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PubMed1999

Cytochrome b phylogeny of the family bovidae: resolution within the alcelaphini, antilopini, neotragini, and tragelaphini.

The family Bovidae is characterized by an incomplete fossil record for the period during which most bovid subfamilies emerged. This, coupled to extensive morphological convergence among species, has given rise to inconsistencies in taxonomic treatments, especially at the tribal and subfamilial levels. In an attempt to clarify some of these issues we analyzed the complete mtDNA cytochrome b gene (1140 bp) from 38 species/subspecies representing at least nine tribes and six subfamilies. Specific emphasis was placed on the evolution of the Alcelaphini (hartebeest and wildebeest), the Tragelaphini (kudu, eland, and close allies), the Antilopini (gazelles), and the Neotragini (dwarf antelope). Saturation plots for the codon positions revealed differences between bovid tribes and this allowed for the exclusion of transitional substitutions that were characterized by multiple hits. There was no significant rate heterogeneity between taxa. By calibrating genetic distance against the fossil record, a transversion-based sequence divergence of 0.22% (+/-0.015%) per million years is proposed for cytochrome b clock calibrations in the Bovidae. All evidence suggests that the Alcelaphini form a monophyletic group; there was no support for the recognition of the Lichtenstein's hartebeest in a separate genus (Sigmoceros), and the acceptance of the previously suggested Alcelaphus is recommended for this species. High bootstrap support was found for a sister taxon relationship between Alcelaphus and Damaliscus, a finding which is in good agreement with allozyme and morphological studies. In the case of the Tragelaphini, the molecular data suggest the inclusion of Taurotragus in the genus Tragelaphus, and no genetic support was found for the generic status of Boocercus. Although associations within the Antilopinae (comprising the tribes Neotragini and Antilopini) could not be unequivocally resolved, there was nonetheless convincing evidence of non-monophyly for the tribe Neotragini, with the Suni antelope (Neotragus moschatus) grouping as a sister taxon to the Impala (Aepyceros melampus, tribe indeterminate, sensu Gentry, 1992) and the Klipspringer (Oreotragus oreotragus) falling within the duiker antelope tribe (Cephalophini).

Animals↗
PubMed2001

Phylogenetic utility of the major opsin in bees (Hymenoptera: Apoidea): a reassessment.

Major opsin (LW Rh) DNA sequence has been reported to provide useful data for resolving phylogenetic relationships among tribes of corbiculate bees based on analyses of 502 bp of coding sequence. However, the corbiculate tribes are believed to be of Cretaceous age, and strong support for insect clades of this age from small data sets of nucleotide sequence data has rarely been demonstrated. To more critically assess opsin's phylogenetic utility we generated an expanded LW Rh data set by sequencing the same gene fragment from 52 additional bee species from 24 tribes and all six extant bee families. Analyses of this data set failed to provide substantial support for monophyly of corbiculate bees, for relationships among corbiculate tribes, or for most other well-established higher-level relationships among long-tongued bees. However, monophyly of nearly all genera and tribes is strongly supported, indicating that LW Rh provides useful phylogenetic signal at lower taxonomic levels. When our expanded LW Rh data set is combined with a morphological and behavioral data set for corbiculate bees, the results unambiguously support the traditional phylogeny of the corbiculate bee tribes: (Euglossini + (Bombini + (Meliponini + Apini))). This implies a single origin of advanced eusocial behavior among bees rather than dual origins, as proposed by several recent studies.

Animals↗
PubMed1995

HLA-B alleles of the Cayapa of Ecuador: new B39 and B15 alleles.

Recent data suggest that HLA-B locus alleles can evolve quickly in native South American populations. To investigate further this phenomenon of new HLA-B variants among Amerindians, we studied samples from another South American tribe, the Cayapa from Ecuador. We selected individuals for HLA-B molecular typing based upon their HLA class II typing results. Three new variants of HLA-B39 and one new variant of HLA-B15 were found in the Cayapa: HLA-B*3905, HLA-B*3906, HLA-B*3907, and HLA-B*1522. A total of thirteen new HLA-B alleles have now been found in the four South American tribes studied. Each of these four tribes studied, including the Cayapa, had novel alleles that were not found in any of the other tribes, suggesting that many of these new HLA-B alleles may have evolved since the Paleo-Indians originally populated South America. Each of these 13 new alleles contained predicted amino acid replacements that were located in the peptide binding site. These amino acid replacements may affect the sequence motif of the bound peptides, suggesting that these new alleles have been maintained by selection. New allelic variants have been found for all common HLA-B locus antigenic groups present in South American tribes with the exception of B48. In spite of its high frequency in South American tribes, no evidence for variants of B48 has been found in all the Amerindians studied, suggesting that B48 may have unique characteristics among the B locus alleles.

Alleles↗
PubMed2005

Phylogenetic relationships in Peniocereus (Cactaceae) inferred from plastid DNA sequence data.

The phylogenetic relationships of Peniocereus (Cactaceae) species were studied using parsimony analyses of DNA sequence data. The plastid rpl16 and trnL-F regions were sequenced for 98 taxa including 17 species of Peniocereus, representatives from all genera of tribe Pachycereeae, four genera of tribe Hylocereeae, as well as from three additional outgroup genera of tribes Calymmantheae, Notocacteae, and Trichocereeae. Phylogenetic analyses support neither the monophyly of Peniocereus as currently circumscribed, nor the monophyly of tribe Pachycereeae since species of Peniocereus subgenus Pseudoacanthocereus are embedded within tribe Hylocereeae. Furthermore, these results show that the eight species of Peniocereus subgenus Peniocereus (Peniocereus sensu stricto) form a well-supported clade within subtribe Pachycereinae; P. serpentinus is also a member of this subtribe, but is sister to Bergerocactus. Moreover, Nyctocereus should be resurrected as a monotypic genus. Species of Peniocereus subgenus Pseudoacanthocereus are positioned among species of Acanthocereus within tribe Hylocereeae, indicating that they may be better classified within that genus. A number of morphological and anatomical characters, especially related to the presence or absence of dimorphic branches, are discussed to support these relationships.

Cactaceae↗
PubMed2001

Genetic relationship of the Guambino, Paez, and Ingano Amerindians of southwest Colombia using major histocompatibility complex class II haplotypes and blood groups.

We analyzed the Amerindian tribes, Guambiano, Ingano, and Paez of the southwest section of Colombia by major histocompatibility complex class II typing and blood group analysis in order to establish their genetic relationship. In addition, genetic admixture with Caucasian and African ancestry were determined based on blood group typing. The Paez showed admixture with Caucasian populations (22.4%), while the Ingano and Guambiano showed some admixture with Black populations (9.2 and 4.6%, respectively). The Ingano had MHC class II haplotypes found mainly in Amerindian and Asian populations with no evidence of class II haplotypes of African origin. MHC class II haplotypes of Amerindian and Asian populations and some haplotypes frequently found in European Caucasians and Asians and haplotypes of European Caucasians were found in Guambiano and Paez tribes. We compared our results with those previously reported for four Amerindian tribes on Northern Colombia. The presence of some MHC class II haplotypes in the Guambiano, Paez, and Ingano tribes and their absence in the Chibcha speaking groups of Northern Colombia suggest that these tribes originated, together with other Amerindians, from a separate migration or by genetic drift from an ancestral population. Therefore they are genetically distant from Chibcha speaking tribes of Colombia.

Asian People↗
PubMed2002

Molecular systematics of the Jacks (Perciformes: Carangidae) based on mitochondrial cytochrome b sequences using parsimony, likelihood, and Bayesian approaches.

The Carangidae represent a diverse family of marine fishes that include both ecologically and economically important species. Currently, there are four recognized tribes within the family, but phylogenetic relationships among them based on morphology are not resolved. In addition, the tribe Carangini contains species with a variety of body forms and no study has tried to interpret the evolution of this diversity. We used DNA sequences from the mitochondrial cytochrome b gene to reconstruct the phylogenetic history of 50 species from each of the four tribes of Carangidae and four carangoid outgroup taxa. We found support for the monophyly of three tribes within the Carangidae (Carangini, Naucratini, and Trachinotini); however, monophyly of the fourth tribe (Scomberoidini) remains questionable. A sister group relationship between the Carangini and the Naucratini is well supported. This clade is apparently sister to the Trachinotini plus Scomberoidini but there is uncertain support for this relationship. Additionally, we examined the evolution of body form within the tribe Carangini and determined that each of the predominant clades has a distinct evolutionary trend in body form. We tested three methods of phylogenetic inference, parsimony, maximum-likelihood, and Bayesian inference. Whereas the three analyses produced largely congruent hypotheses, they differed in several important relationships. Maximum-likelihood and Bayesian methods produced hypotheses with higher support values for deep branches. The Bayesian analysis was computationally much faster and yet produced phylogenetic hypotheses that were very similar to those of the maximum-likelihood analysis.

Animals↗
PubMed2002

The incidence and diversity of Wolbachia in gallwasps (Hymenoptera; Cynipidae) on oak.

Wolbachia bacteria infect approximately 20% of all insect species, and cause a range of alterations to host reproduction, including imposition of thelytoky. The incidence and phenotypic impact of Wolbachia remains to be established in many insect taxa, and considerable research effort is currently focused on its association with particular reproductive modes and the relative importance of the various pathways via which infection occurs. Gallwasps represent an attractive system for addressing these issues for two reasons. First, they show a diversity of reproductive modes (including arrhenotoky, thelytoky and cyclical parthenogenesis) in which the impact of Wolbachia infection can be examined. Second, they occupy two intimately linked trophic niches (gall-inducers and inquilines) between which there is potential for the horizontal exchange of Wolbachia infection. In the arrhenotokous gallwasp lineages screened to date (the herb-galling 'Aylacini' and the rose-galling Diplolepidini), Wolbachia infection always induces thelytoky. The impact of Wolbachia in other arrhenotokous clades, and in the cyclically parthenogenetic clades remains unknown. Here we use polymerase chain reaction (PCR) screening and sequence data for two Wolbachia genes (wsp and ftsZ) to examine the prevalence and incidence of Wolbachia infection in 64 species (a total of 609 individuals) in two further tribes: the arrhenotokous inquilines (tribe Synergini), and the cyclically parthenogenetic oak gallwasps (tribe Cynipini). We ask: (i) whether Wolbachia infection has any apparent impact on host reproduction in the two tribes and (ii) whether there is any correlation between Wolbachia infection and the apparent lack of an arrhenotokous generation in many oak gallwasp life cycles. We show: (i) that Wolbachia infection is rare in the Cynipini. Infected species show no deviation from cyclical parthenogenesis, and infection is no more common in species known only from a thelytokous generation; (ii) that there is a higher incidence of infection within the arrhenotokous inquilines, and generally in gallwasp tribes without cyclical parthenogensis; (iii) all Wolbachia-positive inquiline species are known to possess males, implying either that Wolbachia infection does not result in loss of sex in this tribe or, more probably, that (as for some rose gallwasps) Wolbachia infection leads to loss of sex in specific populations; and (iv) although we find some inquilines and gall inducers to be infected with Wolbachia having the same wsp sequence, these hosts are not members of the same gall communities, arguing against frequent horizontal transmission between these two trophic groups. We suggest that exchange may be mediated by the generalist parasitoids common in oak galls.

Animals↗
PubMed1993

Genetic and linguistic differentiation in the Americas.

The relationship between linguistic differentiation and evolutionary affinities was evaluated in three tribes of the Pacific Northwest. Two tribes (Nuu-Chah-Nulth and Bella Coola) speak Amerind languages, while the language of the third (Haida) belongs to a different linguistic phylum--Na-Dene. Construction of a molecular phylogeny gave no evidence of clustering by linguistic affiliation, suggesting a relatively recent ancestry of these linguistically divergent populations. When the evolutionary affinities of the tribes were evaluated in terms of mitochondrial sequence diversity, the Na-Dene-speaking Haida had a reduced amount of diversity compared to the two Amerind tribes and thus appear to be a biologically younger population. Further, since the sequence diversity between the two Amerind-speaking tribes is comparable to the diversity between the Amerind tribes and the Na-Dene Haida, the evolutionary divergence within the Amerind linguistic phylum may be as great as the evolutionary divergence between the Amerind and Na-Dene phyla. Hence, in the New World, rates of linguistic differentiation appear to be markedly faster than rates of biological differentiation, with little congruence between linguistic hierarchy and the pattern of evolutionary relationships.

Alaska↗
PubMed1975

Plasma cholinesterase studies on south-eastern Bantu of Mozambique.

Blood samples from four Bantu tribes in South-East Mozambique have been phenotyped for the plasma cholinesterase variants of the E1 locus. A control roup of 153 Portuguese residents in Mozambique have also been phenotyped. The frequencies of both the E1a and E1f genes in the Portuguese population is very similar to those in other Caucasian populations. The absence of the E1a gene in the four Bantu tribes provides more evidence of the rarity of this gene in Negroid populations. There is an increased frequency of E1f gene in all tribes as compared with previous surveys. The Ronga and Bitonga tribes have similar E1f frequencies of 0.047 and 0.048, respectively. The Shangana has an E1f frequency of 0.060, and the corresponding figure for the Chopi tribe is 0.089. The latter is the highest recorded frequency for this gene. The results give some support to the doubts concerning the affiliation of the Chopi tribe.

Black People↗
PubMedDate not supplied

Interpopulational and intrapopulational genetic diversity of Amerindians as revealed by six variable number of tandem repeats.

The allele frequencies of six VNTRs (D1S80, D4S43, ApoB 3' VNTR, von Willebrand factor VNTR-I, DXS52 and DYS19) in 123 Amerindians from five tribes (Arara, Wayana-Apalai, Wayampi, Yanomama and Kayapo) were compared with three other Brazilian populations: Whites, Blacks, and individuals of Japanese extraction. The data clearly distinguished the four populations, and measurements of diversity show a decreasing average heterozygosity from Blacks to Whites, Japanese, and Indians. Seven novel alleles were observed: amongst them, two small DYS19 alleles and a large D4S43 allele occurred only in Indians, and may be useful genetic markers for this population. Other prominent features of the Amerindians were: (1) high frequency of ApoB allele 46; (2) absence of a shorter variant of D4S43 allele 1; (3) high frequency, limited to one tribe, of allele 12 of the von Willebrand VNTR. The study also demonstrated a heterogeneity of the Indian tribes, due to both different allele frequencies and the presence or absence of specific alleles. GST was 0.106 for the five Indian populations, and 0.065 for Whites, Blacks and Japanese. HS and HT demonstrated that 11% of the total diversity among Amerindians is caused by interpopulational variability, as compared with 7% for the other three racial groups. In contrast, diversity within each tribe is usually low, as demonstrated by a low average number of alleles per locus. These findings indicate that the study of a small number of tribes may not be representative of the variability of Amerindians, even if a large number of individuals are studied. To capture the whole range of genetic variability of Amerindians, it is necessary to study a large number of populations. The limited genetic diversity thus far observed for Amerindians seems to reflect both a genuine decrease of diversity and a bias caused by the study of limited numbers of tribes.

Alleles↗
PubMed1998

Sma I, Hha I, Msp I and Rsa I restriction fragment length polymorphisms in the von Willebrand factor gene of Chinese population.

OBJECTIVE: To study Sma I, Hha I, Msp I and Rsa I restriction fragment length polymorphisms in vWF gene of Chinese population. METHODS: The vWF gene from 52 unrelated individuals of Han Nationality, 44 of Yi tribe, 42 of Dai tribe was analyzed by polymerase chain reaction and digestion of the endonucleases of Sma I, Hha I, Msp I and Rsa I. RESULTS: The allele frequencies were 0.38:0.62 for Sma I+:Sma I- and 0.38:0.62 for Hha I+:Hha I-; 0.20:0.80 for Msp I+:Msp I-; 0.93:0.07 for Rsa I+:Rsa I- in Chinese Han population. The theoretical heterozygous rates were 0.46, 0.46, 0.36 and 0.13 of these polymorphisms, respectively. The allele frequencies were 0.43:0.57 for Sma I+:Sma I- and 0.43:0.57 for Hha I+:Hha I-, 0.26:0.74 for Msp I+:Msp- in Yi tribe and 0.36:0.64 for Sma I+:Sma I- and Hha I+:Hha I-, 0.17:0.83 for Msp I+:Msp I- in Dai tribe. The theoretical rates were 0.49 for Sma I and Hha I and 0.38 for Msp I in Yi tribe; and 0.45 for Sma I and Hha I, 0.28 for Msp I in Dai tribe, respectively. CONCLUSIONS: The allele frequencies and theoretical rates of these polymorphisms in vWF gene are different between Chinese populations and Caucasians. They should be useful for the carrier detection and prenatal diagnosis in vWD families of Chinese.

Alleles↗
PubMed2001

Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences.

Phylogenetic relationships were inferred using nucleotide sequence variation of the nuclear-encoded chalcone synthase gene (Chs) and the chloroplast gene matK for members of five tribes from the family Brassicaceae to analyze tribal and subtribal structures. Phylogenetic trees from individual data sets are mostly in congruence with the results from a combined matK-Chs analysis with a total of 2721 base pairs, but with greater resolution and higher statistical support for deeper branching patterns. The analysis indicates that tribes Lepidieae, Arabideae, and Sisymbrieae are not monophyletic. Among taxa under study four different lineages each were detected in tribes Arabideae and Lepidieae, interspersed with taxa from tribes Sisymbrieae, Hesperideae, and Brassiceae. It is concluded that tribe Brassiceae might be the only monophyletic group of the traditional tribes. From our data we estimated several divergence times for different lineages among cruciferous plants: 5.8 mya (million years ago) for the Arabidopsis-Cardaminopsis split, 20 mya for the Brassica-Arabidopsis split, and ∼40 mya for the age of the deepest split between the most basal crucifer Aethionema and remaining cruciferous taxa.

Journal Article↗
PubMed2003

Tribal differences in perception of tuberculosis: a possible role in tuberculosis control in Arusha, Tanzania.

SETTING: Arusha, Tanzania. OBJECTIVE: To determine tribal differences in knowledge and practices that might influence tuberculosis control. METHOD: Twenty-seven villages were selected randomly out of 242 villages in four districts. In each village, a general and a livestock keeping group were selected at random. The households were home-visited and 426 family members were interviewed. RESULTS: On average, 40% of respondents practised habits that might expose them to both bovine and human tuberculosis. The Barabaig tribe had a significantly higher number of respondents (50%, chi2(2) = 5.1, P = 0.024) who did not boil milk. Eating uncooked meat or meat products was practised by 17.9% of all respondents. The habit was practised more by Iraqw (21.1%, chi2(2) = 6.9, P = 0.008) and Barabaig (31.6%, chi2(2) = 5.6, P = 0.016) than other tribes. About 75% of the respondents had a poor knowledge of tuberculosis. CONCLUSION: All tribes had habits and beliefs that might expose them to both bovine and human tuberculosis. The Iraqw and Barabaig tribes practised such habits more than other tribes. Knowledge of tuberculosis was limited in all tribes.

Adult↗
PubMed2001

Genetic relationships between Amerindian populations of Argentina.

A total of 495 individuals from five different Argentinian tribes was examined for variation in 23 blood group and protein genetic systems, and the results were integrated with previous data on some of these systems. These tribes generally present RH * R1, PGM1 * 1, and ACP * A frequencies lower and RH * R2, ESD * 1, and GLO * 1 prevalences higher than those observed in other South American Indian groups. Earlier studies with mitochondrial DNA showed that haplogroup A was present in low frequencies in these tribes, but haplogroup B showed a high prevalence among the Mataco. Average heterozygosities are very similar in the five tribes, while estimates of non-Indian ancestry are generally low. Both the blood group and protein, as well as the mtDNA data sets, divide the five tribes into two groups, and the relationships obtained with the blood group and protein systems are exactly those expected on the basis of geography and language. However, the topology obtained with the mtDNA results was different, possibly due to sampling effects or diverse patterns of exchange between the groups related to sex.

Argentina↗
PubMed2006

A common mutation in the CBS gene explains a high incidence of homocystinuria in the Qatari population.

We report the results of a study carried out to delineate genetic and epidemiological aspects of homocystinuria in the Qatari population. Sixty-four patients with homocystinuria (37 males, 27 females, age 1 to 29 years) from 31 nuclear families were ascertained over a period of more than four years. The incidence of homocystinuria in Qatar was calculated to be > or =1:3000, the highest in the world known so far. All patients in whom data were available were vitamin B6-nonresponsive. Molecular studies were performed in all patients. All 53 patients from tribe M and all three patients from tribe K were homozygous for the mutation c.1006C>T (p.R336C) in the CBS gene, with an additional seven patients resulting from mixed marriages between tribe M and tribe K. A single patient from tribe S was homozygous for mutation c.700G>A (p.D234N) in the CBS gene. Both mutations have been previously reported but involve hypermutable CpG dinculeotides and may be recurrent mutations in the Qatari population. The results of this study illustrate a strong founder effect causing a high prevalence of an autosomal recessive disease in a highly consanguineous Arabian population. Molecular neonatal screening may be suitable for early detection of homocystinuria in this population.

Adolescent↗
PubMed1996

Behavioral influences on the evolution of human genetic diversity.

Unique aspects of human behavior account for special features of human evolution. For instance, the best data on the mating patterns of undisturbed hunting-gathering populations are those of Norman Tinsdale for Australian Aborigines. Among some 574 linguistically distinct tribes, he collected information on 755 marriages from the period prior to significant contact with Europeans. One can extrapolate from these data on 1510 individuals. In an average tribe of some 500 individuals, 62-65 of them would have had one parent who was a member of a different tribe and 7 or 8 of them would have been offspring of a parent from a distant tribe, not an adjacent one. Such rates of intergroup marriage, generation after generation, would have produced considerable gene flow, a pattern that likely has occurred during most of human prehistory. The pattern of descent is trellis-like, not one of successive fissioning. Some genetic diversity between tribes must have existed, but most genetic variation would have been within rather than between tribal groups. One implication of this pattern is that ethnically defined groups are not a suitable basis for studying human genetic diversity. Geographically stratified random sampling of the species would be more likely to ensure an unbiased estimate of genome variability.

Animals↗
PubMed1999

The major opsin in bees (Insecta: Hymenoptera): A promising nuclear gene for higher level phylogenetics.

We report the phylogenetic utility of the nuclear gene encoding the long-wavelength opsin (LW Rh) for tribes of bees. Aligned nucleotide sequences were examined in multiple taxa from the four tribes comprising the corbiculate bees within the subfamily Apinae. Phylogenetic analyses of sequence variation in a 502-bp fragment (approx 40% of the coding region) strongly supported the monophyly of each of the four tribes, which are well established from previous studies of morphology and DNA. Trees estimated from parsimony and maximum likelihood analyses of LW Rh sequences show a strongly supported relationship between the tribes Meliponini and Bombini, a relationship that has been found uniformly in studies of other genes (28S, 16S, and cytochrome b). All of the tribal clades as well as relationships among the tribes are supported by high bootstrap values, suggesting the utility of LW Rh in estimating tribal and subfamily rank for these bees. The sequences exhibit minimal base composition bias. Both 1st + 2nd and 3rd position sites provide information for estimating a reliable tree topology. These results suggest that LW Rh, which has not been reported previously in studies of organismal phylogenetics, could provide important new data from the nuclear genome for phylogeny reconstruction.

Animals↗
PubMed1999

Molecular phylogenetic studies of Brassica, rorippa, arabidopsis and allied genera based on the internal transcribed spacer region of 18S-25S rDNA.

The phylogenetic relationships of nine genera in four tribes of the family Brassicaceae were estimated from the sequences of the internal transcribed spacer region (ITS) of the 18S-25S nuclear ribosomal DNA. The entire ITS region of 16 accessions belonging to 10 species of seven genera was sequenced. Eight published sequences of Brassicaceae were also used. A total of 27 sequences were included in this study; four of them were found to be pseudogenes. Both the neighbor-joining and the parsimony trees suggest that the nine genera can be divided into three groups: (1) Arabidopsis, Cardaminopsis, Capsella, and Lepidium; (2) Rorippa and Cardamine; and (3) Brassica, Sinapis, and Raphanus. In contradiction to the proposal that Cardaminopsis and Arabidopsis be put into an expanded tribe Arabideae, our data show that these two genera are more closely related to Capsella and Lepidium (tribe Lepidieae) than to Rorippa and Cardamine (tribe Arabideae). Further, our data show that within the tribe Brassiceae, Raphanus is more closely related to B. nigra than to the B. oleracea/B. rapa clade. This result is in agreement with the nuclear data obtained in several studies, but is in conflict with the RFLP data of mitochondrial and chloroplast DNA. As pointed out by previous authors, it is possible that Raphanus is a hybrid between the B. nigra and B. oleracea/B. rapa lineages with the latter as the maternal parent.

Arabidopsis↗