cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3j8rr
title: Data from: Identifying drivers of breeding success in a long-distance migrant using structural equation modelling

description: In migrant animals, conditions encountered at various times and places
 throughout their annual cycle may affect breeding success. Yet, most
 studies so far have only investigated the effect of specific parts of the
 annual cycle, despite the importance to understand how different stages
 can interact and how these stages compare to intrinsic quality to properly
 modulate breeding success. Using a structural equation modelling approach,
 we investigated drivers of breeding success (migration cycle, individual
 quality, breeding conditions) in hoopoes (Upupa epops), a long-distant
 migrant. Our causal framework explained 75% of the variation in breeding
 success. The effect of the migration schedule was negligible, whereas the
 previous breeding attempt strongly influenced current breeding success. We
 suggest that the interplay of individual quality and environmental
 conditions during both previous and current breeding season may be more
 important drivers of breeding success than migration schedules, even in a
 long-distance migrant. We conclude that structural equation modeling is a
 promising tool to investigate causal relationships. Applied to hoopoes, we
 demonstrated that current breeding success is strongly linked to previous
 breeding success. Complementary analysis integrating weather and climate
 conditions during migration and the breeding season may provide a deeper
 and wider overview of the annual cycle of hoopoes and additional insights
 into the existence of carry-over effects in breeding success.
description: Souchay-et-al_oik.04247_rawdataraw field data of breeding success and migration schedule of surveyed European hoopoes with geolocator. See article and Appendix 2 for a complete description of the data fileSouchay-et-al_ESM3_data.csv
DOI: 10.5061/dryad.42tv030
title: Data from: An experimental test of the relationship between yolk testosterone and the social environment in a colonial passerine

description: Maternal hormones can be transferred to offspring during prenatal
 development in response to the maternal social environment, and may
 adaptively alter offspring phenotype. For example, numerous avian studies
 show that aggressive competition with conspecifics tends to result in
 females allocating more testosterone to their egg yolks, and this may
 cause offspring to have more competitive phenotypes. However, deviations
 from this pattern of maternal testosterone allocation are found, largely
 in studies of colonial species, and have yet to be explained. Colonial
 species may have different life-history constraints causing different yolk
 testosterone allocation strategies in response to conspecific competition,
 but few studies have experimentally tested whether colonial species do
 indeed differ from that of solitary species. To test this, we collected
 eggs from zebra finches (Taeniopygia guttata), a colonial species, in the
 presence and absence of conspecific intrusions. Females did not alter the
 concentration of testosterone deposited in eggs laid during intrusions
 despite becoming more aggressive. These results suggest that maternal
 effects are not characterized by a uniform response to the social
 environment, but rather need to be contextualized with life-history
 traits.
description: Zebra Finch Yolk T and
 AggressionThis file contains the
 ID of each Zebra Finch female ('ID'), the season the experiment
 was conducted ('Date'), the treatment females received (control
 or intrusion; 'Treatment'), which clutch they received the
 treatment during ('Clutch'), how much yolk testosterone they
 allocated ('Yolk T'), how many days of intrusions they received
 prior to clutch initiation ('# of Intrusions'), and their
 average aggression score ('Average
 Aggression').Bentz et al
 2018.csv
DOI: 10.5061/dryad.4gm2r5m
title: Data from: An experimental test of whether pyrodiversity promotes mammal diversity in a northern Australian savanna

description: 1. The increasing awareness that a fire regime that promotes biodiversity
 in one system can threaten biodiversity in another has resulted in a shift
 away from fire management based on vague notions of maximising
 pyrodiversity, towards determining the optimal fire regime based on the
 demonstrated requirements of target species. 2. We utilised a
 long-running, replicated fire experiment on Melville Island, the largest
 island off the northern Australian coast, to test the importance of
 pyrodiversity for native mammals in a northern Australian savanna
 landscape. We first developed statistical models to determine how native
 mammal abundance has responded to nine years of experimentally-manipulated
 fire frequency. Next, given each species’ modelled response to fire
 frequency, we identified the level of pyrodiversity and optimal mix of
 fire frequencies that would be expected to maximise mammal diversity and
 abundance, and minimise extinction risk. This was done for both the entire
 mammal assemblage and for the mammal species currently declining on
 Melville Island. 3. Fire frequency was a significant predictor of
 abundance of the northern brown bandicoot (Isoodon macrourus),
 black-footed tree-rat (Mesembriomys gouldii), brush-tailed rabbit-rat
 (Conilurus penicillatus), grassland melomys (Melomys burtoni), pale
 field-rat (Rattus tunneyi), and mice/dunnarts but not for the common
 brushtail possum (Trichosurus vulpecula). 4. The geometric mean abundance
 (GMA) of the entire mammal assemblage was positively associated with
 pyrodiversity, but peaked at an intermediate value. Hence, maximising
 pyrodiversity would reduce native mammal assemblage GMA below its
 potential maximum. The fire history for an area that maximised the entire
 native mammal assemblage GMA consisted of 57% long-unburnt, 43%
 triennially burnt and &lt;1% annually burnt. Pyrodiversity did not
 reduce the extinction risk, nor increase the GMA of declining mammals
 above that predicted in areas entirely annually or triennially burnt. 5.
 Synthesis and applications: We demonstrate a useful approach with which to
 develop fire management strategies based on the demonstrated requirements
 of target species. By comparing the optimal fire regime identified for the
 conservation of threatened species and that identified for the entire
 mammal assemblage, we demonstrate the flexibility of this approach to
 tailor fire management to address specific management priorities in other
 fire-prone environments.
description: Abundance of mammal
 species by fire treatmentThe number of nights
 each mammal species was detected on camera (relative abundance) in each
 experimental fire plot on Melville Island in 2015. The headings of Iso,
 Tri, Mes, Con, Mel, Rattus and small refer to northern brown bandicoot,
 common brushtail possum, black-footed tree-rat, brush-tailed rabbit-rat,
 Melomys burtoni, Pale field-rat and combined mice and dunnart species,
 respectively.PropGLMs4.csv
DOI: 10.5061/dryad.88h07
title: Data from: Habitat corridors facilitate genetic resilience irrespective of species dispersal abilities or population sizes

description: Corridors are frequently proposed to connect patches of habitat that have
 become isolated due to human-mediated alterations to the landscape. While
 it is understood that corridors can facilitate dispersal between patches,
 it remains unknown whether corridors can mitigate the negative genetic
 effects for entire communities modified by habitat fragmentation. These
 negative genetic effects, which include reduced genetic diversity, limit
 the potential for populations to respond to selective agents such as
 disease epidemics and global climate change. We provide clear evidence
 from a forward-time, agent-based model (ABM) that corridors can facilitate
 genetic resilience in fragmented habitats across a broad range of species
 dispersal abilities and population sizes. Our results demonstrate that
 even modest increases in corridor width decreased the genetic
 differentiation between patches and increased the genetic diversity and
 effective population size within patches. Furthermore, we document a
 tradeoff between corridor quality and corridor design whereby populations
 connected by high quality habitat (i.e., low corridor mortality) are more
 resilient to sub-optimal corridor design (e.g. long and narrow corridors).
 The ABM also revealed that species interactions can play a greater role
 than corridor design in shaping the genetic responses of populations to
 corridors. These results demonstrate how corridors can provide long-term
 conservation benefits that extend beyond targeted taxa and scale up to
 entire communities irrespective of species dispersal abilities or
 population sizes.
description: Corridors
 ModelR script to run
 agent-based model from Habitat Corridors manuscript.Model_4patches.R
DOI: 10.5061/dryad.kn251r8
title: Data from: Riparian reserves help protect forest bird communities in oil palm dominated landscapes

description: 1. Conversion of forest to oil palm agriculture is a significant and
 continuing threat to tropical biodiversity. Despite this, little is known
 about the value of riparian reserves in oil palm and how these
 conservation set-asides might best be managed to maintain biodiversity. 2.
 We characterised bird communities of 28 sites in an oil palm-forest mosaic
 in Sabah, Malaysia using 6104 encounters from 840 point counts. Sites
 included oil palm riparian reserves of various vegetation quality and
 reserve widths, which were compared to oil palm streams without a riparian
 reserve as well as riparian and non-riparian control areas in continuous
 logged forest. 3. Riparian reserves, oil palm waterways, and control sites
 in riparian and non-riparian forest supported distinct avifaunal
 communities. Riparian reserve width, forest quality and amount of forest
 cover were the strongest predictors of bird species richness. For
 forest-dependent species, each of these predictors had stronger effect
 size when compared with all species. On average, reserves held 31% of all
 species and 30% of forest specialists, whereas riparian forest controls
 averaged 32% of all species, but 38% of forest species. 4. Riparian
 reserves with &gt;40 m of natural vegetation on each bank supported
 similar bird diversity to riparian forest control habitats found in
 continuous forest. However, to support equivalent numbers of
 forest-dependent species and species of conservation concern, reserves
 would need to be at least 100 m wide on each bank. The highest numbers of
 species were found in riparian reserves with above-ground carbon densities
 exceeding 75 tC ha-1, highlighting the importance of forest quality, as
 well as width, in supporting riparian bird communities. 5. Synthesis and
 applications. If designed and protected appropriately, riparian reserves
 in oil palm estates support diverse bird communities, including many
 species of conservation concern. This can be achieved by designating large
 reserves (80-200 m total width), but to maximize species numbers forest
 disturbance should also be minimised prior to conversion as well as during
 plantation operations.13-Jun-2018
description: Bird species richness
 and environmental covariates for the SAFE project site and surroundings,
 Sabah, Malaysian Borneo, 2014-2016 [HMTF] (2018)The
 “SAFE_Avian_JAPPL.csv” document contains summary data of bird species
 richness and abundance recorded at the SAFE project between May 2014 and
 September 2016 as well as metadata for the 28 sites from which data were
 collected.SAFE_Avian_JAPPL.csv
DOI: 10.5061/dryad.0rr6pm3
title: Data from: Sperm is a sexual ornament in rose bitterling

description: In many taxa, odour cues mediate mating decisions. A key question is what
 these odours comprise, where they are produced, and what they signal.
 Using rose bitterling, fish that spawn in the gills of freshwater mussels,
 we investigated the role of sperm cues on female oviposition decisions
 using individuals of known MHC genotype. Male bitterling frequently
 released sperm prior to female oviposition and females responded with an
 increased probability of oviposition and released a greater number of
 eggs, particularly if males had a dissimilar MHC genotype. These mating
 preferences by females were shown to be adaptive, with MHC dissimilarity
 of males and females correlated positively with embryo survival. These
 results support a role for indirect benefits to rose bitterling mate
 choice and we propose that sperm acts as a releaser pheromone in
 bitterling, functioning as a sexual ornament signalling male quality as a
 mate.
description: olfactory
 testOlfactory test of female
 response to sperm or water treatmentolf.txtmhc compatibilityData to test spawning response to mhc similar and dissimilar matesmhc.txtegg survivalSurvival of eggs fathered by mhc similar and dissimilar malessurv.txt
DOI: 10.5061/dryad.3sk15
title: Data from: Trait evolution in adaptive radiations: modeling and measuring interspecific competition on phylogenies

description: The incorporation of ecological processes into models of trait evolution
 is important for understanding past drivers of evolutionary change.
 Species interactions have long been thought to be key drivers of trait
 evolution. However, models for comparative data that account for
 interactions between species are lacking. One of the challenges is that
 such models are intractable and difficult to express analytically. Here we
 present phylogenetic models of trait evolution that include interspecific
 competition among chosen species. Competition is modeled as a tendency of
 sympatric species to evolve toward difference from one another, producing
 trait overdispersion and high phylogenetic signal. The model predicts
 elevated trait variance across species and a slowdown in evolutionary rate
 both across the clade and within each branch. The model also predicts a
 reduction in correlation between otherwise correlated traits. We use an
 approximate Bayesian computation approach to estimate model parameters. We
 find reasonable power to detect competition in sufficiently large (20+
 species) trees compared with Brownian trait evolution and with
 Ornstein-Uhlenbeck and early burst models. We apply the model to examine
 the evolution of bill morphology of Darwin’s finches and find evidence
 that competition affects the evolution of bill length.
description: Darwin's finches
 phylogenyDarwin's finches
 phylogeny. Branches in units of millennia. Best estimate tree taken from
 Lamichhaney, S., J. Berglund, M. S. Almén, K. Maqbool, M. Grabherr, A.
 Martinez-Barrio, M. Promerová, et al. Evolution of Darwin/’s Finches and
 Their Beaks Revealed by Genome Sequencing” Nature advance online
 publication (February 11, 2015).finches.phyDarwin's finches allopatry times matrix.Pairwise matrix of the times that species became allopatric. For sympatric species this is 9e9, aka never. For allopatric species this is the time (in millennia) from the tree root to the species' creation node. These times are inferred from the combination of the phylogeny and island data. Species are simply considered sympatric when they share one or more islands.allopatry_timesDarwin's finches trait data.Darwin's finches trait data. Taken from Harmon, L. J., J. B. Losos, T. Jonathan Davies, R. G. Gillespie, J. L. Gittleman, W. B. Jennings, K. H. Kozak, M. A. McPeek, F. Moreno-Roark, T. J. Near, A. Purvis, R. E. Ricklefs, D. Schluter, J. A. Schulte, O. Seehausen, B.L. Sidlauskas, O. Torres-Carvajal, J. T. Weir, A. O. Mooers. 2010. Data from: Early bursts of body size and shape evolution are rare in comparative data. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.f660pfinches.dat
DOI: 10.5061/dryad.35rt2
title: Data from: Nest architecture shapes the collective behavior of harvester ants

description: Structures influence how individuals interact and, therefore, shape the
 collective behaviours that emerge from these interactions. Here I show
 that the structure of a nest influences the collective behaviour of
 harvester ant colonies. Using network analysis, I quantify nest
 architecture and find that as chamber connectivity and redundancy of
 connections among chambers increase, so does a colony's speed of
 recruitment to food. Interestingly, the volume of the chambers did not
 influence speed of recruitment, suggesting that the spatial organization
 of a nest has a greater impact on collective behaviour than the number of
 workers it can hold. Thus, by changing spatial constraints on social
 interactions organisms can modify their behaviour and impact their
 fitness.
description: Nest architecture
 measures and recruitment speedEach nest site (column
 B) has network and volume measures (columns D-H). Column C contains the
 average recruitment speed of the colony whose ID is in column A while it
 occupied the nest site in column B.Architecture and recruitment
 data.csv
DOI: 10.5061/dryad.411hr
title: Data from: Environmental structure and energetic consequences in groups of young mice

description: Microenvironments can have considerable physiological consequences for the
 inhabitants by influencing the movements of individual members. The
 microenvironment can permit more diverse aggregation patterns or restrict
 movements to certain dimensions. Here, we tested whether aspects of the
 microenvironment that influenced aggregation patterns also influenced the
 energetics of groups of young animals. We tested the effects of enclosure
 configuration on the group temperature and respiration of infant mice (Mus
 musculus). We monitored the huddle temperature and respiration of groups
 in flat, concave and conical enclosures, which varied in shape and
 available space, and consequently the types of movements they permitted.
 We found that the amount of available space (or density) had a stronger
 effect on the group temperature than did the shape of the enclosure or
 types of permissible movements. We found no evidence that density or shape
 of the arena strongly affected the respiration rate of the group, with
 groups showing similar levels of oxygen consumption in all treatments. The
 lower density enclosures conveyed a considerable metabolic savings to
 groups in comparison to those tested in a higher density enclosure. These
 findings show density can have a large effect on the energetics of young
 mice, and provide insights on how simple features of the environment will
 influence physiology in a changing world.
description: Temperature and Oxygen
 Consumption DataA .csv file with the
 data for experiments 1 and 2.DataFileDSSheltonetalPhyisiology&Behavior.csv
DOI: 10.5061/dryad.8q78n
title: Data from: Relationships of the Indian phytosaur Parasuchus hislopi Lydekker, 1885

description: The neotype skull of the Indian phytosaur Parasuchus hislopi Lydekker,
 1885 (ISI R42) is re-evaluated and compared with the type material of
 other basal phytosaurs. Parasuchus hislopi is extremely similar to species
 previously placed in Paleorhinus (P. bransoni and P. angustifrons),
 sharing with them such characters as a series of nodes on the lateral
 surface of the jugal, paired ridges on the squamosal and a frontal
 depression. Parasuchus hislopi represents a valid species: it can be
 distinguished from P. bransoni by a relatively low narial eminence and P.
 angustifrons by the absence of paired nasal depressions. Inclusion of
 Parasuchus hislopi in a phylogenetic analysis of phytosaurs recovers it in
 a well-supported clade with P. bransoni and P. angustifrons. Parasuchus is
 considered the senior synonym of Paleorhinus and Arganarhinus. Parasuchus
 (here considered to include P. hislopi, P. angustifrons, P. bransoni and
 P. magnoculus) has a broad circum-Pangaean distribution, with species
 occurring in the south-western United States, Morocco, central Europe and
 India. Phytosaur higher-level taxonomy is also revised: Parasuchidae is
 redefined to include ‘Paleorhinus-grade’ phytosaurs and the
 later-diverging Mystriosuchinae (the group formerly known as
 Phytosauridae), and Pseudopalatinae is renamed Mystriosuchini for reason
 of priority.
description: Parasuchus Phylogenetic
 AnalysisTNT file used in the
 phylogenetic analysis of phytosaurs presented in this paper. Data consists
 of character-taxon matrix in TNT format.ParasuchusV3.tnt
DOI: 10.5061/dryad.1dr06
title: Data from: Anthropogenic impact or anthropogenic accommodation? Distribution range expansion of the common wall lizard (Podarcis muralis) by means of artificial habitats in the north-eastern limits of its distribution range

description: During 2005-2008, field observations were made on the distribution and
 habitat occupation by Podarcis muralis in the middle Bistrita river basin.
 Prior to our study, this lizard was known from only 5 localities in
 Romanian Moldavia (Bicaz, Cheile Bicazului, Lacu Roşu, Gherman and
 Dodeni). Through the present paper the authors acknowledge the existence
 of 28 sites populated by P. muralis in Moldavia and propose a new model
 for the range expansion of the species in the area using man-made
 structures such as road and railway fences and road beds, benefiting from
 the mild climate provided by the Izvorul Muntelui barrier lake and forming
 insular populations to further colonize suitable habitats.
description: Gherghel_et_al_Podarcis_muralisPodarcis muralis distribution records used and discussed in the paper. The records are in shapefile format.
DOI: 10.5061/dryad.28d4t
title: Data from: Controlling population of the molecular rotational state and the alignment theoretically by tailored femtosecond laser pulse

description: We demonstrate that the population of the molecular rotational state
 through a stimulated impulsive Raman excitation can be controlled by
 tailoring the femtosecond laser pulse with a V-style phase modulation. The
 results show that, by precisely manipulating the modulation parameters,
 both the odd and even populations of the molecular rotational state can be
 completely suppressed or reconstructed. Meanwhile, the relative excitation
 between the odd and even populations can be obtained. Finally, we show
 that field-free molecular alignment can be controlled due to the
 modulation of the molecular rotational state populations.
description: prog_populationPopulationOfTheMolecularRotationalState.m
DOI: 10.5061/dryad.8564
title: Data from: Genetic diversity and distinctiveness of the proboscis monkeys (Nasalis larvatus) of the Klias Peninsula, Sabah, Malaysia

description: In this study, we sequenced a partial segment of the mitochondrial control
 region from 21 proboscis monkeys of the Klias peninsula, the last large
 population remaining on the west coast of Sabah, Malaysia. Our results
 showed that this population retains substantial genetic variation, and
 subpopulations from different river systems in the central and southern
 portions of the Klias share multiple haplotypes. We also compared our data
 with previously generated sequences from 2 eastern populations of
 proboscis monkeys in Sabah and found little evidence of regional genetic
 structure. Based on these results, we argue that conservation efforts
 should focus on restoring connectivity between central and southern Klias
 peninsula proboscis monkeys and discuss future analyses needed to better
 understand the mitochondrial structure of proboscis monkeys in Sabah.
description: MunshiSouth.JOH.Nasalis.HaplotypesThis file includes mitochondrial d-loop haplotypes and haplotype frequencies for four populations of proboscis monkeys from Sabah, Malaysia (NE Borneo). The haplotype file is in Arlequin format. Original sequences are available on Genbank.