Biogeography of the Indonesian archipelago: mitochondrial DNA variation in the fruit bat, Eonycteris spelaea (original) (raw)
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Journal of Genetic Engineering and Biotechnology
Background Cynopterus brachyotis (Müller 1838) is a generalist and widespread fruit bat species which inhabits different types of habitats in Southeast Asia. This species plays an essential role as a seed disperser and pollinator. Morphological study and phylogenetic analysis using mtDNA markers (cyt-b and D-loop) revealed that this species had two different forms in peninsular Malaysia and Borneo and six lineages in Southeast Asia that lead to new species formation. In addition, this species is also reported to have high genetic diversity in Malaysia and Thailand based on the D-loop sequence. However, a phylogenetic and genetic variation study of C. brachyotis in Indonesia has not been conducted yet. These two studies are important as additional information for taxonomic and population genetic studies of this species. Thus, we performed the phylogenetic and genetic diversity analysis of the C. brachyotis population collected from seven habitats on Java island, including open-fragme...
Molecular Ecology, 2015
Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and M. recondita are both endemic to Taiwan and are putative sister species. To test for non-allopatric divergence and gene flow in these taxa, we generated sequences using Sanger and Next Generation Sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita, however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species M. eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *BEAST and isolation-with-migration (IM) and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.
Biological Journal of The Linnean Society, 2003
Morphological and genetic analyses of Eonycteris spelaea from 15 islands along the Banda Arc, from Sumatra to Timor and including Kalimantan and Sulawesi, revealed considerable divergence between islands and geographical patterning. On the basis of both morphology and genetics, the populations on the large islands of Greater Sunda (Sumatra, Java, Kalimantan and Sulawesi) are generally distinct from one another and from those on the islands in Nusa Tenggara (Lombok to Timor), which form a more cohesive cluster. These differences may be the result of the Nusa Tenggara populations having been colonized more recently than those on the Greater Sunda, and probably from a single source. All biological measures of the relationships between island populations are positively associated with the extent of the sea-crossing between them, indicating the sea is an important barrier to movement. Multivariate analyses show the presence of a marked trend for body size to increase from west to east. However, individuals from Kalimantan are not consistent with this trend, being smaller than predicted, and on the two outer Banda Arc islands of Sumba and Timor animals are a little larger than predicted from the longitudinal trend. These differences could be due to the relative isolation of these populations or differing environmental conditions. There is also a negative relationship between body size and island area, but this is confounded by the longitudinal trend. No significant longitudinal trends in the genetic data were detected and the trend in body size may be an adaptive response to an environmental cline that is known to occur in this region. © 2003 The Linnean Society of London, Biological Journal of the Linnean Society, 2003, 79, 511–522.
2004
The Azorean bat Nyctalus azoreum is the only endemic mammal native to the remote archipelago of the Azores. It evolved from a continental ancestor related to the Leisler's bat Nyctalus leisleri and is considered threatened because of its restricted and highly fragmented distribution. We studied the genetic variability in 159 individuals from 14 colonies sampled throughout the archipelago. Sequences of the D-loop region revealed moderate but highly structured genetic variability. Half of the 15 distinct haplotypes were restricted to a single island, but the most common was found throughout the archipelago, suggesting a single colonization event followed by limited interisland female gene flow. All N. azoreum haplotypes were closely related and formed a star-like structure typical of expanded populations. The inferred age of demographic expansions was consistent with the arrival of founder animals during the Holocene, well before the first humans inhabited the Azores. Comparisons with a population of N. leisleri from continental Portugal confirmed not only that all N. azoreum lineages were unique to the archipelago, but also that the current levels of genetic diversity were surprisingly high for an insular species. Our data imply that the Azorean bat has a high conservation value. We argue that geographical patterns of genetic structuring indicate the existence of two management units.
Molecular Biology and …, 1988
The Neotropical fruit bat, Artibeus jumaicensis, occurs throughout Latin America and on many islands in the Caribbean. Populations from Jamaica (in the Greater Antilles) to Barbados (in the Lesser Antilles) have been classified as a subspecies (A. j. jumaicensis) separate from that on the Lesser Antillean island of St. Vincent (A. j. schwartzi). Mitochondrial DNA (mtDNA) was isolated from 54 individuals collected on these islands, analyzed by digestion with restriction endonucleases, and the restriction sites were mapped. Three different mtDNA genotypes (16,000 + 200 bp) were identified: J-l (16 animals from Jamaica, one from St. Vincent, 15 from Barbados), J-2 (two animals from Jamaica), and SV-1 (18 animals from St. Vincent, two from Barbados). The J-l and J-2 genotypes were estimated to differ from each other by only 0.4%, but the SV-1 genotype differed from J-l and J-2 by 8.1%-10.5%. The estimated sequence divergence between SV-1 and J-l is unusually large for mammals that are regarded as conspecific. Restriction mapping showed that the differences among the genotypes (presence or absence of particular restriction sites) were located throughout the genome. The presence of the J-1 mtDNA genotype on Jamaica and on St. Vincent and Barbados (1,400 km away) demonstrates that maternal lineages in these bats are not necessarily confined to single islands or limited geographic regions. The presence of the J-l mtDNA genotype within the A. j. schwartzi population on St. Vincent and the presence of the SV-1 genotype in two specimens of A. j. jumaicensis from Barbados document genetic exchange between subspecific populations on these islands, which are separated by 180 km of open water.
Contrasting Genetic Structure in Two Co-Distributed Species of Old World Fruit Bat
PloS one, 2010
The fulvous fruit bat (Rousettus leschenaulti) and the greater short-nosed fruit bat (Cynopterus sphinx) are two abundant and widely co-distributed Old World fruit bats in Southeast and East Asia. The former species forms large colonies in caves while the latter roots in small groups in trees. To test whether these differences in social organization and roosting ecology are associated with contrasting patterns of gene flow, we used mtDNA and nuclear loci to characterize population genetic subdivision and phylogeographic histories in both species sampled from China, Vietnam and India. Our analyses from R. leschenaulti using both types of marker revealed little evidence of genetic structure across the study region. On the other hand, C. sphinx showed significant genetic mtDNA differentiation between the samples from India compared with China and Vietnam, as well as greater structuring of microsatellite genotypes within China. Demographic analyses indicated signatures of past rapid population expansion in both taxa, with more recent demographic growth in C. sphinx. Therefore, the relative genetic homogeneity in R. leschenaulti is unlikely to reflect past events. Instead we suggest that the absence of substructure in R. leschenaulti is a consequence of higher levels of gene flow among colonies, and that greater vagility in this species is an adaptation associated with cave roosting.
Journal of Mammalogy, 2013
Emballonura semicaudata occurs in the southwestern Pacific and populations on many islands have declined or disappeared. One subspecies (E. semicaudata rotensis) occurs in the Northern Mariana Islands, where it has been extirpated from all but 1 island (Aguiguan). We assessed genetic similarity between the last population of E. s. rotensis and 2 other subspecies, and examined genetic diversity on Aguiguan. We sampled 12 E. s. rotensis, sequenced them at 3 mitochondrial loci, and compared them with published sequences from 2 other subspecies. All 12 E. s. rotensis had identical sequences in each of the 3 regions. Using cytochrome-b (Cytb) data E. s. rotensis was sister to E. s. palauensis in a clade separate from E. s. semicaudata. 12S ribosomal RNA (12S) sequences grouped all E. s. semicaudata in 1 clade with E. s. rotensis in a clade by itself. Genetic distances among the 3 subspecies at Cytb were smallest between E. s. palauensis and E. s. rotensis. Distance between E. s. semicaudata and the other 2 subspecies was not different from the distance between E. s. semicaudata and the full species E. raffrayana. A similar relationship was found using the 12S data. These distances are larger than those typically reported for mammalian subspecies using Cytb sequence and within the range of sister species.
Philippine mitochondrial DNA diversity: a populated viaduct between Taiwan and Indonesia?
Molecular biology and …, 2010
Relatively little is known about the genetic diversity of the Philippine population, and this is an important gap in our understanding of Southeast Asian and Oceanic prehistory. Here we describe mitochondrial DNA (mtDNA) variation in 423 Philippine samples and analyze them in the context of the genetic diversity of other Southeast Asian populations. The majority of Philippine mtDNA types are shared with Taiwanese aboriginal groups and belong to haplogroups of postglacial and pre-Neolithic origin that have previously been identified in East Asian and Island Southeast Asian populations. Analysis of hypervariable segment I sequence variation within individual mtDNA haplogroups indicates a general decrease in the diversity of the most frequent types (B4a1a, E1a1a, and M7c3c) from the Taiwanese aborigines to the Philippines and Sulawesi, although calculated standard error measures overlap for these populations. This finding, together with the geographical distribution of ancestral and derived haplotypes of the B4a1a subclade including the Polynesian Motif, is consistent with southward dispersal of these lineages ''Out of Taiwan'' via the Philippines to Near Oceania and Polynesia. In addition to the mtDNA components shared with Taiwanese aborigines, complete sequence analyses revealed a minority of lineages in the Philippines that share their origins-possibly dating back to the Paleolithic-with haplogroups from Indonesia and New Guinea. Other rare lineages in the Philippines have no closely related types yet identified elsewhere.