Conflicting mitochondrial and nuclear paraphyly in small-sized West African house bats (Vespertilionidae) (original) (raw)
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Phylogenetic position of the giant house bat Scotophilus nigrita (Chiroptera, Vespertilionidae)
Mammalia, 2015
The giant house bat Scotophilus nigrita, one of the largest vespertilioniform bat species in the world, is a poorly known taxon, especially with respect to its phylogenetic relationships to congeneric species. Its phylogenetic position was thus assessed by analysing DNA sequences of single mitochondrial and nuclear genes. Based on the mitochondrial cytochrome b, S. nigrita was found to be paraphyletic with respect to continental African species S. colias, S. dinganii, S. nigritellus and S. viridis. Analysis of sequences of the nuclear zinc finger protein gene on the Y chromosome corroborated the general pattern of the cytochrome b phylogeny, although phylogenetic relationships were poorly resolved. These results clearly contradict the published data on S. nigrita from Kenya for both markers, rendering the hypothesis of historical hybridization with S. colias implausible and questioning the taxonomic affiliation of the particular Kenyan sequence. A deep split in the cytochrome b phylogeny between S. nigrita from West and Southern Africa reached sequence divergence values of 7.6% to 8.1%, a finding that supports taxonomic elevation of the two currently recognized subspecies into separate species S. nigrita and S. alvenslebeni.
Sequences of the mitochondrial cytochrome c oxidase subunit I (COI) gene have been shown to be useful for species identification in various groups of animals. However, the DNA barcoding approach has never been tested on African fruit bats of the family Pteropodidae (Mammalia, Chiroptera). In this study, the COI gene was sequenced from 120 bats collected in the Central African Republic and belonging to either Epomophorus gambianus or Micropteropus pusillus, two species easily diagnosed on the basis of morphological characters, such as body size, skull shape and palatal ridges. Two additional molecular markers were used for comparisons: the complete mitochondrial cytochrome b gene and the intron 7 of the nuclear b-fibrinogen (FGB) gene. Our results reveal an unexpected discordance between mitochondrial and nuclear genes. The nuclear FGB signal agrees with our morphological identifications, as the three alleles detected for E. gambianus are divergent from the fourteen alleles found for M. pusillus. By contrast, this taxonomic distinction is not recovered with the analyses of mitochondrial genes, which support rather a polyphyletic pattern for both species. The conflict between molecular markers is explained by multiple mtDNA introgression events from M. pusillus into E. gambianus or, alternatively, by incomplete lineage sorting of mtDNA haplotypes associated with positive selection on FGB alleles of M. pusillus. Our work shows the failure of DNA barcoding to discriminate between two morphologically distinct fruit bat species and highlights the importance of using both mitochondrial and nuclear markers for taxonomic identification.
African Zoology, 2011
The yellow-bellied Scotophilus dinganii is the only African house bat species reported to occur in the Arabian Peninsula. Formerly, the Arabian house bats were referred to similar-looking white-bellied S. leucogaster, which differs from S. dinganii mainly by the colour of ventral pelage. We reassessed the taxonomic status of house bats from southwestern Yemen using genetic and morphological analyses. The Yemeni specimens clustered within two distantly related mitochondrial lineages of African Scotophilus: East African S. aff. dinganii, which is a paraphyletic group to S. dinganii s.str. from South Africa, and West African S. leucogaster. This taxonomic assignation was based on published sequences of reference museum specimens. Differences in external and cranial measurements also indicated the presence of two distinct taxa in Yemen. The Yemeni and comparative Ethiopian populations of S. aff. dinganii showed close morphological similarity to the type specimen of S. nigrita colias from Kenya. Because the Yemeni and Ethiopian yellow-bellied house bats cannot be synonymized with S. dinganii, the designation S. colias is tentatively suggested for this particular East African and Yemeni lineage of the S. dinganii complex. However, final correspondence of this name with the respective populations or applicability of some of other available names must yet be explored. Based on environmental differences of the Yemeni localities of origin, S. colias appears to be ecologically delimited to mountainous habitats, while S. leucogaster to harsh lowland deserts. This is consistent with known habitats of African populations of both species.
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.
BMC Evolutionary Biology
Background: The Old World insectivorous bat genus Rhinolophus is highly speciose. Over the last 15 years, the number of its recognized species has grown from 77 to 106, but knowledge of their interrelationships has not kept pace. Species limits and phylogenetic relationships of this morphologically conservative group remain problematic due both to poor sampling across the Afrotropics and to repeated instances of mitochondrial-nuclear discordance. Recent intensive surveys in East Africa and neighboring regions, coupled with parallel studies by others in West Africa and in Southern Africa, offer a new basis for understanding its evolutionary history. Results: We investigated phylogenetic relationships and intraspecific genetic variation in the Afro-Palearctic clade of Rhinolophidae using broad sampling. We sequenced mitochondrial cytochrome-b (1140 bp) and four independent and informative nuclear introns (2611 bp) for 213 individuals and incorporated sequence data from 210 additional individuals on GenBank that together represent 24 of the 33 currently recognized Afrotropical Rhinolophus species. We addressed the widespread occurrence of mito-nuclear discordance in Rhinolophus by inferring concatenated and species tree phylogenies using only the nuclear data. Well resolved mitochondrial, concatenated nuclear, and species trees revealed phylogenetic relationships and population structure of the Afrotropical species and species groups. Conclusions: Multiple well-supported and deeply divergent lineages were resolved in each of the six African Rhinolophus species groups analyzed, suggesting as many as 12 undescribed cryptic species; these include several instances of sympatry among close relatives. Coalescent lineage delimitation offered support for new undescribed lineages in four of the six African groups in this study. On the other hand, two to five currently recognized species may be invalid based on combined mitochondrial and/or nuclear phylogenetic analyses. Validation of these cryptic lineages as species and formal relegation of current names to synonymy will require integrative taxonomic assessments involving morphology, ecology, acoustics, distribution, and behavior. The resulting phylogenetic framework offers a powerful basis for addressing questions regarding their ecology and evolution.
Frontiers in Ecology and Evolution
The genus Scotophilus contains 21 currently recognized species ranging throughout Africa and Southeast Asia. Among the 13 species recognized from continental Africa, systematic relationships remain poorly understood. Taxonomic uncertainty regarding names, suggestions of polytypic species complexes, and undescribed cryptic diversity all contribute to the current confusion. To gain insights into the systematics of this group, we inferred single locus and multi-locus phylogenies and conducted lineage delimitation analyses using seven unlinked genes for specimens from across Africa. Recent collections from Kenya allowed us to carry out population-level analyses for the diverse assemblage of East African Scotophilus. Multi-locus coalescent delimitation methods indicated strong support for three recently named lineages thought to be restricted to Kenya and Tanzania; it also uncovered two new distinctive lineages at present known only from Kenya. Subsequent taxonomic assessments that integrate these genetic data with phenotypic, distributional, and/or ecological traits are needed to establish these lineages as valid species. Nevertheless, as many as 15 Scotophilus species may occur in continental Africa, 10 of these in Kenya alone. Our analysis highlights the importance of population-level surveys for the detection of cryptic diversity in understudied regions such as the Afrotropics.
Molecular biology and evolution, 1993
Within the tribe Stenodermatini the systematics of the complex of species allied with the genus Artibeus has generated several alternative phylogenetic hypotheses. The most recent treatment recognized four genera (Artibeus, Dermanura, Enchisthenes, and Koopmania) and suggested that the most recent common ancestor of these four genera would include the common ancestor of all other currently recognized Stenodermatini genera except Sturnira. To test this hypothesis, we examined an EcoRI-defined nuclear satellite DNA repeat and 402 bp of DNA sequence variation from the mitochondrial cytochrome b gene. Phylogenetic conclusions based on Southern blot analyses, in situ hybridization, and mitochondrial DNA sequence data indicate that Enchisthenes is not closely related to Dermanura, Artibeus, or Koopmania and that Dermanura, Artibeus, and Koopmania shared a common ancestor after diverging from the remainder of the Stenodermatini. If our conclusions are correct, then justification for recogn...
Journal of Mammalogy, 2005
Abstract The Natal long-fingered bat (Miniopterus natalensis) and lesser long-fingered bat (M. fraterculus) are morphologically almost indistinguishable and occur sympatrically over much of their southern African range. This raises the possibility that they are sister taxa. We employed a multidisciplinary approach to examine their taxonomic relationship to one another and to other Miniopterus species, whose global phylogeny requires review. We examined echolocation, morphological, and dietary differences between M. natalensis ...
Genetic Similarity Amongst Phenotypically Diverse Little Free-Tailed Bats, Chaerephon pumilus
Acta Chiropterologica, 2004
The African molossid Chaerephon pumilus shows extensive variation in colour, size and echolocation across its wide distributional range with a light-winged form in north-eastern Africa and a dark form in southern Africa. There is also much variation in supposedly diagnostic characters (e.g., degree of palatial emargination) amongst the dark form of this species in southern Africa. These differences suggest that there may be cryptic species within C. pumilus. We used phylogenetic and phenetic analyses of sequence data from the mitochondrial cytochrome-b gene of a number of C. pumilus individuals to investigate the status of the light and dark-winged forms of this species and to evaluate the possibility of cryptic species within the dark-winged form of C. pumilus in southern Africa. We evaluated species status by comparing the level of sequence divergence amongst C. pumilus with the level of sequence divergence between known species in the genus. These included C. ansorgei, C. chapini, C. nigeriae and C. jobensis. Intrageneric sequence divergences among the Chaerephon spp. included here ranged from 6.51 to 11.18%, whereas the average sequence divergence between the light and dark forms was 0.9%. This suggests that these two forms are not distinct species. Individuals of the dark form of C. pumilus were genetically indistinguishable from each other having the same cytochrome b haplotype. We thus found no evidence of cryptic species in southern African C. pumilus.
Folia Zoologica, 2016
Evolutionary parallelism complicates taxonomy of the bat genus Scotophilus. This implies the necessity for a careful examination of morphologically similar species. Robbins'-or "nutlet"-house bat Scotophilus nucella is an insufficiently known taxon of the African rainforest zone based on just a handful of recorded specimens previously included in the nut-coloured house bat S. nux. Because its phylogenetic relationship to S. nux and other congeneric species is unknown, it was assessed using analysis of DNA sequences of single mitochondrial and nuclear genes. Based on the mitochondrial cytochrome b sequences, S. nucella was placed in sister position to S. nux. A genetic divergence of 7.8-9.4 % between them supports the recognition of S. nucella as a distinct species. Analysis of partial sequences of the nuclear zinc finger protein gene on the Y-chromosome corroborated the sister relationship of S. nucella and S. nux, while showing sufficient differences to consider them as two species. Mitochondrial genetic diversity in S. nucella was low, whereas S. nux showed a rather complex genetic structure over a large geographic area, despite limited sampling. The origin of the forest group of Scotophilus could be dated to the Miocene-Pliocene transition and the split leading to the contemporary species S. nucella and S. nux to the Pliocene-Pleistocene transition. Both time periods are characterized by an arid climate that led to the retreat of forest environment, which likely promoted speciation in forest refugia. Mid-Pleistocene diversification in S. nux led to a separate lineage from Guinea, West Africa, for which a subspecific status may be considered, as it differs 3.4-4.5 % from other African populations.