cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2g203
title: Data from: Evolutionary history of a dispersal-associated locus across sympatric and allopatric divergent populations of a wing-polymorphic beetle across Atlantic Europe

description: Studying the evolutionary history of trait divergence, in particular those
 related to dispersal capacity, is of major interest for the process of
 local adaptation and metapopulation dynamics. Here, we reconstruct the
 evolution of different alleles at the nuclear encoded mitochondrial
 NADP+-dependent isocitrate dehydrogenase (mtIdh) locus of the ground
 beetle Pogonus chalceus that are differentially and repeatedly selected in
 short- and long-winged populations in response to different hydrological
 regimes at both allopatric and sympatric scales along the Atlantic
 European coasts. We sequenced 2,788 bp of the mtIdh locus spanning a ~7 kb
 genome region and compared its variation with that of two supposedly
 neutral genes. mtIdh sequences show (i) monophyletic clustering of the
 short-winged associated mtIDH-DE haplotypes within the long-winged
 associated mtIDH-AB haplotypes, (ii) a more than tenfold lower haplotype
 diversity associated with the mtIDH-DE alleles compared to the mtIDH-AB
 alleles, and (iii) a high number of fixed nucleotide differences between
 both mtIDH haplotype clusters. Coalescent simulations suggest that this
 observed sequence variation in the mtIdh locus is most consistent with a
 singular origin in a partially isolated subpopulation, followed by a
 relatively recent spread of the mtIDH-DE allele in short-winged
 populations along the Atlantic coast. These results demonstrate that even
 traits associated with decreased dispersal capacity can rapidly spread and
 that reuse of adaptive alleles plays an important role in the adaptive
 potential within this sympatric mosaic of P. chalceus populations.
description: Location and
 codesTable containing code,
 locations, species names and GenBank accession numbersSequence_alignmentsSequence alignments of Pogonus chalcesu mitochondrial NADP+-dependent isocitrate dehydrogenase (mtIdh), cytoplasmic NADP+-dependent isocitrate dehydrogenase (cytIdh), enolase, cytochrome oxidase subunit one (cox1), a mitochondrial region spanning the NADH subunit I (180 bp), the tRNA-Leu gene (64 bp) and the 16S rRNA gene (111 bp) and cytochrome b (cob; 468 bp)Tree_filesNexus files containing Bayasian Interference trees of mitochondrial NADP+-dependent isocitrate dehydrogenase, ctoplasmic NADP+-dependent Isocitrate dehydrogenase, enolase and concatenated alignement of cox1, nad1, cob. Used for phylogentic reconstruction and divergence time estimates.Scripts coalescent simulationsPython script used for performing coalescent simulations, including bash script fro cluster submission and instructions to adjust dendropy module.Scripts_coalescent_simulations.rar
DOI: 10.5061/dryad.d6q6b
title: Data from: Sneeze to leave: African wild dogs (Lycaon pictus) use variable quorum thresholds facilitated by sneezes in collective decisions.

description: In despotically driven animal societies, one or a few individuals tend to
 have a disproportionate influence on group decision-making and actions.
 However, global communication allows each group member to assess the
 relative strength of preferences for different options amongst their
 group-mates. Here, we investigate collective decisions by free-ranging
 African wild dog packs in Botswana. African wild dogs exhibit
 dominant-directed group living and take part in stereotyped social
 rallies: high energy greeting ceremonies that occur before collective
 movements. Not all rallies result in collective movements, for reasons
 that are not well understood. We show that the probability of rally
 success (i.e. group departure) is predicted by a minimum number of audible
 rapid nasal exhalations (‘sneezes’), within the rally. Moreover, the
 number of sneezes needed for the group to depart (i.e. the quorum) was
 reduced whenever dominant individuals initiated rallies, suggesting that
 dominant participation increases the likelihood of a rally’s success, but
 is not a prerequisite. As such, the ‘will of the group’ may override
 dominant preferences when the consensus of subordinates is sufficiently
 great. Our findings illustrate how specific behavioural mechanisms (here,
 sneezing) allow for negotiation (in effect, voting) that shapes
 decision-making in a wild, socially complex animal society.
description: Working Master Data
 SheetsRaw data used for GLMM
 analysis.
DOI: 10.5061/dryad.2q940
title: Data from: Effects of aging and idiopathic Parkinson's disease on tactile temporal order judgment

description: It is generally accepted that the basal ganglia play an important role in
 interval timing that requires the measurement of temporal durations. By
 contrast, it remains controversial whether the basal ganglia play an
 essential role in temporal order judgment (TOJ) of successive stimuli, a
 behavior that does not necessarily require the measurement of durations in
 time. To address this issue, we compared the effects of idiopathic
 Parkinson’s disease (PD) on the TOJ of two successive taps delivered to
 each hand, with the arms uncrossed in one condition and crossed in
 another. In addition to age-matched elderly participants without PD
 (non-PD), we examined young healthy participants so that the effect of
 aging could serve as a control for evaluating the effects of PD. There was
 no significant difference between PD and non-PD participants in any
 parameter of TOJ under either arm posture, although reaction time was
 significantly longer in PD compared with non-PD participants. By contrast,
 the effect of aging was apparent in both conditions. With their arms
 uncrossed, the temporal resolution (the interstimulus interval that
 yielded 84% correct responses) in elderly participants was significantly
 worse compared with young participants. With their arms crossed, elderly
 participants made more errors at longer intervals (~1 s) than young
 participants, although both age groups showed similar judgment reversal at
 moderately short intervals (~200 ms). These results indicate that the
 basal ganglia and dopaminergic systems do not play essential roles in
 tactile TOJ involving both hands and that the effect of aging on TOJ is
 mostly independent of the dopaminergic systems.
description: TOJdata_Nisikawa_etalresponse data of each participant.
DOI: 10.5061/dryad.93ct6
title: Data from: Comparing process-based and constraint-based approaches for modeling macroecological patterns

description: Ecological patterns arise from the interplay of many different processes,
 and yet the emergence of consistent phenomena across a diverse range of
 ecological systems suggests that many patterns may in part be determined
 by statistical or numerical constraints. Differentiating the extent to
 which patterns in a given system are determined statistically, and where
 it requires explicit ecological processes, has been difficult. We tackled
 this challenge by directly comparing models from a constraint-based
 theory, the Maximum Entropy Theory of Ecology (METE) and models from a
 process-based theory, the size-structured neutral theory (SSNT). Models
 from both theories were capable of characterizing the distribution of
 individuals among species and the distribution of body size among
 individuals across 76 forest communities. However, the SSNT models
 consistently yielded higher overall likelihood, as well as more realistic
 characterizations of the relationship between species abundance and
 average body size of conspecific individuals. This suggests that the
 details of the biological processes contain additional information for
 understanding community structure that are not fully captured by the METE
 constraints in these systems. Our approach provides a first step towards
 differentiating between process- and constraint-based models of ecological
 systems and a general methodology for comparing ecological models that
 make predictions for multiple patterns.
description: METE_SSNT_codePython code to allow replication of "Comparing process-based and constraint-based approaches for modeling macroecological patterns" by Xiao Xiao, James O'Dwyer, and Ethan White.
DOI: 10.5061/dryad.6g8t8
title: Data from: Inbreeding depression in a critically endangered carnivore

description: Harmful effects arising from matings between relatives (inbreeding) is a
 long-standing observation that is well founded in theory. Empirical
 evidence for inbreeding depression in natural populations is however rare
 because of the challenges of assembling pedigrees supplemented with
 fitness traits. We examined the occurrence of inbreeding and subsequent
 inbreeding depression using a unique data set containing a genetically
 verified pedigree with individual fitness traits for a critically
 endangered arctic fox (Vulpes lagopus) population. The study covered nine
 years and was comprised of 33 litters with a total of 205 individuals. We
 recorded that the present population was founded by only five individuals.
 Over the study period, the population exhibited a tenfold increase in
 average inbreeding coefficient with a final level corresponding to
 half-sib matings. Inbreeding mainly occurred between cousins, but we also
 observed two cases of full-sib matings. The pedigree data demonstrated
 clear evidence of inbreeding depression on traditional fitness traits
 where inbred individuals displayed reduced survival and reproduction.
 Fitness traits were however differently affected by the fluctuating
 resource abundande. Inbred individuals born at low-quality years displayed
 reduced first-year survival, while inbred individuals born at high-quality
 years were less likely to reproduce. The documentation of inbreeding
 depression in fundamental fitness traits suggests that inbreeding
 depression can limit population recovery. Introducing new genetic material
 to promote a genetic rescue effect may thus be necessary for population
 long-term persistence.
description: Pedigree and life
 history dataSubmitted to
 Dryad.xlsx
DOI: 10.5061/dryad.qt26f
title: Data from: Triplet MaxCut: a new toolkit for rooted supertree

description: The rapid increase of molecular, as well as other types, of available
 classification data has created the need to combine this data into a
 unified hypothesis. Supertree methods are essential when amalgamating
 phylogenetic information from various, possibly conflicting, sources into
 a single tree. The goal of a supertree algorithm is to satisfy maximally
 each such source of information in the output tree. Triplets, rooted trees
 over three leaves, are the minimal piece of such information when dealing
 with rooted trees. Due to its fundamental role in phylogenetics, extensive
 effort has been dedicated to several aspects regarding triplets’ research.
 We have devised a new tool, Triplet MaxCut (TMC), performing various
 operations in rooted supertree, principally amalgamating rooted trees
 based on amalgamating rooted triplets. The utility and efficiency of the
 algorithm is demonstrated by both simulation study and four real data
 supertree inputs.
description: TMC.tarHere we provide executable code for TMC algorithm, instructions for usage, input/output data formats and few examples
DOI: 10.5061/dryad.m066r
title: Data from: Genetic variation in blue whales in the eastern Pacific: implication for taxonomy and use of common wintering grounds

description: Many aspects of blue whale biology are poorly understood. Some of the gaps
 in our knowledge, such as those regarding their basic taxonomy and
 seasonal movements, directly affect our ability to monitor and manage blue
 whale populations. As a step towards filling in some of these gaps,
 microsatellite and mtDNA sequence analyses were conducted on blue whale
 samples from the Southern Hemisphere, the eastern tropical Pacific (ETP),
 and the northeast Pacific. The results indicate that the ETP is
 differentially used by blue whales from the northern and southern eastern
 Pacific, with the former showing stronger affinity to the region off
 Central America known as the Costa Rican Dome, and the latter favoring the
 waters of Peru and Ecuador. Although the pattern of genetic variation
 throughout the Southern Hemisphere is compatible with the recently
 proposed subspecies status of Chilean blue whales, some discrepancies
 remain between catch lengths and lengths from aerial photography, and not
 all blue whales in Chilean waters can be assumed to be of this type. Also,
 the range of the proposed Chilean subspecies, which extends to the
 Galapagos region of the ETP, at least seasonally, perhaps should include
 the Costa Rican Dome and the eastern North Pacific as well.
description: datasummarysuppl.Excel file. One spreadsheet of samples with data, second with haplotype info.
DOI: 10.5061/dryad.v280r0t
title: Data from: Taxonomic revision of the Malagasy Camponotus subgenus Mayria (Hymenoptera, Formicidae) using qualitative and quantitative morphology

description: The Camponotus subgenus Mayria is revised based on the analysis of both
 qualitative morphological characters and morphometric traits. The
 multivariate analysis combined the Nest Centroid (NC)-clustering method
 and Partitioning Algorithm based on Recursive Thresholding (PART) function
 to generate species hypotheses based on 19 continuous morphological traits
 of minor workers. The proposed species hypotheses were confirmed by
 cumulative Linear Discriminant Analysis (LDA). Morphometric ratios for the
 subsets of minor and major workers were used in species descriptions and
 redefinitions. In this study, 14 species are recognized, of which seven
 are newly described: C. lamosy sp. n., C. liandia sp. n., C. mainty sp.
 n., C. manabo sp. n., C. raina sp. n., C. sada sp. n., C. tanosy sp. n.
 Four species are redescribed: C. christi Forel, C. dromedarius Forel, C.
 lubbocki Forel, and C. repens Forel. The following are raised to species
 and redescribed: C. foersteri Forel stat. n., C. maculiventris Emery stat.
 n., and C. pulcher stat. n. The following are synonymized under C.
 foersteri: Camponotus cambouei Forel, syn. n.; C. christi ambustus Forel,
 syn. n.; C. christi ferrugineus Emery, syn. n. and C. pictipes Forel, syn.
 n. The following are synonymized under C. lubbocki: Camponotus lubbocki
 christoides Forel, syn. n. and C. lubbocki rectus Forel, syn. n. Also
 included in this revision are an illustrated species identification key,
 taxonomic discussions, images, and distribution maps for each species
 superimposed with the ecoregions of Madagascar.
description: Morphological
 measurements of individual minor worker specimens of the Malagasy
 Camponotus subgenus MayriaBasic measurements of
 individual specimens of the Malagasy Camponotus subgenus Mayria arranged
 by species code, collection code, and specimen code (unique identification
 number). See text for abbreviations.Supple-material_Mayria_Measurements v1.xlsx
DOI: 10.5061/dryad.br372
title: Data from: Adult sex ratio and operational sex ratio exhibit different temporal dynamics in the wild

description: Adult sex ratio (ASR, the proportion of adult males in the adult
 population) and operational sex ratio (OSR, the proportion of sexually
 active males in the mating pool) are fundamental properties of breeding
 populations and they are often linked to mating systems and sexual
 selection. However, ASR and OSR emerge via different routes in a
 population and may exhibit different temporal patterns. Here, we use data
 from a well-monitored polygamous snowy plover Charadrius nivosus
 population sampled over 3 consecutive breeding seasons to investigate
 whether temporal changes in ASR relate to changes in OSR. We found that
 snowy plovers exhibited male-biased ASR and OSR. Consistent with
 theoretical expectations, OSR was more variable than ASR. However, there
 was no consistent relationship between OSR and ASR: in only 1 of the 3
 study years we found a weak positive relationship (r = 0.22). The lack of
 association was corroborated by time series analyses and sensitivity
 tests. Our work therefore suggests that ASR and OSR exhibit different
 temporal patterns in a polygamous population, and we call for further
 theoretical and empirical studies that analyze their relationship across a
 range of different breeding systems.
description: Data to estimate ASR and
 OSREstimating adult sex
 ratio (ASR) and operational sex ratio (OSR) in a snowy plover population.
 This file contains 2 sheets: 1) Numbers of males and females present in
 the breeding sites each day of the breeding season for three years of
 study to estimate ASR and 2) numbers of males and females present and
 available to breed in the breeding sites each day of the breeding season
 for three years of study to estimate OSR. See ReadMe file for more
 details.
DOI: 10.5061/dryad.9061
title: Data from: Evidence for a Late Pliocene faunal transition based on a new rodent assemblage from Oldowan locality Hadar A.L. 894, Afar Region, Ethiopia

description: The time interval between 3-2 Ma marks several important transitions in
 human evolution, including the extinction of Australopithecus afarensis,
 the origin of the genus Homo, and the appearance of concentrated stone
 tool assemblages forming recognizable archaeological sites. The period
 also marks important changes in Earth's climatic history, with the
 onset of northern hemisphere glaciation starting sometime between 2.8-2.5
 Ma and it remains an unresolved question in paleoanthropology whether or
 not the global climatic events influenced in whole or in part, local
 terrestrial paleoenvironments in Africa and, through this, the course of
 human evolution. Changes in the terrestrial mammalian faunas of East
 Africa during this time interval are an important source of data about
 terrestrial paleoenvironments, and it has been argued that during this
 time period the mammalian faunas of Africa experienced a sudden pulse in
 the extinction and origination of taxa. The data corroborating this
 Turnover Pulse Hypothesis derive from both large-mammal and micromammal
 data, though the fossil record of the former is much more abundant in this
 interval. New micromammal fossils recovered from ca. 2.4 Ma deposits at
 locality A.L. 894, low in the Busidima Formation in the Hadar study area
 of the Afar region, Ethiopia, reveal a significant faunal turnover when
 compared with previously published material from older 3.2 Ma micromammal
 assemblages from the Hadar Formation deposits. The results support the
 hypothesis of a major faunal transition, but larger sample sizes and more
 extensive temporal sampling are needed to refine the time and rate of
 change within this interval at Hadar.
description: al894
 dbal894.dbal894 R scriptal894.R
DOI: 10.5061/dryad.t78c588
title: Data from: Adaptive changes in sexual signaling in response to urbanization

description: Urbanization can cause species to adjust their sexual displays, as the
 effectiveness of mating signals is impacted by environmental conditions.
 Despite many examples showing that mating signals in urban conditions
 differ from those in rural conditions, we do not know whether these
 differences provide a combined reproductive and survival benefit to the
 urban phenotype. Here we show that male túngara frogs have increased the
 conspicuousness of their calls, which is under strong sexual and natural
 selection by signal receivers, as an adaptive response to city life. The
 urban phenotype consequently attracts more females than the forest
 phenotype, while avoiding the costs imposed by eavesdropping bats and
 midges, which we show are rare in urban areas. Finally, we show in a
 translocation experiment that urban frogs can reduce risk of predation and
 parasitism when moved to the forest, but that forest frogs do not increase
 their sexual attractiveness when moved to the city. Our findings thus
 reveal that urbanization can rapidly drive adaptive signal change via
 changes in both natural and sexual selection pressures.
description: dataDryad_Halfwerk-etal
 2018 NEEraw data on call
 behaviour, environmental sampling, female choice experiments and
 translocation experiment
DOI: 10.5061/dryad.qr068
title: Data from: Spatial and temporal variation in hornbill densities in Namdapha Tiger Reserve, Arunachal Pradesh, north-east India

description: Asian hornbill populations are declining across their ranges because of
 hunting and deforestation. Five of the 32 Asian hornbill species occur in
 north-east India. However, vital information on their abundance from the
 region remains scanty. Understanding spatiotemporal variation in densities
 provides crucial information for formulating effective conservation
 strategies based on species-specific abundance patterns and population
 trends. We examined spatiotemporal variation in densities of four hornbill
 species in the Namdapha Tiger Reserve, a site identified as an important
 site for hornbill conservation in Asia. We collected data through
 variable-width line transect sampling (effort=842.1 km) in the
 non-breeding season from 2009-12 to estimate hornbill densities. We had
 458 detections of four hornbill species. We have estimated White-throated
 Brown Hornbill densities (7.9 birds/km2) for the first time throughout its
 entire range. The mean Rufous-necked Hornbill densities (6.9 birds/km2)
 were higher than those reported elsewhere. Great (3.9 birds/km2) and
 Wreathed Hornbill (16.1 birds/km2) densities were comparable with other
 sites. The peak densities of all hornbill species in November-December are
 among the highest reported from Asia. Wreathed Hornbill densities showed
 temporal variation peaking in November-December (68 birds/km2) and
 drastically declining by March-April (1.3 birds/km2), indicating seasonal
 altitudinal movement to low-elevation areas outside the reserve during the
 breeding season. Our results underscored the spatial variation in hornbill
 distribution, with low densities of Great and the White-throated Brown
 hornbills in higher elevations. Our study demonstrates the global
 importance of Namdapha for hornbills, given its large area and high
 densities of four hornbill species.
description: Naniwadekar_Datta_TCS_Hornbill_DataContains details (date, trail identity and length, time, hornbill species identity, perpendicular distance of the sighting, flock size of the bird) of all the hornbill sightings during distance sampling for hornbill density estimation in Namdapha Tiger Reserve. The details of the total number of replicate walks and effort across each trail can also be found here. The details regarding total sampling effort can be found here https://tropicalconservationscience.mongabay.com/content/v6/TCS-2013-Vol6(6)_734-748_Naniwadekar-and-Datta.pdf.Naniwadekar_Datta_TCS_Data.csv