cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d10qb58
title: Data from: Length polymorphisms at two candidate genes explain variation of migratory behaviors in blackpoll warblers (Setophaga striata)

description: Migratory behaviors such as the timing and duration of migration are
 genetically inherited and can be under strong natural selection, yet we
 still know very little about the specific genes or molecular pathways that
 control these behaviors. Studies in candidate genes Clock and Adcyap1 have
 revealed that both of these loci can be significantly correlated with
 migratory behaviors in birds, though observed relationships appear to vary
 across species. We investigated geographic genetic structure of Clock and
 Adcyap1 in four populations of blackpoll warblers (Setophaga striata), a
 Neotropical-Nearctic migrant that exhibits geographic variation in
 migratory timing and duration across its boreal breeding distribution.
 Further, we used data on migratory timing and duration, obtained from
 light-level geolocator trackers to investigate candidate
 genotype-phenotype relationships at the individual level. While we found
 no geographic structure in either candidate gene, we did find evidence
 that candidate gene lengths are correlated with five of the six migratory
 traits. Maximum Clock allele length was significantly and negatively
 associated with spring arrival date. Minimum Adcyap1 allele length was
 significantly and negatively associated with spring departure date and
 positively associated with fall arrival date at the wintering grounds.
 Additionally, we found a significant interaction between Clock and Adcyap1
 allele lengths on both spring and fall migratory duration. Adcyap1
 heterozygotes also had significantly shorter migration duration in both
 spring and fall compared to homozygotes. Our results support the growing
 body of evidence that Clock and Adcyap1 allele lengths are correlated with
 migratory behaviors in birds.
description: Full data
 setGenotype, capture
 location, and migration timing for all analyses in the
 paper.Full
 data for Supplemental.csv
DOI: 10.5061/dryad.6r80s8p
title: Data from: Accelerated epigenetic age and cognitive decline among urban-dwelling adults

description: Objectives. Epigenetic modifications are closely linked with aging, but
 their relationship with cognition remains equivocal. Given known sex
 differences in epigenetic aging, we explored sex-specific associations of
 three DNA methylation-based (DNAm) measures of epigenetic age acceleration
 (EAA) with baseline and longitudinal change in cognitive performance among
 middle-aged urban adults. Methods. We used exploratory data from a
 sub-group of participants in the Healthy Aging in Neighborhoods of
 Diversity across the Life Span (HANDLS) study with complete DNA samples
 and whose baseline ages were &gt;50.0y (2004-2009) to estimate three
 DNAm EAA measures: (A) universal epigenetic age acceleration (AgeAccel);
 (B) intrinsic epigenetic age acceleration (IEAA) ; and (C) extrinsic
 epigenetic age acceleration (EEAA). Cognitive performance was measured at
 baseline visit (2004-2009) and first follow-up (2009-2013) with 11 test
 scores covering global mental status and specific domains such as
 learning/memory, attention, visuo-spatial, psychomotor speed,
 language/verbal and executive function executive. A series of
 mixed-effects regression models were conducted adjusting for covariates
 and multiple testing (N=147-156, ~51% men, k=1.7-1.9
 observations/participant, mean follow-up time~4.7y). Results. EEAA, a
 measure of both biological age and immunosenescence, was consistently
 associated with greater cognitive decline among men on tests of visual
 memory/visuo-constructive ability (Benton Visual Retention Test:
 γ11=0.0512±0.0176, p=0.004) and attention/processing speed (Trail making
 test, part A: γ11=0.219±0.080, p=0.007). AgeAccel and IEAA were not
 associated with cognitive change in this sample. Conclusions. EEAA
 capturing immune system cell aging was associated with faster decline
 among men in domains of attention and visual memory. Larger longitudinal
 studies are needed to replicate our findings.
description: Online Supplemental
 Methods 1 and 2Supplemental method 1:
 Description of cognitive tests, literacy and the CES-D; Supplemental
 Method 2: Description of mixed-effects regression
 modelsOnline Supporting
 Material.docxTable
 S1Table S1. Sample
 selectivity of eligible participants (baseline age&gt;50y) by basic
 characteristics and visit; HANDLS 2004-2013Table
 S2Table S2. Cognitive
 performance test scores by “epigenetic clock” measures, stratified by sex,
 for HANDLS participants &gt;50.0y of age at baseline with complete and
 reliable baseline and/or follow-up cognitive scores: mixed-effects
 regression modelsSTROBE_checklist_v4_combined_PlosMedicine_completed
DOI: 10.5061/dryad.kf17rk8
title: Data from: The first complete mitochondrial genome of the Indian Tent Turtle, Pangshura tentoria (Testudines: Geoemydidae): characterization and comparative analysis

description: Characterization of complete mitogenome is a widely used genomics study
 for species delineation and evolutionary research. However, the sequences
 and structural motifs contained within the mitogenome have been rarely
 examined to understand the phylogeny and evolutionary history among
 Testudines. Hence, the mitogenomic features of several Testudines taxa are
 still anonymous to the scientific communities. The present study decodes
 the first complete mitochondrial genome of the Indian Tent Turtle,
 Pangshura tentoria (16,657 bp) by using next-generation sequencing. This
 denovo assembly encodes 37 genes: 13 protein coding genes (PCGs), 22
 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region
 (CR). The mitogenome contained 19 intergenic spacer and six overlapping
 regions. Most of the genes were encoded on majority strand, except for one
 PCG (NADH dehydrogenase subunit 6) and eight tRNAs. Most of the PCGs were
 started with an ATG initiation codon, except for cytochrome oxidase
 subunit 1 with ‘GTG’ and NADH dehydrogenase subunit 5 with ‘ATA’. The
 termination codons, ‘TAA’ and ‘AGA’ were observed in NADH dehydrogenase
 subunit 4l and NADH dehydrogenase subunit 6 respectively. The Relative
 Synonymous Codon Usage analysis revealed the maximum abundance of Alanine,
 Isoleucine, Leucine, and Threonine. The non-synonymous/synonymous ratios
 were &lt;1 in all PCGs, which indicates strong negative selection
 among all Geoemydid species. The study also found the typical cloverleaf
 secondary structure in most of the tRNA genes, except for Serine (trnS1)
 with lack of the conventional DHU arm. The Wobble base pairing was
 observed in the different stems (DHU, acceptor, and anticodon) of 11
 tRNAs. The comparative study of Geoemydid mitogenomes revealed the
 occurrence of tandem repeats was frequent in the 3´ end of CR. Further,
 two copies of a unique tandem repeat ‘TTCTCTTT’ were identified in P.
 tentoria. The Bayesian and Maximum Likelihood phylogenetic trees using
 concatenation of 13 PCGs revealed the close relationships of P. tentoria
 with Batagur trivittata in the studied dataset. All the Geoemydid species
 showed distinct clustering with high bootstrap support congruent with
 previous evolutionary hypotheses. We suggest that the generations of more
 mitogenomes of Geoemydid species, especially for Batagurinae subfamily,
 are required to improve our understanding their in-depth phylogenetic and
 evolutionary relationships.
description: Testudines_PCGs
 38
DOI: 10.5061/dryad.92b0gq1
title: Data from: Cognitive correlates of cerebellar resting-state functional connectivity in Parkinson disease.

description: Objective: The purpose of this cross-sectional study was to investigate
 the contributions of altered cerebellar resting-state functional
 connectivity (FC) to cognitive impairment in Parkinson disease (PD).
 Methods: We conducted morphometric and resting-state functional
 connectivity MRI (FC-MRI) analyses contrasting 81 PD and 43 age-matched
 healthy controls using rigorous quality assurance measures. To investigate
 the relationship of cerebellar FC to cognitive status, we compared PD
 participants without cognitive impairment (Clinical Dementia Rating scale,
 CDR=0; n=47) to PD participants with impaired cognition (CDR≥0.5; n=34).
 Comprehensive measures of cognition across the five cognitive domains were
 assessed for behavioral correlations. Results: The PD participants had
 significantly weaker FC between the vermis and peristriate visual
 association cortex compared to controls, and the strength of this FC
 correlated with visuospatial function and global cognition. In contrast,
 weaker FC between vermis and dorsolateral prefrontal cortex was found in
 the cognitively impaired PD group compared to PD participants without
 cognitive impairment. This effect correlated with deficits in attention,
 executive functions and global cognition. No group differences in
 cerebellar lobular volumes or regional cortical thickness of the
 significant cortical clusters were observed. Conclusion: These results
 demonstrate a correlation between cerebellar vermal FC and cognitive
 impairment in PD. The absence of significant atrophy in cerebellum or
 relevant cortical areas suggests this could be related to local
 pathophysiology such as neurotransmitter dysfunction.
description: Supplemental_dataSupplemental appendix and figures.
DOI: 10.5061/dryad.8jm8496
title: Climate induced stress and mortality in vervet monkeys

description: As the effects of global climate change become more apparent, animal
 species will become increasingly affected by extreme climate and its
 effect on the environment. There is a pressing need to understand animal
 physiological and behavioural responses to climatic stressors. We used the
 reactive scope model as a framework to investigate the influence of
 drought conditions on vervet monkey (Chlorocebus pygerythrus) behaviour,
 physiological stress and survival across 2.5-years in South Africa. Data
 were collected on climatic, environmental and behavioural variables and
 physiological stress via faecal glucocorticoid metabolites (fGCMs). There
 was a meaningful interaction between water availability and resource
 abundance: when food availability was high but standing water was
 unavailable, fGCMs were higher compared to when food was abundant and
 water was available. Vervet monkeys adapted their behaviour during a
 drought period by spending a greater proportion of time resting at the
 expense of feeding, moving, and social behaviour. As food availability
 decreased, vervet mortality increased. Peak mortality occurred when food
 availability was at its lowest and there was no standing water. A survival
 analysis revealed that higher fGCMs were associated with an increased
 probability of mortality. Our results suggest that with continued climate
 change, the increasing prevalence of drought will negatively affect vervet
 abundance and distribution in our population. Our study contributes to
 knowledge of the limits and scope of behavioural and physiological
 plasticity among vervet monkeys in the face of rapid environmental change.
description: Young_DataContains data for the four different anaylsis run in the paper. It is an excel sheet with four tabs, each one for each model run in the paper. Headings correspond to the headings used in the R code for each model. R codes are attached separately.Mod1_Young_RCodeFile contains R code to run analysis for model 1 in the paperMod2_Young_RCodeFile contains R code to run analysis for model 2 in the paper.Mod3_Young_RCodeFile contains R code to run the analysis for model 3 in the paper.Mod4_Young_RCodeFile contains R code to run the analysis for model 4 in the paper.
DOI: 10.5061/dryad.3sc3c6p
title: Data from: Temporal drop of genetic diversity in Bombus pauloensis

description: Bumblebees are economically important insects which perform essential
 pollination tasks in natural and managed ecosystems. Recent research
 studying Neotropical bumblebee species in Brazil showed a clear decrease
 in genetic diversity over time in Bombus pauloensis. A new temporal
 assessment of genetic diversity is needed to know whether this was a
 location specific result, or a more general phenomenon. This knowledge is
 essential to be able to prioritize conservation and management needs.
 Here, the genetic variability of B. pauloensis populations in Argentina
 was investigated over time using museum collection specimens from 1933 to
 2016, and compared with reanalyzed data from Brazilian populations.
 Furthermore, specific time series were made for two Argentinean locations:
 Candelaria and La Plata, and compared with the time series of Porto Alegre
 (Brazil). All collected specimens were genotyped with 16 microsatellite
 loci to estimate genetic diversity parameters. Our results showed no drop
 in either allelic richness or expected heterozygosity over all Argentinean
 populations. However, a clear drop in genetic diversity was observed in
 two out of three location specific time series. This loss of diversity
 will have negative impacts on population survival, especially over longer
 periods of time. Furthermore, the use and release of mass-reared specimens
 of B. pauloensis, which may be inbred and specifically selected for
 certain commercial but non-adaptive traits, could further diminish the
 genetic pool. Thus, our result implies the urgent need for regional
 conservation policies of B. pauloensis in South Brazil and North
 Argentina.
description: Microsats data B.
 pauloensis_DryadGenepop data of 184 B.
 pauloensis specimens, genotyped with 16 microsatellite DNA
 markers
DOI: 10.5061/dryad.58k2h35
title: Data from: Nonconsumptive predator effects modify crayfish-induced bioturbation as mediated by limb loss: field and mesocosm experiments

description: 1. We addressed the implications of limb loss and regeneration for
 multi-species interactions and their impacts on ecosystem engineering in
 freshwater stream environments. 2. We included regenerative and
 non-regenerative crayfish as well as fish predators in a 2x2 factorial
 design to assess the effects on water turbidity of interactions between
 crayfish ecosystem engineers differing in regenerative status and their
 fish predators. 3. We demonstrated that crayfish limb loss and predation
 risks lead to more turbidity in field and mesocosm conditions. Moreover,
 ongoing regeneration of crayfish increased turbidity, while fish presence
 seemed to hinder crayfish turbidity-inducing behaviors (such as
 tail-flipping and burrowing) in the mesocosm experiment. 4. We confirmed
 that greater numbers of crayfish produce a greater amount of turbidity
 in-situ in streams. 5. Although mechanical burrowing crayfish capacities
 may depend on crayfish burrowing classification (primary, secondary, or
 tertiary), our work emphasizes the implication for turbidity levels of
 crayfish autotomy in freshwater streams.
description: datafullContains the full experimental data.datafull1Same file as datafull, but with NAs for missing data.datafull2Same file as datafull, but with 0s for missing data.Field work 2015R code for analyses heavily commented.HighstatLibNecessary code file to run the R script.summarySENecessary code file to run the R script.
DOI: 10.5061/dryad.34gf741
title: Data from: Mating dynamics and multiple paternity in a long-lived vertebrate

description: Multiple paternity is relatively common across diverse taxa; however, the
 drivers and implications related to paternal and maternal fitness are not
 well understood. Several hypotheses have been offered to explain the
 occurrence and frequency of multiple paternity. One set of hypotheses
 seeks to explain multiple paternity through direct and indirect benefits
 including increased genetic diversity or enhanced offspring fitness,
 whereas another set of hypotheses explains multiple paternity as a
 byproduct of sexual conflict and population-specific parameters such as
 density. Here we investigate mating system dynamics in a historically
 studied population of the American alligator (Alligator mississippiensis)
 in coastal South Carolina. We examine parentage in 151 nests across 6
 years and find that 43% of nests were sired by multiple males and that
 male reproductive success is strongly influenced by male size. Whereas
 clutch size and hatchling size did not differ between singly sired and
 multiple sired nests, fertility rates were observed to be lower in
 multiply sired clutches. Our findings suggest that multiple paternity may
 exert cost in regard to female fitness, and raise the possibility that
 sexual conflict might influence the frequency of multiple paternity in
 wild alligator populations.
description: Multiple Paternity in a
 Long-Lived VertebrateThis file contains all
 allele calls made during the study. All of the paternity and maternity
 assignments made during the study. All assessments made regarding multiple
 paternity as well as each individuals genotype.Zajdel_etal_Data.tar.gz
DOI: 10.7272/q6qn64nk
title: Posttraumatic Stress Disorder (PTSD)

description: This data set was acquired to study various aspects associated with PTSD
 and includes structural neuroimaging data as well as clinical assessments
 including history of physical and sexual abuse or neglect, family history
 of violence, veteran status, presence of alcoholism, and scores on the
 clinician-administered PTSD scale (CAPS).
description: Data Acquisition Location: San Francisco VA Medical Center;
 Scanner Type: Siemens Vision 1.5T; Coronal T1 MPRAGE: TR=10ms, TE=4ms,
 TI=300ms, 1x1mm2, 1.4mm slice thickness; Axial double spin echo PD
 & T2: TR=2500ms, TE=20/80ms, 1x1.4mm2, 3mm slice
 thickness
DOI: 10.5061/dryad.bd4ch22
title: Data from: A phylogenetic analysis of the dirt ants, Basiceros Schulz (Formicidae: Myrmicinae): inferring life histories through morphological convergence

description: Ants of the genus Basiceros (Hymenoptera: Formicidae: Myrmicinae) are
 elusive species known only from Neotropical rainforests. Little
 information is available regarding their natural history, and nothing is
 known about the phylogenetic relationships among species within the genus.
 The genus has been the subject of some controversy regarding generic
 delimitation but is currently a member of the “Basiceros-genus group”
 following recent classification changes. For mouthparts, labral and
 mandibular morphologies present considerable variation in the
 Basiceros-genus group, likely a result of adaptive evolution. In
 Basiceros, those differences can be observed in the labrum shape and the
 various degrees of development of the labral cleft and the
 clypeomandibular space. Here, in an attempt to illuminate the evolution of
 the group, species boundaries are tested for Basiceros. The evolutionary
 relationships of its species are investigated using molecular and
 morphological data. Bayesian inference (BI) and maximum likelihood (ML)
 analyses of a molecular dataset consisting of up to nine genes (three
 mitochondrial, six nuclear) and including samples from multiple
 populations of all known Basiceros taxa recovered the monophyly of the
 genus and of its species, with two well resolved internal clades: the
 singularis clade and the disciger clade. Focusing on the female castes of
 Basiceros, an ancestral state reconstruction is presented for mandibles
 and labrum morphology. The results suggest that the labrum and
 clypeomandibular morphologies are highly labile, although phylogenetically
 important characters in the genus. Mouthpart traits indicate a strong
 correlated evolutionary history potentially associated with specialized
 feeding habits.
description: Alignment matrices and
 data partitioning filesAlignment matrices and
 associated data partitioning files and partition schemes for all analyses
 performed in this study. Includes complete and two pruned data
 sets.alignment_matrices_and_data_partitioning_files.zip
DOI: 10.7272/q66q1v54
title: Gulf War Illness

description: Some veterans who served in the Gulf War subsequently complained of a wide
 variety of physical and neuro-psychological symptoms, termed Gulf War
 Illness (GWI). Several investigators have attributed these symptoms to
 stress. In contrast, Haley and coworkers reported clusters of symptoms
 into three primary syndromes and reported reductions of the neuronal
 marker NAcetyl aspartate (NAA, a marker of neuron integrity and density)
 in the basal ganglia and pons of some GWI subjects. Based on this and
 other data they suggested that GWI has a neurological component. One
 limitation of previous studies is that post traumatic stress disorder
 (PTSD), depresssion, and alcoholism also cause structural and metabolic
 changes in the brain; the previous studies did not carefully control for
 these confounds. The primary goal of this project was to test the
 hypothesis that: subjects with GWI have metabolic and/or morphological
 changes in their brain, which are not accounted for by confounds such as
 post traumatic stress disorder (PTSD), alcohol abuse, and depression. A
 secondary goal was to determine: if these brain changes correlate with CNS
 signs and symptoms of GWI. This project studied 200 subjects with GWI and
 200 Gulf War Veteran (GWV) controls drawn from Northern California and
 surrounding regions. GWI was defined by the same criteria used in previous
 VA cooperative studies. The extent of alcohol abuse and PTSD symptoms was
 measured. MRI/MRS, audiovestibular, neuro-psychological and other
 measurements were also made.
description: Data Acquisition Location: San Francisco VA Medical Center;
 Scanner Type: Siemens Vision 1.5T; Coronal T1 MPRAGE: TR=9ms, TE=4ms,
 TI=300ms, 1x1mm2, 3mm slice thickness; Axial double spin echo PD &
 T2: TR=2500ms, TE=20/80ms, 1x1mm2, 3mm slice thickness