cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.79386ft
title: Data from: Major QTL controls adaptation to serpentine soils in Mimulus guttatus

description: Spatially varying selection is a critical driver of adaptive
 differentiation. Yet, there are few examples where the fitness effects of
 naturally segregating variants that contribute to local adaptation have
 been measured in the field. Plant adaptation to harsh soil habitats
 provides an ideal study system for investigating the genetic basis of
 local adaptation. The work presented here identifies a major locus
 underlying adaptation to serpentine soils in Mimulus guttatus and
 estimates the strength of selection on this locus in native field sites.
 Reciprocal transplant and common garden studies show that serpentine and
 non-serpentine populations of M. guttatus differ in their ability to
 survive on serpentine soils. We directly mapped these field survival
 differences by performing a bulk segregant analysis with F2 survivors from
 a field transplant study and identify a single QTL where individuals that
 are homozygous for the non-serpentine allele do not survive on serpentine
 soils. Genotyping the survivors from an independent mapping population
 reveals that this same QTL controls serpentine tolerance in a second,
 geographically distant population. Finally, we show that this QTL controls
 tolerance to soil properties, as opposed to some other aspect of the field
 sites that may differ, by performing a lab-based common-garden experiment
 in native serpentine soils that replicates the survival differences
 observed in the field. These results indicate that despite the myriad
 chemical and physical challenges that plants face in serpentine habitats,
 adaptation to these soils in M. guttatus has a simple genetic basis.
description: field_dataDirectory contains three files, one for each of the field reciprocal transplant studies.population_locationsGPS coordinates for populations used in reciprocal transplant studiessoil_dataSoil chemical analysis datacommon_gardenThis directory contains two files - the survival data for the common garden experiment and the genotyping results for the RH F2 survivors
DOI: 10.5061/dryad.8nh03
title: Data from: Estrogen receptor alpha distribution and expression in the social neural network of monogamous and polygynous Peromyscus

description: In microtine and dwarf hamsters low levels of estrogen receptor alpha
 (ERa) in the bed nucleus of the stria terminalis (BST) and medial amygdala
 (MeA) play a critical role in the expression of social monogamy in males,
 which is characterized by high levels of affiliation and low levels of
 aggression. In contrast, monogamous Peromyscus males display high levels
 of aggression and affiliative behavior with high levels of testosterone
 and aromatase activity. Suggesting the hypothesis that in Peromyscus ERa
 expression will be positively correlated with high levels of male
 prosocial behavior and aggression. ERa expression was compared within the
 social neural network, including the posterior medial BST, MeA
 posterodorsal, medial preoptic area (MPOA), ventromedial hypothalamus
 (VMH), and arcuate nucleus in two monogamous species, P. californicus and
 P. polionotus, and two polygynous species, P. leucopus and P. maniculatus.
 The results supported the prediction, with male P. polionotus and P.
 californicus expressing higher levels of ERa in the BST than their
 polygynous counter parts, and ERa expression was sexually dimorphic in the
 polygynous species, with females expressing significantly more than males
 in the BST in both polygynous species and in the MeA in P. leucopus.
 Peromyscus ERa expression also differed from rats, mice and microtines as
 in neither the MPOA nor the VMH was ERa sexually dimorphic. The results
 supported the hypothesis that higher levels of ERa are associated with
 monogamy in Peromyscus and that differential expression of ERa occurs in
 the same regions of the brains regardless of whether high or low
 expression is associated with social monogamy. Also discussed are possible
 mechanisms regulating this differential relationship.
description: Estrogen Receptor Alpha
 immunoreactivityThe file contains
 averaged cell counts for estrogen receptor alpha immunoreactivity in males
 and females of four species of Peromyscus. Two that are socially
 monogamous, P. californicus and P. polionotus and two polygynous, P.
 maniculatus and P. leucopus. ER alpha immunoreactive cells counts are
 presented from five regions of the brain, medial amygdala, bed nucleus of
 the stria terminalis, medial preoptic area, arcuate nucleus, and
 ventriomedial hypothalamus.CushingPlosOnePONE-D-15-21334.xls
DOI: 10.5061/dryad.6kb0v
title: Data from: Massive, solidified bone in the wing of a volant courting bird

description: One pervasive morphological feature of tetrapods is the pipe-like, often
 marrow-filled, structure of the limb or long bones. This “hollow” form
 maximizes flexural strength and stiffness with the minimum amount of bony
 material, and is exemplified by truly hollow (air-filled), or pneumatic,
 humeri in many modern birds. High-resolution microCT scans of the wings of
 two male Club-winged Manakins (Machaeropterus deliciosus) uncovered a
 notable exception to the hollow-tube rule in terrestrial vertebrates;
 males exhibited solidified ulnae &gt;3x the volume of birds of
 comparable body size, with significantly higher tissue mineral densities.
 The humeri exhibited similar (but less extreme) modifications. Each of the
 observed osteological modifications increases the overall mass of the
 bone, running counter to pervasive weight-reducing optimizations for
 flight in birds. The Club-winged Manakin is named for a pair of unique
 wing feathers found in adult males; these enlarged feathers attach
 directly to the ulna and resonate to produce a distinctive sound used in
 courtship displays. Given that the observed modifications probably assist
 in sound production, the Club-winged Manakin represents a case in which
 sexual selection by female choice has generated an ecologically “costly”
 forelimb morphology, unique in being specialized for sound production at a
 presumed cost in flight efficiency.
description: Summary Bone Data and
 Charts August 2010Excel file with data
 derived from CT scans indicated in manuscript showing values of individual
 species for each measure. Summary charts included.Bostwick et al Summary CT Data
 and Charts.xls
DOI: 10.5061/dryad.8m0p1
title: Data from: Winter coat color polymorphisms identify global hotspots for evolutionary rescue from climate change

description: Maintenance of biodiversity in a rapidly changing climate will depend on
 the efficacy of evolutionary rescue, whereby population declines due to
 abrupt environmental change are reversed by shifts in genetically-driven
 adaptive traits. However, a lack of traits known to be under direct
 selection by anthropogenic climate change has limited the incorporation of
 evolutionary processes into global conservation efforts. In 22 vertebrate
 species, some individuals undergo a seasonal color molt from summer brown
 to winter white as camouflage against snow, while other individuals remain
 brown. Seasonal snow duration is decreasing globally, and fitness is lower
 for winter white animals on snowless backgrounds. Based on 2,713
 georeferenced samples of known winter coat color – from 8 species across
 trophic levels – we identify environmentally driven clinal gradients in
 winter coat color, including polymorphic zones where winter brown and
 white morphs co-occur. These polymorphic zones, underrepresented by
 existing global protected area networks, indicate hotspots for
 evolutionary rescue in a changing climate.
description: Mills_data_final_2018This is the data used to build models predicting the probability of winter white for each species across their range. It is needed to run the R script. See README file for column descriptions and more information.rasterstack4covThis is the a raster stack of the three covariates (bio_2, bio_3 & snow) used in making the winter white probability maps. It is needed to run the R script.global_phenology_final_scriptThis is the R script associated with the analyses from this publication. Note in order to make species maps you need to download and read into R their range maps from the IUCN red list website: http://www.iucnredlist.org/
DOI: 10.5061/dryad.pm41d
title: Data from: microCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

description: Phenomics, which ideally involves in-depth phenotyping at the
 whole-organism scale, may enhance our functional understanding of genetic
 variation. Here, we demonstrate methods to profile hundreds of phenotypic
 measures comprised of morphological and densitometric traits at a large
 number of sites within the axial skeleton of adult zebrafish. We show the
 potential for vertebral patterns to confer heightened sensitivity, with
 similar specificity, in discriminating mutant populations compared to
 analyzing individual vertebrae in isolation. We identify phenotypes
 associated with human brittle bone disease and thyroid stimulating hormone
 receptor hyperactivity. Finally, we develop allometric models and show
 their potential to aid in the discrimination of mutant phenotypes masked
 by alterations in growth. Our studies demonstrate virtues of deep
 phenotyping in a spatially distributed organ system. Analyzing phenotypic
 patterns may increase productivity in genetic screens, and facilitate the
 study of genetic variants associated with smaller effect sizes, such as
 those that underlie complex diseases.
description: bmp1a -
 -_sa2416_477_nr11bmp1a -
 -_sa2416_265_nr12bmp1a -
 -_sa2416_482_nr14bmp1a +
 +_sa2416_455_nr16bmp1a +
 +_sa2416_218_nr17bmp1a +
 +_sa2416_218_nr19
DOI: 10.5061/dryad.v2t58
title: Data from: Anthropogenic changes in sodium affect neural and muscle development in butterflies

description: The development of organisms is changing drastically because of
 anthropogenic changes in once-limited nutrients. Although the importance
 of changing macronutrients, such as nitrogen and phosphorus, is
 well-established, it is less clear how anthropogenic changes in
 micronutrients will affect organismal development, potentially changing
 dynamics of selection. We use butterflies as a study system to test
 whether changes in sodium availability due to road salt runoff have
 significant effects on the development of sodium-limited traits, such as
 neural and muscle tissue. We first document how road salt runoff can
 elevate sodium concentrations in the tissue of some plant groups by 1.5–30
 times. Using monarch butterflies reared on roadside- and prairie-collected
 milkweed, we then show that road salt runoff can result in increased
 muscle mass (in males) and neural investment (in females). Finally, we use
 an artificial diet manipulation in cabbage white butterflies to show that
 variation in sodium chloride per se positively affects male flight muscle
 and female brain size. Variation in sodium not only has different effects
 depending on sex, but also can have opposing effects on the same tissue:
 across both species, males increase investment in flight muscle with
 increasing sodium, whereas females show the opposite pattern. Taken
 together, our results show that anthropogenic changes in sodium
 availability can affect the development of traits in roadside-feeding
 herbivores. This research suggests that changing micronutrient
 availability could alter selection on foraging behavior for some
 roadside-developing invertebrates.
description: Butterfly and plant raw
 dataThis excel file contains
 three tabs. Tab 1 includes data for the monarch rearing experiment
 including sex (males, females), rearing treatment (roadside collected
 milkweed or prairie collected milkweed), wing length (the measure of body
 size), thoracic protein, dry thoracic weight and the width of each eye
 (note the final analyses used log transformed values of several metrics as
 described in the methods). Tab 2 includes data for the cabbage white
 butterfly rearing experiment, including sex (males, females), rearing
 treatment (low sodium or medium sodium artificial diet), wing length (the
 measure of body size), thoracic protein, dry thoracic weight and brain
 volume of a subset of specimens (note that the final analysis used log
 transformed values of several metrics as described in the methods). Tab 3
 includes element measurements of leaf tissue of plants collected from
 along roadsides and in control sites &gt;100 m from the road. Our analyses
 focused on sodium and nitrogen (note that sodium values were log
 transformed for normality in statistical analyses). Here we also include
 values of other elements that are measured in a standard ICP-AES analysis;
 N values came from a separate analysis of the same samples (using the
 Dumas method).sodium paper data for dryad
 FINAL.xls
DOI: 10.5061/dryad.26qn0
title: Data from: Traces of Medieval migrations in a socially-stratified population from Northern Italy. Evidence from uniparental markers and deep-rooted pedigrees.

description: Social and cultural factors had a critical role in determining the genetic
 structure of Europe. Therefore, socially stratified populations may help
 to focus on specific episodes of European demographic history. In this
 study, we use uniparental markers to analyse the genetic structure of
 Partecipanza in San Giovanni in Persiceto (Northern Italy), a peculiar
 institution whose origins date back to the Middle Ages and whose members
 form the patrilineal descent of a group of founder families. From a
 maternal point of view (mtDNA), Partecipanza is genetically homogeneous
 with the rest of the population. However, we observed a significant
 differentiation for Y-chromosomes. In addition, by comparing 17 Y-STR
 profiles with deep-rooted paternal pedigrees, we estimated a Y-STR
 mutation rate equal to 3.90 * 10−3 mutations per STR per generation and an
 average generation duration time of 33.38 years. When we used these values
 for tentative dating, we estimated 1300-600 years ago for the origins of
 the Partecipanza. These results, together with a peculiar Y-chromosomal
 composition and historical evidence, suggest that Germanic populations
 (Lombards in particular) settled in the area during the Migration Period
 (400–800 AD, approximately) and may have had an important role in the
 foundation of this community.
description: Y-STR haplotypes and
 haplogroups in Partecipanza and S. Giovanni in Persiceto
 samplesSTRdata.xls
DOI: 10.5061/dryad.k291r
title: Data from: Impacts of bioturbation on temporal variation in bacterial and archaeal nitrogen-cycling gene abundance in coastal sediments

description: In marine environments, macrofauna living in or on the sediment surface
 may alter the structure, diversity and function of benthic microbial
 communities. In particular, microbial nitrogen (N)-cycling processes may
 be enhanced by the activity of large bioturbating organisms. Here, we
 study the effect of the burrowing mud shrimp Upogebia deltaura upon
 temporal variation in the abundance of genes representing key N-cycling
 functional guilds. The abundance of bacterial genes representing different
 N-cycling guilds displayed different temporal patterns in burrow sediments
 in comparison with surface sediments, suggesting that the burrow provides
 a unique environment where bacterial gene abundances are influenced
 directly by macrofaunal activity. In contrast, the abundances of archaeal
 ammonia oxidizers varied temporally but were not affected by bioturbation,
 indicating differential responses between bacterial and archaeal ammonia
 oxidizers to environmental physicochemical controls. This study highlights
 the importance of bioturbation as a control over temporal variation in
 nitrogen-cycling microbial community dynamics within coastal sediments.
description: gene_dataGene abundance data from a q-PCR study of nitrogen-cycling genes in a bioturbated coastal sediment.
DOI: 10.5061/dryad.nj2h7
title: Data from: Does the risk of sperm competition help explain cooperation between reproductive competitors? A study in the ocellated wrasse (Symphodus ocellatus)

description: Although cooperating individuals may gain benefits, they risk being
 cheated by their allies. Therefore, to understand the persistence of
 cooperation by mutual benefits, it is important to document both the
 potential benefits of cooperation and the risks of cheating. We
 experimentally examined evidence of cooperation in the ocellated wrasse
 (Symphodus ocellatus), a fish species with males that exercise three
 reproductive strategies: satellite and sneaker males attempt to
 parasitically spawn in the nests of nesting males. Nesting males have been
 hypothesized to tolerate satellites as a result of satellite aid in
 defense against sneaker males and help in courting females. Here, we
 provide evidence that cooperation between reproductive competitors may
 arise in response to sperm competition from other males. After we
 experimentally removed satellites, nesting males had more sneakers at
 their nest and experienced a higher rate of sneaking when they spawned
 (increased sperm competition risk). When we experimentally distracted
 nesting males to prevent their acting aggressively toward satellites,
 satellites spawned with females and ate eggs in the nest. Our results
 suggest that nesting males and satellites gain fitness benefits of reduced
 direct reproductive and sperm competition through cooperation. However,
 nesting males risk losing paternity, while satellites experience increased
 aggression and must invest in aggression themselves (i.e., they act
 aggressively toward sneakers).
description: AmNat-53515-R2
 datafileExcel file of field
 collected behavioral data on Symphodus ocellatus (the ocellated wrasse).
 NM = nesting males, Sat = satellite male, sn = sneaker male, f = female. #
 = number/rate. The removal sheet is of 10 minute observations, and the
 distraction sheet of 5 minute observations.
DOI: 10.5061/dryad.c4tb8
title: Data from: Why does it take two to tango? lifetime fitness consequences of parental care in a burying beetle

description: In species that require parental care, each parent can either care for
 their offspring or leave them in the care of the other parent. For each
 parent this creates three possible parental care strategies: biparental
 care, uniparental (male or female) care, and uniparental desertion by
 either the male or female. The burying beetle, Nicrophorus orbicollis,
 typically exhibits biparental care of offspring, and thus provides a
 unique system that allows us to compare the fitness benefits of these
 parental care strategies in an unconfounded way. In this study, we assess
 the lifetime fitness of biparental care, uniparental care, and uniparental
 desertion strategies in both male and female N. orbicollis. Specifically,
 we tested for increased fitness of the biparental care strategy compared
 to uniparental care strategies. Second, we test for equality of fitness
 between uniparental care and uniparental desertion strategies.
 Surprisingly, biparental care yields lower lifetime fitness for both
 parents compared to the other two strategies. Also, uniparental care and
 uniparental desertion strategies yielded equal fitness. The evolution of
 biparental care in this system is not consistent with the expectation of a
 mutual fitness benefit. We discuss other potential explanations for the
 evolution of biparental care in this system.
description: Data for Smith et al.
 2017 PlosOne PaperThis data is from the
 manuscript titled "Why does it take two to tango? Lifetime fitness
 consequences of parental care in a burying beetle". It includes data
 on lifetime fitness measures (lifespan, number of reproductive attempts,
 number of offspring, total offspring mass, and mean offspring mass) for
 three types of parental care in Nicrophorus orbicollis: biparental care,
 uniparental care, and uniparental desertion.Dryad
 Data.xlsx
DOI: 10.5061/dryad.58pq3
title: Data from: A history of phenotypic plasticity accelerates adaptation to a new environment

description: Can a history of phenotypic plasticity increase the rate of adaptation to
 a new environment? Theory suggests it can through two different
 mechanisms. Phenotypically plastic organisms can adapt rapidly to new
 environments through genetic assimilation, or the fluctuating environments
 that result in phenotypic plasticity can produce evolvable genetic
 architectures. In this article, I studied a model of a gene regulatory
 network that determined a phenotypic character in one population selected
 for phenotypic plasticity and a second population in a constant
 environment. A history of phenotypic plasticity increased the rate of
 adaptation in a new environment, but the amount of this increase was
 dependent on the strength of selection in the original environment.
 Phenotypic variance in the original environment predicted the adaptive
 capacity of the trait within, but not between, plastic and non-plastic
 populations. These results have implications for invasive species, and
 ecological studies of rapid adaptation.
description: Fierst.DryadSimulation results
DOI: 10.5061/dryad.mt7bh
title: Data from: Herbivory facilitates growth of a key reef-building Caribbean coral

description: The decline of reef-building corals in conjunction with shifts to
 short-lived opportunistic species has prompted concerns that Caribbean
 reef framework-building capacity has substantially diminished. Restoring
 herbivore populations may be a potential driver of coral recovery;
 however, the impact of herbivores on coral calcification has been little
 studied. We performed an exclusion experiment to evaluate the impact of
 herbivory on Orbicella faveolata coral growth over 14 months. The
 experiment consisted of three treatments: full exclusion cages; half cage
 procedural controls; and uncaged control plates, each with small O.
 faveolata colonies. We found that herbivorous fish exclusion had a
 substantial impact on both macroalgal cover and coral growth. Fleshy
 macroalgae reached 50% cover within some exclusion cages, but were almost
 absent from uncaged control plates. Critically, O. faveolata calcification
 rates were suppressed by almost half within exclusion cages, with monthly
 coral growth negatively related to overgrowth by fleshy macroalgae. These
 findings highlight the importance of herbivorous fishes for coral growth
 and the detrimental impact of macroalgal proliferation in the Caribbean.
 Policy makers and local managers should consider measures to protect
 herbivorous fishes and reduce macroalgal proliferation to enable coral
 communities to continue to grow and function.
description: Suchley 2017 Ecology and
 Evolution DataExcel spreadsheet
 contains 4 tabs. 1) Monthly_Plate_Data: Monthly plate algal coverage,
 coral polyp count and algal-coral overgrowth data. 2) Coral_Initial_Data:
 Initial coral area, mass and polyp count. 3) Overall_Calcification: Coral
 calcification over study period for 6 coral colonies in cages, 6 coral
 colonies in half cages, and 5 coral colonies on control plates. 4)
 Light_Data: Light intensity time series for one day in one cage, one half
 cage and on one control plate.Suchley 2017 -
 Data.xlsx