cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v9s4mw6r1
title: Data from: Mediterranean marine protected areas have higher biodiversity via increased evenness, not abundance

description: 1. Protected areas are central to biodiversity conservation. For marine
 fish, marine protected areas (MPAs) often harbour more individuals,
 especially of species targeted by fisheries. But precise pathways of
 biodiversity change remain unclear. For example, how local-scale responses
 combine to affect regional biodiversity, important for managing spatial
 networks of MPAs, is not well known. Protection potentially influences
 three components of fish assemblages that determine how species accumulate
 with sampling effort and spatial scale: the total number of individuals,
 the relative abundance of species, and within species aggregation. Here,
 we examined the contributions of each component to species richness
 changes inside MPAs as a function of spatial scale. 2. Using standardised
 underwater visual survey data, we measured the abundance and species
 richness of reef fishes in 43 protected and 41 fished sites in the
 Mediterranean Sea. 3. At both local and regional scales, increased species
 evenness caused by added common species in MPAs compared to fished sites
 was the most important proximate driver of higher diversity. 4.
 Site-to-site variation in the composition (i.e., ß-diversity) of
 common species was also higher among protected sites, and
 depended on sensitivity to exploitation. There were more abundant
 exploited species at regional scales than at local scales, reflecting a
 tendency for different protected sites to harbour different exploited
 species. In contrast, fewer abundant unexploited species were found at the
 regional scale than at the local scale, meaning that relative abundances
 at the regional scale were less even than at the local scale.
 5. Synthesis and applications. Although marine protected
 areas (MPAs) are known to strongly influence fish community abundance and
 biomass, we found that changes to the relative abundance of species (i.e.,
 increased evenness) dominated the biodiversity response to protection.
 MPAs had more relatively common species, which in turn led to higher
 diversity for a given sampling effort. Moreover,
 higher ß-diversity of common species meant that local
 scale responses were magnified at the regional scale due to site-to-site
 variation inside protected areas for exploited species. Regional
 conservation efforts can be strengthened by examining how multiple
 components of biodiversity respond to protection across spatial scales.
description: Fish assemblages were sampled in the northern Mediterranean Sea
 during May-June 2007 and 2008. At each site, similar depths (8-12m) and
 habitats (rocky reefs) were selected to minimise environmental
 heterogeneity, and fish assemblages were surveyed using three 25 x 5m
 strip transects.
description: Code to reproduce results in Blowes et al. 'Mediterranean
 marine protected areas have higher biodiversity via increased evenness,
 not abundance.' <em>J Appl Ecology</em> is available
 at https://github.com/sablowes/MediterraneanMPA
DOI: 10.5061/dryad.bg79cnp74
title: Data from: Biotic interactions help explain variation in elevational range limits of birds among Bornean mountains

description: Physiological tolerances and biotic interactions along habitat gradients
 are thought to influence species occurrence. Distributional differences
 caused by such forces are particularly noticeable on tropical mountains,
 where high species turnover along elevational gradients occurs over
 relatively short distances and elevational distributions of particular
 species can shift among mountains. Such shifts are interpreted as evidence
 of the importance of spatial variation in interspecific competition and
 habitat or climatic gradients. To assess the relative importance of
 competition and compression of habitat and climatic zones in setting range
 limits, we examined differences in elevational ranges of forest bird
 species among four Bornean mountains with distinct features. We
 surveyed the elevational ranges of rain forest birds on four mountains in
 Borneo to test which environmental variables—habitat zone compression or
 presence of likely competitors—best predicted differences in elevational
 ranges of species among mountains. For this purpose, we used two
 complementary tests: a comparison of elevational range limits between
 pairs of mountains, and linear mixed models with naïve occupancy as the
 response variable. We found that lowland species occur at higher
 elevations on two small mountains compared to Mt. Mulu. This result is
 inconsistent with the expectation that distributions of habitats are
 elevationally compressed on small mountains, but is consistent with the
 hypothesis that a reduction in competition (likely diffuse) on short
 mountains, which largely lack montane specialist species, allows lowland
 species to occur higher in elevation. The relative influence of
 competition changes with elevation, and the correlation between lower
 range limits of montane species and the distribution of their competitors
 was weaker than in lowland species. These findings provide
 support for the importance of biotic interactions in setting elevational
 range limits of tropical bird species, although abiotic gradients explain
 the majority of distribution patterns. Thus, models predicting range
 shifts under climate change scenarios must include not only climatic
 variables, as is currently most common, but also information on
 potentially resulting changes in species interactions, especially for
 lowland species.
description: These data estimate the occupancy of each bird species at each
 elevation on each of four mountains in Borneo. Species detected fewer than
 10 times on a given mountain are excluded.  This
 'naive occupancy' value was estimated by dividing the number of
 points where the species was detected on a given mountain at a given
 elevation by the total number of points at that elevation. Points were
 lumped into elevational bins; see the manuscript. Also
 includes estimates of the summed occupancy of potential competitors of the
 same genus and of the same foraging guild (these estimates are obtained as
 above).
DOI: 10.5061/dryad.3n5tb2rch
title: Anatomy of the neural endocranium and stapes of Diadectes absitus (Diadectomorpha) from the early Permian of Germany based on the high‐resolution X‐ray microcomputed tomography

description: A detailed anatomy of the braincase and stapes of the subadult specimen of
 Diadectes absitus from early Permian sediments of Germany based on the
 high-resolution X-ray microcomputed tomography are described for the first
 time. In contrast to previous studies of Diadectes, the bones of the
 braincase (opisthotic, prootic, supraoccipital, basioccipital,
 exoccipital, basisphenoid, sphenethmoid), and parasphenoid of D. absitus
 are not co-ossified, but suturally defined. This has allowed for a
 reconstruction of a complete braincase with all sutures between the
 individual bones. The opisthotic, prootic, and supraocciptal contain a
 well-preserved endosseous labyrinth. The 3D-reconstruction of its cavities
 shows a well-preserved vestibule, three semicircular canals, and
 well-developed cochlear recess. In addition, a shallow subarcuate fossa is
 present on the ventral surface of the supraoccipital, which lies medial to
 the anterior semicircular canal. A typical feature of the diadectid
 braincase is the presence of the otic tube leading from the fenestra
 vestibuli to the vestibule. A revision of the topology of this structure
 is presented here. Here we describe new structures of the stapes,
 especially in its proximal portion, as well as its position to the
 fenestra vestibuli. These structures are described for the first time not
 only in D. absitus, but for the genus.
DOI: 10.5061/dryad.mkkwh70vj
title: In vivo assessment of the neural substrate linked with vocal imitation accuracy

description: Human speech and bird song are acoustically complex communication signals
 that are learned by imitation during a sensitive period early in life.
 Although the brain areas indispensable for speech and song learning are
 known, the neural circuits important for enhanced or reduced vocal
 performance remain unclear. By combining in vivo structural Magnetic
 Resonance Imaging with song analyses in juvenile male zebra finches during
 song learning and beyond, we reveal that song imitation accuracy
 correlates with the structural architecture of four distinct brain areas,
 none of which pertain to the song control system. Furthermore, the
 structural properties of a secondary auditory area in the left hemisphere,
 are capable to predict future song copying accuracy, already at the
 earliest stages of learning, before initiating vocal practicing. These
 findings appoint novel brain regions important for song learning outcome
 and inform that ultimate performance in part depends on fac tors
 experienced before vocal practicing.
DOI: 10.5061/dryad.bzkh1894v
title: Data from: Phenotypic plasticity, but not adaptive tracking, underlies seasonal variation in post-cold hardening freeze tolerance of Drosophila melanogaster

description:     In temperate regions, an organism’s ability
 to rapidly adapt to seasonally varying environments is essential for its
 survival. In response to seasonal changes in selection pressure caused by
 variation in temperature, humidity, and food availability, some organisms
 exhibit plastic changes in phenotype. In other cases, seasonal variation
 in selection pressure can rapidly increase the frequency of genotypes that
 offer survival or reproductive advantages under the current conditions.
 Little is known about the relative influences of plastic and genetic
 changes in short lived organisms experiencing seasonal environmental
 fluctuations. Cold hardening is a seasonally relevant plastic response in
 which exposure to cool, but nonlethal, temperatures significantly
 increases the organism’s ability to later survive at freezing
 temperatures. In the present study, we demonstrate seasonal variation in
 cold hardening in Drosophila melanogaster and test the extent to
 which plasticity and adaptive tracking underlie that seasonal variation.
 We measured the post-cold hardening freeze tolerance of flies from outdoor
 mesocosms over the summer, fall, and winter. We bred outdoor
 mesocosm-caught flies for two generations in the lab and matched each
 outdoor cohort to an indoor control cohort of similar genetic background.
 We cold hardened all flies under controlled laboratory conditions and then
 measured their post-cold hardening freeze tolerance. Comparing indoor and
 field-caught flies and their laboratory-reared G1 and G2 progeny allowed
 us to determine the roles of seasonal environmental plasticity, parental
 effects, and genetic changes on cold hardening. We also tested the
 relationship between cold hardening and other factors, including age,
 developmental density, food substrate, presence of antimicrobials, and
 supplementation with live yeast. We found strong plastic responses to a
 variety of field- and lab-based environmental effects, but no evidence of
 seasonally varying parental or genetic effects on cold hardening. We
 therefore conclude that seasonal variation in post-cold hardening freeze
 tolerance results from environmental influences and not genetic
 changes.
DOI: 10.5061/dryad.wstqjq2gd
title: The Burgess Shale paleocommunity with new insights from Marble Canyon, British Columbia

description: The middle (Wuliuan Stage) Cambrian Burgess Shale is famous for its
 exceptional preservation of diverse and abundant soft-bodied animals
 through the “thick” Stephen Formation. However, with the exception of the
 Walcott Quarry (Fossil Ridge) and the stratigraphically older Tulip Beds
 (Mount Stephen) which are both in Yoho National Park (British Columbia),
 quantitative assessments of the Burgess Shale have remained limited. Here
 we first provide a detailed quantitative overview of the diversity and
 structure of the Marble Canyon Burgess Shale locality based on 16,438
 specimens. Located 40 km southeast of the Walcott Quarry in Kootenay
 National Park (British Columbia), Marble Canyon represents the youngest
 site of the “thick” Stephen Formation. We then combine paleoecological
 datasets from Marble Canyon, Walcott Quarry, Tulip Beds and for the first
 time, the Raymond Quarry, which lies ca. 20 m directly above the Walcott
 Quarry, to yield a combined species abundance dataset of 77,179 specimens
 encompassing 234 taxa. Material from the Tulip Beds comes from talus
 slopes whereas material from all the other localities was collected in
 situ and comes from stratigraphically constrained intervals of at least 2
 m. Marble Canyon shows significant temporal changes in both taxonomic and
 ecological groups, suggesting periods of stasis followed by rapid turnover
 patterns at local and short temporal scales. At wider geographic and
 temporal scales, the different Burgess Shale sites occupy distinct areas
 in multivariate space. Overall, this suggests that the Burgess Shale
 palaeocommunity is far patchier than previously thought and varies at both
 local and regional scales through the “thick” Stephen Formation. This
 underscores that our understanding of Cambrian diversity and ecological
 networks, particularly in early animal ecosystems, remains limited and
 highly dependent on new discoveries.
DOI: 10.5061/dryad.rv15dv44s
title: Winter associations predict social and extra-pair mating patterns in a wild songbird

description: Despite decades of research, our understanding of the underlying causes of
 within-population variation in patterns of extra-pair paternity (EPP)
 remains limited. Previous studies have shown that extra-pair mating
 decisions are linked to both individual traits and ecological factors.
 Here, we examine whether social associations among individuals prior to
 breeding also shape mating patterns, specifically the occurrence of EPP,
 in a small songbird, the blue tit. We test whether associations during the
 non-breeding period predict (1) future social pairs, (2) breeding
 proximity, i.e. the distance between breeding individuals, and (3) the
 likelihood that individuals have extra-pair young together. Individuals
 that were more strongly associated (those that foraged more often
 together) during winter tended to nest closer together. This, by itself,
 predicts EPP patterns, because most extra-pair sires are close neighbours.
 However, even after controlling for spatial effects, female-male dyads
 with stronger social associations prior to breeding were more likely to
 have extra-pair young. Our findings reveal a carry-over from social
 associations into future mating decisions. Quantifying the long-term
 social environment of individuals and studying its dynamics is a promising
 approach to enhance our understanding of the process of (extra-) pair
 formation.
DOI: 10.5061/dryad.dz08kprt4
title: Cold-water coral assemblages on vertical walls: distribution patterns from the Northeast Atlantic

description: Aim: In this study, we assess patterns of cold-water coral assemblages
 observed on deep-sea vertical walls. Similar to their shallow-water
 counterparts, vertical and overhanging walls in the deep sea can host
 highly diverse communities, but because of their geometry, these habitats
 are generally overlooked and remain poorly known.  These vertical
 habitats are however of particular interest, because they can protect
 vulnerable coral ecosystems from trawling activities.  As such,
 it is important to understand their ecology and assess their global
 importance.  Location:  Vertical walls on complex
 geomorphic features, in particular walls of the Rockall Bank Slope Failure
 Escarpment, Whittard and Explorer Canyons, Northeast Atlantic. Methods:
 Video analysis of ROV transects carried out at five sites is used to
 investigate differences in species composition and diversity across walls
 and to compare those to nearby cold-water coral sites on flat
 terrain.  A high-resolution photogrammetric reconstruction is
 further employed to examine whether wall complexity plays a role in
 promoting niche differentiation at very fine spatial scales. 
 Results: The investigated walls showed differences in species assemblage
 both across walls as well as in comparison to flat sites, with the
 fine-scale heterogeneity engendered by walls allowing niche
 differentiation between closely-related taxa.  Main Conclusions:
 Vertical walls represent an important cold-water coral habitat with
 differences in species composition across walls within a region,
 illustrating their role in driving diversity patterns.  Based on
 publicly available bathymetric datasets and a catalogue of broad-scale
 terrain features, globally over 8,000 features are likely to have vertical
 walls and cold-water corals, which highlights the need to consider
 deep-sea vertical habitats in current conservation efforts.
DOI: 10.5061/dryad.rn8pk0p5s
title: Rapid and predictable evolution of admixed populations between two Drosophila species pairs

description: The consequences of hybridization are varied, ranging from the origin of
 new lineages, introgression of some genes between species, to the
 extinction of one of the hybridizing species. We generated replicate
 admixed populations between two pairs of sister species
 of Drosophila: D. simulans and D.
 mauritiana; and D. yakuba and D. santomea. Each
 pair consisted of a continental species and an island endemic. The admixed
 populations were maintained by random mating in discrete generations for
 over 20 generations. We assessed morphological, behavioral, and
 fitness-related traits from each replicate population periodically, and
 sequenced genomic DNA from the populations at generation 20. For both
 pairs of species, species-specific traits and their genomes regressed to
 those of the continental species. A few alleles from the island species
 persisted, but they tended to be proportionally rare among all sites in
 the genome and were rarely fixed within the populations. This paucity of
 alleles from the island species was particularly pronounced on
 the X-chromosome. These results indicate that nearly all foreign
 genes were quickly eliminated after hybridization and that selection
 against the minor species genome might be similar across experimental
 replicates.
DOI: 10.5061/dryad.vdncjsxq9
title: Data from: Strength of species interactions determines biodiversity and stability in microbial communities

description: Organisms, especially microbes, tend to live in complex communities. While
 some of these ecosystems are very bio-diverse, others aren′t, and while
 some are very stable over time others undergo strong temporal
 fluctuations. Despite a long history of research and a plethora of data it
 is not fully understood what sets biodiversity and stability of
 ecosystems. Theory as well as experiments suggest a connection between
 species interaction, biodiversity, and stability of ecosystems, where an
 increase of ecosystem stability with biodiversity could be observed in
 several cases. However, what causes these connections remains unclear.
 Here we show in microbial ecosystems in the lab that the concentrations of
 available nutrients can set the strength of interactions between bacteria.
 At high nutrient concentrations, extensive microbial growth leads to
 strong chemical modifications of the environment, causing more negative
 interactions between species. These stronger interactions exclude more
 species from the community, resulting in a loss of biodiversity. At the
 same time, these stronger interactions also decrease the stability of the
 microbial communities, providing a mechanistic link between species
 interaction, biodiversity and stability.
description: For collection and analysis of the data see our publication.
description: <strong>Raw data for: Strength of species interactions
 determines biodiversity and stability in microbial
 communities</strong>  
 <strong>Raw data for plots (raw data for
 plots.zip)</strong> Contains raw data for the
 plots 1,3 and 4. Data for Fig. 4 is in folder Fig. 4.Except results from
 16S seqeuncing (see below). Datastructure is documented in two readme
 files within the zip folder:
 readme_pairwise_interactions.txt for the data of Fig. 1 and
 3 Readme_complex communities.txt for the data of Fig. 4
 in folder Fig. 4.  
 <strong>Raw data of 16S amplicon sequencing
 (*.fastq.gz)</strong> Dataset contains raw
 sequencing data from Illumina sequencing of soil microbial communities
 that were cultivated in the lab. Data is saved as .fastq.gz files. Data
 structure is explained in the readme_sequencing_raw_data.txt
 file.
DOI: 10.5061/dryad.gmsbcc2hw
title: Phylogeography and population structure of the tsetse fly Glossina pallidipes in Kenya and the Serengeti ecosystem

description: Glossina pallidipes is the main vector of animal African trypanosomiasis
 and a potential vector of human African trypanosomiasis in eastern Africa
 where it poses a large economic burden and public health threat. Vector
 control efforts have succeeded in reducing infection rates, but recent
 resurgence in tsetse fly population density raises concerns that vector
 control programs require improved strategic planning over larger
 geographic and temporal scales. Detailed knowledge of population structure
 and dispersal patterns can provide the required information to improve
 planning. To this end, we investigated the phylogeography and population
 structure of G. pallidipes over a large spatial scale in Kenya and
 northern Tanzania using 11 microsatellite loci genotyped in 600
 individuals. Our results indicate distinct genetic clusters east and west
 of the Great Rift Valley, and less distinct clustering of the northwest
 separate from the southwest (Serengeti ecosystem). Estimates of genetic
 differentiation and first-generation migration indicated high genetic
 connectivity within genetic clusters even across large geographic
 distances of more than 300 km in the east, but only occasional migration
 among clusters. Patterns of connectivity suggest isolation by distance
 across genetic breaks but not within genetic clusters, and imply a major
 role for river basins in facilitating gene flow in G. pallidipes.
 Effective population size (Ne) estimates and results from Approximate
 Bayesian Computation further support that there has been recent G.
 pallidipes population size fluctuations in the Serengeti ecosystem and the
 northwest during the last century, but also suggest that the full extent
 of differences in genetic diversity and population dynamics between the
 east and the west was established over evolutionary time periods
 (tentatively on the order of millions of years). Findings provide further
 support that the Serengeti ecosystem and northwestern Kenya represent
 independent tsetse populations. Additionally, we present evidence that
 three previously recognized populations (the Mbeere-Meru, Central Kenya
 and Coastal “fly belts”) act as a single population and should be
 considered as a single unit in vector control.