were able to skip any question that they did not want to answer. ## Code/software Microsoft Excel
DOI: 10.5061/dryad.wm37pvmhh
title: Data from: Ant seed removal in a non-myrmecochorous Neotropical shrub: implications for seed dispersal

description: This study investigated ant seed removal of Piper sancti-felicis, an early
 successional Neotropical shrub. Neotropical Piper are a classic example of
 bat-dispersed plants, but we suggest that ants are underappreciated
 dispersal agents. We identified eleven ant species from the genera
 Aphaenogaster, Ectatomma, Paratrechina, Pheidole, Trachymyrmex, and
 Wasmannia recruiting to and harvesting P. sancti-felicis seeds in forest
 edge and secondary forest sites at La Selva, Costa Rica. We also tested
 for differences in ant recruitment to five states in which ants can
 commonly encounter seeds: unripe fruit, ripe fruit, overripe fruit, bat
 feces, and cleaned seeds. Overall, ants harvested more seeds from ripe and
 overripe fruits than other states, but this varied among species. To
 better understand the mechanisms behind ant preferences for ripe/overripe
 fruit, we also studied how alkenylphenols, secondary metabolites found in
 high concentrations in P. sancti-felicis fruits, affected foraging
 behavior in one genus of potential ant dispersers, Ectatomma. We found no
 effects of alkenyl- phenols on recruitment of Ectatomma to fruits, and
 thus, these compounds are un- likely to explain differences in ant
 recruitment among fruits of different maturity. Considering that P.
 sancti-felicis seeds have no apparent adaptations for ant disper- sal, and
 few ants removed seeds that were cleaned of pulp, we hypothesize that most
 ants are harvesting its seeds for the nutritional rewards in the attached
 pulp. This study emphasizes the importance of ants as important additional
 dispersers of P. sancti-felicis and suggests that other
 non-myrmecochorous, vertebrate-dispersed plants may similarly benefit from
 the recruitment to fruit by ants.
DOI: 10.5061/dryad.7m0cfxpq9
title: Data from: Rattus population genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management

description: Invasive species have led to precipitous declines in biodiversity,
 especially in island systems. Brown (Rattus norvegicus) and black rats (R.
 rattus) are among the most invasive animals on the planet, with
 eradication being the primary tool for established island populations. The
 need for increased research for defining eradication units and monitoring
 outcomes has been highlighted as a means to maximize success. Haida Gwaii
 is an archipelago ~100 km off the northern coast of British Columbia,
 Canada that hosts globally significant breeding populations of seabirds
 that are at risk due to invasive rats. Here, we paired sampling of brown
 (n=287) and black (n=291) rats across the Haida Gwaii archipelago (British
 Columbia, Canada) with genotyping-by-sequencing (10,770-27,686 SNPs) to
 investigate patterns of population connectivity and infer levels/direction
 of gene flow among invasive rat populations in Haida Gwaii. We
 reconstructed three regional clusters for both species (north, central,
 south), with proximate populations within regions being largely more
 related than those that were more distant, consistent with predictions
 from island biogeography theory. Population assignment of recently
 detected individuals post-eradication on Faraday, Murchison, and the
 Bischof Islands revealed all were re-invaders from Lyell Island, rather
 than being on-island survivors. Based on these results, we identified six
 eradication units constituting single or clusters of islands that would
 limit the potential for re-invasion, some of which will need to be
 combined with biosecurity measures. Overall, our results highlight the
 importance of targeted research prior to conducting eradications and
 demonstrates a framework for applying population genomics for guiding
 invasive species management in island systems.
description: rano_final.vcf: genotypic data for 297 brown rats (Rattus
 norvegicus) at 27,686 SNPs generated via ddRAD
 rara_final.vcf: genotypic data for 242 black rats (Rattus rattus)
 at 10,770 SNPs generated via ddRAD
DOI: 10.5061/dryad.q2bvq83fk
title: Data from: Changes in the diet and body size of a small herbivorous mammal (Sigmodon hispidus, hispid cotton rat) following the Late Pleistocene megafauna extinction

description: The catastrophic loss of large-bodied mammals during the terminal
 Pleistocene likely led to cascading effects within communities. While the
 extinction of the top consumers probably expanded the resources available
 to survivors of all body sizes, little work has focused on the responses
 of the smallest mammals. Here, we use a detailed fossil record from the
 southwestern United States to examine the response of the hispid cotton
 rat (Sigmodon hispidus) to biodiversity loss and climatic change over the
 late Quaternary. In particular, we focus on changes in diet and body size.
 We characterize diet through carbon (d13C) and nitrogen (d15N) isotope
 analysis of bone collagen in fossil jaws and body size through measurement
 of fossil teeth; the abundance of material allows us to examine population
 level responses at millennial scale for the past 16ka. Sigmodon was not
 present at the cave during the full glacial, first appearing at ~16ka
 after ice sheets were in retreat. It remained relatively rare until ~12ka
 when warming temperatures allowed it to expand its species range
 northward. We find variation in both diet and body size of Sigmodon
 hispidus over time: the average body size of the population varied by ~20%
 (90-110g) and mean d13C and d15N values ranged between -13.5 to -16.5‰ and
 5.5 to 7.4‰ respectively. A state-space model suggested changes in mass
 were influenced by diet, maximum temperature and community structure,
 while the modest changes in diet were most influenced by community
 structure. Sigmodon maintained a fairly similar dietary niche
 over time despite contemporaneous changes in climate and herbivore
 community composition that followed the megafauna extinction. Broadly, our
 results suggest that small mammals may be as sensitive to shifts in local
 biotic interactions within their ecosystem as they are to changes in
 climate and large-scale biodiversity loss.
DOI: 10.5061/dryad.qbzkh18d4
title: Co-evolution of cleaning and feeding morphology in the western Atlantic and eastern Pacific gobies

description: Cleaning symbioses are mutualistic relationships where cleaners remove and
 consume ectoparasites from their clients. Cleaning behavior is rare in
 fishes and is a highly specialized feeding strategy only observed in
 around 200 species. Cleaner fishes vary in their degree of specialization,
 ranging from species that clean as juveniles or facultatively as adults,
 to nearly obligate or dedicated cleaners. Here we investigate whether
 these different levels of trophic specialization correspond with similar
 changes in feeding morphology. Specifically, we model the evolution of
 cleaning behavior across the family Gobiidae, which contains the most
 speciose radiation of dedicated and facultative cleaner fishes. We
 compared the cranial morphology and dentition of cleaners and non-cleaners
 across the phylogeny of cleaning gobies and found that facultative
 cleaners independently evolved four times and have converged on an
 intermediate morphology relative to that of dedicated cleaners and
 non-cleaning generalists. This is consistent with their more flexible
 feeding habits. Cleaner gobies also possess a distinct scraping tooth
 morphology, which suggests they are adapted for scraping parasites off
 their clients and show little similarity to other cleaner clades. We
 propose that evolutionary history and pre-adaptation underlie the
 morphological and ecological diversification of cleaner fishes.
DOI: 10.25338/b8903d
title: Data from: The effects of temperature on the defensive strikes of rattlesnakes

description: Movements of ectotherms are constrained by their body temperature owing to
 the effects of temperature on muscle physiology. As physical performance
 often affects the outcome of predator–prey interactions, environmental
 temperature can influence the ability of ectotherms to capture prey and/or
 defend themselves against predators. However, previous research on the
 kinematics of ectotherms suggests that some species may use elastic
 storage mechanisms when attacking or defending, thereby mitigating the
 effects of sub-optimal temperature. Rattlesnakes (Crotalus spp.) are a
 speciose group of ectothermic viperid snakes that rely on crypsis,
 rattling and striking to deter predators. We examined the influence of
 body temperature on the behavior and kinematics of two rattlesnake species
 (Crotalus oreganus helleri and Crotalus scutulatus) when defensively
 striking towards a threatening stimulus. We recorded defensive strikes at
 body temperatures ranging from 15–35°C.We found that strike speed and
 speed of mouth gaping during the strike were positively correlated with
 temperature. We also found a marginal effect of temperature on the
 probability of striking, latency to strike and strike outcome. Overall,
 warmer snakes are more likely to strike, strike faster, open their mouth
 faster and reach maximum gape earlier than colder snakes. However, the
 effects of temperature were less than would be expected for purely
 muscle-driven movements. Our results suggest that, although rattlesnakes
 are at a greater risk of predation at colder body temperatures, their
 decrease in strike performance may be mitigated to some extent by
 employing mechanisms in addition to skeletal muscle contraction (e.g.
 elastic energy storage) to power strikes.