Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals

Neolithic dispersal implications of murids from late Holocene archaeological and modern natural deposits in the Talaud Islands, northern Sulawesi

The Sangihe-Talaud Archipelago represents a group of 77 remote islands located between the Philippines and North Sulawesi, in the northern sector of Wallacea. The Talaud Islands have a rich and significant archaeological record going back to the Pleistocene and are instrumental in understanding Pleistocene colonisation of small islands and later models of Austronesian language dispersal. Here we report on vertebrate material excavated from Leang Mande'et, a late Holocene rockshelter on Karakelang, the main island in the Talaud group. The site represents a periodically occupied shelter used for gardening. Fauna recovered predominately comprises murid elements, with at least four taxa (Rattus rattus, Rattus exulans and two Melomys species) found. The rodents show clear signs of being deposited by raptors rather than humans, unlike the small number of fish remains also recovered. DNA sequences from several Rattus rattus specimens are referrable to Rattus rattus complex lineage IV, a lineage with a southern Indochinese origins and broad modern representation through Indonesia and the Philippines. The lack of any Rattus rattus complex lineage II from Leang Mande’et suggests that the first agricultural inhabitants of this island did not come from Taiwan or northern Indochina, but rather that they either originated from the south or that, once established in the Talauds, opened up significant trade networks to the south and in the process acquired a significant pest

Avian surfactant protein (SP)-A2 first arose in an early tetrapod before the divergence of amphibians and gradually lost the collagen domain

The air-liquid interface of the mammalian lung is lined with pulmonary surfactants, a mixture of specific proteins and lipids that serve a dual purpose-enabling air-breathing and protection against pathogens. In mammals, surfactant proteins A (SP-A) and D (SP -D) are involved in innate defence of the lung. Birds seem to lack the SP-D gene, but possess SP-A2, an additional SP-A-like gene. Here we investigated the evolution of the SP-A and SP-D genes using computational gene prediction, homology, simulation modelling and phylogeny with published avian and other vertebrate genomes. PCR was used to confirm the identity and expression of SP-A analogues in various tissue homogenates of zebra finch and turkey. In silico analysis confirmed the absence of SP-D-like genes in all 47 published avian genomes. Zebra finch and turkey SP-A1 and SP-A2 sequences, confirmed by PCR of lung homogenates, were compared with sequenced and in silico predicted vertebrate homologs to construct a phylogenetic tree. The collagen domain of avian SP-A1, especially that of zebra finch, was dramatically shorter than that of mammalian SP-A. Amphibian and reptilian genomes also contain avian-like SP-A2 protein sequences with a collagen domain. NCBI Gnomon-predicted avian and alligator SP-A2 proteins all lacked the collagen domain completely. Both avian SP-A1 and SP-A2 sequences form separate clades, which are most closely related to their closest relatives, the alligators. The C-terminal carbohydrate recognition domain (CRD) of zebra finch SP-A1 was structurally almost identical to that of rat SP-A. In fact, the CRD of SP-A is highly conserved among all the vertebrates. Birds retained a truncated version of mammalian type SP-A1 as well as a non-collagenous C-type lectin, designated SP-A2, while losing the large collagenous SP-D lectin, reflecting their evolutionary trajectory towards a unidirectional respiratory system. In the context of zoonotic infections, how these evolutionary changes affect avian pulmonary surface protection is not clear

A new species of Rattus (Rodentia: Muridae) from Manus Island, Papua New Guinea

We describe a new species of Rattus, from 3 modern specimens collected on Manus Island in the Admiralty Group, Papua New Guinea, between 2002 and 2012. Subfossil specimens of early to late Holocene age from the Pamwak archaeological site on Manus Island are referred to the new species on morphological criteria; these confirm the species as a long-term resident of Manus Island. The new species is distinguished by its combination of large size; short tail; dorsal pelage that is coarse, spiny, and dark, with prominent black guard hairs; and sharply contrasting cream ventral pelage. Based on its overall body form, the species is almost certainly terrestrial. The dentition combines robust incisors with relatively small molars and the cranium displays a distinctive mélange of characters—including an elongate and anteriorly expanded rostrum and a mesopterygoid fossa that is narrow anteriorly and broadens to the rear. Sequence data from the mitochondrial control region and 3 nuclear genes place the new species as a highly divergent member of the Australo–Papuan Rattus radiation, with no identified close relative among sampled taxa. Morphological comparisons are made between the new species and other pertinent species of Rattus from the region, including R. sanila, a species known only from Late Pleistocene fossil to Late Holocene subfossil remains from an archaeological site on New Ireland. The conservation status of the new species is discussed in the light of a recent survey that failed to locate surviving populations in 2 areas of natural forest on Manus Island. Further survey work is urgently needed to identify any surviving populations and to assess the role of potential threats to the species

First Light And Reionisation Epoch Simulations (FLARES) XI: [OIII] emitting galaxies at 5<z<105<z<10

JWST has now made it possible to probe the rest-frame optical line emission of high-redshift galaxies extending to z~9, and potentially beyond. To aid in the interpretation of these emerging constraints, in this work we explore predictions for [OIII] emission in high-redshift galaxies using the First Light and Reionisation Epoch Simulations (FLARES). We produce predictions for the [OIII] luminosity function, its correlation with the UV luminosity, and the distribution of equivalent widths (EWs). We also explore how the [OIII] EW correlates with physical properties including specific star formation rate, metallicity, and dust attenuation. Our predictions are largely consistent with recent observational constraints on the luminosity function, average equivalent widths, and line ratios. However, they fail to reproduce the observed tail of high-EW sources and the number density of extreme line emitters. Possibilities to explain these discrepancies include an additional source of ionising photons and/or greater stochasticity in star formation in the model or photometric scatter and/or bias in the observations. With JWST now rapidly building larger samples and a wider range of emission lines the answer to this remaining discrepancy should be available imminently.Comment: 15 pages, accepted for publication in MNRAS, minor changes from original versio

Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree–species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets

Cosmic Evolution Early Release Science (CEERS) survey: The colour evolution of galaxies in the distant Universe

The wavelength-coverage and sensitivity of JWST now enables us to probe the rest-frame UV - optical spectral energy distributions (SEDs) of galaxies at high-redshift ($z>4$). From these SEDs it is, in principle, through SED fitting possible to infer key physical properties, including stellar masses, star formation rates, and dust attenuation. These in turn can be compared with the predictions of galaxy formation simulations allowing us to validate and refine the incorporated physics. However, the inference of physical properties, particularly from photometry alone, can lead to large uncertainties and potential biases. Instead, it is now possible, and common, for simulations to be \emph{forward-modelled} to yield synthetic observations that can be compared directly to real observations. In this work, we measure the JWST broadband fluxes and colours of a robust sample of $5<z<10$ galaxies using the Cosmic Evolution Early Release Science (CEERS) Survey. We then analyse predictions from a variety of models using the same methodology and compare the NIRCam/F277W magnitude distribution and NIRCam colours with observations. We find that the predicted and observed magnitude distributions are similar, at least at $58$ the distributions differ somewhat, though our observed sample size is small and thus susceptible to statistical fluctuations. Likewise, the predicted and observed colour evolution show broad agreement, at least at $5<z<8$. There is however some disagreement between the observed and modelled strength of the strong line contribution. In particular all the models fails to reproduce the F410M-F444W colour at $z>8$, though, again, the sample size is small here.Comment: 11 pages, 10 figures, submitted to MNRA

A recent gibbon ape leukemia virus germline integration in a rodent from New Guinea

Germline colonization by retroviruses results in the formation of endogenous retroviruses (ERVs). Most colonization’s occurred millions of years ago. However, in the Australo-Papuan region (Australia and New Guinea), several recent germline colonization events have been discovered . The Wallace Line separates much of Southeast Asia from the Australo-Papuan region restricting faunal and pathogen dispersion. West of the Wallace Line, gibbon ape leukemia viruses (GALVs) have been isolated from captive gibbons. Two microbat species from China appear to have been infected naturally. East of Wallace’s Line, the woolly monkey virus (a GALV) and the closely related koala retrovirus (KoRV) have been detected in eutherians and marsupials in the Australo-Papuan region, often vertically transmitted. The detected vertically transmitted GALV-like viruses in Australo-Papuan fauna compared to sporadic horizontal transmission in Southeast Asia and China suggest the GALV-KoRV clade originates in the former region and further models of early-stage genome colonization may be found. We screened 278 samples, seven bat and one rodent family endemic to the Australo-Papuan region and bat and rodent species found on both sides of the Wallace Line. We identified two rodents ( Melomys ) from Australia and Papua New Guinea and no bat species harboring GALV-like retroviruses. Melomys leucogaster from New Guinea harbored a genomically complete replication-competent retrovirus with a shared integration site among individuals. The integration was only present in some individuals of the species indicating this retrovirus is at the earliest stages of germline colonization of the Melomys genome, providing a new small wild mammal model of early-stage genome colonization

Whole genome duplication potentiates inter-specific hybridisation and niche shifts in Australian burrowing frogs Neobatrachus

Polyploidy plays an important role in evolution because it can lead to increased genetic complexity and speciation. It also provides an extra copy buffer and increases genetic novelty. While both common and well-studied in plants, polyploidy is rare in animals, and most polyploid animals reproduce asexually. Amphibians represent a dramatic vertebrate exception, with multiple independent sexually reproducing polyploid lineages, but very few cases have been studied in any detail. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful model animal polyploid system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We resolve the phylogenetic relationships among Neobatrachus species and provide further support that the three polyploid species have independent origins. We document higher genetic diversity in tetraploids, resulting from widespread gene flow specifically between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and current isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate variation on frogs with differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which in turn corresponds to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow into tetraploid lineages specifically. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on evolution of adaptation in animals