cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.86187
title: Data from: Species selection and the macroevolution of coral coloniality and photosymbiosis

description: Differences in the relative diversification rates of species with variant
 traits is known as species selection. Species selection can produce a
 macroevolutionary change in the frequencies of traits by changing the
 relative number of species possessing each trait over time. But species
 selection is not the only process that can change the frequencies of
 traits, phyletic microevolution of traits within species and phylogenetic
 trait evolution among species, the tempo and mode of microevolution, can
 also change trait frequencies. Species selection, phylogenetic, and
 phyletic processes can all contribute to large-scale trends, reinforcing
 or canceling each other out. Even more complex interactions among
 macroevolutionary processes are possible when multiple covarying traits
 are involved. Here I present a multilevel macroevolutionary framework that
 is useful for understanding how macroevolutionary processes interact. It
 is useful for empirical studies using fossils, molecular phylogenies, or
 both. I illustrate the framework with the macroevolution of coloniality
 and photosymbiosis in scleractinian corals using a time-calibrated
 molecular phylogeny. I find that standing phylogenetic variation in
 coloniality and photosymbiosis deflects the direction of macroevolution
 from the vector of species selection. Variation in these traits constrains
 species selection and results in a 200 million-year macroevolutionary
 equilibrium.
description: Scleractinian
 Coloniality and PhotosymbiosisTable showing the
 presence or absence of coloniality and photosymbiosis for coral species.
 This data was compiled largely from Veron 2002.Scleractinian-data.csv
DOI: 10.5061/dryad.33d6c
title: Data from: Nest predation risk and growth strategies of passerine species: grow fast or develop traits to escape risk?

description: Different body components are thought to trade off in their growth and
 development rates, but the causes for relative prioritization of any trait
 remains a critical question. Offspring of species at higher risk of
 predation might prioritize development of locomotor traits that facilitate
 escaping risky environments over growth of mass. We tested this
 possibility in 12 altricial passerine species that differed in their risk
 of nest predation. We found that rates of growth and development of mass,
 wings, and endothermy increased with nest predation risk across species.
 In particular, species with higher nest predation risk exhibited
 relatively faster growth of wings than of mass, fledged with relatively
 larger wing sizes and smaller mass, and developed endothermy earlier at
 relatively smaller mass. This differential development can facilitate both
 escape from predators and survival outside of the nest environment. Tarsus
 growth was not differentially prioritized with respect to nest predation
 risk, and instead all species achieved adult tarsus size by age of
 fledging. We also tested whether different foraging modes (aerial,
 arboreal, and ground foragers) might explain the variation of differential
 growth of locomotor modules, but we found that little residual variation
 was explained. Our results suggest that differences in nest predation risk
 among species are associated with relative prioritization of body
 components to facilitate escape from the risky nest environment.
description: diffrential growth
 dataappendix A_adult
 size
DOI: 10.5061/dryad.p1r40
title: Data from: Dead before detection: addressing the effects of left truncation on survival estimation and ecological inference for neonates

description: 1. Neonate survival is a key life history trait, yet remains challenging
 to measure in wild populations because neonates can be difficult to
 capture at birth. Estimates of survival from neonates that are
 opportunistically captured might be inaccurate because some individuals
 die before sampling, resulting in data that are left truncated. The
 resulting overestimation of survival rates can further affect ecological
 inference through biased estimates of covariate effects in survival
 models, yet is not addressed in most studies of animal survival. Here, we
 quantify the effects of left truncation on survival estimates and
 subsequent ecological inference. 2. Vaginal implant transmitters (VITs)
 enable capture of ungulates at birth, yielding data without left
 truncation. The effects of left truncation on survival estimation were
 quantified using age-dependent survival models for VIT and
 opportunistically captured neonatal deer. Differences in daily survival
 rates (DSRs) and cumulative survival probability were calculated for the
 first 70 days of life. In addition, left truncation was simulated by
 removing fawns that died during the first 1 or 2 days of life from the
 VIT-caught sample, isolating the effect of left truncation. 3. Cumulative
 probability of survival during the first 70 days of life was overestimated
 by 7–23% for fawns caught opportunistically compared with those caught by
 VIT, depending on model design. Differences in DSRs were large at age 1
 day, but had converged by age 30 days. Simulated left truncation resulted
 in overestimates of survival of up to 31%. Model selection and covariate
 coefficients were strongly affected by left truncation, producing spurious
 ecological inference, including changes to sign and/or magnitude of
 inferred effects of all covariates. 4. We recommend (i) every effort be
 made to capture neonates; (ii) consistent capture methods, using at least
 in part non-truncating techniques, be implemented across years and study
 areas; and (iii) exclusion of left-truncated data from survival estimates
 until DSRs converge with those calculated from non-truncated data. This
 work emphasizes the importance of accounting for left truncation in
 survival estimation for any species with strong age-dependent survival in
 order to prevent biased conclusions produced by sampling method rather
 than true ecological effects.
description: Fawn survival from
 birth/capture to 70 days of ageCapture-mark-recapture
 data for fawns captured at birth or opportunistically until 70 days of
 age, including individual covariates for mass at birth, timber harvest
 regime of capture watershed, age at capture, sex, and
 year.Fawn_survival_70day.csv
DOI: 10.5061/dryad.6mq0n
title: Data from: Shifting to settled cultivation: changing practices among the Adis in Central Arunachal Pradesh, north-east India

description: In the hilly tropics, although shifting cultivation is a widespread
 practice, government policies have attempted to replace it with other land
 uses. However, several factors determine whether farming communities can
 make the shift. We tried understanding the factors that facilitate or
 impede the shift to settled cultivation through interviews with the Adi
 tribe in north-east India. Although settled cultivation was initiated in
 the 60s, about 90% of the families still practise shifting cultivation,
 observing 13 festivals associated with the annual agricultural calendar.
 Our results indicate that the economic status of a household determined
 whether a family undertook settled cultivation, while labour availability
 was important for shifting cultivation. Often, these nuances are ignored
 in the Government policies. We conclude that future policies should be
 mindful of cultural and socio-economic factors that affect the community
 and of the social-ecological resilience of the landscapes and not use a
 one-size-fits-all strategy.
description: Teegalapalli & Datta
 interviews dataThe data contains
 household level socio-economic information collected from five villages in
 the Upper Siang district, Arunachal Pradesh. The information was collected
 based on interview questionnaires.
DOI: 10.5061/dryad.1652m
title: Data from: Extremely reduced dispersal and gene flow in an island bird

description: The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic
 to Réunion Island in the Mascarene archipelago, represents an extreme case
 of microgeographical plumage colour variation in birds, with four distinct
 colour forms occupying different parts of this small island (2512 km2). To
 understand whether such population differentiation may reflect low levels
 of dispersal and gene flow at a very small spatial scale, we examined
 population structure and gene flow by analysing variation at 11
 microsatellite loci among four geographically close localities
 (&lt;26 km apart) sampled within the distribution range of one of the
 colour forms, the brown-headed brown form. Our results revealed levels of
 genetic differentiation that are exceptionally high for birds at such a
 small spatial scale. This strong population structure appears to reflect
 low levels of historical and contemporary gene flow among populations,
 unless very close geographically (&lt;10 km). Thus, we suggest that
 the Réunion grey white-eye shows an extremely reduced propensity to
 disperse, which is likely to be related to behavioural processes.
description: Z_borbonicus_MicrosatellitesGenotypes_GENEPOPThis table corresponds to the genotypes obtained from 67 individuals of Zosterops borbonicus sampled among 4 localities at 11 microsatellite loci. It is given here as a « Genepop » input fileGenotypes-GENEPOP.txt
DOI: 10.5061/dryad.g1372
title: Data from: Climate variability predicts thermal limits of aquatic insects across elevation and latitude

description: Janzen's extension of the climate variability hypothesis posits that
 increased seasonal variation at high latitudes should result in greater
 temperature overlap across elevations, and favor wider thermal breadths in
 temperate organisms compared to their tropical counterparts. We tested
 these predictions by measuring stream temperatures and thermal breadths
 (i.e. the difference between the critical thermal maximum and minimum) of
 62 aquatic insect species from temperate (Colorado, USA) and tropical
 (Papallacta, Ecuador) streams spanning an elevation gradient of ca. 2000m.
 Temperate streams exhibited greater seasonal temperature variation and
 overlap across elevations than tropical streams, and as predicted,
 temperate aquatic insects exhibited broader thermal breadths than tropical
 insects. However, elevation had contrasting effects on patterns of thermal
 breadth. In temperate species, thermal breadth decreased with increasing
 elevation because CTMAX declined with elevation while CTMIN was similar
 across elevations. In tropical insects, by contrast, CTMAX declined less
 sharply than CTMIN with elevation, causing thermal breadth to increase
 with elevation. These macrophysiological patterns are consistent with the
 narrower elevation ranges found in other tropical organisms, and they
 extend Janzen's climate variability hypothesis to freshwater streams.
 Furthermore, because lowland tropical aquatic insects have the narrowest
 thermal breadths of any region, they may be particularly vulnerable to
 short-term extreme changes in stream temperature.
description: Thermal tolerance traits
 of temperate and tropical aquatic insectsThis dataset includes
 critical thermal max and min data along with thermal breadths measured for
 a variety of aquatic insects from low, mid, and high elevation temperate
 and tropical streams. Each individual was assigned to a species using DNA
 barcoding (Taxon) and the taxonomic order is indicated (Order). The
 elevations (in meters) and latitudes (0 = Colorado, 1 = Ecuador) from
 which the insects were collected are provided. Dry weights are provided
 along with critical thermal limits (CTmax and CTmin) and their differences
 where applicable (Thermal Breadth). Stream temperature range is also
 provided (Range).Final_PhysPGLS_Data.csv
DOI: 10.5061/dryad.ts544
title: Data from: Quantification of the zygotic barrier between interbreeding taxa using gene flow data

description: Hybridization and introgression via interspecific gene flow are common
 processes in the plant kingdom. The effectiveness of these processes is
 governed by the strengths of multiple zygotic barriers. These barriers
 have often been quantified in artificial settings using laborious and
 time-consuming hand-pollination experiments, but their quantification is
 nonexistent at the landscape level. In this study, we utilized gene flow
 data within a spatially explicit simulation to assess the strengths of
 zygotic barriers. Our model system consisted of Populusnigra and its
 hybrid, P.×canadensis, which interbreed under natural conditions. The
 study population was located in the floodplain of the Eder River in
 Central Germany. Pollen-mediated introgression rates from hybrid males
 into the seeds of individual female trees were used as the target pattern
 using an inverse modeling approach. Simulations that treated pollen from
 both taxa equally revealed a large discrepancy between the observed and
 modeled rates of introgression for both taxa. The discrepancy was reduced
 by introducing a zygotic barrier against the pollen from the hybrid males.
 The best model outcome indicated comparably strong zygotic barriers acting
 against pollen-mediated introgressive gene flow into the two parental
 taxa, P.nigra and P.×canadensis. The sensitivity of our model was tested
 by applying different dispersal functions. Four common probability density
 functions were used along with a pollen dispersal function that had
 previously been fitted to gene flow data from the same dataset. The best
 barrier value was almost independent of the dispersal functions used here.
 Moreover, it was within the range previously determined in
 hand-pollination-based investigations, validating our model. These data
 indicate that the inverse modeling approach is a powerful method for
 quantifying hidden processes, and we discuss its use as a valuable tool
 for generating new insights into plant mating systems that are relevant to
 evolutionary biology and risk analysis in conservation efforts
description: Introgression
 dataThe file was produced
 using the command 'save()' from the R software. This resulted in
 the file “introgression.RData”, which includes two dataframes: (1)
 intro.rates.paper and (2) tree.data. The first dataframe comprises the
 empirical introgression rates recorded by Bialozyt et al. (2012). The
 columns are the individual tree number followed by the percentage of
 introgression for year 2006 and 2007 respectively. The second dataframe
 (tree.data) comprises the name, coordinates, sex and taxa of all trees
 used in the simulation. In the column 'SEX' females are coded
 '0' and males are coded '1'. In the column
 'SPECIES' Populus nigra are coded '0' and the hybrids
 (Populus × canadenis) are coded '1'.introgression.RData
DOI: 10.5061/dryad.78p62
title: Data from: Sexual isolation promotes divergence between parapatric lake and stream stickleback

description: Speciation can be initiated by adaptive divergence between populations in
 ecologically different habitats, but how sexually based reproductive
 barriers contribute to this process is less well understood. We here test
 for sexual isolation between ecotypes of threespine stickleback fish
 residing in adjacent lake and stream habitats in the Lake Constance basin,
 Central Europe. Mating trials in outdoor mesocosms allowing for natural
 reproductive behavior reveal that mating occurs preferentially between
 partners of the same than of the opposed ecotype. Compared to random
 mating, this sexual barrier reduces gene flow between the ecotypes by some
 36%. This relatively modest strength of sexual isolation is surprising
 because comparing the males between the two ecotypes shows striking
 differentiation in traits generally considered relevant to reproductive
 behavior (body size, breeding coloration, nest size). Analyzing size
 differences among the individuals in the mating trials further indicates
 that assortative mating is not related to ecotype differences in body
 size. Overall, we demonstrate that sexually based reproductive isolation
 promotes divergence in lake-stream stickleback along with other known
 reproductive barriers, but also caution against inferring strong sexual
 isolation from the observation of strong population divergence in sexually
 relevant traits.
description: Dryad.stickleback.mate.choiceComplete data set used for all analyses in the study. The rows are the replicate experimental trials (N = 58). The first column specifies the date of termination of the trials. The subsequent columns describe the experimental females, then the lake males, then the stream males (each trial involved a single female and a male of each ecotype). The last column indicates the male that mated with the female. Missing data are coded as 'NA'.
DOI: 10.5061/dryad.j15ns
title: Data from: Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions

description: Identifying mechanisms driving pathogen persistence is a vital component
 of wildlife disease ecology and control. Asymptomatic, chronically
 infected individuals are an oft-cited potential reservoir of infection but
 demonstrations of the importance of chronic shedding to pathogen
 persistence at the population level remain scarce. Studying chronic
 shedding using commonly collected disease data is hampered by numerous
 challenges, including short-term surveillance that focuses on single
 epidemics and acutely ill individuals, the subtle dynamical influence of
 chronic shedding relative to more obvious epidemic drivers, and poor
 ability to differentiate between the effects of population prevalence of
 chronic shedding versus intensity and duration of chronic shedding in
 individuals. We use chronic shedding of Leptospira interrogans serovar
 Pomona in California sea lions (Zalophus californianus) as a case study to
 illustrate how these challenges can be addressed. Using
 leptospirosis-induced strands as a measure of disease incidence, we fit
 models with and without chronic shedding, and with different seasonal
 drivers, to determine the timescale over which chronic shedding is
 detectable and the interactions between chronic shedding and seasonal
 drivers needed to explain persistence and outbreak patterns. Chronic
 shedding can enable persistence of L. interrogans within the sea lion
 population. However, the importance of chronic shedding was only apparent
 when surveillance data included at least two outbreaks and the intervening
 inter-epidemic trough during which fadeout of transmission was most
 likely. Seasonal transmission, as opposed to seasonal recruitment of
 susceptibles, was the dominant driver of seasonality in this system, and
 both seasonal factors had limited impact on long-term pathogen
 persistence. We show that the temporal extent of surveillance data can
 have a dramatic impact on inferences about population processes, where the
 failure to identify both short- and long-term ecological drivers can have
 cascading impacts on understanding higher-order ecological phenomena, such
 as pathogen persistence.
description: Weekly numbers of
 California sea lions stranding due to leptospirosisIncluded are the number
 of California sea lions stranding due to leptospirosis (LeptoStrands) in
 each week (Week) for four 2.5 year (Year) eras. The four eras are
 1984-1986, 1988-1990, 1991-1993, and 2004-2006, with each beginning in the
 24th week to reflect a June 17 start date.CSL_WeeklyLeptoStrandings_Buhnerkempe_etal.txt
DOI: 10.5061/dryad.66767
title: Data from: Analysis of cytochrome P450 contribution to evolved plant toxin resistance in Drosophila sechellia

description: Drosophila sechellia is a dietary specialist species of fruit fly that has
 evolved resistance to the toxic secondary defence compounds produced by
 the fruit of its preferred host plant Morinda citrifolia. The genetic
 basis of adult toxin resistance is the result of evolution at five loci
 across the genome. Genetic mapping between D. sechellia and Drosophila
 simulans and subsequent functional studies in Drosophila melanogaster have
 identified candidate genes potentially underlying one locus involved in
 toxin resistance but the remainder of the genes involved are unknown.
 Genes in the mixed function oxidase or cytochrome P450 gene family are
 frequently utilized in evolved toxin resistance in insects, yet whether
 they play a role in D. sechellia's resistance to the toxins found in
 its host plant is unknown. Here we test the role of cytochrome P450
 enzymatic activity in evolved resistance to the two primary toxins found
 in M. citrifolia fruit: octanoic acid and hexanoic acid. We found that
 although cytochrome P450 enzymatic activity is involved in basal
 resistance it is not involved in derived toxin resistance in D. sechellia.
description: Peyser_et_al_2017Adult drosophila species survival over 1 hour exposure to octanoic or hexanoic acid survival with and without piperonyl butoxide (PBO)
DOI: 10.5061/dryad.sp45r
title: Data from: Persist or produce: a community trade-off tuned by species evenness

description: Understanding the effects of biodiversity on community persistence and
 productivity is key to managing both natural and production systems.
 Because rare species face greater danger of extinction, species evenness,
 a measure of how similar abundances are across species in a community, is
 seen as a key component of biodiversity. However, previous studies have
 failed to find a consistent association of species evenness with species
 survival and biomass production. Here we provide a theoretical framework
 for the relationship among these three elements. We demonstrate that the
 lack of consistent outcomes is not an idiosyncratic artifact of different
 studies but can be unified under one common framework. Applying a niche
 theory approach, we confirm that under demographic stochasticity evenness
 is a general indicator of the risk of future species extinctions in a
 community, in accordance with the majority of empirical studies. In
 contrast, evenness cannot be used as a direct indicator of the level of
 biomass production in a community. When a single species dominates, as
 expressed by the constraints imposed by the population dynamics, biomass
 production depends on the niche position of the dominating species and can
 increase or decrease with evenness. We demonstrate that high species
 evenness and an intermediate level of biomass production is the
 configuration that maximizes the average species survival probability in
 response to demographic stochasticity.
description: R-codeThe code generates niche
 overlap matrices and gradient of species evenness, and calculates relative
 biomass production and species survival probability. It reproduces figures
 1 and 4.code.R