cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4r8q3
title: Data from: Pronounced genetic structure and site fidelity among native Muskellunge populations in Lake Huron and Georgian Bay

description: Conservation and management issues related to genetic diversity and stock
 structure of native populations of Muskellunge Esox masquinongy have
 largely been unexplored. In Lake Huron’s North Channel and Georgian Bay,
 Muskellunge populations have been impacted by historical commercial
 fisheries, recreational fisheries, loss of spawning habitat, historical
 water quality issues, and ecosystem changes. To determine the spatial
 genetic structure of native Muskellunge in Lake Huron and Georgian Bay,
 spawning adults were sampled from 10 sites in the North Channel and
 eastern Georgian Bay. Genotyping with 20 microsatellite DNA loci showed
 substantial spatial genetic structure, with significant pairwise
 divergences among spawning sites. Individual- and population-based
 analyses revealed hierarchical population structuring, with strong
 patterns of spawning site fidelity and isolation by distance; very low
 levels of dispersal and gene flow over historical and contemporary
 timescales were indicated. Estimation of effective population sizes
 highlighted the limited genetic resources that are present in these
 localized populations. The present results show that Muskellunge in Lake
 Huron and Georgian Bay consist of multiple small populations with limited
 ranges and high site fidelity and should be managed accordingly.
description: Georgian Bay muskellunge
 microsatellite genotypesMicrosatellite genotypes
 of muskellunge (Esox masquinongy) from native populations in Lake Huron,
 OntarioGBay_muskie_genotypes.xlsx
DOI: 10.5061/dryad.t0d447t7
title: Data from: Associated evolution of bipedality and cursoriality among Triassic archosaurs: a phylogenetically controlled evaluation.

description: Bipedalism evolved more than twice among archosaurs, and it is a
 characteristic of basal dinosaurs and a prerequisite for avian flight.
 Nevertheless, the reasons for the evolution of bipedalism among archosaurs
 have barely been investigated. Comparative analysis using phylogenetically
 independent contrasts showed a significant correlation between bipedality
 (relative length of forelimb) and cursoriality (relative length of
 metatarsal III) among Triassic archosaurs. This result indicates that,
 among Triassic archosaurs, bipeds could run faster than quadrupeds.
 Bipedalism is probably an adaptation for cursoriality among archosaurs,
 which may explain why bipedalism evolved convergently in the crocodilian
 and bird lineages. This result also indicates that the means of acquiring
 cursoriality may differ between archosaurs and mammals.
description: AppendixResults of correlation tests between cursoriality index and body size, and between cursoriality index and bipedality index after the effect of body size was removed, among Triassic archosaurs. The default settings of the correlation tests were (1) a branch length of one set for all branches and (2) reconstructed phylogenetic relationships among Triassic archosaurs (Fig. 2). Additional sensitivity analyses with arbitrary branch length (Grafen, Nee, and Pagel), temporal duration as branch lengths, or polytomic relationship (Fig. 2B) did not alter the result significantly. The analysis was also conducted with restricted taxa, which are crurotarsans, ornithodirans, and ornithodirans without sauropodomorphs except Eoraptor.rev kubo 11015 suppl. appendix.docrev kubo 11015 suppl. appendix.pdf
DOI: 10.5061/dryad.v7d6t
title: Data from: Comparative riverscape genetics reveals reservoirs of genetic diversity for conservation and restoration of Great Plains fishes.

description: We used comparative landscape genetics to examine the relative roles of
 historical events, intrinsic traits, and landscape factors in determining
 the distribution of genetic diversity of river fishes across the North
 American Great Plains. Spatial patterns of diversity were overlaid on a
 patch-based graphical model, and then compared within and among three
 species that co-occurred across five Great Plains watersheds. Species
 differing in reproductive strategy (benthic vs. pelagic spawning) were
 hypothesized to have different patterns of genetic diversity, but the
 overriding factor shaping contemporary patterns of diversity was the
 signature of past climates and geological history. Allelic diversity was
 significantly higher at southern latitudes for Cyprinella lutrensis and
 Hybognathus placitus, consistent with northward expansion from southern
 Pleistocene refugia. Within the historical context, all species exhibited
 lowered occupancy and abundance in heavily fragmented and drier upstream
 reaches, particularly H. placitus; a pelagic-spawning species, suggesting
 rates of extirpation have outpaced losses of genetic diversity in this
 species. Within most basins, genetically diverse populations of each
 species persisted. Hence, reconnecting genetically diverse populations
 with those characterized by reduced diversity (regardless of their
 position within the riverine network) would provide populations with
 greater genetic and demographic resilience. We discuss cases where
 cross-basin transfer may be appropriate to enhance genetic diversity and
 mitigate negative effects of climate change. Overall, striking
 similarities in genetic patterns and response to fragmentation and
 dewatering suggest a common strategy for genetic resource management in
 this unique riverine fish assemblage.
description: Microsatellite data and
 geospatial coordinates for three study speciesExcel file with three
 digit microsatellite data for Hybognathus placitus, Cyrinella lutrensis
 and Notropis atherinoides. File also contains geospatial coordinates for
 each sample collection.Mol_ecology_Dryad.xlsx
DOI: 10.5061/dryad.110qd
title: Data from: Duplication and sub/neofunctionalization of Malvolio, an insect homolog of Nramp, in the subsocial beetle Nicrophorus vespilloides

description: With growing numbers of sequenced genomes, increasing numbers of duplicate
 genes are uncovered. Here we examine Malvolio, a gene in the natural
 resistance-associated macrophage protein (Nramp) family, that has been
 duplicated in the subsocial beetle, Nicrophorus vespilloides, which
 exhibits advanced parental behavior. There is only one copy of Mvl in
 honey bees and Drosophila, whereas in vertebrates there are two copies
 that are subfunctionalized. We first compared amino acid sequences for
 Drosophila, beetles, mouse and humans. We found a high level of
 conservation between the different species, though there was greater
 variation in the C-terminal regions. A phylogenetic analysis across
 multiple insect orders suggests that Mvl has undergone several independent
 duplications. To examine the potential for different functions where it
 has been duplicated, we quantified expression levels of Mvl1 and Mvl2 in
 eight tissues in N. vespilloides. We found that while Mvl1 was expressed
 ubiquitously, albeit at varying levels, expression of Mvl2 was limited to
 brain and midgut. Because Mvl has been implicated in behavior, we examined
 expression during different behavioral states that reflected differences
 in opportunity for social interactions and expression of parental care
 behaviors. We found differing expression patterns for the two copies, with
 Mvl1 increasing in expression during resource preparation and feeding
 offspring, and Mvl2 decreasing in these same states. Given these patterns
 of expression, along with the protein analysis, we suggest that Mvl in N.
 vespilloides has experienced sub/neofunctionalization following its
 duplication, and may be evolving differing and tissue-specific roles in
 behavior and physiology.
description: Mvl1_2_Expression_Social_ConditionLevel of expression of Mvl1 and Mvl2 under different social conditions. Head tissue (fat body and brain).Malvolio_All_Tissues_RT-qPCRLevel of expression of Mvl1 and Mvl2 in tissues from females (except testes from males). All virgin. Expression measured using qRT-PCR with ttbp as reference gene.
DOI: 10.5061/dryad.rh807jp
title: Data from: Microsite conditions in retrogressive thaw slumps may facilitate increased seedling recruitment in the Alaskan Low Arctic

description: In Low Arctic tundra, thermal erosion of ice-rich permafrost soils
 (thermokarst) has increased in frequency since the 1980s. Retrogressive
 thaw slumps (RTS) are thermokarst disturbances forming large open
 depressions on hillslopes through soil wasting and vegetation
 displacement. Tall (&gt; 0.5 m) deciduous shrubs have been observed in
 RTS a decade after disturbance. RTS may provide conditions suitable for
 seedling recruitment, which may contribute to arctic shrub expansion. We
 quantified in situ seedling abundance, and size and viability of soil
 seedbanks in greenhouse trials for two RTS chronosequences near lakes on
 Alaska’s North Slope. We hypothesized recent RTS provide microsites for
 greater recruitment than mature RTS or undisturbed tundra. We also
 hypothesized soil seedbanks demonstrate quantity-quality trade-offs:
 younger seedbanks contain smaller numbers of mostly viable seed that
 decrease in viability as seed accumulates over time. We found five times
 as many seedlings in younger RTS as in older RTS, including birch and
 willow, and no seedlings in undisturbed tundra. Higher seedling counts
 were associated with bare soil, warmer soils, higher soil available
 nitrogen, and less plant cover. Seedbank viability was unrelated to size.
 Older seedbanks were larger at one chronosequence, with no difference in
 percent germination. At the other chronosequence, germination was lower
 from older seedbanks but seedbank size was not different. Seedbank
 germination was positively associated with in situ seedling abundance at
 one RTS chronosequence, suggesting post-disturbance revegetation from
 seedbanks. Thermal erosion may be important for recruitment in tundra by
 providing bare microsites that are warmer, more nutrient rich, and less
 vegetated than in undisturbed conditions. Differences between two
 chronosequences in seedbank size, viability, and species composition
 suggest disturbance interacts with local conditions to form seedbanks. RTS
 may act as seedling nurseries to benefit many arctic species as climate
 changes, particularly those that do not produce persistent seed.
description: Seedling and seedbank
 dataEnvironmental
 characterization, seedling count data, seedbank size and germination
 dataDCHuebner_data.xlsx
DOI: 10.5061/dryad.s81k3
title: Data from: The role of human outdoor recreation in shaping patterns of grizzly bear-black bear co-occurrence

description: Species distributions are influenced by a combination of landscape
 variables and biotic interactions with other species, including people.
 Grizzly bears and black bears are sympatric, competing omnivores that also
 share habitats with human recreationists. By adapting models for
 multi-species occupancy analysis, we analyzed trail camera data from 192
 trail camera locations in and around Jasper National Park, Canada to
 estimate grizzly bear and black bear occurrence and intensity of trail
 use. We documented (a) occurrence of grizzly bears and black bears
 relative to habitat variables (b) occurrence and intensity of use relative
 to competing bear species and motorised and non-motorised recreational
 activity, and (c) temporal overlap in activity patterns among the two bear
 species and recreationists. Grizzly bears were spatially separated from
 black bears, selecting higher elevations and locations farther from roads.
 Both species co-occurred with motorised and non-motorised recreation,
 however, grizzly bears reduced their intensity of use of sites with
 motorised recreation present. Black bears showed higher temporal activity
 overlap with recreational activity than grizzly bears, however differences
 in bear daily activity patterns between sites with and without motorised
 and non-motorised recreation were not significant. Reduced intensity of
 use by grizzly bears of sites where motorised recreation was present is a
 concern given off-road recreation is becoming increasingly popular in
 North America, and can negatively influence grizzly bear recovery by
 reducing foraging opportunities near or on trails. Camera traps and
 multi-species occurrence models offer non-invasive methods for identifying
 how habitat use by animals changes relative to sympatric species,
 including humans. These conclusions emphasise the need for integrated
 land-use planning, access management, and grizzly bear conservation
 efforts to consider the implications of continued access for motorised
 recreation in areas occupied by grizzly bears.
description: Raw
 DataIncludes data for
 multi-species analysis and for activity overlap
 analysisRaw
 data.zipR CodeR Code for multi-species
 analysis (adapted from Rota et al. 2016. A multi-species occupancy model
 for two or more interacting species. Methods in Ecology and Evolution. 7:
 1164-1173) and for activity overlap analysis.R
 code.zip
DOI: 10.5061/dryad.j647p
title: Data from: Dietary studies in birds: testing a non-invasive method using digital photography in seabirds

description: Dietary studies give vital insights into foraging behaviour, with
 implications for understanding changing environmental conditions and the
 anthropogenic impacts on natural resources. Traditional diet sampling
 methods may be invasive or subject to biases, so developing non-invasive
 and unbiased methods applicable to a diversity of species is essential. We
 used digital photography to investigate the diet fed to chicks of a
 prey-carrying seabird and compared our approach (photo-sampling) to a
 traditional method (regurgitations) for the greater crested tern
 Thalasseus bergii. Over three breeding seasons, we identified &gt;24
 000 prey items of at least 48 different species, more than doubling the
 known diversity of prey taken by this population of terns. We present a
 method to estimate the length of the main prey species (anchovy Engraulis
 encrasicolus) from photographs, with an accuracy &lt;1 mm and
 precision ~ 0·5 mm. Compared to regurgitations at two colonies,
 photo-sampling produced similar estimates of prey composition and size, at
 a faster species accumulation rate. The prey compositions collected by two
 researchers photo-sampling concurrently were also similar. Photo-sampling
 offers a non-invasive tool to accurately and efficiently investigate the
 diet composition and prey size of prey-carrying birds. It reduces biases
 associated with observer-based studies and is simple to use. This
 methodology provides a novel tool to aid conservation and management
 decision-making in the light of the growing need to assess environmental
 and anthropogenic change in natural ecosystems.
description: DATA ARCHIVE ANCHOVY
 STANDARD LENGTHData include: 1) The
 measurements of the anchovy used for the allometric regressions (training
 set) 2) The measurements of the anchovy in the test set. 3) The
 measurements of the anchovy measured from photos and regurgitates at
 Robben Island and from Seal Island.DATA ARCHIVE
 PHOTO-SAMPLE & REGURGITATIONSThis file include: The
 ordered list of species in the photo samples from Observer A and B and
 Seal Island and the ordered list of species in the regurgitation in both
 Robben Island and Seal Island.List of species
 recordedList of species recorded
 using photo-sampling method in Robben Island
 (2013-2015)
DOI: 10.5061/dryad.67v66m9
title: Data from: The onset of ecological diversification 50 years after colonization of a crater lake by haplochromine cichlid fishes

description: Adaptive radiation research typically relies on the study of evolution in
 retrospective, leaving the predictive value of the concept hard to
 evaluate. Several radiations, including the cichlid fish in the East
 African Great Lakes, have been studied extensively, yet no study has
 investigated the onset of the intraspecific processes of niche expansion
 and differentiation shortly after colonization of an adaptive zone by
 cichlids. Haplochromine cichlids of one of the two lineages that seeded
 the Lake Victoria radiation recently arrived in Lake Chala, a lake
 perfectly suited for within-lake cichlid speciation. Here we infer the
 colonization and demographic history, quantify phenotypic, ecological and
 genomic diversity and diversification, and investigate the selection
 regime to ask if the population shows signs of diversification resembling
 the onset of adaptive radiation. We find that since their arrival in the
 lake, haplochromines have colonized a wide range of depth habitats
 associated with ecological and morphological expansion and the beginning
 of phenotypic differentiation and potentially nascent speciation,
 consistent with the very early onset of an adaptive radiation process.
 Moreover, we demonstrate evidence of rugged phenotypic fitness surfaces,
 indicating that current ecological selection may contribute to the
 phenotypic diversification.
description: Phenotypic data for
 Astatotilapia cf. bloyeti from Lake ChalaPhenotypic data for
 Astatotilapia cf. bloyeti from Lake Chala, fish were collected in fall
 2014. Data includes individual ID number (column A), number of circuli (as
 an age estimate, column B), depth of capture (C), wet weight (D), genus
 (E), capture site (F), morph assignement (G), linear morphological
 distances (H to V), mitochondrial haplotype (W), stable isotopes (X-Y),
 intestine length (Z), volumetric proportion of prey items in the stomachs
 (AA-AL), fullness index of the stomachs from 1 (empty) to 5 (full, AM),
 and colouration (AN-AU).AstatotilapiaChalaPhenotypicData.xlsx
DOI: 10.5061/dryad.d826h
title: Data from: Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population

description: Understanding the causes of population decline is crucial for conservation
 management. We therefore used genetic analysis both to provide baseline
 data on population structure and to evaluate hypotheses for the
 catastrophic decline of the South American sea lion (Otaria flavescens) at
 the Falkland Islands (Malvinas) in the South Atlantic. We genotyped 259
 animals from 23 colonies across the Falklands at 281 bp of the
 mitochondrial hypervariable region and 22 microsatellites. A weak
 signature of population structure was detected, genetic diversity was
 moderately high in comparison with other pinniped species, and no evidence
 was found for the decline being associated with a strong demographic
 bottleneck. By combining our mitochondrial data with published sequences
 from Argentina, Brazil, Chile and Peru, we also uncovered strong
 maternally directed population structure across the geographical range of
 the species. In particular, very few shared haplotypes were found between
 the Falklands and South America, and this was reflected in correspondingly
 low migration rate estimates. These findings do not support the prominent
 hypothesis that the decline was caused by migration to Argentina, where
 large-scale commercial harvesting operations claimed over half a million
 animals. Thus, our study not only provides baseline data for conservation
 management but also reveals the potential for genetic studies to shed
 light upon long-standing questions pertaining to the history and fate of
 natural populations.
description: Data_fileExcel file with 22 microsatellites loci y mitochondrial control region.Data_SL.xlsx
DOI: 10.5061/dryad.nf61r
title: Data from: Strong population genetic structure and contrasting demographic histories for the small-spotted catshark (Scyliorhinus canicula) in the Mediterranean Sea

description: Coastal and demersal chondrichthyans, such as the small-spotted catshark,
 are expected to exhibit genetic differentiation in areas of complex
 geomorphology like the Mediterranean Basin because of their limited
 dispersal ability. To test this hypothesis, we used a fragment of the
 mitochondrial cytochrome c oxidase subunit I gene and 12 nuclear
 microsatellite loci in order to investigate the genetic structure and
 historical demography of this species, and to identify potential barriers
 to gene flow. Samples were collected from the Balearic Islands, the
 Algerian Basin, the Ionian Sea, the Corinthian Gulf and various locations
 across the Aegean Sea. Additional sequences from the Atlantic and the
 Levantine Basin retrieved from GenBank were included in the mitochondrial
 DNA analysis. Both mitochondrial and nuclear microsatellite DNA data
 revealed a strong genetic subdivision, mainly between the western and
 eastern Mediterranean, whereas the Levantine Basin shared haplotypes with
 both areas. The geographic isolation of the Mediterranean basins seems to
 enforce the population genetic differentiation of the species, with the
 deep sea acting as a strong barrier to its dispersal. Contrasting
 historical demographic patterns were also observed in different parts of
 the species' distribution, most notably a population growth trend in
 the western Mediterranean/Atlantic area and a slight decreasing one in the
 Aegean Sea. The different effects of the Pleistocene glacial periods on
 the habitat availability may explain the contrasting demographic patterns
 observed. The current findings suggest that the small-spotted catshark
 exhibits several genetic stocks in the Mediterranean, although further
 study is needed.
description: Microsatellite raw data
 of Scyliorhinus caniculaKousteni_etal_Scanicula_msat_data.csv
DOI: 10.5061/dryad.6r6pn
title: Data from: A simple experimental set-up to disentangle the effects of altered temperature and moisture regimes on soil organisms

description: 1. Climate manipulation experiments in the field and laboratory
 incubations are common methods to study the impact of climate change on
 soils and their biota. However, both types of methods have drawbacks
 either on their mechanistic interpretation or ecological relevance. 2. We
 propose an experimental setup that combines the best of both methods, and
 can be easily obtained by modifying widely available Tullgren soil fauna
 extractors. This setup creates or alters temperature and moisture
 gradients within intact field soil cores, after which soil biota, their
 activity, and vertical movements can be studied. We assessed the
 performance and demonstrate the applicability of this setup through a case
 study on Collembola response to changes in microclimatic gradients in peat
 bogs. 3. Warming created a vertical temperature gradient of 14°C in peat
 cores without varying soil moisture conditions, while at a given
 temperature regime precipitation and drought treatments shifted natural
 soil moisture gradients to ‘wetter’ and ‘drier’, respectively. This
 allowed for disentangling interacting warming and moisture effects on soil
 fauna. In our case study Collembola communities showed peat layer-specific
 responses to these climate treatments. Warming decreased Collembola
 density and altered community composition in the shallowest layer, whereas
 precipitation increase affected Collembola community composition in the
 deepest layer. 4. We showed that climate change can have layer-specific
 effects on soil organisms that are ‘hidden’ by not taking microclimatic
 vertical gradients into account. This experimental setup facilitates
 studying (multi-trophic) organism responses to climate changes, with only
 a small adjustment of equipment that is often already present in soil
 ecology laboratories. Moreover, this setup can be easily customized to
 study many more other research questions related to wide-ranging organisms
 and ecosystems.
description: Temperature and soil
 moisture data climate manipulationTemperature and Soil
 moisture data of a peat core that was exposed to experimental climate
 manipulation by placement into a modified Tullgren
 setupMEE_Krab_temp&soilmoist..xlsxCollembola community data climate manipulationCollembola community data of peatcores exposed to climate manipulation by placement into a modified Tullgren setupMEE_Krab_Collembola_density.xlsx