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Mitochondrial genomics identifies major haplogroups in Aboriginal Australians

van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM

Am. J. Phys. Anthropol., 2006 Oct;131(2):282-94.
PMID: 16596590

We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.

Matched MeSH terms: Phylogeny
Seed dispersal and spatial pattern in tropical trees

Seidler TG, Plotkin JB

PLoS Biol, 2006 Oct;4(11):e344.
PMID: 17048988

Theories of tropical tree diversity emphasize dispersal limitation as a potential mechanism for separating species in space and reducing competitive exclusion. We compared the dispersal morphologies, fruit sizes, and spatial distributions of 561 tree species within a fully mapped, 50-hectare plot of primary tropical forest in peninsular Malaysia. We demonstrate here that the extent and scale of conspecific spatial aggregation is correlated with the mode of seed dispersal. This relationship holds for saplings as well as for mature trees. Phylogenetically independent contrasts confirm that the relationship between dispersal and spatial pattern is significant even after controlling for common ancestry among species. We found the same qualitative results for a 50-hectare tropical forest plot in Panama. Our results provide broad empirical evidence for the importance of dispersal mode in establishing the long-term community structure of tropical forests.

Matched MeSH terms: Phylogeny
Possible conservation units of the sun bear (Helarctos malayanus) in Sarawak based on variation of mtDNA control region

Onuma M, Suzuki M, Ohtaishi N

Jpn. J. Vet. Res., 2006 Nov;54(2-3):135-9.
PMID: 17201199

The mitochondrial DNA control region of the sun bear (Helarctos malayanus) was sequenced using 21 DNA samples collected from confiscated sun bears to identify conservation units, such as evolutionarily significant units and management units, in Sarawak, Borneo Island. A total of 10 haplotypes were observed, indicating the presence of at least two lineages in the sun bear population in Sarawak. Presumably, these two lineages could represent evolutionarily significant units. However, the geographical distributions of the two lineages remained unknown due to the lack of information regarding the exact capture locations of the confiscated sun bears. It is essential to elucidate the geographical distributions of these lineages in order to create a proper conservation plan for the sun bears in Sarawak. Therefore, further studies examining the haplotype distributions using DNA samples from known localities are essential.

Matched MeSH terms: Phylogeny
Determination of molecular types and genetic heterogeneity of Cryptococcus neoformans and C. gattii in Malaysia

Tay ST, Lim HC, Tajuddin TH, Rohani MY, Hamimah H, Thong KL

Med Mycol, 2006 Nov;44(7):617-22.
PMID: 17071555

The molecular types and genetic heterogeneity of Cryptococcus neoformans and C. gattii clinical isolates in Malaysia were determined in this study. Of 44 C. neoformans collected between 1980 and 2003, 42 (95.5%) were molecular type VNI, 2 (4.5%) were molecular type VNII. Of 17 C.gattii isolates, 13 (76.5%) were molecular type VGI, and 4 (23.5%) were molecular type VGII. A difference was noted when comparing the molecular types of cryptococcal isolates in the earlier and recent cases of cryptococcosis. While both molecular types VNI and VGI were equally predominant in the earlier cases of cryptococcosis, VNI was the most predominant molecular type isolated from the recent cases. VNII was a new molecular type, isolated from 5.1% of the recent cases. All the bird dropping isolates were molecular type VNI. The genetic heterogeneity of the two predominant molecular types, i.e., VNI, VGI clinical isolates and bird dropping isolates of C. neoformans were further determined by polymerase chain reaction (PCR) fingerprinting method, using (GTG)5 as single primer. Two clusters of cryptococcal isolates were distinguished at 68.5% of similarity, with cluster I consisting of VNI isolates and cluster II consisting of VGI isolates. Each cluster was further subdivided into three subtypes at >/=80% of similarity. Fourteen bird dropping isolates were grouped into a subtype within VN1, sharing 82.7% of similarity with the clinical isolates. A higher degree of similarities, ranging from 93.4-97.6% was noted between 3 bird dropping isolates with the clinical isolates in another subtype. This study demonstrated the existence of various molecular types of C. neoformans isolates in Malaysia and the genetic heterogeneity within the predominant molecular types. The study also provides evidence for genetic relatedness of clinical isolates with bird dropping isolates in the environment.

Matched MeSH terms: Phylogeny
Emergence and predominance of an H5N1 influenza variant in China

Smith GJ, Fan XH, Wang J, Li KS, Qin K, Zhang JX, et al.

Proc Natl Acad Sci U S A, 2006 Nov 07;103(45):16936-41.
PMID: 17075062

The development of highly pathogenic avian H5N1 influenza viruses in poultry in Eurasia accompanied with the increase in human infection in 2006 suggests that the virus has not been effectively contained and that the pandemic threat persists. Updated virological and epidemiological findings from our market surveillance in southern China demonstrate that H5N1 influenza viruses continued to be panzootic in different types of poultry. Genetic and antigenic analyses revealed the emergence and predominance of a previously uncharacterized H5N1 virus sublineage (Fujian-like) in poultry since late 2005. Viruses from this sublineage gradually replaced those multiple regional distinct sublineages and caused recent human infection in China. These viruses have already transmitted to Hong Kong, Laos, Malaysia, and Thailand, resulting in a new transmission and outbreak wave in Southeast Asia. Serological studies suggest that H5N1 seroconversion in market poultry is low and that vaccination may have facilitated the selection of the Fujian-like sublineage. The predominance of this virus over a large geographical region within a short period directly challenges current disease control measures.

Matched MeSH terms: Phylogeny
Phylogeography and ethnogenesis of aboriginal Southeast Asians

Hill C, Soares P, Mormina M, Macaulay V, Meehan W, Blackburn J, et al.

Mol Biol Evol, 2006 Dec;23(12):2480-91.
PMID: 16982817

Studying the genetic history of the Orang Asli of Peninsular Malaysia can provide crucial clues to the peopling of Southeast Asia as a whole. We have analyzed mitochondrial DNA (mtDNAs) control-region and coding-region markers in 447 mtDNAs from the region, including 260 Orang Asli, representative of each of the traditional groupings, the Semang, the Senoi, and the Aboriginal Malays, allowing us to test hypotheses about their origins. All of the Orang Asli groups have undergone high levels of genetic drift, but phylogeographic traces nevertheless remain of the ancestry of their maternal lineages. The Semang have a deep ancestry within the Malay Peninsula, dating to the initial settlement from Africa >50,000 years ago. The Senoi appear to be a composite group, with approximately half of the maternal lineages tracing back to the ancestors of the Semang and about half to Indochina. This is in agreement with the suggestion that they represent the descendants of early Austroasiatic speaking agriculturalists, who brought both their language and their technology to the southern part of the peninsula approximately 4,000 years ago and coalesced with the indigenous population. The Aboriginal Malays are more diverse, and although they show some connections with island Southeast Asia, as expected, they also harbor haplogroups that are either novel or rare elsewhere. Contrary to expectations, complete mtDNA genome sequences from one of these, R9b, suggest an ancestry in Indochina around the time of the Last Glacial Maximum, followed by an early-Holocene dispersal through the Malay Peninsula into island Southeast Asia.

Matched MeSH terms: Phylogeny*
Identification of a novel circulating recombinant form (CRF33_01B) disseminating widely among various risk populations in Kuala Lumpur, Malaysia

Tee KK, Li XJ, Nohtomi K, Ng KP, Kamarulzaman A, Takebe Y

J Acquir Immune Defic Syndr, 2006 Dec 15;43(5):523-9.
PMID: 17031320

A molecular epidemiological investigation was conducted among various risk populations (n = 184) in Kuala Lumpur, Malaysia, in 2003 to 2005, on the basis of nucleotide sequences of protease and reverse transcriptase regions. In addition to circulating HIV-1 strains, including CRF01_AE (57.1%), subtype B (20.1%), and subtype C (0.5%), we detected a candidate with a new circulating recombinant form (CRF). We determined four near-full-length nucleotide sequences with identical subtype structure from epidemiologically unlinked individuals of different risk and ethnic groups. In this chimera, two short subtype B segments were inserted into the gag-RT region in a backbone of CRF01_AE. The recombinant structure was distinct from previously identified CRF15_01B in Thailand. In agreement with the current HIV nomenclature system, this constitutes a novel CRF (CRF33_01B). The overall prevalence of CRF33_01B is 19.0% (35/184). Although the prevalence of CRF33_01B is particularly high among injecting drug users (42.0%, 21/50), it is also detected in a substantial proportion of homo-/bisexual males (18.8%, 3/16) and heterosexuals (9.8%, 9/92). Moreover, unique recombinant forms composed of CRF01_AE and subtype B that have a significant structural relationship with CRF33_01B were detected in 1.6% (3/184) of study subjects, suggesting an ongoing recombination process in Malaysia. This new CRF seems to be bridging viral transmission between different risk populations in this country.

Matched MeSH terms: Phylogeny
Molecular characterization of recent infectious bursal disease virus isolates from Malaysia

Nurulfiza I, Hair-Bejo M, Omar AR, Aini I

Acta Virol., 2006;50(1):45-51.
PMID: 16599185

Three isolates of Infectious bursal disease virus (IBDV), designated UPM04178, UPM04190 and UPM04238, were obtained from severe outbreaks of infectious bursal disease (IBD) in Malaysia in 2004. The hypervariable region (HPVR) of VP2 gene of these isolates was sequenced. The obtained sequences were compared with those of other isolates. The highest similarity (98%) concerning both nucleotide and amino acid sequences was found to very virulent IBDV (vvIBDV) strains. Phylogenetic analysis revealed clustering of the three isolates with vvIBDV strains. Evolutionary relatedness of the three isolates to vvIBDV strains was demonstrated by three phylogenetic methods: bootstrap values of 100%, 95% and 90% for nucleotide sequences and those of 58%, 86% and 96% for amino acid sequences were obtained by the distance, maximum parsimony and maximum likehood methods, respectively. It is concluded that UPM04178, UPM04190 and UPM04238 are vvIBDV isolates of serotype 1, which originate from a common ancestor of IBDV strains present in Malaysia.

Matched MeSH terms: Phylogeny
Fulltext Molecular genetic approaches for the conservation of endangered orchids

Rodrigues, K. F., Yeoh, K. A., Kumar, S. V.

Buletin Persatuan Genetik Malaysia, 2006;12(1):13-14.
MyJurnal

Geographically isolated populations of endemic orchids have evolved and adapted to an existence within specifi c ecological niches. These populations are highly susceptible to anthropogenic
infl uences on their microhabitats. The primary objective of conservation programs is the restoration of endangered populations to their ecologically sustainable levels, and the fi rst stage in the process of conservation involves estimation of molecular diversity at the level of the population. The approach described in this article involves the application of RAPD, Microsatellites and Chloroplast DNA markers for the characterization of the genetic structure of Paphiopedilum rothschildianum and Phalaenopsis gigantea, two endangered and endemic orchids of Sabah. This study has isolated a total of 96 microsatellite loci in P. rothschildianum and P. gigantea, 42 specifi c primer pairs have been designed for amplifi cation of microsatellite loci and are currently being applied to screen the breeding pools. The Chloroplast DNA regions amplifi ed by the primer pairs trnH-psbA and trnL-trnF exhibit distinct polymorphisms and can be used to establish phylogenetic
relationships. The ability of microsatellite loci to cross-amplify selected varieties of orchids has been determined. The molecular markers developed will be applied to estimate population diversity
levels and to formulate long-term management strategies for the conservation of endangered species of orchids of Sabah.

Matched MeSH terms: Phylogeny
Fulltext Oil palm microsatellites: implications and potentials

Chua, B. H., Rajinder, S., Tan, S. G., Faridah, Q. Z., Cheah, S. C.

Buletin Persatuan Genetik Malaysia, 2006;12(1):1-5.
MyJurnal

Microsatellites or simple sequence repeats (SSRs) are tandem repeats of DNA of 1-6 bp long. They ubiquitously occur in both eukaryotic and prokaryotic genomes. Because of their abundance,
they have widespread applications in both animal and plant sciences; such as varietal identification, genetic mapping, QTL mapping, phylogenetic and diversity studies. Thus, SSRs have become valuable DNA markers for molecular biologists and geneticists. Microsatellites are markers
of choice for many molecular geneticists because of their hypervariability, codominant
inheritance, multi-allelism and PCR-based assaying of variations that are amenable to automation and high throughput assay. However, the utilization of microsatellite markers in the past was
hampered by its laborious de novo isolations and species-specific nature.

Matched MeSH terms: Phylogeny
Fulltext Tracking the source and origin of H5N1 avian influenza viruses in Malaysia

Sharifah, S .H., Suriani, M. N., Hassuzana, K., Aini, I.

Buletin Persatuan Genetik Malaysia, 2006;12(1):1-3.
MyJurnal

Malaysia, experienced two epidemic waves of HPAI; its fi rst outbreak of HP H5N1 in August 2004 that occurred in the state of Kelantan and the second and subsequent outbreaks in February–March 2006 in three states on the west coast of Malaysia namely Wilayah Persekutuan
Kuala Lumpur, Perak and Penang. Five outbreaks occurred in village chickens and one in a multi-species enclosure of birds in a bird park resort facility. Molecular epidemiological studies by genomic sequencing and phylogenetic analyses of the viruses isolated showed that the
virus isolated from WP Kuala Lumpur is of the V-genotype and it originated from Hunan China, two viruses were found to be similar to the Fujian/Hunan strains and other viruses were similar to the Vietnam/ Thailand strains.

Matched MeSH terms: Phylogeny
Resurrection of Staurois parvus from S. tuberilinguis from Borneo (Amphibia, Ranidae)

Matsui M, Mohamed M, Shimada T, Sudin A

Zoolog Sci, 2007 Jan;24(1):101-6.
PMID: 17409723

Two forms of Staurois that are differentiated by body size occur parapatrically in the Crocker Range, Sabah, Borneo. Analyses of a total of 1,499 bp of the mitochondrial cytochrome b, 12S rRNA, and 16S rRNA genes revealed that the two forms could be completely split genetically. The two forms could be also clearly differentiated morphologically, not only by snout-vent length but also by the relative sizes of snout, eye, and finger disk. Comparisons of the two forms with all known species of the genus revealed the large and small forms to be S. tuberilinguis and S. parvus, respectively. The latter species has long been synonymized with the former, but we here consider them to represent different species.

Matched MeSH terms: Phylogeny*
Genetic diversity and molecular identification of mosquito species in the Anopheles maculatus group using the ITS2 region of rDNA

Walton C, Somboon P, O'Loughlin SM, Zhang S, Harbach RE, Linton YM, et al.

Infect Genet Evol, 2007 Jan;7(1):93-102.
PMID: 16782411

The species diversity and genetic structure of mosquitoes belonging to the Anopheles maculatus group in Southeast Asia were investigated using the internal transcribed spacer 2 (ITS2) of ribosomal DNA (rDNA). A molecular phylogeny indicates the presence of at least one hitherto unrecognised species. Mosquitoes of chromosomal form K from eastern Thailand have a unique ITS2 sequence that is 3.7% divergent from the next most closely related taxon (An. sawadwongporni) in the group. In the context of negligible intraspecific variation at ITS2, this suggests that chromosomal form K is most probably a distinct species. Although An. maculatus sensu stricto from northern Thailand and southern Thailand/peninsular Malaysia differ from each other in chromosomal banding pattern and vectorial capacity, no intraspecific variation was observed in the ITS2 sequences of this species over this entire geographic area despite an extensive survey. A PCR-based identification method was developed to distinguish five species of the group (An. maculatus, An. dravidicus, An. pseudowillmori, An. sawadwongporni and chromosomal form K) to assist field-based studies in northwestern Thailand. Sequences from 187 mosquitoes (mostly An. maculatus and An. sawadwongporni) revealed no intraspecific variation in specimens from Thailand, Cambodia, mainland China, Malaysia, Taiwan and Vietnam, suggesting that this identification method will be widely applicable in Southeast Asia. The lack of detectable genetic structure also suggests that populations of these species are either connected by gene flow and/or share a recent common history.

Matched MeSH terms: Phylogeny
Fulltext Reemergence of endemic Chikungunya, Malaysia

AbuBakar S, Sam IC, Wong PF, MatRahim N, Hooi PS, Roslan N

Emerg Infect Dis, 2007 Jan;13(1):147-9.
PMID: 17370532

Chikungunya virus infection recently reemerged in Malaysia after 7 years of nondetection. Genomic sequences of recovered isolates were highly similar to those of Malaysian isolates from the 1998 outbreak. The reemergence of the infection is not part of the epidemics in other Indian Ocean countries but raises the possibility that chikungunya virus is endemic in Malaysia.

Matched MeSH terms: Phylogeny
Allozyme variation in the camaenid tree snails Amphidromus atricallosus (Gould, 1843) and A. inversus (Müller, 1774)

Prasankok P, Ota H, Toda M, Panha S

Zoolog Sci, 2007 Feb;24(2):189-97.
PMID: 17409732

We examined allozyme variation in two camaenid tree snails, Amphidromus atricallosus and A. inversus, across two principal regions of Thailand and from Singapore, plus for A. inversus, one site in peninsular Malaysia. Using horizontal starch gel electrophoresis, 13 allozyme loci (11 polymorphic) were screened for A. atricallosus and 18 (5 polymorphic) for A. inversus. Heterozygosity was higher in A. atricallosus (Hexp=0.018-0.201, mean=0.085) than in A. inversus (Hexp=0-0.023, mean= 0.002). Genetic heterogeneity among samples was higher in A. inversus (Fst=0.965) than in A. atricallosus (Fst=0.781). Within A. atricallosus, populations were more differentiated in southern Thailand (Fst=0.551) than in eastern Thailand (Fst=0.144). The high Fst and low Hexp in populations of A. inversus suggest that this species is likely to have experienced a series of strong bottlenecks, perhaps occurring chiefly on offshore continental-shelf islands. The low Fst values of A. atricallosus in eastern Thailand suggest frequent gene flows among populations in this region. The southern and eastern samples of A. atricallosus exhibited fixed allele differences at four loci and great genetic distance (Nei's D=0.485-0.946), suggesting that these two samples may actually represent, or else be evolving into, separate species.

Matched MeSH terms: Phylogeny
Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques

Smith DG, McDonough JW, George DA

Am J Primatol, 2007 Feb;69(2):182-98.
PMID: 17177314

An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was sequenced to characterize genetic variation within and among 1,053 samples comprising five regional populations each of longtail macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta), and one sample each of Japanese (M. fuscata) and Taiwanese (M. cyclopis) macaques. The mtDNA haplotypes of longtail macaques clustered in two large highly structured clades (Fas1 and Fas2) of a neighbor-joining tree that were reciprocally monophyletic with respect to those representing rhesus macaques, Japanese macaques, and Taiwanese macaques. Both clades exhibited haplotypes of Indonesian and Malaysian longtail macaques widely dispersed throughout them; however, longtail macaques from Indochina, Philippines, and Mauritius each clustered in a separate well-defined clade together with one or a few Malaysian and/or Indonesian longtail macaques, suggesting origins on the Sunda shelf. Longtail macaques from Malaysia and Indonesia were far more genetically diverse, and those from Mauritius were far less diverse than any other population studied. Nucleotide diversity between mtDNA sequences of longtail macaques from different geographic regions is, in some cases, greater than that between Indian and Chinese rhesus macaques. Approximately equal amounts of genetic diversity are due to differences among animals in the same regional population, different regional populations, and different species. A greater proportion of genetic variance was explained by interspecies differences when Japanese and Taiwanese macaques were regarded as regional populations of rhesus macaques than when they were treated as separate species. Rhesus macaques from China were more closely related to both Taiwanese and Japanese macaques than to their own conspecifics from India.

Matched MeSH terms: Phylogeny
Phylogeography illuminates maternal origins of exotic Coptotermes gestroi (Isoptera: Rhinotermitidae)

Jenkins TM, Jones SC, Lee CY, Forschler BT, Chen Z, Lopez-Martinez G, et al.

Mol Phylogenet Evol, 2007 Mar;42(3):612-21.
PMID: 17254806

Coptotermes gestroi, the Asian subterranean termite (AST), is an economically important structural and agricultural pest that has become established in many areas of the world. For the first time, phylogeography was used to illuminate the origins of new found C. gestroi in the US Commonwealth of Puerto Rico; Ohio, USA; Florida, USA; and Brisbane, Australia. Phylogenetic relationships of C. gestroi collected in indigenous locations within Malaysia, Thailand, and Singapore as well as from the four areas of introduction were investigated using three genes (16S rRNA, COII, and ITS) under three optimality criteria encompassing phenetic and cladistic assumptions (maximum parsimony, maximum likelihood, and neighbor-joining). All three genes showed consistent support for a close genetic relationship between C. gestroi samples from Singapore and Ohio, whereas termite samples from Australia, Puerto Rico, and Key West, FL were more closely related to those from Malaysia. Shipping records further substantiated that Singapore and Malaysia were the likely origin of the Ohio and Australia C. gestroi, respectively. These data provide support for using phylogeography to understand the dispersal history of exotic termites. Serendipitously, we also gained insights into concerted evolution in an ITS cluster from rhinotermitid species in two genera.

Matched MeSH terms: Phylogeny*
Human enterovirus 71 disease in Sarawak, Malaysia: a prospective clinical, virological, and molecular epidemiological study

Ooi MH, Wong SC, Podin Y, Akin W, del Sel S, Mohan A, et al.

Clin Infect Dis, 2007 Mar 01;44(5):646-56.
PMID: 17278054

BACKGROUND: Human enterovirus (HEV)-71 causes large outbreaks of hand-foot-and-mouth disease with central nervous system (CNS) complications, but the role of HEV-71 genogroups or dual infection with other viruses in causing severe disease is unclear.
METHODS: We prospectively studied children with suspected HEV-71 (i.e., hand-foot-and-mouth disease, CNS disease, or both) over 3.5 years, using detailed virological investigation and genogroup analysis of all isolates.
RESULTS: Seven hundred seventy-three children were recruited, 277 of whom were infected with HEV-71, including 28 who were coinfected with other viruses. Risk factors for CNS disease in HEV-71 included young age, fever, vomiting, mouth ulcers, breathlessness, cold limbs, and poor urine output. Genogroup analysis for the HEV-71-infected patients revealed that 168 were infected with genogroup B4, 68 with C1, and 41 with a newly emerged genogroup, B5. Children with HEV-71 genogroup B4 were less likely to have CNS complications than those with other genogroups (26 [15%] of 168 vs. 30 [28%] of 109; odds ratio [OR], 0.48; 95% confidence interval [CI], 0.26-0.91; P=.0223) and less likely to be part of a family cluster (12 [7%] of 168 vs. 29 [27%] of 109; OR, 0.21; 95% CI, 0.10-0.46; P

Matched MeSH terms: Phylogeny
Amycolatopsis nigrescens sp. nov., an actinomycete isolated from a Roman catacomb

Groth I, Tan GYA, González JM, Laiz L, Carlsohn MR, Schütze B, et al.

Int J Syst Evol Microbiol, 2007 Mar;57(Pt 3):513-519.
PMID: 17329776 DOI: 10.1099/ijs.0.64602-0

The taxonomic status of two actinomycetes isolated from the wall of a hypogean Roman catacomb was established based on a polyphasic investigation. The organisms were found to have chemical and morphological markers typical of members of the genus Amycolatopsis. They also shared a range of chemical, molecular and phenotypic markers which served to separate them from representatives of recognized Amycolatopsis species. The new isolates formed a branch in the Amycolatopsis 16S rRNA gene sequence tree with Amycolatopsis minnesotensis NRRL B-24435(T), but this association was not supported by a particularly high bootstrap value or by the product of the maximum-parsimony tree-making algorithm. The organisms were distinguished readily from closely related Amycolatopsis species based on a combination of phenotypic properties and from all Amycolatopsis strains by their characteristic menaquinone profiles, in which tetra-hydrogenated menaquinones with 11 isoprene units predominated. The combined genotypic and phenotypic data indicate that the isolates merit recognition as representing a novel species of the genus Amycolatopsis. The name proposed for this novel species is Amycolatopsis nigrescens sp. nov., with type strain CSC17Ta-90(T) (=HKI 0330(T)=DSM 44992(T)=NRRL B-24473(T)).

Matched MeSH terms: Phylogeny
A molecular epidemiological study targeting the glycoprotein gene of rabies virus isolates from China

Meng SL, Yan JX, Xu GL, Nadin-Davis SA, Ming PG, Liu SY, et al.

Virus Res, 2007 Mar;124(1-2):125-38.
PMID: 17129631

A group of 31 rabies viruses (RABVs), recovered primarily from dogs, one deer and one human case, were collected from various areas in China between 1989 and 2006. Complete G gene sequences determined for these isolates indicated identities of nucleotide and amino acid sequences of >or=87% and 93.8%, respectively. Phylogenetic analysis of these and some additional Chinese isolates clearly supported the placement of all Chinese viruses in Lyssavirus genotype 1 and divided all Chinese isolates between four distinct groups (I-IV). Several variants identified within the most commonly encountered group I were distributed according to their geographical origins. A comparison of representative Chinese viruses with other isolates retrieved world-wide indicated a close evolutionary relationship between China group I and II viruses and those of Indonesia while China group III viruses formed an outlying branch to variants from Malaysia and Thailand. China group IV viruses were closely related to several vaccine strains. The predicted glycoprotein sequences of these RABVs variants are presented and discussed with respect to the utility of the anti-rabies biologicals currently employed in China.

Matched MeSH terms: Phylogeny

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