Phylogenetics of small horseshoe bats from East Asia based on mitochondrial DNA sequence variation (original) (raw)
Related papers
Journal of Mammalogy, 2009
A new species of horseshoe bat (Chiroptera: Rhinolophidae) is described from southwestern China. The presence of a wedge-shaped sella and pointed connecting process of the nose leaf aligns the new species to the landeri group in the Afro-Palearctic lineage of Rhinolophus. However, the new species is distinctly separable from these allopatrically distributed species by its noticeably larger body size. Other sympatric large-sized species of Rhinolophus have rounded connecting processes. Molecular systematic analyses based on mitochondrial cytochrome-b sequences confirmed the affinity of the new species to the Afro-Palearctic lineage, but in a clade most closely related to the ferrumequinum, fumigatus, and maclaudi groups. Of these species, only R. ferrumequinum ranges into Asia and overlaps in distribution with the new species. R. ferrumequinum is similar in general body size and external appearance; however, the new species is distinct in the characteristics of the nose leaf, skull, and baculum. The presence of a new species from southwestern China in the Afro-Palearctic lineage indicates a more complex historical biogeographic scenario within Rhinolophus than previously known. The difficulties found in allocating the new species to one of the phenetically described traditional species groups stress the convenience of using a phylogenetically based systematic organization of the genus Rhinolophus.
Mammalian Biology - Zeitschrift für Säugetierkunde, 2009
There have been few studies of the structural and evolutionary characteristics of the mitochondrial control region (CR) in rhinolophids, yet this could have important consequences for the interpretation of phylogenetic relationships within this group. Here we sequenced and analyzed the CR of 37 individuals from 12 Rhinolophus species, including 2 species from GenBank. The length of the CR ranged from 1335 to 1514 bp, and the base composition was very similar among species. The CR of horseshoe bats, like that of other mammals, could be subdivided into a central conserved domain (CD) and two flanking variable domains, extended termination associated sequences (ETAS), and conserved sequence blocks (CSB). Besides the common conserved blocks (ETAS1, ETAS2, F-B boxes, CSB1, CSB2 and CSB3) found in 3 domains, an ETAS2-like and a CSB1-like element were also detected in the ETAS and CSB domains, respectively, in all individuals. Notwithstanding a short tandem repeat (11 or 13 bp) between CSB1 and CSB2 in all specimens, the base composition, copy number and arrays are all variable. A long tandem repeat (79 bp) was only identified in the ETAS domain in one individual of R. pusillus. Phylogenetic reconstructions based on the CR sequences indicated that the molecular phylogenetic relationships among some Rhinolophus species were inconsistent with the results of phenetic analyses, but similar to phylogenetic constructions using cytochrome b. An unidentified species R. sp and 3 species from the philippinensis-group that were clearly morphologically different comprised a monophyletic group, which could have resulted from morphological independent evolution.
Molecular …, 2009
Phylogeographical studies are typically based on haplotype data, occasionally on nuclear markers such as microsatellites, but rarely combine both. This is unfortunate because the use of markers with contrasting modes of inheritance and rates of evolution might provide a more accurate and comprehensive understanding of a species' history. Here we present a detailed study of the phylogeography of the greater horseshoe bat, Rhinolophus ferrumequinum, using 1098 bp of the mitochondrial ND2 gene from 45 localities from across its Palaearctic range to infer population history. In addition, we re-analysed a large microsatellite data set available for this species and compared the results of both markers to infer population relationships and the historical processes influencing them. We show that mtDNA, the most popular marker in phylogeography studies, yielded a misleading result, and would have led us to conclude erroneously that a single expansion had taken place in Europe. Only by combining the mitochondrial and microsatellite data sets are we able to reconstruct the species' history and show two colonization events in Europe, one before the Last Glacial Maximum (LGM) and one after it. Combining markers also revealed the importance of Asia Minor as an ancient refugium for this species and a source population for the expansion of the greater horseshoe bat into Europe before the LGM.
Zoologica Scripta, 2013
. Systematics and biogeography of the arcuate horseshoe bat species complex (Chiroptera: Rhinolophidae). -Zoologica Scripta, 00, 000-000. The present study sheds light on species delimitation in what has been previously described as Rhinolophus arcuatus, a morphologically conservative bat species complex nominally distributed throughout archipelagic South-East Asia from New Guinea to Sumatra. Given that rhinolophids tend to be relatively weak fliers, hence have low vagility, we hypothesized that some specimens attributed to R. arcuatus, but originating from geographically disjunct populations, may in fact represent distinct species. To test this hypothesis, we examined specimens attributed to R. arcuatus as well as to other species in the Rhinolophus euryotis species group using both morphological techniques and mitochondrial cytochrome b and control region sequences. Careful morphological analysis reveals heretofore cryptic but nevertheless distinct, species-level morphological differences among specimens derived from geographically isolated locations. Furthermore, molecular data illuminate the existence of several species-level sequence divergences among specimens heretofore attributed to R. arcuatus. These analyses similarly suggest the existence of additional species in other South-East Asian Rhinolophus taxa previously considered monotypic. We suggest at least one description to be undertaken of a previously unrecognized species as well as the elevation of several others from sub-specific to specific status.
The utility and reliability of mitochondrial DNA sequences in phylogenetic and phylogeographic studies may be compromised by widespread and undetected nuclear mitochondrial copies (numts) as well as heteroplasmy within individuals. Both numts and heteroplasmy are likely to be common across diverse taxa yet few studies have characterised their frequencies and variation at the intra-specific level. Here we report the presence of both numts and heteroplasmy in the mitochondrial control region of the Chinese horseshoe bat Rhinolophus sinicus. In total we generated 123 sequences from 18 bats, which contained two different numt clades (i.e. Numt-1 and Numt-2) and one mtDNA clade. The sequence divergence between Numt-1 and Numt-2 was 16.8% and each numt type was found in all four R. sinicus taxa, suggesting either two ancient translocations of mitochondrial DNA into the nucleus from the same source taxon, or a single translocation from different source taxa that occurred before the split of R. sinicus into different lineages. Within the mtDNA clade, phylogenetic relationships among the four taxa of R. sinicus were similar to those seen in previous results. Based on PCR comparisons, heteroplasmy was inferred between almost all individuals of R. sinicus with respect to sequence variation. Consistent with introgression of mtDNA between Central sinicus and septentrionalis, individuals from these two taxa exhibited similar signatures of repeated sequences in the control region. Our study highlights the importance of testing for the presence of numts and heteroplasmy when applying mtDNA markers to phylogenetic studies. Citation: Mao X, Dong J, Hua P, He G, Zhang S, et al. (2014) Heteroplasmy and Ancient Translocation of Mitochondrial DNA to the Nucleus in the Chinese Horseshoe Bat (Rhinolophus sinicus) Complex. PLoS ONE 9(5): e98035.
Phylogenetic discordance among taxa can provide powerful insights into past episodes of introgressive hybridization, as well as lineage sorting. Previously, we showed that the taxonomically distinct taxon Rhinolophus sinicus septentrionalis has undergone historical introgression with its sympatric sister subspecies Rhinolophus sinicus sinicus. To examine in more detail the extent of gene flow between these two taxa, and also between these and their sister species Rhinolophus thomasi, we obtained new samples from China, Myanmar, and Vietnam, and combined new and published genetic data from these, Rhinolophus rouxii, and Rhinolophus indorouxii from India. Phylogenetic analyses revealed three separate cases of discordance: between R. s. septentrionalis and adjacent populations of R. s. sinicus, between R. s. septentrionalis and R. thomasi and between eastern populations of R. s. sinicus and a newly-identified lineage. In both former cases, the mitochondrial DNA introgression appears to be asymmetric, which is likely to have resulted from mating between R. s. septentrionalis females with smaller R. s. sinicus and R. thomasi males, although we cannot rule out other scenarios completely. Further conflicts between genetic data and accepted species arrangements across the genus, with paraphyly of members of the rouxii-group, suggest the need for a thorough systematic revision of relationships within this group.
Journal of Biogeography, 2011
Aim The extent to which the ranges of temperate biota in East Asia have been shaped by geological and climatic changes during the Pleistocene remains poorly understood. Previous molecular-based studies of the greater horseshoe bat (Rhinolophus ferrumequinum), which is widespread across China and Japan, suggest that this species was able to persist in multiple refugia in this region. However, limited availability of samples precluded a detailed analysis of past distributions. By integrating ecological niche modelling with phylogenetic analyses, we aim to resolve the impact of past events on the population genetic structure of R. ferrumequinum and provide detailed descriptions of potential distribution patterns during this time.
Lineage Divergence and Historical Gene Flow in the Chinese Horseshoe Bat (Rhinolophus sinicus)
PloS one, 2013
Closely related taxa living in sympatry provide good opportunities to investigate the origin of barriers to gene flow as well as the extent of reproductive isolation. The only two recognized subspecies of the Chinese rufous horseshoe bat Rhinolophus sinicus are characterized by unusual relative distributions in which R. s. septentrionalis is restricted to a small area within the much wider range of its sister taxon R. s. sinicus. To determine the history of lineage divergence and gene flow between these taxa, we applied phylogenetic, demographic and coalescent analyses to multi-locus datasets. MtDNA gene genealogies and microsatellite-based clustering together revealed three divergent lineages of sinicus, corresponding to Central China, East China and the offshore Hainan Island. However, the central lineage of sinicus showed a closer relationship with septentrionalis than with other lineages of R. s. sinicus, in contrary to morphological data. Paraphyly of sinicus could result from either past asymmetric mtDNA introgression between these two taxa, or could suggest septentrionalis evolved in situ from its more widespread sister subspecies. To test between these hypotheses, we applied coalescent-based phylogenetic reconstruction and Approximate Bayesian Computation (ABC). We found that septentrionalis is likely to be the ancestral taxon and therefore a recent origin of this subspecies can be ruled out. On the other hand, we found a clear signature of asymmetric mtDNA gene flow from septentrionalis into central populations of sinicus yet no nuclear gene flow, thus strongly pointing to historical mtDNA introgression. We suggest that the observed deeply divergent lineages within R. sinicus probably evolved in isolation in separate Pleistocene refugia, although their close phylogeographic correspondence with distinct eco-environmental zones suggests that divergent selection might also have promoted broad patterns of population genetic structure.
Journal of Mammalogy, 2003
We examined the systematics of round-eared bats (Tonatia and Lophostoma) using sequence data from the nuclear recombination activator gene-2 (Rag2) gene and the mitochondrial valine transfer RNA, 12S ribosomal RNA (rRNA), and 16S rRNA. Some analyses of the mitochondrial and combined data sets indicate that round-eared bats may be paraphyletic relative to the genera Phyllostomus, Phylloderma, and Mimon. Both nuclear and mitochondrial data sets indicate substantial genetic divergence between Tonatia and Lophostoma, and neither data set unambiguously demonstrates monophyly of round-eared bats. However, our analyses cannot exclude the possibility that round-eared bats form a monophyletic lineage that separated anciently into Tonatia and Lophostoma. Within the Tonatia lineage, T. bidens and T. saurophila are sister taxa but are divergent for both nuclear and mitochondrial sequences. Nuclear data suggest that L. silvicolum may be paraphyletic, as currently recognized, because L. evotis appears within this clade.
Journal of Biogeography
Aim The extent to which the ranges of temperate biota in East Asia have been shaped by geological and climatic changes during the Pleistocene remains poorly understood. Previous molecular-based studies of the greater horseshoe bat (Rhinolophus ferrumequinum), which is widespread across China and Japan, suggest that this species was able to persist in multiple refugia in this region. However, limited availability of samples precluded a detailed analysis of past distributions. By integrating ecological niche modelling with phylogenetic analyses, we aim to resolve the impact of past events on the population genetic structure of R. ferrumequinum and provide detailed descriptions of potential distribution patterns during this time.