cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g4f4qrfp5
title: Genetic divergence across glacial refugia despite interglacial gene flow in a crested newt

description: MtDNA-based phylogeography has illuminated the impact of the Pleistocene
 Ice Age on species distribution dynamics and the build-up of genetic
 divergence. The well-known shortcomings of mtDNA in biogeographical
 inference can be compensated by integrating multilocus data and species
 distribution modelling into phylogeography. We re-visit the phylogeography
 of the Italian crested newt (Triturus carnifex), a species distributed in
 two of Europe’s main glacial refugia, the Balkan and Italian Peninsulas.
 While a new 51 nuclear DNA marker dataset supports the existence of three
 lineages previously suggested by mtDNA (Balkan, northern Italy and
 southern Italy), the nuclear DNA dataset also provides improved resolution
 where these lineages have obtained secondary contact. We observe
 geographically restricted admixture at the contact between the Balkan and
 northern Italy gene pools and identify a potential mtDNA ghost lineage
 here. At the contact between the northern and southern Italy gene pools we
 find admixture over a broader area, as well as asymmetric mtDNA
 introgression. Our species distribution model is in agreement with a
 distribution restricted to distinct refugia during Pleistocene glacial
 cycles and postglacial expansion with secondary contact. Our study
 supports: (1) the relevance of the north-western Balkan Peninsula as a
 discrete glacial refugium; (2) the importance of north-eastern Italy and
 the northern Apennine as suture zones; and (3) the applicability of a
 refugia-within-refugia scenario within the Italian Peninsula.
DOI: 10.5061/dryad.m37pvmd0v
title: IS-mediated mutations both promote and constrain evolvability during a long-term experiment with bacteria

description: The long-term dynamics of IS elements and their effects on
 bacteria are poorly understood, including whether they are
 primarily genomic parasites or important drivers of adaptation by
 natural selection. Here, we investigate the dynamics of IS
 elements and their contribution to genomic evolution and fitness during
 a long-term experiment with Escherichia coli. This data set
 includes the Rmd file to analyze the genomic and metagenomic data
 (Tenaillon et al. 2016 and Good et al. 2017) in light with the IS dynamics
 and their correlation with fitness improvements described in the present
 work. 
description: This data set includes and RMD file containing metadata,
 markdown-formatted plain text and code. For further information on
 methods, please refer to the paper.
DOI: 10.6084/m9.figshare.31164904
title: Data for Ornithology publication: Female and male song rates but not female testosterone are elevated early in the breeding season in a temperate songbird (<i>Troglodytes aedon</i>)

description: In this study, we investigated associations between male and female song rates and circulating plasma testosterone in wild, nest box breeding <i>Troglodytes aedon</i> (Northern House Wrens) throughout the breeding cycle. We (1) explored how song rates and testosterone concentrations changed across the breeding cycle for each sex and (2) examined whether individual testosterone concentrations related to individual song rates in either sex. We used linear mixed models or a generalized linear mixed effect hurdle model (female song analysis only) to explore how song rate and testosterone concentrations change over the breeding cycle. See the R script and associated metadata and manuscript for more details.The file "Testosterone.and.song.csv" contains all the data relevant to this study.The file "HOWR.testosterone.vs.song.seasonal.analysis.r" is a script that provides the data analysis and figure generation for this study.
DOI: 10.6084/m9.figshare.31164904.v1
title: Data for Ornithology publication: Female and male song rates but not female testosterone are elevated early in the breeding season in a temperate songbird (<i>Troglodytes aedon</i>)

description: In this study, we investigated associations between male and female song rates and circulating plasma testosterone in wild, nest box breeding <i>Troglodytes aedon</i> (Northern House Wrens) throughout the breeding cycle. We (1) explored how song rates and testosterone concentrations changed across the breeding cycle for each sex and (2) examined whether individual testosterone concentrations related to individual song rates in either sex. We used linear mixed models or a generalized linear mixed effect hurdle model (female song analysis only) to explore how song rate and testosterone concentrations change over the breeding cycle. See the R script and associated metadata and manuscript for more details.The file "Testosterone.and.song.csv" contains all the data relevant to this study.The file "HOWR.testosterone.vs.song.seasonal.analysis.r" is a script that provides the data analysis and figure generation for this study.
DOI: 10.5068/d1m38q
title: Data from: The utility of environmental DNA from sediment and water samples for recovery of observed plant and animal species from four Mojave Desert springs

description: Background: Mojave Desert springs are fragile ecosystems, hosting endemic
 plants and animals, which are threatened by the increasing human demand
 for water and climate change. To develop management practices that will
 protect the groundwater-dependent ecosystems at Mojave Desert springs,
 real-time, low cost biodiversity monitoring and assessments are required.
 Environmental DNA (eDNA) metabarcoding uses DNA shed from organisms (e.g.
 skin cells, feces, pollen, etc.) that is present in water, air, soil, or
 sediment samples to assess community composition. This approach can
 increase the detection sensitivity for rare and elusive species, compared
 to expensive and time-consuming conventional methods, which also require
 taxonomic expertise. Aims: This study tests the effectiveness of eDNA
 techniques in capturing the observed Mojave Desert spring biodiversity in
 the winter and spring of 2019 at four distinct, naturally occurring
 springs. We also test the utility of sample types (water versus sediment)
 for capturing biodiversity. Results: We found that each of the four Mojave
 Desert springs supports a unique biological community. Sediment samples
 contained the greatest biodiversity, but all sample types captured species
 observed in the field by humans or camera-traps. We also found no
 statistical difference in species richness captured in winter and spring
 except for the Cytochrome Oxidase I marker, for which winter had greater
 biodiversity. Conclusion: This study supports the use of eDNA
 metabarcoding as an effective tool to mirror observation by human
 observers of ecological communities in desert springs. It demonstrates the
 importance of appropriately timing eDNA field sampling, primer selection,
 and using field-based surveys of wildlife and plants in addition to eDNA
 detection. This study also identified gaps in reference sequence databases
 for Mojave biodiversity and encourages collaboration of eDNA researchers
 with managers for effective conservation management plans.
DOI: 10.5061/dryad.cjsxksn4q
title: Clearcutting and selective logging have inconsistent effects on liana diversity and abundance but not on liana–tree interaction networks

description: Understanding the effects of forest management on lianas and their
 interaction with trees is an important step towards effective forest
 management. Our study therefore aimed at quantifying the patterns of liana
 diversity and abundance, and liana-tree interaction network structure in
 response to logging disturbance in a moist semi-deciduous forest in Ghana.
 We sampled lianas (diameter at 1.3 m ≥ 1 cm) and their host trees
 (diameter at breast height ≥ 5 cm) in 90 20 × 20 m plots among three
 forest management regimes: clearcut-logged, selectively-logged and
 old-growth forests. Liana species diversity and abundance in the
 selectively-logged forest was similar to that of the old-growth forest,
 while that in clearcut-logged forest was significantly lower than both
 above-mentioned forest types. Liana-tree interaction networks showed
 anti-nested structure, which is a form of nonrandom community
 organization. There were significant modularity and degree of
 specialization, but no significant connectance in the network structure.
 Largely, most of the species were peripherals, while a few species acted
 as structurally important species (i.e. module hubs, network hubs and
 connectors) in the three networks. A different set of species acted as
 structurally important species in the different forest management regimes.
 Our findings call for a re-examination of clearcutting logging in forest
 management in view of its negative effects on lianas, and we recommend
 prioritizing important modules in liana-tree network for future
 conservation.
description: Plant species were identified by plant taxonomists, and recourse
 to identification manuals.
DOI: 10.5061/dryad.cz8w9gj27
title: Noise distracts foraging bats

description: Predators frequently must detect and localize their prey in challenging
 environments. Noisy environments have been prevalent across the
 evolutionary history of predator-prey relationships, but now with
 increasing anthropogenic activities noise is becoming a more prominent
 feature of many landscapes. Here, we use the gleaning pallid bat,
 Antrozous pallidus, to investigate the mechanism by which noise disrupts
 hunting behavior. Noise can primarily function to mask – obscure by
 spectrally overlapping a cue of interest, or distract – occupy an animal’s
 attentional or other cognitive resources. Using band-limited white noise
 treatments that either overlapped the frequencies of a prey cue or did not
 overlap this cue, we find evidence that distraction is a primary driver of
 reduced hunting efficacy in an acoustically-mediated predator. Under
 exposure to both noise types successful prey localization declined by
 half, search time nearly tripled, and bats used 25% more sonar pulses than
 when hunting in ambient conditions. Overall, the pallid bat does not seem
 capable of compensating for environmental noise. These findings have
 implications for mitigation strategies, specifically the importance of
 reducing sources of noise on the landscape rather than attempting to
 reduce the bandwidth of anthropogenic noise.
description: Included with the dataset is a ReadMe file
 "Allen_etal2021_DATASET_Readme.txt"
DOI: 10.5061/dryad.4j0zpc895
title: Influence of past and current factors on the beta diversity of coastal lagoon fish communities in South America

description: Aim: We aimed to assess the relative influence of past (Quaternary
 paleodrainage characteristics) and current factors on the beta diversity
 of freshwater fishes in coastal lagoons and explore the main processes
 involved. Location: Atlantic coast of South America. Taxon: Fishes (173
 species) Methods: We built a dataset of species occurrence in 129 lagoons
 across eight freshwater ecoregions of the world (FEOWs) located between
 latitudes 0° and 36° and calculated beta diversity (βjac) and its turnover
 (βjtu) and nestedness (βjne) components. We used a partial Mantel test and
 multiple regressions on distance matrices to evaluate the importance of
 past and current factors, and of geographical distance in determining beta
 diversity. Past variables were those representing the historical
 freshwater habitat during the last glacial maximum (LGM), and contemporary
 variables were those related to current habitat. Results: We found high
 values of βjac within the FEOWs, with βjtu prevailing over βjne. Both past
 (paleodrainage) and current (drainage area, salinity, and lagoon area)
 factors affected species dissimilarity (βjac = 46%) and its components
 (βjtu = 44% and βjne =20%), although explanation was, in part, shared with
 geographical distance. Individually, the influence of past factors was
 prevalent in beta diversity and its components. Main Conclusions: The
 results suggest that major changes in the availability of freshwater
 habitats and connectivity since the Pleistocene must have affected the
 colonization, extinction and recolonization processes of fishes along the
 eastern coast of South America. We suggest that the high beta diversity
 values may result from limited dispersal after extinctions in the LGM and
 that the dissimilar freshwater fish communities currently seen were formed
 mainly by heterogeneous subsets of the regional species pool that
 persisted in landscape refuges during past sea level increases and then
 recolonized coastal lagoons.
description: We compiled fish species composition data for 129 lagoons along
 the Atlantic coast of South America between latitudes 0° and 36° S, which
 encompass eight freshwater ecoregions of the world (FEOW). The fish data
 consisted of a presence/absence matrix of species by lagoon. Most data
 were compiled by Petry et al. (2016), but we added new data by searching
 fish collection records in the SpeciesLink database
 (http://splink.cria.org.br/) and in primary research papers. A taxonomic
 and nomenclatural verification was performed across the dataset to
 validate all the species records. We included only lagoons that were
 subjected to specific community sampling protocols. Exclusively estuarine
 species or occasional marine species were not included, since we were
 interested in biogeographical processes related to freshwater species
 only.
DOI: 10.5061/dryad.5qfttdz3g
title: Nematodes carried by beetles and remaining in malt extract agar (MEA)

description: To show the importance of vector switching of nematodes in the evolution
 of the  Bursaphelenchus xylophilus group, we tested a hypothesis
 that “Bursaphelenchus doui (or its ancestor) was transferred by Acalolepta
 fraudatrix, Acalolepta sejuncta, and/or Monochamus subfasciatus (or their
 ancestral species) from broad-leaved trees to conifers, switched vectors
 from these cerambycid beetles to Monochamus beetles in conifers, and then
 evolved into the common ancestor of Bursaphelenchus mucronatus and B.
 xylophilus.” We used a simple nematode-loading method to beetles and
 produced 20 binary combinations of five B. xylophilus group species and
 four cerambycid beetle species in the tribe Lamiini. The affinity of the
 nematodes for the beetles was examined based on phoretic stage formation
 of the nematodes. Phoretic stages of B. doui appeared in all beetle
 species examined, namely Acalolepta luxuriosa, Psacothea hilaris, A.
 fraudatrix, and Monochamus alternatus, although the affinity of the
 nematode for M. alternatus was weak. This finding indicates that B. doui
 could switch vectors to conifer-using Monochamus beetles after transfer by
 A. fraudatrix from broad-leaved trees to conifers. We conclude that vector
 switching of nematodes could have potentially happened during the
 evolutionary history of the B. xylophilus group.
description: See README file for column descriptions.
DOI: 10.5061/dryad.mcvdncjzr
title: In vivo transcriptome of Lactobacillus acidophilus and colonization impact on murine host intestinal gene expression

description: Lactobacillus acidophilus NCFM is a probiotic strain commonly used in
 dairy products and dietary supplements. Post-genome in vitro
 studies of NCFM thus far have linked potential key genotypes to its
 probiotic-relevant attributes including gut survival, prebiotic
 utilization, host interactions and immunomodulatory
 activities. To corroborate and extend beyond previous in vivo and
 in vitro functional studies, we employed a dual RNA-seq transcriptomic
 approach to identify genes potentially driving the gut fitness and
 activities of L. acidophilus NCFM in vivo, and in parallel, examine the
 ileal transcriptional response of its murine hosts during
 monocolonization. Spatial expression profiling of NCFM from the
 ileum through the colon revealed a set of 134 core genes that were
 consistently overexpressed during gut transit. These in vivo core
 genes are predominantly involved in the metabolism of carbohydrates, amino
 acids and nucleotides, along with mucus-binding proteins and adhesion
 factors, confirming their functionally important roles in nutrient
 acquisition and gut retention.  Functional characterization of
 the highly expressed major S-layer encoding gene established its
 indispensable role as a cell shape determinant and maintenance of cell
 surface integrity, essential for viability and probiotic
 attributes.  Host colonization by L. acidophilus resulted in
 significant down-regulation of several pro-inflammatory cytokines and
 tight junction proteins. Genes related to redox signaling, mucin
 glycosylation and circadian rhythm modulation were induced, suggesting
 impacts on intestinal development and immune
 functions. Metagenomic analysis of NCFM populations
 post-colonization demonstrated the genomic stability of L. acidophilus as
 a gut transient and further established its safety as a probiotic and
 biotherapeutic delivery platform.
DOI: 10.5061/dryad.4f4qrfj9j
title: UCE and Sanger sequenced data for phylogenetic analysis of jumping spiders (Baviini and Nungia, Salticidae)

description: The systematics and taxonomy of the tropical Asian jumping spiders of the
 tribe Baviini is reviewed, with a molecular phylogenetic study (UCE
 sequence capture, traditional Sanger sequencing) guiding a
 reclassification of the group's genera. The well-studied members of
 the group are placed into six genera: Bavia Simon, 1877, Indopadilla Caleb
 & Sankaran, 2019, Padillothorax Simon, 1901, Piranthus Thorell,
 1895, Stagetillus Simon, 1885, and one new genus, Maripanthus Maddison.
 The identity of Padillothorax is clarified, and Bavirecta Kanesharatnam
 & Benjamin, 2018 synonymized with it. Hyctiota Strand, 1911 is
 synonymized with Stagetillus. The molecular phylogeny divides the baviines
 into three clades, the Piranthus clade with a long embolus (Piranthus,
 Maripanthus), the genus Padillothorax with a flat body and short embolus,
 and the Bavia clade with a higher body and (usually) short embolus
 (remaining genera). In general, morphological synapomorphies support or
 extend the molecularly-delimited groups. Eighteen new species are
 described (all with taxonomic authority W. Maddison): Bavia nessagyna,
 Indopadilla bamilin, I. kodagura, I. nesinor, I. redunca, I. redynis, I.
 sabivia, I. vimedaba, Maripanthus draconis (type species of Maripanthus),
 M. jubatus, M. reinholdae, Padillothorax badut, P. mulu, Piranthus api, P.
 bakau, P. kohi, P. mandai, and Stagetillus irri. The distinctions between
 baviines and the astioid Nungia Żabka, 1985 are reviewed, leading to four
 species being moved into Nungia from Bavia and other genera. Fifteen new
 combinations are established, and one combination is restored. Five of
 these new or restored combinations correct previous errors of placing
 species in genera that have superficially similar palps but extremely
 different body forms, in fact belonging in distantly related tribes —
 emphasizing that the general shape of male palps should be used with
 caution in determining relationships. A little-studied genus,
 Padillothorus Prószyński, 2018, is tentatively assigned to the Baviini.
 Ligdus Thorell, 1895 is assigned to the Ballini.
description: A mix of UCE sequence capture using both spider and arachnid
 probesets, and Sanger sequencing on a few traditional genes.
DOI: 10.5061/dryad.1c59zw3t7
title: Thermoelectric performances for both p- and n- type GeSe

description: The thermoelectric properties of p-type and n-type GeSe are studied
 systematically by using first principles and Boltzmann transport theory.
 The calculation includes electronic structure, electron relaxation time,
 lattice thermal conductivity and thermoelectric transport properties. The
 results show that GeSe is an indirect band gap semiconductor with band gap
 1.34 eV. Though p-type GeSe has high density of states near Fermi level,
 the electronic conductivity is relative low because there is no carrier
 transport pathway along a-axis direction. For n-type GeSe, a charge
 density channel is formed near CBM, which improves the electrical
 conductivity of n-type GeSe along the a-axis direction. At 700 K, the
 optimal ZT value reaches 2.5 at 4×1019 cm-3 for n-type GeSe, while that is
 0.6 at 1×1020 cm-3 for p-type GeSe. The results show n-type GeSe has
 better thermoelectric properties than p-type GeSe, indicating that n-type
 GeSe is a promising thermoelectric material in middle temperature. The
 data include electronic structure, electron relaxation time, lattice
 thermal conductivity and thermoelectric transport properties for p- and
 n-type GeSe.
description: First principles and Boltzmann
 transport theory.
DOI: 10.5061/dryad.pzgmsbcjn
title: Mapped read data and files and scripts from: Vicariance followed by secondary gene flow in a young gazelle species complex

description: Grant’s gazelles have recently been proposed to be a species complex
 comprising three highly divergent mtDNA lineages (Nanger granti, N. notata
 and N. petersii). The three lineages have non-overlapping distributions in
 East Africa, but without any obvious geographical divisions, making them
 an interesting model for studying the early stage evolutionary dynamics of
 allopatric speciation in detail. Here we use genomic data obtained by
 restriction site-associated (RAD) sequencing of 106 gazelle individuals to
 shed light on the evolutionary processes underlying Grant's gazelle
 divergence, to characterize their genetic structure and to assess the
 presence of gene flow between the main lineages in the species complex. We
 date the species divergence to 134,000 years ago, which is recent in
 evolutionary terms. We find population subdivision within N. granti, which
 coincides with the previously suggested two subspecies, N.g. granti and
 N.g. robertsii. Moreover, these two lineages seem to have hybridized in
 Masai Mara. Perhaps more surprisingly given their extreme genetic
 differentiation, N. granti and N. petersii also show signs of prolonged
 admixture in Mkomazi, which we identified as a hybrid population most
 likely founded by allopatric lineages coming into secondary contact.
 Despite the admixed composition of this population, elevated X-chromosomal
 differentiation suggests that selection may be shaping the outcome of
 hybridization in this population. Our results therefore provide detailed
 insights into the processes of allopatric speciation and secondary contact
 in a recently radiated species complex.
description: BAM files with RAD sequencing data of 106 Grant's gazelle
 and 4 Thomson's gazelle mapped to the goat reference genome bosTau8.
 Contains also scripts used to generate all analyses starting from these
 BAM files for the publication "Vicariance followed by secondary gene
 flow in a young gazelle species complex".
description: bamfiles.zip: contains the 110 bam files.
 README.md has information on how to use the scripts.
 infoFiles.zip contains lists with sample information
 corresponding to bam files and variants excluded during QC
 scripts.zip contains the scripts, including model specification
 files for all models used with fastsimcoal2 and qpGraph
   Raw sequence data availabe in SRA accession
 PRJNA673069.