cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.tht76hf16
title: The interplay of fungal and bacterial microbiomes on rainforest frogs following a disease outbreak

description: Emerging infectious diseases are a serious threat to wildlife populations,
 and there is growing evidence that host microbiomes play important roles
 in infection dynamics, possibly even mitigating diseases. Nevertheless,
 most research on this topic has focused only on bacterial microbiomes,
 while fungal microbiomes have been largely neglected. To help fill this
 gap in our knowledge, we examined both the bacterial and fungal
 microbiomes of four sympatric Australian frog species which had different
 population-level responses to the emergence of chytridiomycosis, a
 widespread disease caused by the fungal pathogen Batrachochytrium
 dendrobatids (Bd). We sequenced 16,884 fungal amplicon sequence variants
 (ASVs) and 41,774 bacterial ASVs. Bacterial communities had higher
 richness and were less variable within frog species than were fungal
 communities. Nevertheless, both communities were correlated for ASV
 richness and beta diversity (i.e., frogs with similar bacterial richness
 and community composition tended to also have similar fungal richness and
 community composition). This suggests that either one microbial community
 was having a large impact on the other, or that they were both being
 driven by similar environmental factors. For both microbial taxa, we found
 little evidence of associations between Bd (prevalence or intensity) and
 either individuals’ ASVs or beta-diversity. However, there was mixed
 evidence of associations between richness (both bacterial and fungal) and
 Bd, with high richness potentially providing a protective effect.
 Surprisingly, the relative abundance of bacteria that have previously been
 shown to inhibit Bd was also positively associated with Bd infection
 intensity, suggesting that a high relative abundance of those bacteria
 provides poor protection against infection.
description: These data are ASV tables from skin swabs of frogs. See methods
 section of "The interplay of fungal and bacterial microbiomes on
 rainforest frogs following a disease outbreak" for details.
DOI: 10.5061/dryad.ksn02v761
title: SCUBA belt transects for abundance data H. cochlea and H. aequicostatus

description: Marine symbioses are integral to the persistence of ecosystem functioning
 in coral reefs. Solitary corals of the species Heteropsammia cochlea and
 Heterocyathus aequicostatus have been observed to live in symbiosis with
 the sipunculan worm Aspidosiphon muelleri muelleri, which inhabits a
 cavity within the coral, in Zanzibar (Tanzania). The symbiosis of these
 photosymbiotic corals enables the coral holobiont to move, in fine to
 coarse unconsolidated substrata, a process termed as “walking”. This
 allows the coral to escape sediment cover in turbid conditions which is
 crucial for these light-dependent species. An additional commensalistic
 symbiosis of this coral-worm holobiont is found between the Aspidosiphon
 worm and the cryptoendolithic bivalve Jousseaumiella sp., which resides
 within the cavity of the coral skeleton. To understand the morphological
 alterations caused by these symbioses, interspecific relationships, with
 respect to the carbonate structures between these three organisms, are
 documented using high-resolution imaging techniques (scanning electron
 microscopy and µCT scanning). Documenting multi-layered symbioses can shed
 light on how morphological plasticity interacts with environmental
 conditions to contribute to species persistence.
description: SCUBA Dive transects. 20 m x 2
 m belt transect method (English et al. 1994).
DOI: 10.5061/dryad.cjsxksn76
title: Data from: Phylogenomics of elongate-bodied Springtails reveals independent transitions from aboveground to belowground habitats in deep time

description: Soil has become a major hotspot of biodiversity studies, yet the pattern
 and timing of the evolution of soil organisms are poorly known because of
 the scarcity of palaeontological data. To overcome this limitation, we
 conducted a genome-based macroevolutionary study of an ancient,
 diversified, and widespread lineage of soil fauna, the elongate-bodied
 springtails (class Collembola, order Entomobryomorpha). To build the first
 robust backbone phylogeny of this previously refractory group, we sampled
 representatives of major higher taxa (6 out of 8 families, 11 out of 16
 subfamilies) of the order with an emphasis on the most problematic
 superfamily Tomoceroidea, applied whole-genome sequencing (WGS) methods,
 and compared the performance of different combinations of datasets
 (universal single-copy orthologues/USCO versus ultraconserved
 elements/UCE) and modelling schemes. The fossil-calibrated timetree was
 used to reconstruct the evolution of body size, sensory organs, and
 pigmentation to establish a time frame of the ecomorphological
 divergences. The resultant trees based on different analyses were
 congruent in most nodes. Several discordant nodes were carefully evaluated
 by considering method fitness, morphological information, and topology
 test. The evaluation favoured the well-resolved topology from analyses
 using USCO amino acid matrices and complex site-heterogeneous models
 (CAT+GTR and LG+PMSF (C60)). The preferred topology supports the
 monophyletic superfamily Tomoceroidea as an early-diverging lineage and a
 sister relationship between Entomobryoidea and Isotomoidea. The family
 Tomoceridae was recovered as monophyletic, while Oncopoduridae was
 recovered as paraphyletic, with Harlomillsia as a sister to Tomoceridae
 and hence deserving a separate family status as Harlomillsiidae Yu and
 Zhang fam. n. Ancestral Entomobryomorpha were reconstructed as
 surface-living, supporting independent origins of soil-living groups
 across the Palaeozoic–Mesozoic, and highlighting the ancient evolutionary
 interaction between aboveground and belowground fauna.
DOI: 10.5061/dryad.18931zczx
title: Metabarcoding of the microbial community inhabiting the phosphogypsum stockpiles of the city of Huelva (SW, Spain)

description: In this work, metabarcoding of 16S and 18S rRNA gene coding sequences were
 employed to characterize the prokaryotic and eukaryotic
 communities in the phosphogypsum stacks located in the city of Huelva (SW
 Spain). In this environment around 100 Mt of phosphogypsum with
 extreme acidity and high concentrations of heavy metals and radionuclides
 have been accumulated for more than forty years on the marshlands of the
 Tinto River estuary. The microbial community inhabiting these adverse
 conditions remains unknown, although it can have an effect on the
 biogeochemical cycle of the phosphogypsum components and contain new
 species with biotechnological interest.
description: Water
 samples were collected from seawater, the Tinto River lower course, and
 two different points in phosphogypsum stacks, the perimeter channel and
 the piezometer. Fresh biomass was harvested from each water sample by
 filtering through a 0.7 μm glass fiber filter (Whatman, GF/G), and DNA was
 extracted by using the GeneJET Genomic Purification kit (Thermo Fisher
 Scientific, Waltham, MA, USA), following the manufacturer's
 instructions. The genomic DNA was used as a template for PCR amplification
 of specific regions of 16S rRNA and 18S rRNA coding genes. The
 hypervariable region V3-V4 of the 16S rRNA coding gen was amplified by
 using the primer set 341F/806R, while the primer pair 1380F/1510R was used
 for the amplification of the region V9 of the 18S rRNA coding gene. PCR
 reactions were carried out with Phusion® High-Fidelity PCR Master Mix
 (New England Biolabs, MA, USA). PCR products were mixed in equal ratios
 and purified following the Qiagen Gel Extraction Kit (Qiagen, Germany).
 Purified PCR products were employed for the generation of libraries with
 NEBNext® UltraTM DNA Library Prep Kit for Illumina and quantified via
 Qubit and Q-PCR. Finally, amplicons were sequenced on the Illumina
 platform to generate paired-end raw reads. To keep the reliability of the
 data, quality controls were performed at each step of the procedure, from
 the raw DNA samples to the final data (Q&gt;36).
description: Description of samples in Readme file.
DOI: 10.5061/dryad.fj6q573wq
title: Roe deer microsatellite genotype data

description: In the early 1800s, the European roe deer (Capreolus capreolus) was
 probably extirpated from Switzerland, due to overhunting and
 deforestation. After a federal law was enacted in 1875 to protect
 lactating females and young, and limiting the hunting season, the roe deer
 successfully recovered and recolonised Switzerland. In this study, we use
 mitochondrial DNA and nuclear DNA markers to investigate the
 recolonisation and assess contemporary genetic structure in relation to
 broad topographic features, in order to understand underlying ecological
 processes, inform future roe deer management strategies and explore the
 opportunity for development of forensic traceability tools. The results
 concerning the recolonisation origin support natural, multidirectional
 immigration from neighbouring countries. We further demonstrate that there
 is evidence of weak genetic differentiation within Switzerland among
 topographic regions. Finally, we conclude that the genetic data support
 the recognition of a single roe deer management unit within Switzerland,
 within which there is a potential for broad scale geographic origin
 assignment using nuclear markers to support law enforcement.
description: Roe deer samples were collected in Switzerland between 2004 and
 2017, by local hunters. Additional tissue samples were collected from
 Northern Italy close to the Swiss border (Lombardy) and Central Italy
 (Emilia-Romagna region). Samples were grouped into six regions based on
 broad landscape features, primarily according to topographic variation, as
 follows: Swiss regions: North, n=25; Central-East, n=106; Central-West,
 n=102; South-West, n=20; South-East, n= 54. The samples from Lombardy were
 included in the southeastern Swiss region as they originated close to the
 Swiss border with no barrier to free movement.The sixth group consisted of
 9 individuals from central Italy, resulting in a total of 316 samples. DNA
 from tissue and blood samples was extracted using the DNeasy® Blood and
 Tissue kit (Qiagen). DNA from blood swab samples was extracted using a
 chelex protocol followed by a Qiagen PCR purification kit (Qiagen,
 Switzerland) as described in Morf et al. (2021).
description: <strong>Microsatellite genotypes for Capreolus
 capreolus</strong> CSV file which contains
 original individual genotypes
 <strong>README_roe_deer_genotypes</strong>
 Short description of the csv file included in this
 submission
DOI: 10.5061/dryad.3r2280ghx
title: Data from: Leaching potential of phosphite fertilizer in sandy soils of the Southern Coastal Plain, USA

description: This is digital research data corresponding to a published
 manuscript, Leaching potential of phosphite fertilizer in sandy
 soils of the southern coastal plain, USA. Environments 2021, 8,
 126, https://doi.org/10.3390/environments8110126 Novel biotechnology on
 transgenic plants capable of metabolizing phosphite (Phi), a reduced form
 of P, could improve the effectiveness of P fertilizers and reduce the P
 footprint in agriculture with the benefit of suppressing weed growth.
 However, potassium Phi (K-Phi) salts used as fertilizer are highly soluble
 in water. At the same time, sandy soils of the Southern Coastal Plain are
 vulnerable to leaching losses resulting from long-term Pi fertilizer
 application. We performed a replicated leaching trial using five soil
 materials that included three surface and two subsurface layers from
 cultivated topsoil (Ap horizon) with contrasting Phi and Pi sorption
 capacities. Each soil received three treatments K-Phi at rates 0
 (control), 24, and 49 kg P ha−1 and leached twice with de-ionized water.
 All K-Phi-treated soils leached Phi except for the controls.
DOI: 10.5061/dryad.4j0zpc8d9
title: Aligned and curated mtDNA sequences from: Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period

description: Aim: Many species experienced population turnover and local extinction
 during the Late Pleistocene. In the case of megafauna, it remains
 challenging to disentangle climate change and the activities of
 Palaeolithic hunter-gatherers as the main cause. In contrast, the impact
 of humans on rodent populations is likely to be negligible. This
 study investigated which climatic and/or environmental factors affect the
 population dynamics of the common vole. This temperate rodent is
 widespread across Europe and was one of the most abundant small mammal
 species throughout the Late Pleistocene. Location: Europe Taxon: Common
 vole (Microtus arvalis) Methods: We generated a dataset comprised of a
 4.2-kb-long fragment of mitochondrial DNA (mtDNA) from 148 ancient and 51
 modern specimens sampled from multiple localities across Europe and
 covering the last 60 thousand years (ka). We used Bayesian inference to
 reconstruct their phylogenetic relationships and to estimate the age of
 the specimens that were not directly dated. Results: We estimated the time
 to the most recent common ancestor of all last glacial and extant common
 vole lineages to be 90 ka ago and the divergence of the main mtDNA
 lineages present in extant populations to between 55 and 40 ka ago, which
 is earlier than previous estimates. We detected several lineage
 turnovers in Europe during the period of high climate variability at the
 end of Marine Isotope Stage 3 (MIS 3; 57–29 ka ago) in addition to those
 found previously around the Pleistocene/Holocene transition. In
 contrast, data from the Western Carpathians suggest continuity throughout
 the Last Glacial Maximum (LGM), even at high latitudes. Main conclusions:
 The main factor affecting the common vole populations during the last
 glacial period was the decrease in open habitat during the interstadials,
 whereas climate deterioration during the LGM
 had little impact on population dynamics. This suggests that the rapid
 environmental change rather than other factors was the major force shaping
 the histories of the Late Pleistocene faunas.
description: This is a curated alignment of ca. 4.2 kb fragment of mtDNA of
 ancient and modern common voles (<em>M.arvalis</em>). Indels
 around polinucleotide tracts were removed.
DOI: 10.5061/dryad.9s4mw6mj8
title: Supplementary data and files for: The importance of contact zones for distinguishing interspecific from intraspecific geographic variation

description: With limited sampling, geographic variation within a single species can be
 difficult to distinguish from interspecific variation, confounding our
 ability to draw accurate species boundaries. We argue that thorough
 sampling and analysis of contact zones between putative taxa can determine
 if assortative mating or selection against hybrids exists (supporting the
 presence of two distinct species), or alternatively if mating is random
 among genotypes and admixture among adjacent populations is gradual and
 continuous (supporting geographic variation within a single species).
 Here, we test two alternative hypotheses for two pairs of named taxa at
 contact zones within the American milksnake (Lampropeltis triangulum)
 complex. A prior morphological analysis found areas of gradual
 intergradation among named taxa, and concluded that the taxa represented
 geographical races of a single polytypic species. In contrast, a
 subsequent analysis of gene sequence data, but with limited sampling near
 the contact zones, hypothesized distinct boundaries between species at the
 contact zones. At the contact zone between proposed species L. triangulum
 and L. gentilis, we examined a ~700 km-wide transect across the states of
 Kansas and Missouri, with thorough sampling and reduced-representation
 genomic-level sequencing, to test the two opposing taxonomic hypotheses.
 Our transect analyses included examinations of population structure, fixed
 differences, cline-fitting, and an admixture index analysis. These
 analyses all supported a gradual and continuous geographic cline across a
 broad intergrade zone between two geographic forms of L. triangulum, thus
 providing strong support for a single species in this region (and no
 support for the recognition of L. gentilis as a distinct species). At a
 second contact zone between proposed species L. triangulum and L.
 elapsoides (but variously treated as species or subspecies by different
 researchers) in Kentucky and Tennessee, we re-evaluated morphological
 data. In this case, the contact zone analysis indicated sympatry and
 reproductive isolation of the two taxa, and thus strongly supported L.
 triangulum and L. elapsoides as distinct species. We conclude that
 detailed studies of contact zones, based on either genetic or
 morphological data, are essential for distinguishing intraspecific from
 interspecific variation in the case of widely and continuously distributed
 taxa.
description: (1) Sequencing method: ddRAD sequencing (2)
 Bioinformatics pipeline: iPyrad (3) Analyses:
 Phylogenetic tree (RAxML)
 Population genetics (PCA, sNMF, conStruct)
 Admixture index HZAR
 Fixed difference analysis (4)
 Data visualization (custom scripts)
description: Please see README.txt for full details.
DOI: 10.5061/dryad.4qrfj6qc1
title: Data from: Patterns of genomic and allochronic strain divergence in the fall armyworm, Spodoptera frugiperda

description: Speciation is the process through which reproductive isolation develops
 between distinct populations. Because this process takes time, speciation
 studies often necessarily examine populations within a species that are at
 various stages of divergence. The fall armyworm, Spodoptera frugiperda
 (J.E.Smith), is comprised of two strains (R=Rice & C=Corn) that
 serve as a novel system to explore population divergence in sympatry.
 Here, we use ddRADSeq data to show that fall armyworm strains in the field
 are largely genetically distinct, but some interstrain hybridization
 occurs. Although we detected F1 hybrids of both R- and C-strain maternal
 origin, only hybrids with R-strain mtDNA were found to contribute to
 subsequent generations, possibly indicating a unidirectional barrier to
 gene flow. Although these strains have been previously defined as ‘host
 plant-associated,’ we recovered an equal proportion of R- and C-strain
 individuals in fields dominated by C-strain host plants. As an alternative
 to host associated divergence, we tested the hypothesis that differences
 in nightly activity patterns could account for reproductive isolation by
 genotyping temporally-collected moths. Our data indicates that strains
 exhibit a significant shift in the timing of their nightly activities in
 the field. This divergence in phenology creates a prezygotic reproductive
 barrier that likely maintains the genetic isolation between strains. Thus,
 we conclude that it may be ecologically inaccurate to refer to the C- and
 R- strain as ‘host-associated’ and they should more appropriately be
 considered ‘allochronic strains.’
DOI: 10.5061/dryad.pzgmsbcp5
title: Revisiting a classic hybrid zone: movement of the northern flicker hybrid zone in contemporary times

description: Natural hybrid zones have provided important insights into the
 evolutionary process, and their geographic dynamics over time can help to
 disentangle the underlying biological processes that maintain them. Here,
 we leverage replicated sampling of an identical transect across the hybrid
 zone between yellow-shafted and red-shafted flickers in the Great Plains
 to assess its stability over ~60 years (1955-1957 to 2016-2018). We
 identify a ~73 km westward shift in the hybrid zone center towards the
 range of the red-shafted flicker, but find no associated changes in width
 over our sampling period. In fact, the hybrid zone remains remarkably
 narrow, suggesting some kind of selective pressure maintains the zone. By
 comparing to previous work in the same geographic region, it appears
 likely that the movement in the hybrid zone has occurred in the years
 since the early 1980s. This recent movement may be related to changes in
 climate or land management practices that have allowed asymmetric westward
 movement of yellow-shafted flickers into the Great Plains.
description: <strong>INCLUDED FILES:</strong>
 1. <strong>scoring_locality_distances.txt</strong> =
 information on sampling localities (unprocessed file)
 2. <strong>flicker-scoring-HZonly.txt</strong> =
 phenotypic scoring of all samples included in the study (unprocessed
 file) 3-4.
 <strong>scoring_historic_input.txt</strong> /
 <strong>scoring_contempory_input.txt</strong> = files produced
 by processing flicker-scoring-HZonly.txt;<br> includes the mean and
 SE of phenotypic scores at each sampling locality for the historic or
 contemporary sampling period 5-8.
 <strong>scoring_historic_input_males.txt</strong> /
 <strong>scoring_historic_input_females.txt</strong> /
 <strong>scoring_contemporary_input_males.txt</strong> /
 <strong>scoring_contemporary_input_females.txt</strong>
 = <br> same as above, but separates males and females within the
 historic or contemporary sampling periods 9.
 <strong>photo_scores_HZonly.txt</strong> = ImageJ values from
 multi-spectral photography of all samples included in the study
 (unprocessed file)   Data processing
 scripts are available at https://github.com/stepfanie-aguillon/. Note that file names are consistent with those used in the GitHub Repository.
DOI: 10.5061/dryad.n02v6wx05
title: Mapping and assembly of the Midas cichlid male-specific region supports molecular parallelism in the evolution of a master sex-determining role for amhr2

description: The evolution of sex chromosomes and their differentiation from autosomes
 is a major event during genome evolution that happened many times in
 several lineages. The repeated evolution and lability of sex-determination
 mechanisms in fishes makes this a well-suited system to test for general
 and predictable patterns in evolution. According to current theory,
 differentiation is triggered by the suppression of recombination following
 the evolution of a new master-sex determining gene. However, the molecular
 mechanisms that establish recombination suppression are known from few
 examples, owing to the intrinsic difficulties of assembling sex
 determining regions (SDRs). Forward-genetics data and the development of
 long-read sequencing have generated a wealth of data questioning central
 aspects of the current theory. Here, we demonstrate that sex in Midas
 cichlids is determined by an XY system, identify and assemble the SDR by
 combining forward-genetics, long-read sequencing and optical mapping. We
 show how long-reads aid in the detection of artifacts in
 genotype-phenotype mapping that arise from incomplete genome assemblies.
 The male-specific region is restricted to a 100 kb segment on chromosome 4
 that harbors transposable elements and a Y-specific duplicate of the
 anti-Mullerian receptor 2 locus, a known sex-determining gene. Our data
 suggests that amhr2Y originated by an interchromosomal
 translocation from chromosome 20 to 4 predating the split of Midas and
 Flier cichlids. In the later, it is pseudogenized and translocated to
 another chromosome. Duplication of anti-Mullerian genes is a common route
 to establishing new sex determiners, highlighting the role of molecular
 parallelism in the evolution of sex determination.