Kyle N. Armstrong

Molecular Phylogeny, Biogeography, and Habitat Preference Evolution of Marsupials

Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation.

Evolution of craniofacial novelty in parrots through developmental modularity and heterochrony

SUMMARY Parrots (order Psittaciformes) have developed novel cranial morphology. At the same time, they show considerable morphological diversity in the cranial musculoskeletal system, which includes two novel structures: the suborbital arch and the musculus (M.) pseudomasseter. To understand comprehensively the evolutionary pattern and process of novel cranial morphology in parrots, phylogenetic and developmental studies were conducted. Firstly, we undertook phylogenetic analyses based on mitochondrial ribosomal RNA gene sequences to obtain a robust phylogeny among parrots, and secondly we surveyed the cranial morphology of parrots extensively to add new information on the character states. Character mapping onto molecular phylogenies indicated strongly the repeated evolution of both the suborbital arch and the well‐developed M. pseudomasseter within parrots. These results also suggested that the direction of evolutionary change is not always identical in the two characters, implying that these characters are relatively independent or decoupled structures behaving as separate modules. Finally, we compared the developmental pattern of jaw muscles among bird species and found a difference in the timing of M. pseudomasseter differentiation between the cockatiel Nymphicus hollandicus (representative of a well‐developed condition) and the peach‐faced lovebird Agapornis roseicollis (representative of an underdeveloped condition). On the basis of this study, we suggest that in the development of novel traits, modularity and heterochrony facilitate the diversification of parrot cranial morphology.

DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.

Genetic and acoustic population structuring in the Okinawa least horseshoe bat: are intercolony acoustic differences maintained by vertical maternal transmission?

The origin and meaning of echolocation call frequency variation within rhinolophid bats is not well understood despite an increasing number of allopatric and sympatric examples being documented. A bimodal distribution of mean regional call frequency within the Okinawa‐jima Island population of Rhinolophus cornutus pumilus (Rhinolophidae) provided a unique opportunity to investigate geographic call frequency variation early in its development. Individual resting echolocation frequencies, partial mitochondrial DNA D‐loop sequences and genotypes from six microsatellite loci were obtained from 288 individuals in 11 colonies across the entire length of the island, and nearby Kume‐jima Island. Acoustic differences (5–8 kHz) observed between the north and south regions have been maintained despite evidence of sufficient nuclear gene flow across the middle of the island. Significant subdivision of maternally inherited D‐loop haplotypes suggested a limitation of movement of females between regions, but not within the regions, and was evidence of female philopatry. These results support a ‘maternal transmission’ hypothesis whereby the difference in the constant frequency (CF) component between the regions is maintained by mother–offspring transmission of CF, the restricted dispersal of females between regions and small effective population size. We suggest that the mean 5–8 kHz call frequency difference between the regions might develop through random cultural drift.

How and Why Overcome the Impediments to Resolution: Lessons from rhinolophid and hipposiderid Bats

Abstract The phylogenetic and taxonomic relationships among the Old World leaf-nosed bats (Hipposideridae) and the closely related horseshoe bats (Rhinolophidae) remain unresolved. In this study, we generated a novel approximately 10-kb molecular data set of 19 nuclear exon and intron gene fragments for 40 bat species to elucidate the phylogenetic relationships within the families Rhinolophidae and Hipposideridae. We estimated divergence times and explored potential reasons for any incongruent phylogenetic signal. We demonstrated the effects of outlier taxa and genes on phylogenetic reconstructions and compared the relative performance of intron and exon data to resolve phylogenetic relationships. Phylogenetic analyses produced a well-resolved phylogeny, supporting the familial status of Hipposideridae and demonstrated the paraphyly of the largest genus, Hipposideros. A fossil-calibrated timetree and biogeographical analyses estimated that Rhinolophidae and Hipposideridae diverged in Africa during the Eocene approximately 42 Ma. The phylogram, the timetree, and a unique retrotransposon insertion supported the elevation of the subtribe Rhinonycterina to family level and which is diagnosed herein. Comparative analysis of diversification rates showed that the speciose genera Rhinolophus and Hipposideros underwent diversification during the Mid-Miocene Climatic Optimum. The intron versus exon analyses demonstrated the improved nodal support provided by introns for our optimal tree, an important finding for large-scale phylogenomic studies, which typically rely on exon data alone. With the recent outbreak of Middle East respiratory syndrome, caused by a novel coronavirus, the study of these species is urgent as they are considered the natural reservoir for emergent severe acute respiratory syndrome (SARS)-like coronaviruses. It has been shown that host phylogeny is the primary factor that determines a virus’s persistence, replicative ability, and can act as a predictor of new emerging disease. Therefore, this newly resolved phylogeny can be used to direct future assessments of viral diversity and to elucidate the origin and development of SARS-like coronaviruses in mammals.

Late Pleistocene Australian Marsupial DNA Clarifies the Affinities of Extinct Megafaunal Kangaroos and Wallabies

Understanding the evolution of Australias extinct marsupial megafauna has been hindered by a relatively incomplete fossil record and convergent or highly specialized morphology, which confound phylogenetic analyses. Further, the harsh Australian climate and early date of most megafaunal extinctions (39-52 ka) means that the vast majority of fossil remains are unsuitable for ancient DNA analyses. Here, we apply cross-species DNA capture to fossils from relatively high latitude, high altitude caves in Tasmania. Using low-stringency hybridization and high-throughput sequencing, we were able to retrieve mitochondrial sequences from two extinct megafaunal macropodid species. The two specimens, Simosthenurus occidentalis (giant short-faced kangaroo) and Protemnodon anak (giant wallaby), have been radiocarbon dated to 46-50 and 40-45 ka, respectively. This is significantly older than any Australian fossil that has previously yielded DNA sequence information. Processing the raw sequence data from these samples posed a bioinformatic challenge due to the poor preservation of DNA. We explored several approaches in order to maximize the signal-to-noise ratio in retained sequencing reads. Our findings demonstrate the critical importance of adopting stringent processing criteria when distant outgroups are used as references for mapping highly fragmented DNA. Based on the most stringent nucleotide data sets (879 bp for S. occidentalis and 2,383 bp for P. anak), total-evidence phylogenetic analyses confirm that macropodids consist of three primary lineages: Sthenurines such as Simosthenurus (extinct short-faced kangaroos), the macropodines (all other wallabies and kangaroos), and the enigmatic living banded hare-wallaby Lagostrophus fasciatus (Lagostrophinae). Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.

Modelling the prey detection performance of Rhinonicteris aurantia (Chiroptera: Hipposideridae) in different atmospheric conditions discounts the notional role of relative humidity in adaptive evolution.

We examined a recent notion that differences in echolocation call frequency amongst geographic groups of constant frequency (CF)-emitting bats is the result of a trade-off between maximising prey detection range at lower frequencies and enhancing small-prey resolution at higher frequencies in different atmospheric (relative humidity; RH) environments. Isolated populations of the endemic Australian orange leaf-nosed bat Rhinonicteris aurantia were used as an example since geographic isolation in different environments has been a precursor to differences in their characteristic echolocation call frequencies (mean difference c. 6 kHz; means of 114.64 and 120.99 kHz). The influence of both atmospheric temperature and RH on maximum prey detection range was explored through mathematical modelling. This revealed that temperature was of similar importance to relative humidity and that under certain circumstances, each could reduce the effect of the other on ultrasound attenuation rates. The newly developed models contain significant conceptual improvements in method compared to other recent approaches, and can be applied to the situation of any other species of bat. For a given set of atmospheric conditions, the prey detection range of R. aurantia was reduced slightly when call frequency increased by 6 kHz, but an increase in RH, temperature or both reduced detection range significantly. A similar trend was also evident in prey detection volume ratios calculated for the same conditions. Spatial volume ratios were applied to assess the impact of changed atmospheric conditions and prey size on foraging ecology. Reductions in detection range associated with increases in RH and/or temperature also varied in relation to the size (cross sectional area) of insect prey. Modelling demonstrated that small (6 kHz) movements in call frequency could not compensate for the changes in prey detection range and spatial detection volumes that result from significant changes in atmospheric temperature or RH. The notion that differences in RH are the primary cause leading to adaptive evolution and speciation in CF-emitting bats by precipitating intraspecific differences in the mean call frequency of geographically isolated bat populations was not supported by the results of this case study.

A plethora of planigales: genetic variability and cryptic species in a genus of dasyurid marsupials from northern Australia

Abstract. Multiple mitochondrial and nuclear gene sequences reveal substantial genetic variation within the dasyurid marsupial genus Planigale, suggesting greater taxonomic diversity than is currently recognised. To further investigate planigale relationships 116 new mitochondrial and nuclear gene sequences, including 16 new specimens, were added to our database. We confirm the presence of an unrecognised species (Planigale ‘species 1’) limited to the Pilbara region of Western Australia and suggest that the ‘Mt Tom Price’ animals may be closely related to Planigale ingrami subtilissima. We also confirm that at least four distinct genetic lineages make up what is currently recognised as P. maculata. This complex of closely related taxa represents a radiation of sibling species rather than a single, genetically diverse one. Three of these lineages (M1 + M2, M3 and M4) are distributed sympatrically across the Top End of Australia and one (M5 = P. maculata sensu stricto) is localised to the eastern coast of Australia. Within the Planigale ingrami complex, Planigale ‘Mt Tom Price’ (lineage Ing. 1) occurs in the Pilbara in sympatry with Planigale ‘species 1’ and lineage Ing. 2 is found in the Northern Territory in sympatry with species of the P. maculata complex. There is thus a plethora of northern Australian planigales, many of which are formally undescribed and whose geographic ranges require careful re-evaluation.

Networking Networks for Global Bat Conservation

Conservation networks link diverse actors, either individuals or groups, across space and time. Such networks build social capital, enhance coordination, and lead to effective conservation action. Bat conservation can benefit from network approaches because the taxonomic and ecological diversity of bats, coupled with the complexity of the threats they face, necessitates a wide range of expert knowledge to effect conservation. Moreover, many species and issues transcend political boundaries, so conservation frequently requires or benefits from international cooperation. In response, several regional bat conservation networks have arisen in recent years, and we suggest that, with the globalization of threats to bats, there is now a need for a global network to strengthen bat conservation and provide a unified voice for advocacy. To retain regional autonomy and identity, we advocate a global network of the regional networks and develop a roadmap toward such a meta-network using a social network framework. We first review the structure and function of existing networks and then suggest ways in which existing networks might be strengthened. We then discuss how regional gaps in global coverage might best be filled, before suggesting ways in which regional networks might be linked for global coverage.

Research priorities for the Pilbara leaf-nosed bat (Rhinonicteris aurantia Pilbara form)

Significant biodiversity offset funds have been allocated towards conservation research on threatened species as part of the environmental approvals process for resource development in the Pilbara region of Western Australia. One of these species is the Pilbara leaf-nosed bat (Rhinonicteris aurantia Pilbara form), which is entirely reliant on roosting in a limited number of caves and disused mines, many of which exist in the mineral-bearing strata that are the focus of mining activity. A research agenda for the Pilbara leaf-nosed bat was developed during a workshop attended by scientists, environmental consultants and mining industry representatives. Five research priorities were identified: (1) collate existing data contained within unpublished environmental surveys; (2) clarify and better characterise the number and distribution of day roosts; (3) better understand habitat requirements, particularly foraging habitat, and the movement of bats between roosts; (4) provide more robust estimates of total population and colony size, and improve understanding of social behaviour; and (5) investigate appropriate buffers in a range of mining contexts and protocols for artificial roost construction. Meta-analysis of current data, confirmation of potential day roosts, and long-term monitoring of activity patterns would rapidly increase our knowledge of the Pilbara leaf-nosed bat to enable effective conservation actions.