cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r6c36
title: Data from: Assortative flocking in crossbills and implications for ecological speciation

description: How reproductive isolation is related to divergent natural selection is a
 central question in speciation. Here we focus on several ecologically
 specialised taxa or “call types” of red crossbills (Loxia curvirostra
 complex), one of the few groups of birds providing much evidence for
 ecological speciation. Call types differ in bill sizes and feeding
 capabilities, and also differ in vocalizations, such that contact calls
 provide information on crossbill phenotype. We found that two call types
 of red crossbills were more likely to approach playbacks of their own call
 type than those of heterotypics, and that their propensity to approach
 heterotypics decreased with increasing divergence in bill size. Although
 call similarity also decreased with increasing divergence in bill size,
 comparisons of responses to familiar versus unfamiliar call types indicate
 that the decrease in the propensity to approach heterotypics with
 increasing divergence in bill size was a learned response, and not a
 byproduct of calls diverging pleiotropically as bill size diverged.
 Because crossbills choose mates while in flocks, assortative flocking
 could lead indirectly to assortative mating as a byproduct. These patterns
 of association therefore provide a mechanism by which increasing divergent
 selection can lead to increasing reproductive isolation.
description: assortative
 flockingThese are the data that
 were analyzed in this manuscript. They were collected using playbacks to
 free-flying (responding) crossbills in the field. The columns from left to
 right are: the identity (call type) of the crossbills flying over or
 responding call type; the identity of the calls (call type) on the
 playback tape to which the free-flying call types were responding; the
 mean probability that the free-flying crossbills landed in response to the
 playbacks; the difference in bill depth between the call types
 (free-flying and playback); the call similarity of the two groups of
 crossbills; whether the responding and playback crossbills were the same
 call type (homotypic) or not (heterotypic); whether the free-flying call
 types were familiar with the playback call type; and whether the
 comparison involved call type 4.
DOI: 10.5061/dryad.n50jf
title: Data from: Assessing the effects of iron enrichment across holobiont compartments reveals reduced microbial nitrogen fixation in the Red Sea coral Pocillopora verrucosa

description: The productivity of coral reefs in oligotrophic tropical waters is
 sustained by an efficient uptake and recycling of nutrients. In
 reef-building corals, the engineers of these ecosystems, this nutrient
 recycling is facilitated by a constant exchange of nutrients between the
 animal host and endosymbiotic photosynthetic dinoflagellates
 (zooxanthellae), bacteria, and other microbes. Due to the complex
 interactions in this so-called coral holobiont, it has proven difficult to
 understand the environmental limitations of productivity in corals. Among
 others, the micronutrient iron has been proposed to limit primary
 productivity due to its essential role in photosynthesis and bacterial
 processes. Here, we tested the effect of iron enrichment on the physiology
 of the coral Pocillopora verrucosa from the central Red Sea during a
 12-day experiment. Contrary to previous reports, we did not see an
 increase in zooxanthellae population density or gross photosynthesis.
 Conversely, respiration rates were significantly increased, and microbial
 nitrogen fixation was significantly decreased. Taken together, our data
 suggest that iron is not a limiting factor of primary productivity in Red
 Sea corals. Rather, increased metabolic demands in response to iron
 enrichment, as evidenced by increased respiration rates, may reduce carbon
 (i.e., energy) availability in the coral holobiont, resulting in reduced
 microbial nitrogen fixation. This decrease in nitrogen supply in turn may
 exacerbate the limitation of other nutrients, creating a negative feedback
 loop. Thereby, our results highlight that the effects of iron enrichment
 appear to be strongly dependent on local environmental conditions and
 ultimately may depend on the availability of other nutrients.
description: Rädecker_etal_EcoEvo2017Overview of raw measurement data for P. verrucosa holobionts from the Central Red Sea after 12 days under control or iron enriched conditions. Units of response parameters identical to those provided in the manuscript.
DOI: 10.5061/dryad.5c409
title: Data from: Exceptional body sizes but typical trophic structure in a Pleistocene food web

description: In this study, we focused on the exceptionally large mammals inhabiting
 the Americas during the Quaternary period and the paramount role of body
 size in species ecology. We evaluated two main features of Pleistocene
 food webs: the relationship between body size and (i) trophic position and
 (ii) vulnerability to predation. Despite the large range of species sizes,
 we found a hump-shaped relationship between trophic position and body
 size. We also found a negative trend in species vulnerability similar to
 that observed in modern faunas. The largest species lived near the
 boundary of energetic constraints, such that any shift in resource
 availability could drive these species to extinction. Our results
 reinforce several features of megafauna ecology: (i) the negative
 relationship between trophic position and body size implies that
 large-sized species were particularly vulnerable to changes in energetic
 support; (ii) living close to energetic imbalance could favour the
 incorporation of additional energy sources, for example, a transition from
 a herbivorous to a scavenging diet in the largest species (e.g.
 Megatherium) and (iii) the interactions and structure of Quaternary
 megafauna communities were shaped by similar forces to those shaping
 modern fauna communities.
description: Data from Body Mass and
 feeding habits of Pleistocene megafaunal of South
 AmericaFeeding group
 (Carnivore/herbivore) of the Pleistocene assemblage of South American.
 Part of the data is available from table 3 in the article "Splendid
 oddness: revisiting the curious trophic relationships of South American
 Pleistocene mammals and their abundance" authored by RICHARD A.
 FARIÑA, ADA CZERWONOGORA and MARIANA DI GIACOMO in Anais da Academia
 Brasileira de Ciências (2014) 86(1): 311-331, Printed version ISSN
 0001-3765 / Online version ISSN 1678-2690
 http://dx.doi.org/10.1590/0001-3765201420120010Splendid_oddness_Farinia2014_V2_unified.csv
DOI: 10.5061/dryad.0r31r
title: Data from: Estimating age and age class of harvested hog deer from eye lens mass using frequentist and Bayesian methods

description: Estimation of the age or age class of harvested animals is often necessary
 to interpret the condition and dynamics of wildlife populations. The
 mammalian eye lens continues to grow until death and hence the dry mass of
 the eye lens has commonly been used to estimate the age of mammals. The
 method requires the relationship between eye lens mass and age to be
 parameterized using individuals of known age. However, predicting age is
 complicated by the curvilinear relationship between eye lens mass and age.
 We used frequentist and Bayesian methods to predict the ages and age
 classes of harvested hog deer Axis porcinus from eye lens mass. Deer were
 tagged as calves and harvested 4–177 months later in southeastern
 Australia. Lenses were extracted, fixed and oven-dried. Of the five growth
 models evaluated, the Lord model best described the relationship between
 age and eye lens dry mass (R2 = 95%). The precision of age predictions
 obtained using the Lord model in a Bayesian mode of inference decreased
 with increasing eye lens dry mass, with the size of the 95% CI equaling or
 exceeding predicted age for hog deer &gt; 6 years. However, most
 predictions of hog deer age will have reasonable precision because few
 animals &gt; 6 years are harvested. Linear discriminant analysis had
 high predictive power for classifying hog deer to four widely-used age
 classes (juvenile, yearling, prime-age and senescent). The Bayesian method
 is recommended for inverse non-linear prediction of age and the
 frequentist linear discriminant analysis method is recommended for
 estimating age class. We provide tables of correspondence between hog deer
 eye lens dry mass and predicted age and age class. Our statistical methods
 can be used to estimate age and age class for other mammalian species,
 including from other ageing techniques such as tooth eruption-wear
 criteria.
description: Ages and eye lens masses
 of the 111 known-age hog deer used in our analyses.The data file is
 composed of two named columns. 'Age' is the age (days) of the
 hog deer since birth. 'Mass' is the eye lens dry mass (g) for
 either (i) the heaviest of the two eye lenses (if two eye lenses were
 collected) or (ii) the one eye lens if only one eye lens was collected.
 There are data for 111 hog deer (i.e. one individual per row). Ages range
 from 130 to 5393 days and eye lens dry masses range from 0.2092 to 0.5485
 g.hog.txt
DOI: 10.5061/dryad.j5r33
title: Data from: Rapid change in the thermal tolerance of a tropical lizard

description: The predominant view is that the thermal physiology of tropical
 ectotherms, including lizards, is not labile over ecological timescales.
 We used the recent introduction (∼35 years ago) of the Puerto Rican lizard
 Anolis cristatellus to Miami, Florida, to test this thermal rigidity
 hypothesis. We measured lower (critical thermal minimum [CTmin]) and upper
 (critical thermal maximum [CTmax]) thermal tolerances and found that the
 introduced population tolerates significantly colder temperatures (by
 ∼3°C) than does the Puerto Rican source population; however, CTmax did not
 differ. These results mirror the thermal regimes experienced by each
 population: Miami reaches colder ambient temperatures than Puerto Rico,
 but maximum ambient temperatures are similar. The differences in CTmin
 were observed even though lizards from both sites experienced nearly
 identical conditions for 49 days before CTmin measurement. Our results
 demonstrate that changes in thermal tolerance occurred relatively rapidly
 (∼35 generations), which strongly suggests that the thermal physiology of
 tropical lizards is more labile than previously proposed.
description: am nat dryad
 ctdata
DOI: 10.5061/dryad.c170h
title: Data from: Heterospecific courtship, minority effects and niche separation between cryptic butterfly species.

description: Species interacting in varied ecological conditions often evolve in
 different directions in different local populations. The butterflies of
 the cryptic Leptidea complex are sympatrically distributed in different
 combinations across their Eurasian range. Interestingly, the same species
 is a habitat generalist in some regions and a habitat specialist in
 others, where a sibling species has the habitat generalist role. Previous
 studies suggest that this geographically variable niche divergence is
 generated by local processes in different contact zones. By varying the
 absolute and relative densities of Leptidea sinapis and Leptidea juvernica
 in large outdoor cages, we show that female mating success is unaffected
 by conspecific density, but strongly negatively affected by the density of
 the other species. Whereas 80% of the females mated when a conspecific
 couple was alone in a cage, less than 10% mated when the single couple
 shared the cage with five pairs of the other species. The heterospecific
 courtships can thus affect the population fitness, and for the species in
 the local minority, the suitability of a habitat is likely to depend on
 the presence or absence of the locally interacting species. If the local
 relative abundance of the different species depends on the colonization
 order, priority effects might determine the ecological roles of
 interacting species in this system.
description: Mating data
 tableData collected in the
 field experiment. Column headers: Day (experiment day), Cage (the specific
 cage used), Species (Leptidea sinapis or L. juvernica), Prop (the
 proportion of the focal species of all butterflies in the cage), Density
 (the density of the focal species/square meter in the cage), Mated (the
 number of mated females), Ncons (the number of couples of the focal
 species in the treatment), and Treatment (the number of couples of the
 focal species and the number of couples of the other species in the
 treatment).data-JEB-2012-00580.R1.txt
DOI: 10.5061/dryad.th08v
title: Data from: Use of long-term opportunistic surveys to estimate trends in abundance of hibernating Townsend's big-eared bats

description: The advent of broad-scale threats to bats such as white-nose syndrome and
 climate change highlights the need for reliable baseline assessment of
 their populations. However few long-term, rigorously-designed assessments
 of bats populations exist, particularly in western North America.
 Consequently, results of informal monitoring efforts are often the only
 data available upon which to base population assessments. We evaluated
 whether an opportunistic collection of surveys recorded over a 22-year
 period could be used to assess population trend of Townsend's
 big-eared bats (Corynorhinus townsendii) at Lava Beds National Monument in
 northern California. We used records of counts of hibernating bats
 conducted during 1991-2012 to estimate the number of bats in 52 individual
 caves as well as cumulatively. Seventeen of 22 caves surveyed in {greater
 than or equal to} 4 years had an increasing trend in the number of
 hibernating bats. We estimated the cumulative annual growth rate over the
 period to be 1.79%. Stable or increasing number of hibernating
 Townsend's big-eared bats may be a result of management actions taken
 to limit disturbance of bats during maternity and hibernation seasons. We
 found no evidence that annual counts depressed the number of hibernating
 bats, thereby broadening monitoring options and the ability to link
 population trends to extrinsic factors. Our results demonstrate that
 opportunistically collected, long-term data sets may be useful for
 establishing first approximations of population trends for bats.
description: WellerEtAl_DataNumber of Townsend’s big-eared bats (Corynorhinus townsendii) counted in 52 individual caves during each year from 1991 – 2012 at Lava Beds National Monument, Siskiyou County, California.
DOI: 10.5061/dryad.pd2p5
title: Data from: The effect of weathering on bird bone survivorship in modern and fossil saline-alkaline lake environments

description: A modern Lesser Flamingo (Phoeniconaias minor) assemblage was collected
 along the shoreline of Lake Emakat, a saline-alkaline lake in northern
 Tanzania. Taphonomic analysis found the assemblage to be heavily
 weathered. This is likely due to the bone’s heightened exposure to solar
 radiation and corrosive soil and water chemistries, as is expected to
 occur in such depositional environments. Analysis found that deep, wide,
 longitudinal cracks penetrate the medullar cavities of both weathered and
 unweathered long bones. The cause and taphonomic consequence of these
 cracks are addressed here, using data from Lake Emakat and from controlled
 studies. Results support repeated (episodic) submersion, followed by
 drying, as the causal mechanism behind these wet-dry cracks. Mineral salt
 uptake by bone may explain the early appearance and prevalence of these
 cracks in saline-alkaline lake settings, as compared to other depositional
 settings. The rate of weathering and incidence of wet-dry cracking varies
 significantly across limb elements. This difference correlates to element
 specific resistance properties to external loading forces. Heavy
 weathering weakens the structural integrity of bone and can accelerate its
 fragmentation. This can lead to bird bone loss in nearshore and ephemeral
 wetland settings, which may then affect resulting skeletal part,
 diversity, and richness profiles. Heavy weathering can therefore obscure
 important taphonomic and paleoecological information. The weathering data
 collected here are then applied to a fossil bird assemblage from the FLK
 Complex, (late Pliocene), Olduvai Gorge, in Tanzania. Results provide
 evidence for the effect of weathering on paleoecological and behavioral
 interpretations. Weathering should be considered when analyzing fossil
 bird assemblages.
description: Prassack Supplement
 1Data
 is on weathering of modern Lesser Flamingo bird bone. Bone is from a
 ground surface assemblage collected by the author at Lake Emakat, a
 saline-alklaine lake in Empakaai Crater, Ngorongoro Highlands, northern
 Tanzania. WS stands for Weathering Stage. Numbers are in NISP (Number of
 Identified Specimens Present)
DOI: 10.5061/dryad.92j80
title: Data from: Modelling tooth–prey interactions in sharks: the importance of dynamic testing

description: The shape of shark teeth varies among species, but traditional testing
 protocols have revealed no predictive relationship between shark tooth
 morphology and performance. We developed a dynamic testing device to
 quantify cutting performance of teeth. We mimicked head-shaking behaviour
 in feeding large sharks by attaching teeth to the blade of a reciprocating
 power saw fixed in a custom-built frame. We tested three tooth types at
 biologically relevant speeds and found differences in tooth cutting
 ability and wear. Teeth from the bluntnose sixgill (Hexanchus griseus)
 showed poor cutting ability compared with tiger (Galeocerdo cuvier),
 sandbar (Carcharhinus plumbeus) and silky (C. falciformis) sharks, but
 they also showed no wear with repeated use. Some shark teeth are very
 sharp at the expense of quickly dulling, while others are less sharp but
 dull more slowly. This demonstrates that dynamic testing is vital to
 understanding the performance of shark teeth.
description: Compared cutting
 abilityComparative cutting
 ability.csvWear cutting
 ability
DOI: 10.5061/dryad.1q7q4
title: Data from: Phylogenetic and comparative genomics of the family Leptotrichiaceae and introduction of a novel fingerprinting MLVA for Streptobacillus moniliformis

description: Background: The Leptotrichiaceae are a family of fairly unnoticed bacteria
 containing both microbiota on mucous membranes as well as significant
 pathogens such as Streptobacillus moniliformis, the causative organism of
 streptobacillary rat bite fever. Comprehensive genomic studies in members
 of this family have so far not been carried out. We aimed to analyze 47
 genomes from 20 different member species to illuminate phylogenetic
 aspects, as well as genomic and discriminatory properties. Results: Our
 data provide a novel and reliable basis of support for previously
 established phylogeny from this group and give a deeper insight into
 characteristics of genome structure and gene functions. Full genome
 analyses revealed that most S. moniliformis strains under study form a
 heterogeneous population without any significant clustering. Analysis of
 infra-species variability for this highly pathogenic rat bite fever
 organism led to the detection of three specific variable number tandem
 analysis loci with high discriminatory power. Conclusions: This highly
 useful and economical tool can be directly employed in clinical samples
 without laborious prior cultivation. Our and prospective case-specific
 data can now easily be compared by using a newly established MLVA database
 in order to gain a better insight into the epidemiology of this presumably
 under-reported zoonosis.
description: FIG1+FIG2FIG1: Phylogeny of 29 strains of S. moniliformis, S. ratti, S. notomytis, S. felis and S. hongkongensis FIG2: Phylogeny of 23 S. moniliformis strains, both phylogenies are in nexus formatTree_submission.zip
DOI: 10.5061/dryad.f16b0
title: Data from: Decline in milkweed (Asclepias syriaca) populations in central New Jersey over a one year period

description: Milkweed (Asclepias syriaca) is the primary food source of the eastern
 North American Monarch butterfly (Danaus plexippus), and numbers have been
 steadily declining. Between 2012 to 2013 we conducted a survey measure to
 milkweed numbers in Montgomery Township New Jersey. The purpose of this
 survey was to examine and measure the change in milkweed numbers after a 1
 year period. In October 2012, publicly accessible areas of Montgomery
 Township were surveyed. This same survey was repeated in 2013, and the
 change in mean number of milkweed plants per plot recorded. Global
 positioning satellite data were collected using GPS tracker 1.0 for
 iPhone. All plots from publicly accessible areas were measured except one
 plot that was intentionally cultivated. Apart from the single
 intentionally cultivated plot, only 2 plots remained from the original 30
 in the 2012 survey (6%). From the original 302 stalks, only 87 remained
 one year later (a decrease of 71.9 %). A total of 3 new plots were found,
 indicating new growth. There was a notable decrease in the mean number of
 milkweed stalks per plot from 2012 (10.4 ± 2.3) to 2013 (4.3 ± 2.4). This
 decrease was statistically significant at the 5% level (P = 0.03958). Over
 a one year period, a statistically significant decline in milkweed plants
 was observed in central New Jersey. More should be done to conserve
 milkweed populations.
description: Repository Nikhil Gopal
 2Spreadsheet containing
 raw data for milkweed analyses (2012 to 2013). Data variables includes:
 GPS coordinates, number of stalks, fertilizer status and mowed status are
 also included.
DOI: 10.5061/dryad.098c4
title: Data from: Markov-modulated Poisson processes as a new framework for analyzing capture-recapture data

description: 1.Opportunistic capture-recapture data consists of observations over
 non-constant time-intervals and so fails to satisfy the basic assumptions
 of traditional capture-recapture models. Analyzing opportunistic
 capture-recapture data is often done by discretizing time-intervals or
 summarizing data, but without taking into account the continuous-time
 process of the state and/or the capture. 2.To deal with non-constant
 time-intervals, continuous-time closed capture-recapture models have been
 proposed by Yip et al. (1996), Hwang & Chao (2002), Schofield et
 al. (2017) for estimating population size. More recently, a
 continuous-time Cormack-Jolly-Seber model has been proposed by Fouchet et
 al. (2016) to reduce bias in survival rates, and a two-state process has
 been proposed by Choquet et al. (2017) to estimate reproduction rates and
 survival rates of young within a season. 3.The aim of the current study is
 to demonstrate how an approach based on a Markov-modulated Poisson process
 (MMPP) (Freed & Shepp, 1982) allows, in a similar way to a
 multistate model, to model opportunistic data using several states. To
 this end, several multistate models were rewritten as MMPP models,
 showing, the potential for this approach to address the ecological
 questions as multistate models, but using an extended data framework. In
 particular, it is a useful framework for dealing with data that has
 unordered levels of uncertainty. 4.The methods were illustrated using
 simulations and analysis of data on the Alpine ibex (Capraibex).
description: Capra ibex observed
 during spring 20111st column: the
 observation number (overall there is 127 observations); 2nd column: the
 identity of the individual; 3rd column: The day of the observation (1 to
 89); 4th column: The observation: 1 to 5, 1 = Not breeding, 2 = Certainly
 breeding, 3 = Probably breeding, 4 = Possibly breeding, 5 =
 Undefinedspring2011.txt