cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bnzs7h492
title: Urban specialization reduces habitat connectivity by a highly mobile wading bird

description: Background Mobile animals transport nutrients and propagules across
 habitats, and are crucial for the functioning of food webs and for
 ecosystem services. Human activities such as urbanization can alter animal
 movement behavior, including site fidelity and resource use. Because many
 urban areas are adjacent to natural sites, mobile animals might connect
 natural and urban habitats. More generally, understanding animal movement
 patterns in urban areas can help predict how urban expansion will affect
 the roles of highly mobile animals in ecological processes. Methods Here,
 we examined movements by a seasonally nomadic wading bird, the American
 white ibis (Eudocimus albus), in South Florida, USA. White ibis are
 colonial wading birds that forage on aquatic prey; in recent years, some
 ibis have shifted their behavior to forage in urban parks, where they are
 fed by people. We used a spatial network approach to investigate how
 individual movement patterns influence connectivity between urban and
 non-urban sites. We built a network of habitat connectivity using GPS
 tracking data from ibis during their non-breeding season and compared this
 network to simulated networks that assumed individuals moved
 indiscriminately with respect to habitat type. Results We found that the
 observed network was less connected than the simulated networks, that
 urban-urban and natural-natural connections were strong, and that
 individuals using urban sites had the least-variable habitat use.
 Importantly, the few ibis that used both urban and natural habitats
 contributed the most to connectivity. Conclusions Habitat specialization
 in urban-acclimated wildlife could reduce the exchange of propagules and
 nutrients between urban and natural areas, which has consequences both for
 beneficial effects of connectivity such as gene flow and for detrimental
 effects such as the spread of contaminants or pathogens.
DOI: 10.5061/dryad.bzkh1897b
title: Gene family amplification facilitates adaptation in freshwater Unionid bivalve Megalonaias nervosa

description: As organisms are faced with intense rapidly changing selective pressures,
 new genetic material is required to facilitate adaptation. Among sources
 of genetic novelty, gene duplications and transposable elements (TEs)
 offer new genes or new regulatory patterns that can facilitate
 evolutionary change. With advances in genome sequencing it is possible to
 gain a broader view of how gene family proliferation and TE content evolve
 in non-model species when populations become threatened. Freshwater
 bivalves (Unionidae) currently face severe anthropogenic challenges. Over
 70% of species in the United States are threatened, endangered or extinct
 due to pollution, damming of waterways, and overfishing. We have created a
 reference genome for M. nervosa to determine how genome content has
 evolved in the face of these widespread environmental challenges. We
 observe a burst of recent transposable element proliferation causing a 382
 Mb expansion in genome content. Gene family expansion is common, with a
 duplication rate of 1.16 x 10^-8 per gene per generation. Cytochrome P450,
 ABC transporters, Hsp70 genes, von Willebrand proteins, chitin metabolism
 genes, mitochondria eating proteins, and opsin gene families have
 experienced significantly greater amplification and show signatures of
 selection. We use evolutionary theory to assess the relative contribution
 of SNPs and duplications in evolutionary change. Estimates suggest that
 gene family evolution may offer an exceptional substrate of genetic
 variation in M. nervosa, with Psgv=0.185 compared with Psgv=0.067 for
 single nucleotide changes. Hence, we suggest that gene family evolution is
 a source of "hopeful monsters" within the genome that facilitate
 adaptation.
description: Genome assembly and annotation using Illumina+nanopore, RNAseq
 data.  De novo assembled transcriptomes using the oyster river protocol.
 TEs identified using RepDeNovo and RepeatScout.  
description: Megalonaias nervosa collected from Pickwick Reservoir near Muscle
 Shoals, AL in 2017
DOI: 10.5061/dryad.31zcrjdjp
title: Data for: Innate immune function and antioxidant capacity of nestlings of an African raptor co-vary with the level of urbanization around breeding territories

description: Urban areas provide breeding habitats for many species. However, animals
 raised in urban environments face challenges such as altered food
 availability and quality, pollution, and pathogens assemblages. These
 challenges can affect physiological processes like immune function and
 antioxidant defences which are important for fitness. Here, we explore how
 levels of urbanisation influence innate immune function, immune response
 to a mimicked bacterial infection and antioxidant capacity of nestling
 Black Sparrowhawks Accipiter melanoleucus in South Africa. We also explore
 the effect of timing of breeding and rainfall on physiology since both can
 influence the environmental condition under which nestlings are raised.
 Finally, because urbanisation can influence immune function indirectly, we
 use path analyses to explore direct and indirect associations between
 urbanisation, immune function, and oxidative stress. We obtained measures
 of innate immunity (haptoglobin, lysis, agglutination and bactericidal
 capacity), indices of antioxidant capacity (total non-enzymatic
 antioxidant capacity (tAOX), and total glutathione from nestlings from
 2015 - 2019. In addition, in 2018 and 2019, we mimicked a bacterial
 infection by injecting nestlings with lipopolysaccharide and quantified
 their immune response. Increased urban cover was associated with an
 increase in lysis and a decrease in tAOX, but not with any of the other
 physiological parameters. Furthermore, except for agglutination, no
 physiological parameters were associated with the timing of breeding.
 Lysis and bactericidal capacity, however, varied consistently with the
 annual rainfall pattern. Immune response to a mimicked a bacterial
 infection decreased with urban cover but not with the timing of breeding
 nor rainfall. Our path analyses suggested indirect associations between
 urban cover and some immune indices via tAOX but not via the timing of
 breeding. Our results show that early-life development in an urban
 environment is associated with variation in immune and antioxidant
 functions. The direct association between urbanisation and antioxidant
 capacity and their impact on immune function is likely an important factor
 mediating the impact of urbanisation on urban-dwelling animals. Future
 studies should explore how these results are linked to fitness and whether
 the responses are adaptive for urban-dwelling species.
description: Field data including morphometric measurements, sampling history
 and individual identifiers of nestling of Black Sparrowhawk
 <em>Accipiter melanoleucus</em>, measures of immune function
 and antioxidant capacity generated from laboratory analyses of plasma and
 whole blood, estimation of cover around breeding territories using
 landcover images, and Cape Town rainfall data collected from the South
 African Weather Services. All data compiled in Office Microsoft Excel
 spreadsheets.
DOI: 10.5061/dryad.zw3r22871
title: Thermal tolerance of Lasius americanus across urbanization and geographical gradients

description: Cities are emerging as a new venue to overcome the challenges of obtaining
 data on compensatory responses to climatic warming through phenotypic
 plasticity and evolutionary change. In this review, we highlight how
 cities can be used to explore physiological trait responses to
 experimental warming and also how cities can be used as human-made
 space-for-time substitutions. We synthesized the current literature and
 found evidence for significant plasticity and evolution in thermal
 tolerance trait responses to urban heat islands. For those studies that
 reported both plastic and evolved components of thermal tolerance, we
 found evidence that both mechanisms contributed to phenotypic shifts in
 thermal tolerance, rather than plastic responses precluding or limiting
 evolved responses. Interestingly though, for a broader range of studies,
 we found that the magnitude of evolved shifts in thermal tolerance was not
 significantly different from the magnitude of shift in those studies that
 only reported phenotypic results, which could be a product of evolution,
 plasticity, or both. Regardless, the magnitude of shifts in urban thermal
 tolerance phenotypes was comparable to more traditional space-for-time
 substitutions across latitudinal and altitudinal clines in environmental
 temperature. We conclude by considering how urban-derived estimates of
 plasticity and evolution of thermal tolerance traits can be used to
 improve forecasting methods including macrophysiological models and
 species distribution modelling approaches. Finally, we consider areas for
 further exploration including sub-lethal performance traits and thermal
 performance curves, assessing the adaptive nature of trait shifts, and
 taking more full advantage of the environmental thermal variation that
 cities generate.
description: Usage information can be found in the file
 "LasiusMetadata". This document provides information on the
 contents of the 4 dataset files corresponding with heat and cold tolerance
 values of Lasius americanus ants across a biogeographic gradient and an
 urbanization gradient.
DOI: 10.5061/dryad.hdr7sqvgk
title: Peregrine Falcon Site Occupancy along Delmarva Peninsula, VA (2006-2009)

description: We monitored the breeding activity of peregrine falcons along the seaside
 of the Delmarva Peninsula (2006-2009) to determine their influence on the
 distribution of foraging red knots along the Virginia barrier
 islands.  Twelve breeding territories were used during the study
 period.  Both activity status and productivity varied across
 sites.  Activity status was used to examine the influence of
 peregrines on the distribution of foraging red knots relative to peregrine
 eyries.  This database contains the results of survey efforts
 (2006-2009).
description: We determined the number of nesting pairs, productivity, and
 nesting success of peregrine falcons breeding along the seaside of the
 Delmarva Peninsula in Virginia by regular monitoring.  The Delmarva
 Peninsula study area considered here includes the barrier island lagoon
 system from the Virginia-Maryland boundary south to the mouth of the
 Chesapeake Bay.  Artificial structures have been established within this
 study area specifically for use by breeding peregrines.  Nesting
 structures were surveyed early in the breeding season (March) to determine
 occupancy by falcons.  We monitored sites determined to be occupied during
 a given year an additional 2-5 times from March through July to document
 breeding activity, to band young, and to document fledging success. For
 our purposes here, we considered a breeding territory to be active if a
 pair of adult peregrines was resident during the breeding
 season.
DOI: 10.5061/dryad.573n5tb68
title: Ambulatory physicians’ electronic health record self-efficacy

description: Objective: To assess ambulatory providers’ confidence in learning about
 and using the electronic health record (EHR). Materials and Methods:
 Providers were administered an EHR skills self-assessment survey. Results:
 71 providers participated. Only 35% of respondents felt that they had
 strong EHR skills, 92% felt confident that they could learn new skills,
 and 90% felt they could improve with practice. 45% of faculty physicians
 felt confident that they could use the EHR in a time-efficient manner and
 52% felt could keep up with advances but 16% felt apprehensive about using
 the EHR. 94% of faculty would welcome opportunities to learn more.
 Discussion: Most providers viewed using the EHR as a clinical skill they
 could master with training and practice. Conclusion: Physicians may be
 engaged by EHR training programs that focus on the use of the EHR as a
 clinical skill. This work has informed new training programs at our
 institution.
description: Data was collected by survey, on paper or via Google
 Survey.  The "Top 10 Score" was calculated
 and compiled by the author from Epic Provider Efficiency Data.
 Any potentially identifying information has been
 removed.
description: Survey results range from 1 to 5 with 1 equal to strongly
 disagree and 5 equal to strongly agree.
DOI: 10.5061/dryad.hmgqnk9fm
title: Geophyte ecophysiology and traits

description: Premise of the study: In semi-arid regions, decreasing rainfall
 presents a challenge to perennial seedlings that must reach sufficient
 size to survive the first year’s seasonal drought. Attaining a large
 storage organ size has been hypothesized to enhance drought resilience in
 geophytes, but building larger storage organs requires greater growth
 rates, and paradoxically, some traits conferring faster growth are highly
 sensitive to drought. We examine if tuber size confers greater drought
 resilience in seedlings of four closely related geophytic species
 of Pelargonium. Methods: We imposed two drought
 treatments when seedlings were two months old: chronic low water and acute
 water restriction for ten days. Plants in the acute dry-down treatment
 were then rewatered at control levels. We compared morphological and
 ecophysiological traits at two, three and six months of age and used
 mixed-effects models to identify traits determining tuber biomass at
 dormancy.      Key
 results: Despite ten-fold variation in size, species had similar
 physiological trait values under well-watered conditions. Chronic and
 acute droughts negatively affected tuber size at the end of the season,
 but only in the two species with large tubers. Chronic drought did not
 affect physiological traits of any species, but in response to acute
 drought, larger species showed reduced photosynthetic performance. Canopy
 area was the best predictor of final tuber biomass. 
 Conclusions: Contradictory to the hypothesis that large tubers
 provide greater drought resiliency,
 in Pelargonium seedlings smallness actually increased
 drought tolerance, although at the expense of more vigorous growth
 compared to species with larger tubers under well-watered
 conditions.
DOI: 10.5061/dryad.r7sqv9sb1
title: Unraveling the predictive role of temperature in the gut microbiota of the sea urchin Echinometra sp. EZ across spatial and temporal gradients

description: Shifts in microbial communities represent a rapid response mechanism for
 host organisms to respond to changes in environmental conditions.
 Therefore, they are likely to be important in assisting the
 acclimatization of hosts to seasonal temperature changes as well as to
 variation in temperatures across a species’ range. The Persian/Arabian
 Gulf is the world's warmest sea, with large seasonal fluctuations in
 temperature (20℃ - 37℃) and is connected to the Gulf of Oman which
 experiences more typical oceanic conditions (&lt;32℃ in the summer).
 This system is an informative model for understanding how symbiotic
 microbial assemblages respond to thermal variation across temporal and
 spatial scales. Here, we elucidate the role of temperature on the
 microbial gut community of the sea
 urchin Echinometra sp. EZ and identify
 microbial taxa that are tightly correlated with the thermal environment.
 We generated two independent datasets with a high degree of geographic and
 temporal resolution. The results show that microbial communities vary
 across thermally variable habitats, display temporal shifts that correlate
 with temperature, and can become more disperse as temperatures rise. The
 relative abundances of several ASVs significantly correlate with
 temperature in both independent datasets despite the
 &gt;300 km distance between the furthest sites and the
 extreme seasonal variations. Notably, over 50% of the temperature
 predictive ASVs identified from the two datasets belonged to the family
 Vibrionaceae. Together, our results identify temperature as a robust
 predictor of community-level variation and highlight specific microbial
 taxa putatively involved in the response to thermal environment.
description: Please see manuscript.
description: metadata_season_var - Metadata for the temporal series with
 metadata values metadata_site.tsv - Metadata for the
 summer winter spatial series with metadata values 
 seqdna.fasta - All 16S sequences with corresponding ASV
 identifier  siteseason.featuretable.txt - ASV table for
 both datasets, nonrarified, not filtered. Contains ASV ID from QIIME with
 our shortened ASV ID  totaluniqtax.tsv - ASV ID with
 taxonomic identifier TemporalSeries.zip 
 SWSiteSeries.zip   *Please
 note the identifiers CG and MS, as well as AF and AH are used
 interchangeably throughout some of these documents.
DOI: 10.5061/dryad.83bk3j9qd
title: Defensive structures influence fighting outcomes

description: In many animal species, individuals engage in fights with conspecifics
 over access to limited resources (e.g. mates, food, or shelter). Most
 theory about these intraspecific fights assumes that damage has an
 important role in determining the contest winner. Thus, defensive
 structures that reduce the amount of damage an individual accrues during
 intraspecific competition should provide a fighting advantage. 
 Examples of such damage-reducing structures include the dermal shields of
 goats, the dorsal osteoderms of crocodiles, and the armored telsons of
 mantis shrimps. Although numerous studies have identified these defensive
 structures, no study has investigated whether they influence the outcomes
 of intraspecific fights.   Here, we investigated whether
 inhibiting damage by enhancing an individual’s armor influenced fighting
 behavior and success in the giant mesquite bug, Thasus
 neocalifornicus (Insecta: Hemiptera: Coreidae).  We
 found that experimentally manipulated individuals (i.e. those provided
 with additional armor) were 1.6 times more likely to win a fight when
 compared to the control. These results demonstrate that damage, and
 damage-reducing structures, can influence fighting success. The
 implications of these results are twofold. First, our results
 experimentally support a fundamental assumption of most theoretical
 fighting models: that damage is a fighting cost that can influence contest
 outcomes. Second, these results highlight the importance of an
 individual’s defensive capacity, and why defense should not be
 ignored.
DOI: 10.5061/dryad.wm37pvmm8
title: Data from: Morphological conservatism of the Family Naticidae (Gastropoda) through time: potential causes and consequences

description: Taxonomic status of several members of the Family Naticidae is extremely
 vague because of its simple shell morphology. Conventional taxonomic
 classification schemes suggest that most of the morphological characters
 tend to be homoplastic and exhibit convergence. Such morphological
 convergence complicates naticid taxonomy and makes it difficult to
 understand the evolutionary history of this group; several unrelated taxa
 are often misidentified as naticids, thereby exaggerating the actual
 diversity of this group. Here, we employ a standard landmark–based
 approach to understand the pattern of morphological evolution of this
 family. Ordination methods such as Principal Components Analysis and
 Canonical Variate Analysis were used to create morphospaces, and disparity
 was quantified using variance and range. Our results reveal, when naticids
 are compared with their sister taxon, Ampullinidae, the two families show
 significant differences in their average shapes, despite their superficial
 resemblances. Among naticids, although the mean shapes of the individual
 subfamilies are different, overall, the family Naticidae has displayed
 extreme morphological conservatism from the Jurassic to the Holocene.
 Interestingly, this conservatism has been unaffected by taxonomic
 changes — neither the extinction of the subfamily
 Gyrodinae nor the appearance of the subfamily Sininae affected this
 morphological conservatism. Naticids have always shown strong ecological
 preference towards an infaunal mode of life, and strict behavioural
 selectivity in handling and preying upon infaunal organisms, and this
 ecological and behavioural conservatism could have enabled them
 to diversify, without undergoing a change in their basic bauplan.
description: <b>File Name </b> <b>Description
 </b> Naticids and Ampullinids
 taxa Tps
 file containing raw landmark data of all ampullinid and naticid
 species Naticids taxa Overall
 Tps file containing
 raw landmark data of all naticid species representing overall
 shape Naticids taxa Aperture
 Tps file containing
 raw landmark data of all naticid species representing aperture
 shape Naticids taxa Outline
 Tps file containing
 raw landmark data of all naticid species representing outline
 shape Sharma_et_al._SOM_Tables
 Document containing
 all supplementary tables 
 
 Sharma_et_al._SOM_Figures Document containing all supplementary
 figures
DOI: 10.5061/dryad.g1jwstqpt
title: Moving in fast waters: the exaggerated claw gape of the new river crayfish (Cambarus chasmodactlyus) aids in locomotor performance

description: Humans are inherently fascinated by exaggerated and conspicuous
 morphological structures such as the elk antlers and the peacock trains.
 Because these traits are costly to develop and wield, the environment in
 which they are used can select for specific sizes or shapes to minimize
 such costs. In aquatic environments, selection to reduce drag can
 constrain the form of exaggerated structures; this is presumably why
 exaggerated morphologies are less common in aquatic environments compared
 to terrestrial ones. Interestingly, multiple species of crayfish possess
 claws with an exaggerated gape between their pinching fingers, but the
 function of this claw gape is unknown. Here, I describe and test the
 function of the exaggerated claw gape of the New River Crayfish, Cambarus
 chasmodactylus. Specifically, I test the hypothesis that the claw gape
 aids in movement throughout fast-flowing streams. I found that both claw
 size and gape size were sexually dimorphic in this species and that males
 had disproportionately larger gapes compared to females. Further, by
 experimentally manipulating gape size and testing crayfish locomotor
 performance, I found that individuals with their gape blocked were 30%
 slower than crayfish with a natural gape. My results highlight a unique
 adaptation that compensates for wielding an exaggerated structure in
 aquatic environments.