cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qrfj6q5d0
title: The roles of climate, geography and natural selection as drivers of genetic and phenotypic differentiation in a widespread amphibian Hyla annectans (Anura: Hylidae)

description: The role of geological events and Pleistocene climatic fluctuations as
 drivers of current patterns of genetic variation in extant species has
 been a topic of continued interest among evolutionary biologists.
 Nevertheless, comprehensive studies of widely distributed species are
 still rare, especially from Asia. Using geographically extensive sampling
 of many individuals and a large number of nuclear single nucleotide
 polymorphisms (SNPs), we studied the phylogeography and historical
 demography of Hyla annectans populations in southern China. Thirty-five
 sampled populations were grouped into seven clearly defined genetic
 clusters that closely match phenotype-based subspecies classification.
 These lineages diverged 2.32–5.23 million years ago, a timing that closely
 aligns with the rapid and drastic uplifting of the Qinghai-Tibet Plateau
 and adjacent southwest China. Demographic analyses and species
 distribution models indicate that different populations of this species
 have responded differently to past climatic changes. In the Hengduan
 Mountains, most populations experienced a bottleneck, whereas the
 populations located outside of the Hengduan Mountains have gradually
 declined in size since the end of the last glaciation. In addition, the
 levels of phenotypic and genetic divergence were strongly correlated
 across major clades. These results highlight the combined effects of
 geological events and past climatic fluctuations, as well as natural
 selection, as drivers of contemporary patterns of genetic and phenotypic
 variation in a widely distributed anuran in Asia.
description: 'SNP_data_for_H.annectans' is the SNP data for Hyla
 annectans in vcf formats.  Which is used for the phylogeney tree, genetic
 structure, genetic differentiation, demographic analyses.
 'Morphological_data_info' are the statistic data of
 snout-vent length (SVL), weight and spots numbers used for morphological
 analyses and QST-FST comparison.
 'SDM_input_ascii' are the SDM ascii files used for
 SDMs. 'SDM_locality_info' are the occurrence
 data points of five genetic clusters for the H. annectans.
DOI: 10.5061/dryad.q83bk3jg1
title: Data from: Oxidative stress experienced during early development influences the offspring phenotype

description: Oxidative stress (OS) experienced early in life can affect an individual’s
 phenotype. However, its consequences for the next generation remain
 largely unexplored. We manipulated the OS level endured by zebra finches
 (Taeniopygia guttata) during their development by transitorily inhibiting
 the synthesis of the key antioxidant glutathione (‘early-high-OS’). The
 offspring of these birds and control parents were cross-fostered at
 hatching to enlarge or reduce its brood size. Independently of parents’
 early-life OS levels, the chicks raised in enlarged broods showed lower
 erythrocyte glutathione levels, revealing glutathione sensitivity to
 environmental conditions. Control (“early-low-OS”) biological mothers
 produced females, not males, that attained a higher body mass when raised
 in a benign environment (i.e. the reduced brood). In contrast, biological
 mothers exposed to early-life OS produced heavier males, not females, when
 allocated in reduced broods. Early-life OS also affected the parental
 rearing capacity because 12d-old nestlings raised by a foster pair with
 both early-high-OS members grew shorter legs (tarsus) than chicks from
 other groups. The results indicate that environmental conditions during
 development can affect early glutathione levels, which may, in turn,
 influence the next generation through both pre- and postnatal parental
 effects. The results also demonstrate that early-life OS can constrain the
 offspring phenotype.
description: Dataset collected from a transgenerational study. F0 pairs
 produced F1 offspring that were early treated with every two days BSO
 injections inducing a reduction in total glutathione (tGSH) synthesis at
 14d old. A random subsample of F1 adult birds was allowed to freely mate
 and breed in a large outdoor aviary. Hatchlings (F2) were cross-fostered
 during the first days of their life (mean 2-d old) to increase or reduce
 the original brood size to test the effect of the early development
 treatment of their parents under two differentiated environments (adverse
 or benign, respectively).
description: The dataset has two sheets. The information and phenotype
 variables of the F2 nestlings are on the first sheet and the information
 about the reproductive events of the F1 parents is on the second sheet.
 The explanation of the variables is included as a comment on the variable
 name.
DOI: 10.6084/m9.figshare.28295672
title: Andrias fossil sample cytb.fasta

description: Partial cytb gene sequence of<i> </i><i>Andrias japonicus</i> fossil sample.
DOI: 10.6084/m9.figshare.28295672.v1
title: Andrias fossil sample cytb.fasta

description: Partial cytb gene sequence of<i> </i><i>Andrias japonicus</i> fossil sample.
DOI: 10.6084/m9.figshare.29656007
title: Clinical Metagenomics

description: Clinical metagenomics for diagnosis of febrile illness.
DOI: 10.6084/m9.figshare.29656007.v1
title: Clinical Metagenomics

description: Clinical metagenomics for diagnosis of febrile illness.
DOI: 10.5061/dryad.h9w0vt4g3
title: Extending the footprint record of Pareiasauromorpha to the Cisuralian: earlier appearance and wider palaeobiogeography of the group

description: Pareiasauromorpha is one of the most important tetrapod groups of the
 Permian. Skeletal evidence suggests a late Kungurian origin in North
 America, whereas the majority of occurrences come from the Guadalupian and
 Lopingian of South Africa and Russia. Pareiasauromorpha footprints include
 the ichnogenus Pachypes, that is, however, unknown from strata older than
 late Guadalupian. A revision of several Pachypes-like footprints from the
 Cisuralian–Guadalupian of Europe and North America confirm the occurrence
 of this ichnogenus and of the ichnospecies Pachypes ollieri n. comb.
 beginning in the Artinskian. This is the earliest known occurrence of
 Pachypes and it coincides with the Artinskian reptile radiation. Based on
 a synapomorphy-based track-trackmaker correlation, Pachypes ollieri n.
 comb. can be attributed to nycteroleter pareiasauromorphs such as
 Macroleter. Therefore, the earliest occurrences of pareiasauromorph
 footprints precede by at least 10 Myr the earliest occurrence of this
 group in the skeletal record. Moreover, the palaeobiogeography of the
 group is extended to the Cisuralian and Guadalupian of western Europe.
DOI: 10.5061/dryad.nvx0k6dq6
title: Magnetic transfection with superparamagnetic chitosan-loaded IGFBP5 nanoparticles and their in vitro biosafety

description: Purpose: To study the application of superparamagnetic chitosan
 nanoparticles (SPCIONPs) as gene vectors using a magnetic transfection
 system for the targeted treatment of lung metastasis of osteosarcoma.
 Methods: The superparamagnetic chitosan nanoparticles were characterized
 by Transmission Electron Microscopy, Fourier Transform Infrared
 spectrometry, a Superconducting Quantum Interference Device and Atomic
 Force Microscopy. Their biosafety was determined by cell counting kit-8
 (CCK8) and live-dead staining assays. In vitro transfection was detected
 by laser confocal microscopy. Results: SPCIONPs, which can bind closely to
 plasmids and protect them from DNA enzyme degradation, were prepared with
 an average particle size of 95.60 nm and zeta potential of 11 mV. The
 results of the CCK8 and live-dead staining assays showed that
 superparamagnetic chitosan nanoparticles loaded with Insulin-like growth
 factor-binding protein 5 (SPCIONPs/pIGFBP5) induced no significant
 cytotoxicity compared to the control group. The in vitro transfection
 result suggested that pIGFBP5 emitted a greater amount of red fluorescence
 in the SPCIONPs/pIGFBP5 group than that in the chitosan-loaded IGFBP5
 (CS/pIGFBP5) group. Conclusion: The prepared SPCIONPs had good biosafety
 and could be effectively used to transfer pIGFBP5 into 143B cells, and
 they thus have good application prospects for the treatment of lung
 metastasis of osteosarcoma.
description: We used CCK8 to detect cytotoxicity, with 5 accessory holes in
 each group. After removing the maximum and minimum values, 3 values were
 left for statistical analysis to eliminate errors.
DOI: 10.5061/dryad.k0p2ngf63
title: A genomic footprint of a moving hybrid zone in marbled newts

description: We developed a panel of 44 nuclear genetic markers and applied this to two
 species of marbled newts in the north (Triturus marmoratus) and the south
 (T. pygmaeus) of the Iberian Peninsula, to document pattern and process of
 interspecific gene flow. The northernmost occurrence of T. pygmaeus
 genetic material was in a T. marmoratus population north of the Vouga
 river estuary. This suggested the past presence of a hybrid zone, possibly
 coinciding with a natural river outlet at ca. 1200 A.D. Since 1808, the
 species contact has moved back south to a by then completed, man-made
 Vouga channel. We also found a T. marmoratus genomic footprint in T.
 pygmaeus from the Serra de Sintra, near Lisbon. In combination with a
 previously reported southern, relic occurrence of T. marmoratus in between
 both areas, the data point to the superseding with hybridization of T.
 marmoratus by T. pygmaeus. We estimate that the species hybrid zone has
 moved over a distance of ca. 215 km.
description: Provided are the raw Ion Torrent reads and the reads processed
 through the bioinformatics pipeline described
 in<strong>:</strong> Wielstra, B., Duijm,
 E., Lagler, P., Lammers, Y., Meilink, W.R.M., Ziermann, J.M., Arntzen,
 J.W. (2014). Parallel tagged amplicon sequencing of transcriptome-based
 genetic markers for <em>Triturus</em> newts with the Ion
 Torrent next-generation sequencing platform. <em>Molecular Ecology
 Resources</em> 14(5): 1080-1089.
 (https://onlinelibrary.wiley.com/doi/full/10.1111/1755-0998.12242)
DOI: 10.5061/dryad.m0cfxpp1j
title: Chromosome-level genome of the peach fruit moth Carposina sasakii (Lepidoptera: Carposinidae) provides a resource for evolutionary studies on moths

description: Here we provide scripts and parameters for genome assembly and annotation,
 as well as the manually annotated circadian genes of period (PER),
 timeless (TIM), Clock (CLK), cycle (CYC) and cryptochrome (CRY), five
 detoxification gene families of cytochrome P450 monooxygenase (P450s),
 glutathione S-transferase (GSTs), carboxyl/cholinesterases (CCEs),
 UDP-glycosyltransferases (UGTs) and ATP-binding cassette (ABC)
 transporters, IR, OR, OBP, GR genes from the genome of the peach fruit
 moth (PFM), Carposina sasakii Matsumura (Lepidoptera: Carposinidae,
 superfamily Copromorphoidea) and genomes of its related species.
description: <b>Manual annotation of
 circadian genes</b> We further manually annotated
 well-studied circadian genes: <i>period</i> (PER),
 <i>timeless</i> (TIM), <i>Clock</i> (CLK),
 <i>cycle</i> (CYC) and cryptochrome (CRY), using BLAST v2.2.31
 (Altschul<i> et al.</i> 1990). Reference protein sequences of
 insect circadian genes were obtained from the Uniprot database. Conserved
 domains within proteins were annotated against the conserved domain
 database (Lu<i> et al.</i> 2020). Circadian genes of the other
 15 insect species were annotated in the same way. For a common domain of
 three genes (CLK, PER and CYC), a neighbor-joining tree was constructed
 using MEGA7 (Kumar<i> et al.</i> 2016) with 500 bootstrap
 replicates. <b>Manual annotation of
 detoxification gene families</b> We manually annotated five
 detoxification gene families of cytochrome P450 monooxygenase (P450s),
 glutathione S-transferase (GSTs), carboxyl/cholinesterases (CCEs),
 UDP-glycosyltransferases (UGTs) and ATP-binding cassette (ABC)
 transporters. We used the bioinformatic pipeline BITACORA
 (Vizueta<i> et
 al.</i> 2019) to conduct HMMER v3.3
 (Finn<i> et al.</i>
 2011)and BLAST
 v2.2.31 (Altschul<i> et
 al.</i> 1990) analyses under a
 full mode. Hits were
 filtered with a default cut-off E-value of 10e-5. The HMMs
 of P450 were downloaded from Pfam v32.0 (El-Gebali<i> et
 al.</i> 2018), while other HMMs of
 detoxification gene families were created by HMMER v3.3
 (Finn<i> et al.</i>
 2011). Orthologs from
 <i>Bombyx
 mori</i> and <i>D.
 melanogaster</i> were used as evidence. The annotated genes were
 further filtered manually based on gene length and the presence of
 conserved domains. Genes with a length shorter than 80 amino acids were
 removed. Orthologs were aligned with the G-INS-I algorithm implemented in
 MAFFT v7.450 (Katoh & Standley
 2013). A
 neighbor-joining tree was constructed for each gene family using MEGA7
 (Kumar<i> et al.</i>
 2016) with 500 bootstrap
 replicates.
description: Sequences are in fasta format by gene.
DOI: 10.5061/dryad.pzgmsbchw
title: Phylogenomic discordance in the Eared Seals is best explained by incomplete lineage sorting following explosive radiation in the Southern Hemisphere

description: The phylogeny and systematics of fur seals and sea lions (Otariidae) have
 long been studied with diverse data types, including an increasing amount
 of molecular data. However, only a few phylogenetic relationships have
 reached acceptance pointing at strong gene-tree species tree discordance.
 Divergence times in the group also vary largely between studies. These
 uncertainties impeded the understanding of the biogeographical history of
 the group, such as when and how trans-equatorial dispersal and subsequent
 speciation events occurred. Here we used high-coverage genome-wide
 sequencing for 14 of the 15 species of Otariidae to elucidate the
 phylogeny of the family and its bearing on the taxonomy and
 biogeographical history. Despite extreme topological discordance among
 gene trees, we found a fully supported species tree that agrees with the
 few well-accepted relationships and establishes monophyly of the genus
 Arctocephalus. Our data support a relatively recent trans-hemispheric
 dispersal at the base of a southern clade, which rapidly diversified into
 six major lineages between 3 to 2.5 Mya. Otaria diverged first, followed
 by Phocarctos and then four major lineages within Arctocephalus. However,
 we found Zalophus to be non-monophyletic, with California (Z.
 californianus) and Steller sea lions (Eumetopias jubatus) grouping closer
 than the Galapagos sea lion (Z. wollebaeki) with evidence for
 introgression between the two genera. Overall, the high degree of
 genealogical discordance was best explained by incomplete lineage sorting
 resulting from quasi-simultaneous speciation within the southern clade
 with introgresssion playing a subordinate role in explaining the
 incongruence among and within prior phylogenetic studies of the family.
DOI: 10.5061/dryad.gtht76hjh
title: Data from: Wintering grounds, population size and evolutionary history of a cryptic passerine species from isotopic and genetic data

description: Cryptic species pose a particular challenge to biologists in the context
 of life history investigations because of the difficulty in their field
 discrimination. Additionally, there is normally a lag in their widespread
 acceptance by the scientific community once they are formally recognised.
 These two factors might constrain our ability to properly assess the
 conservation status of the different species conforming a cryptic complex.
 In this study, we analysed isotopic and genetic data to shed light into
 the still unclear wintering grounds, population size and evolutionary
 history of the Iberian chiffchaff (Phylloscopus ibericus), a species
 included within the Common chiffchaff (Phylloscopus collybita) until two
 decades ago due to their phenotypic similarity. We used molecular methods
 to identify spring-migrating Phylloscopus species captured in northern
 Iberia, and by comparing the Hydrogen isotopic ratios of their claw tips
 (δ2Hc; which would reflect the signatures of their wintering grounds), we
 detected that δ2Hc values of Iberian chiffchaffs were similar to Willow
 warblers (Phylloscopus trochilus; a renowned trans-Saharan migrant), and
 higher than Common chiffchaffs (mostly a pre-Saharan migrant). These
 results strongly support the idea that Iberian chiffchaffs winter in
 tropical Africa. We additionally reconstructed the phylogeny and
 evolutionary history of the Iberian chiffchaff’s clade using mitochondrial
 and nuclear markers. Our results revealed relatively high values of
 nucleotide diversity (and, hence, high Ne) for the species that were
 greater than the values of the Common/Iberian most recent common ancestor.
 This suggests that the Iberian chiffchaff did not experience strong
 bottlenecks after diverging from the Common chiffchaff approximately one
 million years ago. Ultimately, our study provides another illustrative
 example of how isotopic and genetic analysis tools can help to enhance our
 understanding of avian ecology and evolution.
description: This dataset shows the list of birds considered in our study. For
 each individual we indicated the capture site in Araba province (Basque
 Country, Northern Iberia), ring number, capture date, species assignation
 in the field according to external phenotypic characteristics, species
 assignation according to its COI sequence, and the isotopic measurements
 (δ<sup>2</sup>Hc) of their claws (n=40
 individuals). 
description: We provide an Excel file with a first sheet where the meaning of
 each variable is briefly explained and a second sheet with the
 dataset.
DOI: 10.5061/dryad.6wwpzgmwd
title: Networks of physiological adjustments and defenses, and their synergy with sodium (Na+) homeostasis explain the hidden variation for salinity tolerance across the cultivated Gossypium hirsutum germplasm

description: The abilities to mobilize and/or sequester excess ions within and outside
 the plant cell are important components of salt-tolerance mechanisms.
 Mobilization and sequestration of Na+ involves three transport systems
 facilitated by the plasma membrane H+/Na+ antiporter (SOS1), vacuolar
 H+/Na+ antiporter (NHX1), and Na+/K+ transporter in vascular tissues
 (HKT1). Many of these mechanisms are conserved across the plant kingdom.
 While Gossypium hirsutum (upland cotton) is significantly more
 salt-tolerant relative to other crops, the critical factors contributing
 to the phenotypic variation hidden across the germplasm have not been
 fully unraveled. In this study, the spatio-temporal patterns of Na+
 accumulation along with other physiological and biochemical interactions
 were investigated at different severities of salinity across a meaningful
 genetic diversity panel across cultivated upland Gossypium. The aim was to
 define the importance of holistic or integrated effects relative to the
 direct effects of Na+ homeostasis mechanisms mediated by GhHKT1, GhSOS1,
 and GhNHX1. Multi-dimensional physio-morphometric attributes were
 investigated in a systems-level context using univariate and multivariate
 statistics, randomForest, and path analysis. Results showed that mobilized
 or sequestered Na+ contributes significantly to the baseline tolerance
 mechanisms. However, the observed variance in overall tolerance potential
 across a meaningful diversity panel were more significantly attributed to
 antioxidant capacity, maintenance of stomatal conductance, chlorophyll
 content, and divalent cation (Mg2+) contents other than Ca2+ through a
 complex interaction with Na+ homeostasis. The multi-tier
 macro-physiological, biochemical and molecular data generated in this
 study, and the networks of interactions uncovered strongly suggest that a
 complex physiological and biochemical synergy beyond the first-line-of
 defense (Na+ sequestration and mobilization) accounts for the total
 phenotypic variance across the primary germplasm of Gossypium hirsutum.
 These findings are consistent with the recently proposed Omnigenic Theory
 for quantitative traits and should contribute to a modern look at
 phenotypic selection for salt tolerance in cotton breeding.
description: BLASTP queries with segments of protein sequences from
 <i>GhHKT1,</i> <i>GhSOS1, </i>and <i>GhNHX1
 </i>were performed<i> </i>against published genomes to
 identify potential orthologs. The cDNA sequences for the target genes were
 aligned using ClustalW.
DOI: 10.25553/5z8j-vr48
title: Gateway Harmonized TILDA COVID, Version A
DOI: 10.5061/dryad.6wwpzgmwf
title: Down feather morphology reflects adaptation to habitat and thermal conditions across the avian phylogeny

description: Down feathers are the first feather types that appear in both the
 phylogenetic and the ontogenetic history of birds. Although it is widely
 acknowledged that the primary function of downy elements is insulation,
 little is known about the interspecific variability in the structural
 morphology of these feathers, and the environmental factors that have
 influenced their evolution. Here, we collected samples of down and
 afterfeathers from 156 bird species and measured key morphological
 characters that define the insulatory properties of the downy layer. We
 then tested if habitat and climatic conditions could explain the observed
 between-species variation in down feather structure. We show that habitat
 has a very strong and clearly defined effect on down feather morphology.
 Feather size, barbule length and nodus density all decreased from
 terrestrial towards aquatic birds, with riparian species exhibiting
 intermediate characters. Wintering climate, expressed as windchill (a
 combined measure of the ambient temperature and wind speed) had limited
 effects on down morphology, colder climate only being associated with
 higher nodus density in dorsal down feathers. Overall, an aquatic
 lifestyle selects for a denser plumulaceous layer, while the effect of
 harsh wintering conditions on downy structures appear limited. These
 results provide key evidence of adaptations to habitat at the level of the
 downy layer, both on the scale of macro- and micro-elements of the
 plumage. Moreover, they reveal characters of convergent evolution in the
 avian plumage and mammalian fur, that match the varying needs of
 insulation in terrestrial and aquatic modes of life.
description: Feathers were collected from dead birds and from a museum
 collection. Feathers were photographed and feather traits were measured
 from pictures using a software. For further details see the
 Methods.
description: All important information is included in the Methods.