Widespread support for a global species list with a formal governance system.

Taxonomic data are a scientific common. Unlike nomenclature, which has strong governance institutions, there are currently no generally accepted governance institutions for the compilation of taxonomic data into an accepted global list. This gap results in challenges for conservation, ecological research, policymaking, international trade, and other areas of scientific and societal importance. Consensus on a global list and its management requires effective governance and standards, including agreed mechanisms for choosing among competing taxonomies and partial lists. However, governance frameworks are currently lacking, and a call for governance in 2017 generated critical responses. Any governance system to which compliance is voluntary requires a high level of legitimacy and credibility among those by and for whom it is created. Legitimacy and credibility, in turn, require adequate and credible consultation. Here, we report on the results of a global survey of taxonomists, scientists from other disciplines, and users of taxonomy designed to assess views and test ideas for a new system of taxonomic list governance. We found a surprisingly high degree of agreement on the need for a global list of accepted species and their names, and consistent views on what such a list should provide to users and how it should be governed. The survey suggests that consensus on a mechanism to create, manage, and govern a single widely accepted list of all the world's species is achievable. This finding was unexpected given past controversies about the merits of list governance.

Trophic niche shifts and phenotypic trait evolution are largely decoupled in Australasian parrots.

BACKGROUND: Trophic shifts from one dietary niche to another have played major roles in reshaping the evolutionary trajectories of a wide range of vertebrate groups, yet their consequences for morphological disparity and species diversity differ among groups. METHODS: Here, we use phylogenetic comparative methods to examine whether the evolution of nectarivory and other trophic shifts have driven predictable evolutionary pathways in Australasian psittaculid parrots in terms of ecological traits such as body size, beak shape, and dispersal capacity. RESULTS: We found no evidence for an 'early-burst' scenario of lineage or morphological diversification. The best-fitting models indicate that trait evolution in this group is characterized by abrupt phenotypic shifts (evolutionary jumps), with no sign of multiple phenotypic optima correlating with different trophic strategies. Thus, our results point to the existence of weak directional selection and suggest that lineages may be evolving randomly or slowly toward adaptive peaks they have not yet reached. CONCLUSIONS: This study adds to a growing body of evidence indicating that the relationship between avian morphology and feeding ecology may be more complex than usually assumed and highlights the importance of adding more flexible models to the macroevolutionary toolbox.

Dense sampling of bird diversity increases power of comparative genomics.

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1-4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families-including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species.

Principles for creating a single authoritative list of the world's species.

Lists of species underpin many fields of human endeavour, but there are currently no universally accepted principles for deciding which biological species should be accepted when there are alternative taxonomic treatments (and, by extension, which scientific names should be applied to those species). As improvements in information technology make it easier to communicate, access, and aggregate biodiversity information, there is a need for a framework that helps taxonomists and the users of taxonomy decide which taxa and names should be used by society whilst continuing to encourage taxonomic research that leads to new species discoveries, new knowledge of species relationships, and the refinement of existing species concepts. Here, we present 10 principles that can underpin such a governance framework, namely (i) the species list must be based on science and free from nontaxonomic considerations and interference, (ii) governance of the species list must aim for community support and use, (iii) all decisions about list composition must be transparent, (iv) the governance of validated lists of species is separate from the governance of the names of taxa, (v) governance of lists of accepted species must not constrain academic freedom, (vi) the set of criteria considered sufficient to recognise species boundaries may appropriately vary between different taxonomic groups but should be consistent when possible, (vii) a global list must balance conflicting needs for currency and stability by having archived versions, (viii) contributors need appropriate recognition, (ix) list content should be traceable, and (x) a global listing process needs both to encompass global diversity and to accommodate local knowledge of that diversity. We conclude by outlining issues that must be resolved if such a system of taxonomic list governance and a unified list of accepted scientific names generated are to be universally adopted.

Towards reconciliation of the four world bird lists: hotspots of disagreement in taxonomy of raptors.

There are currently four world bird lists referenced by different stakeholders including governments, academic journals, museums and citizen scientists. Consolidation of these lists is a conservation and research priority. In reconciling lists, care must be taken to ensure agreement in taxonomic concepts-the actual groups of individual organisms circumscribed by a given scientific epithet. Here, we compare species-level taxonomic concepts for raptors across the four lists, highlighting areas of disagreement. Of the 665 species-level raptor taxa observed at least once among the four lists, only 453 (68%) were consistent across all four lists. The Howard and Moore Checklist of the Birds of the World contains the fewest raptor species (528), whereas the International Ornithological Community World Bird List contains the most (580) and these two lists are in the most disagreement. Of the disagreements, 67% involved owls, and Indonesia was the country containing the most disagreed upon species (169). Finally, we calculated the amount of species-level agreement across lists for each avian order and found raptor orders spread throughout the rankings of agreement. Our results emphasize the need to reconcile the four world bird lists for all avian orders, highlight broad disagreements across lists and identify hotspots of disagreement for raptors, in particular.

Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.

The bowerbirds in New Guinea and Australia include species that build the largest and perhaps most elaborately decorated constructions outside of humans. The males use these courtship bowers, along with their displays, to attract females. In these species, the mating system is polygynous and the females alone incubate and feed the nestlings. The bowerbirds also include 10 species of the socially monogamous catbirds in which the male participates in most aspects of raising the young. How the bower-building behavior evolved has remained poorly understood, as no comprehensive phylogeny exists for the family. It has been assumed that the monogamous catbird clade is sister to all polygynous species. We here test this hypothesis using a newly developed pipeline for obtaining homologous alignments of thousands of exonic and intronic regions from genomic data to build a phylogeny. Our well-supported species tree shows that the polygynous, bower-building species are not monophyletic. The result suggests either that bower-building behavior is an ancestral condition in the family that was secondarily lost in the catbirds, or that it has arisen in parallel in two lineages of bowerbirds. We favor the latter hypothesis based on an ancestral character reconstruction showing that polygyny but not bower-building is ancestral in bowerbirds, and on the observation that Scenopoeetes dentirostris, the sister species to one of the bower-building clades, does not build a proper bower but constructs a court for male display. This species is also sexually monomorphic in plumage despite having a polygynous mating system. We argue that the relatively stable tropical and subtropical forest environment in combination with low predator pressure and rich food access (mostly fruit) facilitated the evolution of these unique life-history traits. [Adaptive radiation; bowerbirds; mating system, sexual selection; whole genome sequencing.].

Physiological changes in post-hatchling green turtles (Chelonia mydas) following short-term fasting: implications for release protocols.

Relocation of sea turtle nests and the retention of post-hatchlings for head-starting programs are both commonly used to improve conservation outcomes and facilitate eco-tourism ventures. Currently, there is little literature surrounding the husbandry protocols required during these programs to optimize post-release outcomes. To assess the impact of varied feeding regimes on exercise performance, (which will hereafter be referred to as 'fitness'), 40 10-month-old captive post-hatchling green turtles (Chelonia mydas) were divided into four groups of 10 and fasted for either 3, 9, 10 or 15 h. The animals were then subjected to a fitness test via repetitive use of the 'righting reflex' on land. Health assessments were conducted prior to the fitness test, including; heart rate, haematocrit (Hct), heterophil to lymphocyte ratio and the measurement of 11 biochemical analytes, including pH, partial pressures of carbon dioxide (PvCO2) and oxygen (PvO2), lactate, bicarbonate (HCO3 -), sodium (Na+), potassium (K+), chloride (Cl-), ionized calcium (iCa2+), glucose and urea. Results were corrected for multiple comparisons and significant differences among groups were demonstrated for temperature, pH, HCO3 -, iCa2+, urea and lactate. To investigate physiological relationships between analytes, correlation coefficients were calculated between fitness and glucose, fitness and lactate, glucose and lactate, pH and iCa2+, pH and K+, pH and PvCO2, pH and HCO3 - and Hct and K+. Following correction for multiple comparisons, significant relationships were seen between pH and iCa2+ and pH and HCO3 -. Post-hatchling turtles appear to enter a catabolic state when exposed to short-term fasting. While this did not have a direct impact on fitness, the production of an intense energetic output from a catabolic state may induce a physiological debt. This study suggests that handling that induces a physical response should be minimized and animals should be fed within 10 h of release.

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.

Songbirds have a species number close to that of mammals and are classic models for studying speciation and sexual selection. Sex chromosomes are hotspots of both processes, yet their evolutionary history in songbirds remains unclear. We characterized genomes of 11 songbird species, with 5 genomes of bird-of-paradise species. We conclude that songbird sex chromosomes have undergone four periods of recombination suppression before species radiation, producing a gradient of pairwise sequence divergence termed 'evolutionary strata'. The latest stratum was probably due to a songbird-specific burst of retrotransposon CR1-E1 elements at its boundary, instead of the chromosome inversion generally assumed for suppressing sex-linked recombination. The formation of evolutionary strata has reshaped the genomic architecture of both sex chromosomes. We find stepwise variations of Z-linked inversions, repeat and guanine-cytosine (GC) contents, as well as W-linked gene loss rate associated with the age of strata. A few W-linked genes have been preserved for their essential functions, indicated by higher and broader expression of lizard orthologues compared with those of other sex-linked genes. We also find a different degree of accelerated evolution of Z-linked genes versus autosomal genes among species, potentially reflecting diversified intensity of sexual selection. Our results uncover the dynamic evolutionary history of songbird sex chromosomes and provide insights into the mechanisms of recombination suppression.

DNA barcoding a unique avifauna: an important tool for evolution, systematics and conservation.

BACKGROUND: DNA barcoding utilises a standardised region of the cytochrome c oxidase I (COI) gene to identify specimens to the species level. It has proven to be an effective tool for identification of avian samples. The unique island avifauna of New Zealand is taxonomically and evolutionarily distinct. We analysed COI sequence data in order to determine if DNA barcoding could accurately identify New Zealand birds. RESULTS: We sequenced 928 specimens from 180 species. Additional Genbank sequences expanded the dataset to 1416 sequences from 211 of the estimated 236 New Zealand species. Furthermore, to improve the assessment of genetic variation in non-endemic species, and to assess the overall accuracy of our approach, sequences from 404 specimens collected outside of New Zealand were also included in our analyses. Of the 191 species represented by multiple sequences, 88.5% could be successfully identified by their DNA barcodes. This is likely a conservative estimate of the power of DNA barcoding in New Zealand, given our extensive geographic sampling. The majority of the 13 groups that could not be distinguished contain recently diverged taxa, indicating incomplete lineage sorting and in some cases hybridisation. In contrast, 16 species showed evidence of distinct intra-species lineages, some of these corresponding to recognised subspecies. For species identification purposes a character-based method was more successful than distance and phylogenetic tree-based methods. CONCLUSIONS: DNA barcodes accurately identify most New Zealand bird species. However, low levels of COI sequence divergence in some recently diverged taxa limit the identification power of DNA barcoding. A small number of currently recognised species would benefit from further systematic investigations. The reference database and analysis presented will provide valuable insights into the evolution, systematics and conservation of New Zealand birds.

Better governance will lead to better taxonomy: response to Raposo et al. (2017).

We welcome the recent paper by Raposo et al. (2017) debating our Nature Comment on inadequacies in taxonomic governance and the impact this has on conservation and society (Garnett Christidis 2017), as well as the opportunity to clarify our views. We admit to surprise at meanings read into our paper by Raposo et al. (2017) that we never intended and that we had not thought were there. As we have also made clear in a separate discussion of our paper (Garnett Christidis 2018 in response to Thomson et al. 2018), we wish to make clear at the start: (i) that we have no wish to stifle taxonomic research, only to strengthen the legitimacy of its findings; and (ii) we believe that taxonomic research should not consider the consequences for conservation, or society, in its conclusions once transparent taxonomic criteria have been established (Garnett Christidis 2007), but that taxonomists have an obligation to improve their governance to ensure taxonomic conclusions are of the highest standard.

Environmental determinism, and not interspecific competition, drives morphological variability in Australasian warblers (Acanthizidae).

Interspecific competition is thought to play a key role in determining the coexistence of closely related species within adaptive radiations. Competition for ecological resources can lead to different outcomes from character displacement to, ultimately, competitive exclusion. Accordingly, divergent natural selection should disfavor those species that are the most similar to their competitor in resource use, thereby increasing morphological disparity. Here, we examined ecomorphological variability within an Australo-Papuan bird radiation, the Acanthizidae, which include both allopatric and sympatric complexes. In addition, we investigated whether morphological similarities between species are related to environmental factors at fine scale (foraging niche) and/or large scale (climate). Contrary to that predicted by the competition hypothesis, we did not find a significant correlation between the morphological similarities found between species and their degree of range overlap. Comparative modeling based on both a priori and data-driven identification of selective regimes suggested that foraging niche is a poor predictor of morphological variability in acanthizids. By contrast, our results indicate that climatic conditions were an important factor in the formation of morphological variation. We found a significant negative correlation between species scores for PC1 (positively associated to tarsus length and tail length) and both temperature and precipitation, whereas PC2 (positively associated to bill length and wing length) correlated positively with precipitation. In addition, we found that species inhabiting the same region are closer to each other in morphospace than to species outside that region regardless of genus to which they belong or its foraging strategy. Our results indicate that the conservative body form of acanthizids is one that can work under a wide variety of environments (an all-purpose morphology), and the observed interspecific similarity is probably driven by the common response to environment.

Hematologic and biochemical characteristics of stranded green sea turtles.

To improve understanding of pathophysiologic processes occurring in green sea turtles ( Chelonia mydas) stranded along the east coast of Australia, we retrospectively examined the hematologic and biochemical blood parameters of 127 green turtles admitted to 2 rehabilitation facilities, Dolphin Marine Magic (DMM) and Taronga Zoo (TZ), between 2002 and 2016. The predominant size class presented was small immature animals (SIM), comprising 88% and 69% of admissions to DMM and TZ, respectively. Significant differences in blood profiles were noted between facility, size, and outcome. Elevated levels of aspartate aminotransferase (AST) and heterophils were poor prognostic indicators in animals from TZ, but not DMM. SIM animals at both institutions had lower protein levels than large older (LO) animals. SIM animals at DMM also had lower hematocrit and monocyte concentration; SIM animals at TZ had lower heterophil counts. Urea was measured for 27 SIM animals from TZ, but the urea-to-uric acid ratio was not prognostically useful. Strong correlations were seen between AST and glutamate dehydrogenase (GDH; r = 0.68) and uric acid and bile acids ( r = 0.72) in the 45 SIM animals from DMM in which additional analytes were measured. χ2 contingency tests showed that the most recently published reference intervals were not prognostically useful. A paired t-test showed that protein levels rose and heterophil numbers fell in the 15 SIM animals from TZ during the rehabilitation process. Our results indicate that further work is required to identify reliable prognostic biomarkers for green turtles.

A new subspecies of Short-toed Snake-eagle from Wallacea determined from morphological and DNA comparison.

The taxonomic status of the geographically isolated population of Short-toed Snake-eagle Circaetus gallicus on the Lesser Sundas (=Nusa Tenggara) has been controversial. In the past they have been regarded as either a migrant population or a recently arrived resident population. Here we obtained DNA sequences from the mitochondrial cytochrome-b gene and combined genetic data with assessments of published and novel morphological data to clarify the taxonomic status of the Lesser Sundas population of C. gallicus. The cytochrome-b distance between the Lesser Sundas and Palearctic populations of C. gallicus is consistent with subspecific differentiation, indicating a possible divergence during one of the most recent Pleistocene glaciations. Although some of the morphological distinctions show overlap, the new subspecies can generally be diagnosed from nominate C. gallicus gallicus by being smaller and paler, and exhibiting less spotting and barring. Unlike nominate populations from mainland Eurasia, the new subspecies seems to lack pronounced sexual dimorphism. We here describe this new subspecies to science and discuss its biology and conservation status.

Speciation in Indo-Pacific swiftlets (Aves: Apodidae): integrating molecular and phenotypic data for a new provisional taxonomy of the Collocalia esculenta complex.

White-bellied swiftlets of the Collocalia esculenta complex constitute a radiation of colony-breeding swifts distributed throughout the tropical Indo-Pacific region. Resolution of their taxonomy is challenging due to their morphological uniformity. To analyze the evolutionary history of this complex, we combine new biometric measurements and results from plumage assessment of museum specimens with novel as well as previously published molecular data. Together, this body of information constitutes the largest systematic dataset for white-bellied swiftlets yet compiled, drawn from 809 individuals belonging to 32 taxa for which new molecular, biometric, and/or plumage data are presented. We propose changing the classification of white-bellied swiftlets, for which two species are currently recognized, to elevate eight regional forms to species level, and we also describe two new subspecies. The ten taxa we recommend recognizing at the species level are: Collocalia linchi (Java to Lombok, Sumatran hills), C. dodgei (montane Borneo), C. natalis (Christmas Island), C. affinis (Greater Sundas, including the Thai-Malay Peninsula and Andaman-Nicobar Islands), C. marginata (Philippines), C. isonota (Philippines), C. sumbawae (west Lesser Sundas), C. neglecta (east Lesser Sundas), C. esculenta (Sulawesi, Moluccas, New Guinea, Bismarck Archipelago, Solomon Islands), and C. uropygialis (Vanuatu, New Caledonia). Future molecular and morphological work is needed to resolve questions of speciation and population affinities in the Philippines, Christmas Island, Wallacea and central Melanesia, and to shed light on historic diversification and patterns of gene flow in the complex.

Phylogeny and new taxonomy of the Booted Eagles (Accipitriformes: Aquilinae).

We present a phylogeny of all booted eagles (38 extant and one extinct species) based on analysis of published sequences from seven loci. We find molecular support for five major clades within the booted eagles: Nisaetus (10 species), Spizaetus (4 species), Clanga (3 species), Hieraaetus (6 species) and Aquila (11 species), requiring generic changes for 14 taxa. Additionally, we recommend that the Long-crested Eagle (Lophaetus occipitalis) and the Black Eagle (Ictinaetus malaiensis) remain in their monotypic genera, due to their distinctive morphology. We apply the recently resurrected genus Clanga for the spotted eagles (previously Aquila spp.) to resolve the paraphyly of the genus Aquila such that the clade including the Booted Eagle (H. pennatus), Little Eagle (H. morphnoides), Pygmy Eagle (H. weiskei), Ayres's Eagle (H. ayresii) and Wahlberg's Eagle (H. wahlbergi) can remain in the genus Hieraaetus. The Rufous-bellied Eagle should be retained in the genus Lophotriorchis. For consistency in English names, we recommend that the term "hawk-eagles" be used only for the species in the genera Nisaetus and Spizaetus. We suggest following new or modified English names: Cassin's Eagle (Aquila africana), Bonaparte's Eagle (A. spilogaster), Ayres's Eagle (Hieraaetus ayresii), and Black-and-chestnut Hawk-Eagle (Spizaetus isidori).

Bioacoustic and multi-locus DNA data of Ninox owls support high incidence of extinction and recolonisation on small, low-lying islands across Wallacea.

Known for their rich biodiversity and high level of endemism, the islands of Wallacea serve as natural laboratories for the study of spatio-temporal evolution and patterns of species diversification. Our study focuses on the owl genus Ninox, particularly the Southern Boobook (N. novaeseelandiae) and Moluccan Boobook (N. squamipila) complexes, which are widely distributed across Australasia. We conducted bioacoustic and multi-locus DNA analyses of 24 Ninox owl taxa to evaluate relationships and levels of divergence within the two complexes and ultimately assess the relationship between patterns of taxonomic differentiation and bioclimatic factors. We found that taxa that are vocally and/or genetically distinct from populations on the Australian mainland are found on islands that are significantly larger and higher in altitude than taxa that are vocally and/or genetically indistinct from populations on the Australian mainland. This pattern suggests that taxa occurring on small, low-lying Wallacean islands are likely to be recent colonisers that have dispersed from Australia. Overall, our observations demonstrate that the genus Ninox is likely to have colonised the Wallacean region multiple times as small, low-lying islands undergo frequent extinction, whereas populations on large and high-altitude islands are more resilient.

Ecological opportunity and the evolution of habitat preferences in an arid-zone bird: implications for speciation in a climate-modified landscape.

Bioclimatic models are widely used to investigate the impacts of climate change on species distributions. Range shifts are expected to occur as species track their current climate niche yet the potential for exploitation of new ecological opportunities that may arise as ecosystems and communities remodel is rarely considered. Here we show that grasswrens of the Amytornis textilis-modestus complex responded to new ecological opportunities in Australia's arid biome through shifts in habitat preference following the development of chenopod shrublands during the late Plio-Pleistocene. We find evidence of spatially explicit responses to climatically driven landscape changes including changes in niche width and patterns of population growth. Conservation of structural and functional aspects of the ancestral niche appear to have facilitated recent habitat shifts, while demographic responses to late Pleistocene climate change provide evidence for the greater resilience of populations inhabiting the recently evolved chenopod shrubland communities. Similar responses could occur under future climate change in species exposed to novel ecological conditions, or those already occupying spatially heterogeneous landscapes. Mechanistic models that consider structural and functional aspects of the niche along with regional hydro-dynamics may be better predictors of future climate responses in Australia's arid biome than bioclimatic models alone.