Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern

Avian Island Radiations Shed Light on the Dynamics of Adaptive and Nonadaptive Radiation

Understanding the mechanisms underlying species formation and differentiation is a central goal of evolutionary biology and a formidable challenge. This understanding can provide valuable insights into the origins of the astonishing diversity of organisms living on our planet. Avian evolutionary radiations on islands have long fascinated biologists as they provide the ideal variation to study the ecological and evolutionary forces operating on the continuum between incipient lineages to complete speciation. In this review, we summarize the key insights gained from decades of research on adaptive and nonadaptive radiations of both extant and extinct insular bird species. We present a new comprehensive global list of potential avian radiations on oceanic islands, based on published island species checklists, taxonomic studies, and phylogenetic analyses. We demonstrate that our understanding of evolutionary processes is being greatly enhanced through the use of genomic tools. However, to advance the field, it is critical to complement this information with a solid understanding of the ecological and behavioral traits of both extinct and extant avian island species.

Museomics help resolving the phylogeny of snowfinches (Aves, Passeridae, Montifringilla and allies)

Historical specimens from museum collections provide a valuable source of material also from remote areas or regions of conflict that are not easily accessible to scientists today. With this study, we are providing a taxon-complete phylogeny of snowfinches using historical DNA from whole skins of an endemic species from Afghanistan, the Afghan snowfinch, Pyrgilauda theresae. To resolve the strong conflict between previous phylogenetic hypotheses, we generated novel mitogenome sequences for selected taxa and genome-wide SNP data using ddRAD sequencing for all extant snowfinch species endemic to the Qinghai-Tibet Plateau (QTP) and for an extended intraspecific sampling of the sole Central and Western Palearctic snowfinch species (Montifringilla nivalis). Our phylogenetic reconstructions unanimously refuted the previously suggested paraphyly of genus Pyrgilauda. Misplacement of one species-level taxon (Onychostruthus tazcanowskii) in previous snowfinch phylogenies was undoubtedly inferred from chimeric mitogenomes that included heterospecific sequence information. Furthermore, comparison of novel and previously generated sequence data showed that the presumed sister-group relationship between M. nivalis and the QTP endemic M. henrici was suggested based on flawed taxonomy. Our phylogenetic reconstructions based on genome-wide SNP data and on mitogenomes were largely congruent and supported reciprocal monophyly of genera Montifringilla and Pyrgilauda with monotypic Onychostruthus being sister to the latter. The Afghan endemic P. theresae likely originated from a rather ancient Pliocene out-of-Tibet dispersal probably from a common ancestor with P. ruficollis. Our extended trans-Palearctic sampling for the white-winged snowfinch, M. nivalis, confirmed strong lineage divergence between an Asian and a European clade dated to 1.5 - 2.7 million years ago (mya). Genome-wide SNP data suggested subtle divergence among European samples from the Alps and from the Cantabrian mountains.

Disseminating "hidden" scientific collections: the medium and large-sized terrestrial mammals at the Museo di Anatomia Comparata "Giovanni Battista Grassi", Roma, Italy

The dissemination of specimen data in scientific collections is a crucial step in making them available to the scientific community. However, even today, especially in some countries, little or nothing is known about the contents of the naturalistic collections of some museums. This is regrettable, especially in cases where the collections include historic specimens and endangered species. The Museum of Comparative Anatomy "Giovanni Battista Grassi", situated in Rome, Italy, houses historical anatomical and didactic collections, with specimens gathered from 1600s and almost worldwide. The collection holds 444 specimens of medium and large-sized terrestrial mammals, comprising 25 fossils, 40 skins, 186 skulls, 70 skeletons and 123 anatomical pieces, representing 63% of recent mammal orders, mainly from localities of Africa and Europe. A list of this material, indexed by the orders and families, is provided, as well as comments on the conservation status of the species. Remarkable data are summarised, including new data on a hippopotamus specimen from an extinct population and the record of three rhinoceros species from 1600s. Besides comparative anatomical studies, the Museum of Comparative Anatomy of Sapienza University emerges as a source of important material for biodiversity genomics.

Multiple mutations in the Nav1.4 sodium channel of New Guinean toxic birds provide autoresistance to deadly batrachotoxin

Toxicity has evolved multiple times across the tree of life and serves important functions related to hunting, defence and parasite deterrence. Toxins are produced either in situ by the toxic organism itself or associated symbionts, or acquired through diet. The ability to exploit toxins from external sources requires adaptations that prevent toxic effects on the consumer (autoresistance). Here, we examine genomic adaptations that could facilitate autoresistance to the diet-acquired potent neurotoxic alkaloid batrachotoxin (BTX) in New Guinean toxic birds. Our work documents two new toxic bird species and shows that toxic birds carry multiple mutations in the SCN4A gene that are under positive selection. This gene encodes the most common vertebrate muscle Nav channel (Nav1.4). Molecular docking results indicate that some of the mutations that are present in the pore-forming segment of the Nav channel, where BTX binds, could reduce its binding affinity. These mutations should therefore prevent the continuous opening of the sodium channels that BTX binding elicits, thereby preventing muscle paralysis and ultimately death. Although these mutations are different from those present in Neotropical Phyllobates poison dart frogs, they occur in the same segments of the Nav1.4 channel. Consequently, in addition to uncovering a greater diversity of toxic bird species than previously known, our work provides an intriguing example of molecular-level convergent adaptations allowing frogs and birds to ingest and use the same neurotoxin. This suggests that genetically modified Nav1.4 channels represent a key adaptation to BTX tolerance and exploitation across vertebrates.

Lack of country-wide systematic herpetology collections in Portugal jeopardizes future research and conservation

Natural History Collections (NHCs) represent the world's largest repositories of long-term biodiversity datasets. Specimen collection and voucher deposition has been the backbone of NHCs since their inception, but recent decades have seen a drastic decline in rates of growth via active collecting. Amphibians and reptiles are amongst the most threatened zoological groups on the planet and are historically underrepresented in most worldwide NHCs. As part of an ongoing project to review the Portuguese zoological collections in the country's NHCs, herpetological data from its three major museums and smaller collections was gathered and used to examine the coverage and representation of the different taxa extant in Portugal. These collections are not taxonomically, geographically, or temporally complete. Approximately 90% of the Portuguese herpetological taxa are represented in the country's NHCs, and around half of the taxa are represented by less than 50 specimens. Geographically, the collections cover less than 30% of the country's territory and almost all of the occurring taxa have less than 10% of their known distribution represented in the collections. A discussion on the implications for science of such incomplete collections and a review of the current status of Portuguese NHCs is presented.

Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex

Genetic isolation and morphological differentiation are two important factors in the speciation process that not always act in concert. A rapid morphological change in a lineage can hide its close relationship to another lineage, while slight morphological differentiation between two taxa can give the appearance of a closer relationship than is actually the case. The Dollarbird (Eurystomus orientalis) and the Azure Roller (Eurystomus azureus) is such an example. Today the Dollarbird and the Azure Roller are unanimously considered to constitute two distinct species, but in a recent genetic study it has been shown that the latter taxon, despite being larger and having a distinctly different coloration, is phylogenetically nested within the former. Its precise placement within this complex has not been determined, however. In this study, we investigate the phylogenetic relationships within the Dollarbird/Azure Roller complex. We estimate divergence times and infer phylogenetic relationships using sequence data from 6,475 genome-wide intronic regions, as well as complete mitochondrial genomes, using both concatenation and multispecies coalescence approaches. We find that within the Dollarbird/Azure Roller complex there are several examples of discrepancies between genetic and morphological differentiation. The Dollarbird is currently divided into between nine to twelve subspecies. Some of these subspecies are poorly differentiated, whereas others are morphologically more clearly discernable. Our data suggest that the complex consist of at least seven distinct genetic lineages that do not entirely match the morphological variation within the group. For instance, our results show that the subspecies solomonensis from the Solomon Islands, despite being morphologically very similar to its geographically closest neighbors, in fact is a highly distinct lineage that became isolated more than 700,000 years ago. In contrast, the morphologically distinct Azure Roller, which is currently treated as a distinct species, is nested within the Dollarbird and forms a slightly younger lineage than solomonensis and is the sister group to a clade with Australian and New Guinean Dollarbirds. Our results also show a deep genetic split within the Dollarbirds on the Asian mainland. This stands in contrast to the apparent clinal morphological variation reported for the birds on the Asian mainland. We also find support for the presence of a genetically distinct clade in the Wallacea region. The birds from the Wallacea region has previously been recognized as a distinct subspecies, connectens, but is currently placed in synonymy of other subspecies. Our results are thus at odds with the current division of the Dollarbird/Azure Roller complex into two species. Given that the species status of azureus is undisputed, the apparent genetic isolation of solomonensis and its clear separation from the other lineages suggests that this taxon also warrants species status. Based on the genetic and morphological variation observed within the Dollarbird/Azure Roller complex there is little doubt that even more taxa should regarded as species, but this require further examination.

Museomics and phylogenomics of lovebirds (Psittaciformes, Psittaculidae, Agapornis) using low-coverage whole-genome sequencing

Natural history collections contain specimens that provide important insights into studies of ecology and evolution. With the advancement of high-throughput sequencing, historical DNA (hDNA) from museum specimens has become a valuable source of genomic data to study the evolutionary history of organisms. Low-coverage whole genome sequencing (WGS) has been increasingly applied to museum specimens for analyzing organelle genomes, but is still uncommon for genotyping the nuclear DNA fraction. In this study, we applied low-coverage WGS to phylogenomic analyses of parrots in the genus Agapornis by including both modern samples and historical specimens of ∼100-year-old. Agapornis are small-sized African and Malagasy parrots with diverse characters. Earlier phylogenetic studies failed to resolve the positions of some key lineages, prohibiting a robust interpretation of the biogeography and evolution of these African parrots. Here, we demonstrated the use of low-coverage WGS for generating both mitochondrial and nuclear genomic data, and evaluated data quality differences between modern and historical samples. Our resolved Agapornis phylogeny indicates the ancestor of Agapornis likely colonized Madagascar from Australasia by trans-oceanic dispersal events before dispersing to the African continent. Genome-wide SNPs also allowed us to identify the parental origins of hybrid Agapornis individuals. This study demonstrates the potential of applying low-coverage WGS to phylogenomics and population genomics analyses and illustrates how including historical museum specimens can address outstanding questions regarding the evolutionary history of contemporary lineages.