Complete Mitochondrial Cytochrome Research Articles

Age structure and genetic diversity of Homatula pycnolepis in the Nujiang River basin

This study examined the age structure of the Loach, Homatula pycnolepis through the otolith growth rings in 204 individual specimens collected from the Xiaomengtong River of the Nujiang River (Salween River) basin in April, 2008. There were only two different age classes, 1 and 2 years of age-no 3 year olds were detected. The age structure of H. pycnolepis was simple. The complete mitochondrial DNA cytochrome b gene sequences (1140) of 80 individuals from 4 populations collected in the Nujiang River drainage were sequenced and a total of 44 variable sites were found among 4 different haplotypes. The global haplotype diversity (Hd) and nucleotide diversity (Pi) were calculated at 0.7595, 0.0151 respectively, and 0, 0 in each population, indicating a consistent lack of genetic diversity in each small population. There was obvious geographic structure in both the Nujiang River basin (NJB) group, and the Nanding River (NDR) group. The genetic distance between NJB and NDR was calculated at 0.0356, suggesting that genetic divergence resulted from long-term isolation of individual population. Such a simple age structure and a lack of genetic diversity in H. pycnolepis may potentially be due to small populations and locale fishing pressures. Accordingly, the results of this study prompt us to recommend that the NJB, NDR and Lancang River populations should be protected as three different evolutionary significant units or separated management units.

Use of mitochondrial cytochrome b sequences to determine the origin of captive Asian tapirs Tapirus indicus: implications for conservation

ESR Endangered Species Research Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsSpecials ESR 21:97-103 (2013) - DOI: https://doi.org/10.3354/esr00509 Use of mitochondrial cytochrome b sequences to determine the origin of captive Asian tapirs Tapirus indicus: implications for conservation Yuttamol Muangkram1,2, Worawidh Wajjwalku2,*, Chaleow Salakij2, Nongnid Kaolim2, Boripat Siriaroonrut3, Sumate Kamolnorranath3, Wanlaya Tipkantha3, Umaporn Maikaew4, Warisara Thomas5, Kanda Polsrila6, Kwanreaun Dong sa-ard7, Saowaphang Sananu8, Anuwat Wattananorrasate9 1The Graduate School, Kasetsart University, Chatuchak, Bangkok 10900, Thailand2Department of Pathology, Faculty of Veterinary Medicine, Kasetsart University, Kamphaengsaen, Nakhon Pathom 73140, Thailand3Endangered Species Conservation and Research Institute, Zoological Park Organization, Dusit, Bangkok 10300, Thailand4Khao Kheow Open Zoo, Sriracha, Chonburi 20110, Thailand5Nakhon Ratchasima Zoo, Muang, Nakhon Ratchasima 30000, Thailand6Song Khla Zoo, Muang, Song Khla 90000, Thailand7Chiang Mai Zoo, Muang, Chiang Mai 50000, Thailand8Dusit Zoo, Dusit, Bangkok 10300, Thailand9Safari World Public Company Limited, Klongsamwa, Bangkok 10510, Thailand *Corresponding author. Email: fvetwww@yahoo.com ABSTRACT: Populations of the Endangered Asian tapir Tapirus indicus in Thailand have been severely fragmented and isolated and may be facing a high risk of extinction. Their genetic diversity and population viability remains unknown. The main aim of this study was to assess the genetic diversity of the Asian tapir using the complete mitochondrial cytochrome b gene (1140 bp). We collected 31 blood samples from captive individuals. Two polymorphic sites were found, contributing to 3 maternal lineages: Ti-1 (n = 15), Ti-2 (n = 11), and Ti-3 (n = 5). Comparative analysis with GenBank sequences of other Asian tapirs found another 17 variable sites. These results suggest that there may be up to 7 distinct haplotypes of T. indicus. Furthermore, the pattern of the haplotype distribution corresponded to natural geographic boundaries, including the Isthmus of Kra and the Malacca Strait. One unique haplotype found in Sumatra was genetically distinct from 3 haplotypes found in Thailand and 3 haplotypes from Malaysia. One haplotype shared between Thai and Malaysian populations indicated a possible origin in the tropical rainforest along the Thai-Malay border. In general, the diverged geographic distribution of these haplotypes illustrates the phylogeographic history of the family Tapiridae (T. indicus, T. terrestris, T. pinchaque, and T. bairdii) based on our 963 bp cytochrome b sequences. These baseline genetic data have the potential to enhance effective management of tapirs held in captive breeding programs. However, there is still an urgent need to identify and maintain the genetic diversity of these distinct populations in the wild. KEY WORDS: Cytochrome b gene · Genetic diversity · Malayan tapir · Phylogenetic analysis · Thailand Full text in pdf format NextCite this article as: Muangkram Y, Wajjwalku W, Salakij C, Kaolim N and others (2013) Use of mitochondrial cytochrome b sequences to determine the origin of captive Asian tapirs Tapirus indicus: implications for conservation. Endang Species Res 21:97-103. https://doi.org/10.3354/esr00509 Export citation RSS - Facebook - Tweet - linkedIn Cited by Published in ESR Vol. 21, No. 2. Online publication date: August 13, 2013 Print ISSN: 1863-5407; Online ISSN: 1613-4796 Copyright © 2013 Inter-Research.

Mitochondrial diversity and distribution of African green monkeys (chlorocebus gray, 1870).

African green monkeys (Chlorocebus) represent a widely distributed and morphologically diverse primate genus in sub-Saharan Africa. Little attention has been paid to their genetic diversity and phylogeny. Based on morphological data, six species are currently recognized, but their taxonomy remains disputed. Here, we aim to characterize the mitochondrial (mt) DNA diversity, biogeography and phylogeny of African green monkeys. We analyzed the complete mitochondrial cytochrome b gene of 126 samples using feces from wild individuals and material from zoo and museum specimens with clear geographical provenance, including several type specimens. We found evidence for nine major mtDNA clades that reflect geographic distributions rather than taxa, implying that the mtDNA diversity of African green monkeys does not conform to existing taxonomic classifications. Phylogenetic relationships among clades could not be resolved suggesting a rapid early divergence of lineages. Several discordances between mtDNA and phenotype indicate that hybridization may have occurred in contact zones among species, including the threatened Bale monkey (Chlorocebus djamdjamensis). Our results provide both valuable data on African green monkeys’ genetic diversity and evolution and a basis for further molecular studies on this genus. Am. J. Primatol. 75:350-360, 2013. © 2013 Wiley Periodicals, Inc.

A novel semi-multiplex PCR assay for identification of tropical eels of genus Anguilla in Indonesian waters

A one-step semi-multiplex polymerase chain reaction (PCR) is proposed to distinguish seven species and subspecies of tropical eels, i.e., Anguilla celebesensis, A. interioris, A. nebulosa nebulosa, A. marmorata, A. borneensis, A. bicolor bicolor, and A. bicolor pacifica, known in Indonesian waters. Seven pairs of species-specific primers, including two forward and seven reverse sequences, were designed after alignment of published and new complete mitochondrial cytochrome b (1,140 bp) and 16S ribosomal RNA (rRNA) (1,120 bp) sequences. All species-specific primer pairs are included in one PCR mix, but only one pair of them can amplify a specific fragment from the template DNA that is analyzed. The semi-multiplex PCR amplified a fragment of 230 bp for A. b. bicolor, 372 bp for A. n. nebulosa, 450 bp for A. borneensis, 620 bp for A. marmorata, 670 bp for A. b. pacifica, 720 bp for A. celebesensis, and 795 bp for A. interioris, which are then separated by DNA agarose gel electrophoresis.

Migration route estimation of the Jeju striped field mouse Apodemus agrarius chejuensis (Rodentia, Muridae)

The taxonomic relationship between two Korean field mice species, Apodemus agrarius coreae and A. a. chejuensis, as well as their possible historic migration routes, was examined by molecular genetic analysis of the complete mitochondrial cytochrome b gene of 73 mice collected from the Korean Peninsula and Jeju Island. Our findings suggest that A. a. coreae and A. a. chejuensis populations expanded and dispersed rapidly. Bayesian and network analysis showed that A. a. chejuensis is a clearly distinct population, and that A. a. chejuensis originated from the ancestral lineage of A. a. coreae. Based on our data, we hypothesize that the A. a. coreae population originated from eastern China or elsewhere. After the last glacial epoch, the lineage isolated from A. a. coreae had adapted to the new environment of Jeju Island, and with the reproductive isolation caused by the geographic barrier, this lineage eventually became a distinct population.

White-toothed shrews (Mammalia, Soricomorpha, Crocidura) of coastal islands of Vietnam

New findings of the white-toothed shrews (Crocidura spp.) from offshore islands of Vietnam are reported. The species identifications have been confirmed by the analysis of complete mitochondrial cytochrome b gene (1140 bp). Crocidura phuquocensis is the only species found in the Phu Quoc Island. Crocidura fuliginosa has been recorded from two islands of the Con Dao Archipelago (Con Son and Bai Canh). The occurrence of Crocidura fuliginosa in Vietnam has been genetically confirmed for the first time. Crocidura attenuata has been collected from the Cat Ba Island for the first time, and this finding corresponds well with the proposal that the species’ distribution is confined to the north and east of the Red River only.

Species identification of Cyprinidae fish in Taiwan by FINS and PCR–RFLP analysis

Cyprinidae fish are widely distributed in Taiwan, and processed products made from them are favored by consumers. To identify the species used for these processed products, complete mitochondrial cytochrome b genes (cytb, 1141 bp) of 8 Cyprinidae were established. Then, a rapid PCR–RFLP method was used to amplify a 426 bp fragment of cytb using primer set Lnew1/Hnew1, and the fragment was co-digested with NlaIII and BstXI. The results show that using this PCR–RFLP technique for the species identification of the 8 Cyprinidae was successful. The method was further applied to investigate 16 commercial samples of processed Cyprinidae products from traditional markets. The results indicate that 9 of the samples were Carassius auratus auratus, Cyprinus carpio carpio, or Ctenopharyngodon idella. The other 6 samples did not belong to the Cyprinidae family according to PCR–RFLP. These samples were further analyzed with the forensically informative nucleotide sequencing (FINS) and BLAST methods. The results show that these 6 processed products were Oreochromis spp., a monophyletic fish group. The last commercial product could not be amplified to obtain a 426 bp fragment, so its species remains unknown. This study shows that PCR–RFLP and FINS can be used to identify processed products fraudulently labeled as Cyprinidae.

Molecular phylogenetic relationships of pangasiid and schilbid catfishes in Thailand

In this study, the phylogenetic relationships among 13 pangasiids and six schilbids of Thailand were reconstructed based on the almost complete mitochondrial cytochrome b (cyt b), 12S rRNA, tRNA-Val and 16S rRNA, as well as the partial nuclear recombination-activating gene 1 (rag1) sequences by using the maximum likelihood and the Bayesian inference methods of phylogenetic reconstruction. The reconstructed phylogeny based on the concatenated sequence data set recovered Pangasiidae and Schilbidae as reciprocally monophyletic groups. Within Pangasiidae, four major clades were recovered, which according to the cyt b genetic distances can be categorized into four genera: Pangasius, Pseudolais, Helicophagus and Pangasianodon. The genus Pangasianodon was strongly supported as the most basal taxon within pangasiids, whereas Pseudolais + Helicophagus were recovered as a sister group of Pangasius. Within the latter, the giant pangasius Pangasius sanitwongsei was recovered as a sister group of the spot pangasius Pangasius larnaudii, Pangasius krempfi as a sister group of Pangasius nasutus + Pangasius conchophilus and Pangasius polyuranodon as a sister species of Pangasius macronema. Other internal phylogenetic relationships, however, were unresolved. Within Schilbidae, Pseudeutropius was supported as the most basal lineage. Eutropiichthys was recovered as a sister group of Clupisoma. The enigmatic Clupisoma sinense was recognized as more closely related to Laides longibarbis than to Clupisoma prateri. Thus, based on the cyt b genetic distances, a recategorization of C. sinense to the genus Laides is suggested. On the basis of a relaxed clock fossil calibration, the divergence of pangasiids and schilbids was estimated to have occurred 14·93 million years before present (b.p.) during the Miocene epoch. The separation between Pangasiidae and Schilbidae took place c. 13·12 Mb.p. during the early middle Miocene. The estimated divergence time of pangasiids is similar to the age of the calibrated fossil, Cetopangasius chaetobranchus, which was discovered in north-central Thailand. This suggests that the oldest pangasiid ancestor diverged into diverse genera in the area.

Phylogenetic relationship between Callosciurus caniceps andC. inornatus (Rodentia, Sciuridae): Implications for zoogeographical isolation by the Mekong River

To test the riverine barrier hypothesis in small arboreal mammals, we examined phylogenetic relationship between two Callosciurus squirrel species (C. caniceps and C. inornatus) geographically isolated in the northeastern part of the Indochina Peninsula by the Mekong River. We did this by comparing complete mitochondrial DNA cytochrome b gene sequences of these two squirrels and five other Callosciurus species: C. erythraeus, C. finlaysonii, C. nigrovittatus, C. notatus, and C. prevostii. Phylogenetic trees showed that there are three major lineages: (1) a lineage containing C. caniceps, C. erythraeus, C. finlaysonii, and C. inornatus; (2) a C. notatus lineage; and (3) a lineage containing C. nigrovittatus and C. prevostii. Callosciurus caniceps was most closely related to C. inornatus. Based on transversional divergence rate at the third codon position of cytochrome b gene, they diverged about 1.2 million years ago. The drastic eastward shift of the Mekong River may have isolated ancestors of C. caniceps and C. inornatus. Then, these two species might have evolved in the different environments of each side of the Mekong River. This phylogeographic history suggests a typical case of allopatric speciation.

DNA barcoding of African fruit bats (Mammalia, Pteropodidae). The mitochondrial genome does not provide a reliable discrimination between Epomophorus gambianus and Micropteropus pusillus

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 β-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.

Molecular phylogeny of the Sinocyclocheilus (Cypriniformes: Cyprinidae) fishes in northwest part of Guangxi, China

The northwestern part of Guangxi is a typical karst landform. There are about ten species of the genus Sinocyclocheilus distributed in the region. To investigate the phylogenetic relationships and resolve the taxonomic status of these species, we determined nucleotide sequences of complete mitochondrial cytochrome b gene of 11 ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony and maximum likelihood analyses. Phylogenetic results showed that these species cluster as one clade with strong support. The 95% credibility interval (CI) of the divergence time between the species in the northwest part of Guangxi and other species in the genus Sinocyclocheilus is 8.28–12.40Mya. For the karst environment, these species show marked, recent genetic differentiation. From the overall consideration of morphology and molecular data Sinocyclocheilus tianeensis should be a valid species.

Analysis of global and local population stratification of finless porpoises Neophocaena phocaenoides in Chinese waters

The existence of three distinct populations is widely accepted for the finless porpoise (Neophocaena phocaenoides) in Chinese waters: the Yellow Sea, Yangtze River, and South China Sea populations. Here, we use nine species-specific microsatellite loci, the complete mitochondrial DNA control region (912 bp), and the complete mitochondrial cytochrome b gene (1,140 bp) to further investigate potential population stratification in the Yellow Sea using 147 finless porpoise samples from the Bohai Sea and adjacent northern Yellow Sea, two regions that were largely underrepresented in previous genetic studies. Our F-statistics analyses confirm the previously described three populations, but further demonstrate significant genetic differentiation between the [Bohai + northern Yellow] Sea and the southern Yellow Sea. On the other hand, median-joining network analyses do not exhibit well-differentiated haplotype groups among different geographic populations, suggesting the existence of shared ancestral haplotypes. Levels of microsatellite diversity are moderate to high (mean HE = 0.794) among the 147 [Bohai + northern Yellow] Sea finless porpoises and no recent bottleneck was detected, whereas mtDNA control region and cytochrome b gene diversity is low to moderate. The microsatellite genotypic and mtDNA haplotypic data also confirm the presence of mother-calf pairs in single-net bycatch cases. The results presented here highlight the necessity to treat the [Bohai + northern Yellow] Sea population (highly impacted by anthropogenic threats) as a separate Management Unit.

Ancient DNA Suggests Dwarf and ‘Giant’ Emu Are Conspecific

BackgroundThe King Island Emu (Dromaius ater) of Australia is one of several extinct emu taxa whose taxonomic relationship to the modern Emu (D. novaehollandiae) is unclear. King Island Emu were mainly distinguished by their much smaller size and a reported darker colour compared to modern Emu.Methodology and ResultsWe investigated the evolutionary relationships between the King Island and modern Emu by the recovery of both nuclear and mitochondrial DNA sequences from sub-fossil remains. The complete mitochondrial control (1,094 bp) and cytochrome c oxidase subunit I (COI) region (1,544 bp), as well as a region of the melanocortin 1 receptor gene (57 bp) were sequenced using a multiplex PCR approach. The results show that haplotypes for King Island Emu fall within the diversity of modern Emu.ConclusionsThese data show the close relationship of these emu when compared to other congeneric bird species and indicate that the King Island and modern Emu share a recent common ancestor. King Island emu possibly underwent insular dwarfism as a result of phenotypic plasticity. The close relationship between the King Island and the modern Emu suggests it is most appropriate that the former should be considered a subspecies of the latter. Although both taxa show a close genetic relationship they differ drastically in size. This study also suggests that rates of morphological and neutral molecular evolution are decoupled.

Population genetic structure and conservation genetics of threatened Okaloosa darters (Etheostoma okaloosae)

Imperiled Okaloosa darters (Etheostoma okaloosae) are small, benthic fish limited to six streams that flow into three bayous of Choctawhatchee Bay in northwest Florida, USA. We analyzed the complete mitochondrial cytochrome b gene and 10 nuclear microsatellite loci for 255 and 273 Okaloosa darters, respectively. Bayesian clustering analyses and AMOVA reflect congruent population genetic structure in both mitochondrial and microsatellite DNA. This structure reveals historical isolation of Okaloosa darter streams nested within bayous. Most of the six streams appear to have exchanged migrants though they remain genetically distinct. The U.S. Fish and Wildlife Service recently reclassified Okaloosa darters from endangered to threatened status. Our genetic data support the reclassification of Okaloosa darter Evolutionary Significant Units (ESUs) in the larger Tom’s, Turkey, and Rocky creeks from endangered to threatened status. However, the three smaller drainages (Mill, Swift, and Turkey Bolton creeks) remain at risk due to their small population sizes and anthropogenic pressures on remaining habitat. Natural resource managers now have the evolutionary information to guide recovery actions within and among drainages throughout the range of the Okaloosa darter.

Genetic diversity of mitochondrial cytochrome b gene in Chinese native buffalo

The origins of the domestic water buffalo remain contentious. To better understand the origins of Chinese water buffalo, we sequenced the complete mitochondrial cytochrome b (MT-CYB) gene from 270 individuals representing 13 Chinese domestic swamp buffalo populations. We found genetic evidence of introgression of river buffalo into Chinese swamp buffalo herds. Swamp buffalo haplotypes can be divided into two highly divergent lineages (A and B), suggesting that Chinese native swamp buffalo have two maternal origins. We found that the A→G transition in the buffalo MT-CYB gene stop codon resulted in buffalo haplotypes being terminated by one of two stop codons: AGA or AGG. AGA is common to river buffalo and lineage A of swamp buffalo, while AGG is specific to lineage B of swamp buffalo. Lineage A appears to have been domesticated in China. Further genetic evidence is required to clarify the origins of lineage B.

Comparing chromosomal and mitochondrial phylogenies of the Indriidae (Primates, Lemuriformes)

The Malagasy primate family Indriidae comprises three genera with up to 19 species. Cytogenetic and molecular phylogenies of the Indriidae have been performed with special attention to the genus Propithecus. Comparative R-banding and FISH with human paints were applied to karyotypes of representatives of all three genera and confirmed most of the earlier R-banding results. However, additional chromosomal rearrangements were detected. A reticulated and a cladistic phylogeny, the latter including hemiplasies, have been performed. Cladistic analysis of cytogenetic data resulted in a phylogenetic tree revealing (1) monophyly of the family Indriidae, (2) monophyly of the genus Avahi, (3) sister–group relationships between Propithecus diadema and Propithecus edwardsi, and (4) the grouping of the latter with Indri indri, Propithecus verreauxi, and Propithecus tattersalli, and thus suggesting paraphyly of the genus Propithecus. A molecular phylogeny based on complete mitochondrial cytochrome b sequences of 16 species indicated some identical relationships, such as the monophyly of Avahi and the sister–group relationships of the eastern (P. diadema and P. edwardsi) to the western Propithecus species (P. verreauxi, Propithecus coquereli, and P. tattersalli). However, the main difference between the molecular and cytogenetic phylogenies consists in an early divergence of Indri in the molecular phylogeny while in the chromosomal phylogeny it is nested within Propithecus. The similarities and differences between molecular and cytogenetic phylogenies in relation to data on the species’ geographic distributions and mating systems allow us to propose a scenario of the evolution of Indriidae. Chromosomal and molecular processes alone or in combination created a reproductive barrier that was then followed by further speciation processes.Electronic supplementary materialThe online version of this article (doi:10.1007/s10577-011-9188-5) contains supplementary material, which is available to authorized users.

Mitochondrial phylogeny of tamarins (Saguinus, Hoffmannsegg 1807) with taxonomic and biogeographic implications for theS. nigricollisspecies group

Tamarins of the genus Saguinus, subfamily Callitrichinae, represent one of the most diverse primate radiations. So far, about 35 taxa have been described, but detailed information about their taxonomy and phylogeny is still lacking. To further elucidate the phylogenetic relationships and the biogeographic history within the genus, and to contribute to a more reliable classification of its taxa, we sequenced the complete mitochondrial cytochrome b gene and the hypervariable region I of the D-loop. Therefore, we mainly used fecal samples from wild tamarins collected during two expeditions to the Peruvian Amazon, an area of high tamarin diversity. Our data suggest that the numerous taxa of the S. nigricollis species group are derived from a common ancestor that separated from the other representatives of the genus ~10 mya. Most taxa of the S. nigricollis group form monophyletic clusters, which mainly originated in a single rapid radiation ~2.9 mya. S. fuscicollis and S. nigricollis appear as polyphyletic taxa, but we could identify various clusters, which are mainly consistent with differences in coat coloration. We could confirm most of the existing taxa as distinct entities and suggest species status for fuscicollis, illigeri, lagonotus, leucogenys, nigricollis, nigrifrons, tripartitus, and weddelli. Our genetic data do not support a separate status for melanoleucus and graellsi, but due to differences in fur coloration, we give them subspecies status. The species group most likely originated in western Amazonia and diversified during the decline of the Acre wetland and the formation of the Amazonian river system.

A new mtDNA COI gene lineage closely related to Anopheles janconnae of the Albitarsis complex in the Caribbean region of Colombia

An understanding of the taxonomic status and vector distribution of anophelines is crucial in controlling malaria. Previous phylogenetic analyses have supported the description of six species of the Neotropical malaria vector Anopheles (Nyssorhynchus) albitarsis s.l. (Diptera: Culicidae): An. albitarsis, Anopheles deaneorum, Anopheles marajoara, Anopheles oryzalimnetes, Anopheles janconnae and An. albitarsis F. To evaluate the taxonomic status of An. albitarsis s.l. mosquitoes collected in various localities in the Colombian Caribbean region, specimens were analyzed using the complete mitochondrial DNA cytochrome oxidase I (COI) gene, the ribosomal DNA (rDNA) internal transcribed spacer 2 (ITS2) region and partial nuclear DNA white gene sequences. Phylogenetic analyses of the COI gene sequences detected a new lineage closely related to An. janconnae in the Caribbean region of Colombia and determined its position relative to the other members of the complex. However, the ITS2 and white gene sequences lacked sufficient resolution to support a new lineage closely related to An. janconnae or the An. janconnae clade. The possible involvement of this new lineage in malaria transmission in Colombia remains unknown, but its phylogenetic closeness to An. janconnae, which has been implicated in local malaria transmission in Brazil, is intriguing.

Phylogeny and distribution of crested gibbons (genus Nomascus) based on mitochondrial cytochrome b gene sequence data

Crested gibbons, genus Nomascus, are endemic to the Indochinese bioregion and occur only in Vietnam, Laos, Cambodia, and southern China. However, knowledge about the number of species to be recognized and their exact geographical distributions is still limited. To further elucidate the evolutionary history of crested gibbon species and to settle their distribution ranges, we analyzed the complete mitochondrial cytochrome b gene from 79 crested gibbon individuals from known locations. Based on our findings, crested gibbons should be classified into seven species. Within N. concolor, we recognize two subspecies, N. concolor concolor and N. concolor lu. Phylogenetic reconstructions indicate that the northernmost species, N. hainanus, N. nasutus, and N. concolor branched off first, suggesting that the genus originated in the north and successively migrated to the south. The most recent splits within Nomascus occurred between N. leucogenys and N. siki, and between Nomascus sp. and N. gabriellae. Based on our data, the currently postulated distributions of the latter four species have to be revised. Our study shows that molecular methods are a useful tool to elucidate phylogenetic relationships among crested gibbons and to determine species boundaries.

Phylogenetic relationships of some Sylviidae species based on complete mtDNA cyt b and partial COI sequence data

Members of the passerine family Sylviidae are distributed widely around the Old World and the phylogenetic relationships of many species still remain controversial. In this study, we investigated the phylogeny and relationships among 37 species of 11 genera by analyzing DNA sequences obtained from the complete mitochondrial cytochrome b (cyt b) and partial cytochrome oxidase I (COI) genes. The data were analyzed by maximum-likelihood analysis and Bayesian inference. The results demonstrate that the current genus Phylloscopus is non-monophyletic, while Seicercus is synonymized with Phylloscopus or is a group within the genus Phylloscopus. We may conclude that within Phylloscopus there are close relations between P. magnirostris and P. borealis; among P. proregulus, P. yunnanensis, P. pulcher and P. maculipennis, as well as among P. occisinensis, P. schwarzi, P. armandii, P. collybita and P. fuscatus. Monophyly of the genus Cettia could not be corroborated; it is closely related to the genera Abroscopus and Tesia. However monophyly of Acrocephalus is supported. Furthermore, the close relationships between Sylvia and Zosterops and among Prinia, Orthotomus and Cisticola are also supported.