Phylogeography and population genetics of the endemic Malagasy bat, Macronycteris commersoni s.s. (Chiroptera: Hipposideridae)

Full-Length Transcriptome of the Great Himalayan Leaf-Nosed Bats (Hipposideros armiger) Optimized Genome Annotation and Revealed the Expression of Novel Genes

The Great Himalayan Leaf-nosed bat (Hipposideros armiger) is one of the most representative species of all echolocating bats and is an ideal model for studying the echolocation system of bats. An incomplete reference genome and limited availability of full-length cDNAs have hindered the identification of alternatively spliced transcripts, which slowed down related basic studies on bats' echolocation and evolution. In this study, we analyzed five organs from H. armiger for the first time using PacBio single-molecule real-time sequencing (SMRT). There were 120 GB of subreads generated, including 1,472,058 full-length non-chimeric (FLNC) sequences. A total of 34,611 alternative splicing (AS) events and 66,010 Alternative Polyadenylation (APA) sites were detected by transcriptome structural analysis. Moreover, a total of 110,611 isoforms were identified, consisting of 52% new isoforms of known genes and 5% of novel gene loci, as well as 2112 novel genes that have not been annotated before in the current reference genome of H. armiger. Furthermore, several key novel genes, including Pol, RAS, NFKB1, and CAMK4, were identified as being associated with nervous, signal transduction, and immune system processes, which may be involved in regulating the auditory nervous perception and immune system that helps bats to regulate in echolocation. In conclusion, the full-length transcriptome results optimized and replenished existing H. armiger genome annotation in multiple ways and offer advantages for newly discovered or previously unrecognized protein-coding genes and isoforms, which can be used as a reference resource.

Phylogeny of the Madagascar-centred tribe Danaideae (Rubiaceae) as a precursor to taxonomic revision: insights into its generic and species limits, affinities and distribution

BACKGROUND AND AIMS

The tribe Danaideae (Rubiaceae) is almost exclusively endemic to the Western Indian Ocean Region (WIOR), and encompasses the genera Danais, Payera and Schismatoclada that occur in humid, sub-humid and mountain and mountain bio climate zones. Much of the species diversity is endemic to restricted, remote and/or mountainous areas of Madagascar and recent field work on the island indicates substantial unknown diversity of the Danaideae. Furthermore, the monophyly of the Malagasy genera Payera and Schismatoclada has been questioned in previous work, species delimitations and phylogenetic relationships within the genera are poorly understood, and the distribution and evolution of gross morphological features have not been assessed.

METHODS

We conducted morphological investigations, and produced robust phylogenies of Danaideae based on nuclear and plastid sequence data from 193 terminals. Ample plant material has been newly collected in the WIOR for the purpose of the present study, including potentially new species unknown to science. We performed Bayesian non-clock and relaxed-clock analyses employing three alternative clock models of a dataset with a dense sample of taxa from the entire geographical ranges of Danaideae. Based on the results, we discuss species diversity and distribution, relationships, and morphology in Danaideae.

KEY RESULTS

Our results demonstrate the monophyly of Danaideae, its three genera and 42 species. Nine species are resolved as non-monophyletic. Many geographically distinct but morphologically heterogeneous lineages were identified, and morphological features traditionally considered diagnostic of subgroups of the genera, used for example in species identification keys, are not clade-specific.

CONCLUSIONS

Our results demonstrate that Madagascar contains ample previously undocumented morphological and species diversity of Danaideae. Our novel approach to molecular phylogenetic analyses as a precursor to taxonomic revisions provides numerous benefits for the latter. There are tentative indications of parallel northward diversification in Payera and Schismatoclada on Madagascar, and of geographical phylogenetic clustering despite the anemochorous condition of Danaideae.

Population diversification in the frog Mantidactylus bellyi on an isolated massif in northern Madagascar based on genetic, morphological, bioacoustic and ecological evidence

In the processes that give rise to new species, changes first occur at the population level. But with the continuous nature of the divergence process, change in biological properties delimiting the shift from “individuals of divergent populations” towards “individuals of distinct species”, as well as abiotic factors driving the change, remain largely ambivalent. Here we study diversification processes at the population level in a semi-aquatic frog, Mantidactylus (Brygoomantis) bellyi, across the diverse vegetation types of Montagne d’Ambre National Park (MANP), Madagascar. Genetic diversity was assessed with seven newly developed microsatellite markers as well as mitochondrial DNA sequences and concordance with patterns of ecological, morphological, and bioacoustic divergence evaluated. We found M. bellyi lacking mitochondrial differentiation within MANP, while microsatellite datasets partitioned them into three highly differentiated, geographically separated subpopulations (with indications for up to five subpopulations). The molecular grouping–primarily clustering individuals by geographic proximity–was coincident with differences in mean depth and width of waters, suggesting a possible role of fluvial characteristics in genetic exchange in this stream-breeding species. Genetic clustering not consistent with differences in call properties, except for dominant call frequencies under the two-subpopulations model. Morphological divergence was mostly consistent with the genetic clustering; subpopulations strongly differed by their snout-vent length, with individuals from high-elevation subpopulations smaller than those from populations below 1000 m above sea level. These results exemplify how mountains and environmental conditions might primarily shape genetic and morphological divergence in frog populations, without strongly affecting their calls.

Evolutionary relationships and population genetics of the Afrotropical leaf-nosed bats (Chiroptera, Hipposideridae)

The Old World leaf-nosed bats (Hipposideridae) are aerial and gleaning insectivores that occur throughout the Paleotropics. Both their taxonomic and phylogenetic histories are confused. Until recently, the family included genera now allocated to the Rhinonycteridae and was recognized as a subfamily of Rhinolophidae. Evidence that Hipposideridae diverged from both Rhinolophidae and Rhinonycteridae in the Eocene confirmed their family rank, but their intrafamilial relationships remain poorly resolved. We examined genetic variation in the Afrotropical hipposiderids Doryrhina, Hipposideros, and Macronycteris using relatively dense taxon-sampling throughout East Africa and neighboring regions. Variation in both mitochondrial (cyt-b) and four nuclear intron sequences (ACOX2, COPS, ROGDI, STAT5) were analyzed using both maximum likelihood and Bayesian inference methods. We used intron sequences and the lineage delimitation method BPP—a multilocus, multi-species coalescent approach—on supported mitochondrial clades to identify those acting as independent evolutionary lineages. The program StarBEAST was used on the intron sequences to produce a species tree of the sampled Afrotropical hipposiderids. All genetic analyses strongly support generic monophyly, with Doryrhina and Macronycteris as Afrotropical sister genera distinct from a Paleotropical Hipposideros; mitochondrial analyses interpose the genera Aselliscus, Coelops, and Asellia between these clades. Mitochondrial analyses also suggest at least two separate colonizations of Africa by Asian groups of Hipposideros, but the actual number and direction of faunal interchanges will hinge on placement of the unsampled African-Arabian species H.megalotis. Mitochondrial sequences further identify a large number of geographically structured clades within species of all three genera. However, in sharp contrast to this pattern, the four nuclear introns fail to distinguish many of these groups and their geographic structuring disappears. Various distinctive mitochondrial clades are consolidated in the intron-based gene trees and delimitation analyses, calling into question their evolutionary independence or else indicating their very recent divergence. At the same time, there is now compelling genetic evidence in both mitochondrial and nuclear sequences for several additional unnamed species among the Afrotropical Hipposideros. Conflicting appraisals of differentiation among the Afrotropical hipposiderids based on mitochondrial and nuclear loci must be adjudicated by large-scale integrative analyses of echolocation calls, quantitative morphology, and geometric morphometrics. Integrative analyses will also help to resolve the challenging taxonomic issues posed by the diversification of the many lineages associated with H.caffer and H.ruber.