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PubMed1998

Subfamily divergence in the multigene family of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcS) in Triticeae and its relatives.

To investigate genetic mechanisms acting on multigene family in plants, we analyzed sequence variation in the rbcS gene of 13 species of Triticeae and one species each of related tribes (Bromeae and Aveneae). A total of 36 rbcS genes were analyzed. Based on dimorphism in the length of intron, the rbcSs of investigated species were classified into two subfamilies A and B. The difference in intron length was caused by an indel of about 200 bp in the middle of the intron. The two subfamilies of rbcS were present in the three tribes, indicating that the divergence of rbcS subfamilies occurred before the split of these tribes. Generally, variation between the two subfamilies of rbcS was larger than that within subfamily, but these two measures were about the same at the tribe level. This result suggested that divergence of the subfamilies of rbcS occurred at about the same time of tribe diversification. The level of nucleotide variation in the exon region between subfamilies was reduced in the Triticeae, but clear change was not detected in the intron sequence. This result suggested that the exon sequences between subfamilies of rbcS were homogenized without affecting the intron sequence in the Triticeae lineage.

Base Sequence↗
PubMed2004

Burkitt's lymphoma in Kenya: geographical, age, gender and ethnic distribution.

OBJECTIVE: To show the geographical (Provincial), age, gender and ethnic distribution of Burkitt's lymphoma in patients in Kenya. DESIGN: A retrospective review of patients' records for the years 1988-1992 and a prospective evaluation of patients with BL between 1993 and 1997. These were descriptive and hospitals based studies. SETTING: Kenyatta National Hospital; Kenya's main referral and teaching hospital and seven provincial hospitals. MAIN OUTCOME MEASURES: For each tissue proven Burkitt's lymphoma case the following were required; province of birth and residence, tribe, age, sex, chief complains, physical examination findings, investigation results and tissues result confirming the diagnosis of BL. STATISTICAL METHOD: Mainly proportions were used to compare variables, however Pearson's liner correlation was used to assess the time trends. RESULTS: This study registered 1005 patients; 961 (95.6%) children and 44 (4.4%) adults. 0-14 years the age standardized incidence rate (ASR) of 0.83. Variations documented in the provinces' BL ASR range; 1.8 Coast to 0.23 Rift Valley and increasing yearly trend for both children and adults. The major tribes in Kenya consisted; Luo 29.5%. Luhya (24.1%) and Coastal (16.5%). No patient of Asian or European or Arab extraction was recorded in the study. The age distribution showed no case below two years, a rapid rise from three year 3 (5.6%), and peak at 6 (19.5%) for children and at 17 years (13.6%) years for the adult. Age group 5-9 years had the highest ASR. The male to female (M:F) ratios were; 1.5:1 and 1:1 in children and adults respectively, provincial ratios range; 2.6:1 in Nairobi to 1.2:1 in Nyanza, the tribes range; 3.5:1 in Somali to 1:1 in other tribes between 2 and 14 years old when also males were more than females. Peak time of presentation of symptoms was 4 weeks. Tumour sites were in children; jaw 51.6%, abdomen (25%), combined jaw and abdomen 13.8% and others 9.6% and adults; jaw (4.5%), abdomen (43.2%), combined jaw and abdomen (25%) and other sites (27.3%) 67.6% males and 42.4% female adults had HIV infection and disseminated BL disease. CONCLUSION: The study demonstrates that Burkitt's lymphoma is a childhood disease. The disease distribution is consistent with intermediate risk Burkitt's lymphoma level. Furthermore the distribution varied by province, tribe, age and gender. The variations could be due to environmental factors.

Abdominal Neoplasms↗
PubMed1999

Phylogeny of the core Malvales: evidence from ndhF sequence data.

The monophyly of the group comprising the core malvalean families, Bombacaceae, Malvaceae, Sterculiaceae, and Tiliaceae, was recently confirmed by molecular studies, but the internal structure of this clade is poorly understood. In this study, we examined sequences of the chloroplast ndhF gene (aligned length 2226 bp) from 70 exemplars representing 35 of the 39 putative tribes of core Malvales. The monophyly of one traditional family, the Malvaceae, was supported in the trees resulting from these data, but the other three families, as traditionally circumscribed, are nonmonophyletic. In addition, the following relationships were well supported: (1) a clade, /Malvatheca, consisting of traditional Malvaceae and Bombacaceae (except some members of tribe Durioneae), plus Fremontodendron and Chiranthodendron, which are usually treated as Sterculiaceae; (2) a clade, /Malvadendrina, supported by a unique 21-bp (base pair) deletion and consisting of /Malvatheca, plus five additional subclades, including representatives of Sterculiaceae and Tiliaceae, and Durionieae; (3) a clade, /Byttneriina, with genera traditionally assigned to several tribes of Tiliaceae, plus exemplars of tribes Byttnerieae, Hermannieae, and Lasiopetaleae of Sterculiaceae. The most striking departures from traditional classifications are the following: Durio and relatives appear to be more closely related to Helicteres and Reevesia (Sterculiaceae) than to Bombacaceae; several genera traditionally considered as Bombacaceae (Camptostemon, Matisia, Phragmotheca, and Quararibea) or Sterculiaceae (Chiranthodendron and Fremontodendron) appear as sister lineages to the traditional Malvaceae; the traditional tribe Helictereae (Sterculiaceae) is polyphyletic; and Sterculiaceae and Tiliaceae, as traditionally circumscribed, represent polyphyletic groups that cannot sensibly be maintained with their traditional limits for purposes of classification. We discuss morphological characters and conclude that there has been extensive homoplasy in characters previously used to delineate major taxonomic groups in core Malvales. The topologies here also suggest that /Malvatheca do not have as a synapormophy monothecate anthers, as has been previously supposed but, instead, may be united by dithecate, transversely septate (polysporangiate) anthers, as found in basal members of both /Bombacoideae and /Malvoideae. Thus, "monothecate" anthers may have been derived at least twice, independently, within the /Bombacoideae (core Bombacaceae) and /Malvoideae (traditional Malvaceae).

Journal Article↗
PubMed1999

Factors associated with suicide ideation among American Indian adolescents: does culture matter?

Data from self-report surveys of 1,353 high school students representing three culturally distinct American Indian tribes were analyzed for tribal differences in factors associated with suicidal ideation. In the multivariate analysis, no single correlate of suicide ideation was common to all three tribes. The correlates of suicide ideation were consistent with each tribe's social structure, conceptualization of individual and gender roles, support systems, and conceptualization of death. These results underscore the heterogeneity of suicide ideation across three distinct American Indian tribes consistent with their cultural heterogeneity. Suicide prevention and screening programs may be difficult to adapt from one tribe to another.

Adolescent↗
PubMed1999

Hereditary hemolytic disorders among the Ashram school children in Mayurbhanj district of Orissa.

Hemoglobinopathy and allied hemolytic disorders are important genetic and public health problems in Orissa. These cause high degree of hemolytic anemia, morbidity and mortality in the vulnerable populations. A total of 465 Ashram School children aged 6-15 years belonging to Bathudi, Bhumiz, Kolha and Santal tribes in six localities of Mayurbhanj district of Orissa were screened for hemoglobinopathy, glucose-6-phosphate dehydrogenase (G-6-PD) deficiency, ABO and Rhesus blood groups serology and any other hereditary condition. The sickle cell trait (Hb AS) was detected in Santal (1.0%), Bathudi (1.0%) and Bhumiz (0.9%) tribals. No case of homozygous sickle cell disease was detected among the tribes of Mayurbhanj district. The beta-thalassemia trait was detected in Santal (8.0%), Kolha (2.0%), Bhumiz (1.7%) and other tribal (3.8%) students. Sickle cell hemoglobinopathy and beta-thalassemia are prevalent in this district among the tribes, but the frequency is very low. The prevalence of G-6-PD deficiency is considerably high (7.7-9.8%) among the tribes of Mayurbhanj district in Orissa. Out of total 43 G-6-PD deficient subjects, there were 32 males, 9 heterozygote females and 2 homozygous females. This shows that the antimalarial drugs should be administered with caution as these cause hemolytic anemia, sometimes fatal also. The distribution of ABO and Rhesus blood groups shows the preponderance of B blood group (33.8%) over O (29.6%) and 2.1% cases of Rhesus negativity were detected among the Bathudi tribe. This pattern is consistent with the characteristic features of tribal populations in India.

Adolescent↗
PubMed2000

Phylogenetic relationships among eighteen neotropical Culicini species.

The subgeneric relationships among 8 generic and infrageneric taxa of the Culicini tribe were examined by cladistic analysis based on 30 larval mouthpart characters (maxillae and mandibles) of 7 subgenera of Culex L. and 1 of Deinocerites Theobald. We analyzed 18 ingroup species as well as Deinocerites melanophylum Dyar and Knab as a sister group, and Aedes taeniorhynchus Wiedemann as an outgroup. A parsimony analysis using the Nona program resulted in 2 trees each of 109 steps (consistency and retention indices = 0.88). The topologies obtained were similar to the current classification of the tribe, based on nonexplicit methods mainly including adult characters, with 2 exceptions. In the present work, the monophyly of the tribe Culicini (Culex + Deinocerites) was supported by 4 synapomorphies. The subgenus Lutzia Theobald formed the most basal clade in the tribe Culicini and the placement of Phenacomyia Harbach and Peyton as a subgenus was validated by its location as a sister group of the subgenus Culex and other subgenera. The subgenus Carrollia Lutz was the most robust taxon, supported by 5 synapomorphies, and was congruent with the infragroups of the current classification. The relationships among Deinocerites, Anoedioporpa Dyar, Microculex Theobald, and Melanoconion Theobald were unresolved, but were placed in the most internal clade of the tribe. The 1st exception to the accepted classification was the poorly resolved boundary between Anoedioporpa and Microculex The 2nd was the strong support (with 11 synapomorphies) for the inclusion of Deinocerites as a subgenus of Culex in the Culicini, which is proposed here.

Animals↗
PubMed2000

Further data on the microsatellite locus D12S67 in worldwide populations: an unusual distribution of D12S67 alleles in Native Americans.

We report the frequencies of alleles at the microsatellite locus D12S67 in 2 widely separated ethnic groups of the world: 2 populations from Sulawesi, an island in the Indonesian archipelago, and 5 Native American tribes of Colombia, South America. The allele frequencies in the Minihasans and Torajans of Sulawesi are similar to each other (but the modal class allele is different) and in general agreement with those reported in mainland Asian groups, but different from both Europeans and Chinese Han of Taiwan. The 5 Native American tribes (Arsario, Kogui, Ijka, Wayuu, and Coreguaje) display different allele frequencies from those seen in Sulawesi populations, in other groups from Europe and mainland Asia, and in Chinese Han of Taiwan. Native Americans exhibit a bimodal distribution of alleles, unlike other groups, with significant differences among the tribes. The Arsario and Kogui have no admixture with Europeans or Africans and are the most distinctive, while the Wayuu have the most admixture and show most similarity to other groups. The data suggest that nonadmixed Native Americans may be quite distinctive with respect to this marker. The most common allele varies across the 5 tribes, from 249 base pairs to 261 base pairs. All samples exhibit Hardy-Weinberg genotype proportions; heterozygosities are lowest in the 2 nonadmixed Native American tribes. Examination of all the available data indicates that some east Asian and southeast Asian groups are characterized by a high frequency of smaller sized D12S67 alleles, while other populations have a greater proportion of the larger sized alleles. The cumulative, though still highly restricted, population data on locus D12S67 demonstrate that it may be of considerable value in anthropological genetic studies of ethnic groups. Data are required on Native Americans outside Colombia before this marker can be used in admixture studies of this group.

Base Pairing↗
PubMed2001

Disintegration of the scrophulariaceae.

A molecular systematic study of Scrophulariaceae sensu lato using DNA sequences of three plastid genes (rbcL, ndhF, and rps2) revealed at least five distinct monophyletic groups. Thirty-nine genera representing 24 tribes of the Scrophulariaceae s.l. (sensu lato) were analyzed along with representatives of 15 other families of Lamiales. The Scrophulariaceae s.s. (sensu stricto) include part or all of tribes Aptosimeae, Hemimerideae, Leucophylleae, Manuleae, Selagineae, and Verbasceae (= Scrophularieae) and the conventional families Buddlejaceae and Myoporaceae. Veronicaceae includes all or part of tribes Angelonieae, Antirrhineae, Cheloneae, Digitaleae, and Gratioleae and the conventional families Callitrichaceae, Globulariaceae, Hippuridaceae, and Plantaginaceae. The Orobanchaceae include tribes Buchnereae, Rhinantheae, and the conventional Orobanchaceae. All sampled members of Orobanchaceae are parasitic, except Lindenbergia, which is sister to the rest of the family. Family Calceolariaceae Olmstead is newly erected herein to recognize the phylogenetic distinctiveness of tribe Calceolarieae. The Calceolariaceae are close to the base of the Lamiales. The Stilbaceae are expanded by the inclusion of Halleria. Mimulus does not belong in any of these five groups.

Journal Article↗
PubMed1990

[Epidemiological study on ossification of the posterior longitudinal ligament (OPLL) in the cervical spine--comparison of the prevalence between Japanese and Taiwanese].

The etiology of OPLL still remains obscure. The purpose of this study is to clarify whether OPLL in the cervical spine occurs more often in the Japanese than in the Chinese and the Takasago tribe (native tribe) in Taiwan. Lateral X-ray films of the cervical spine in these inhabitants over the age of 30 years were studied. Results were as follows. The prevalent rate of OPLL in the cervical spine was significantly lower in the Chinese (p less than 0.01) and in the Takasago tribe (p less than 0.05) as compared to the Japanese in Kagoshima. OPLL was found in 2 out of 1,004 Chinese (0.2%), in 2 out of 529 Takasago tribe (0.4%), and in 9 out of 514 Japanese in Kagoshima (1.8%). The incidence of ossification of the anterior longitudinal ligament, Barsony's disease and posterior osteophyte was significantly higher in the Chinese, while there was no significant difference of their incidence between the Takasago tribe and the Japanese in Kagoshima. This study suggests that the difference in the prevalence of cervical OPLL exists between Japanese and Taiwanese. However, further epidemiological survey is needed to ascertain this point.

Adult↗
PubMed1996

Population structure and genetic differentiation among 16 tribal populations of central India.

Genetic polymorphisms for six blood groups, three red cell enzymes, three serum proteins, and hemoglobin were examined in sixteen central Indian tribal populations. Nine of the tribes belonged to Orissa, five to Madhya Pradesh, and two to Maharashtra. Eleven tribes spoke the Dravidian language, three Indo-Ayran, and two the language of the Austro-Asiatic families. The population structure of these tribal populations was analyzed at the inter- and intrastate and linguistic levels, using data for 13 genetic systems (38 alleles or haplotypes). Nine of the 13 loci showed significant heterogeneity in the 16 tribes, and the pattern of heterogeneity was also discernible in the different states and in the Dravidian-speaking tribes. As expected, the extent of genetic differentiation or gene diversity was the highest so far reported from central India. The mean FIS and HS for each locus in the different state, linguistic, and total tribal groups were consistently higher than the FST and GST values, respectively, showing that the genetic structure of each tribe is highly influenced by inbreeding. In a genetic affinity analysis by genetic distance the Indo-Aryan and Austro-Asiatic language groups showed little affinity with each other, although there was some tendency toward geographic affinity. The present analysis indicates that, in addition to genetic drift, gene flow, and selection, the genetic structure of the populations of central India is also highly influenced by sociocultural adaptation and inbreeding.

Ethnicity↗
PubMed1997

Factor IX gene haplotypes in Amerindians.

We have determined the haplotypes of the factor IX gene for 95 Indians from 5 Brazilian Amazon tribes: Wayampí, Wayana-Apalaí, Kayapó, Arára, and Yanomámi. Eight polymorphisms linked to the factor IX gene were investigated: MseI (at 5', nt -698), BamHI (at 5', nt -561), DdeI (intron 1), BamHI (intron 2), XmnI (intron 3), TaqI (intron 4), MspI (intron 4), and HhaI (at 3', approximately 8 kb). The results of the haplotype distribution and the allele frequencies for each of the factor IX gene polymorphisms in Amerindians were similar to the results reported for Asian populations but differed from results for other ethnic groups. Only five haplotypes were identified within the entire Amerindian study population, and the haplotype distribution was significantly different among the five tribes, with one (Arára) to four (Wayampí) haplotypes being found per tribe. These findings indicate a significant heterogeneity among the Indian tribes and contrast with the homogeneous distribution of the beta-globin gene cluster haplotypes but agree with our recent findings on the distribution of alpha-globin gene cluster haplotypes and the allele frequencies for six VNTRs in the same Amerindian tribes. Our data represent the first study of factor IX-associated polymorphisms in Amerindian populations and emphasizes the applicability of these genetic markers for population and human evolution studies.

Brazil↗
PubMed1996

Molecular phylogeny of the New World monkeys (Platyrrhini, primates) based on two unlinked nuclear genes: IRBP intron 1 and epsilon-globin sequences.

Nuclear sequences of the 1.8 kilobase (kb) long intron 1 of the interstitial retinol-binding protein gene (IRBP), previously determined for 11 of the 16 extant genera of New World monkeys (superfamily Ceboidea, infraorder Platyrrhini), have now been determined for the remaining 5 genera. The maximum parsimony trees found, first with IRBP sequences alone and then with tandemly combined IRBP and epsilon-globin gene sequences from the same species, supported a provisional cladistic classification with the following clusters. Subtribes Callitrichina (Callithrix, Cebuella), Callimiconina (Callimico), Leontopithecina (Leontopithecus) and Saguina (Saguinus) constitute subfamily Callitrichinae, and subfamilies Callitrichinae, Aotinae (Aotus), and Cebinae (Cebus, Saimiri) constitute family Cebidae. Subtribes Chiropotina (Chiropotes, Cacajao) and Pitheciina (Pithecia) constitute tribe Pitheciini; and tribes Pitheciini and Callicebini (Callicebus) constitute subfamily Pitheciinae. Subtribes Brachytelina (Brachyteles, Lagothrix) and Atelina (Ateles) constitute tribe Atelini, and tribes Atelini and Alouattini (Alouatta) constitute subfamily Atelinae. The parsimony results were equivocal as to whether Pitheciinae should be grouped with Atelinae in family Atelidae or have its own family Pitheciidae. The cladistic groupings of extant ceboids were also examined by different stochastic evolutionary models that employed the same stochastic process of nucleotide substitutions but alternative putative phylogenetic trees on which the nucleotide substitutions occurred. Each model, i.e., each different tree, predicted a different multinomial distribution of nucleotide character patterns for the contemporary sequences. The predicted distributions that were closest to the actual observed distributions identified the best fitting trees. The cladistic relationships depicted in these best fitting trees agreed in almost all cases with those depicted in the maximum parsimony trees.

Animals↗
PubMedDate not supplied

Asian and non-Asian origins of Mon-Khmer- and Mundari-speaking Austro-Asiatic populations of India.

In the present study, we analyzed 1,686 samples from 31 tribal populations of India for the mitochondrial DNA 9-base-pair deletion/insertion polymorphism, and characterized them based on the relevant mitochondrial DNA coding-region single nucleotide polymorphisms and hypervariable region I motifs, to test the genetic origins of the ethnically and linguistically heterogeneous Austro-Asiatic tribes of India. A comparative analysis of our results with the existing data suggests multiple origins of Austro-Asiatic tribes in India, and particularly the Asian and non-Asian origins of the Mon-Khmer and the Mundari populations. We also identified a novel subclade of haplogroup B in the Mon-Khmer Khasi tribes that distinguishes them from the Nicobarese, indicating two different waves of migration of the Mon-Khmer tribes in India.

Classification↗
PubMed2004

Atelinae phylogenetic relationships: the trichotomy revived?

This research examines phylogenetic relationships between members of the Atelinae subfamily (Alouatta, Ateles, Brachyteles, and Lagothrix), based on analysis of three genetic regions. Two loci, cytochrome c oxidase subunit II (COII) and the hypervariable I portion of the control region, are part of the mitochondrial genome. The other is a single-copy nuclear gene, Aldolase A Intron V. Analysis of these genetic regions provides support for tribe Alouattini containing the Alouatta species, while tribe Atelini contains the other three genera. However, these three genetic regions produce conflicting results for relationships among tribe Atelini members. Previous genetic studies supported grouping Brachyteles with Lagothrix, leaving Ateles in a separate subclade. The present data sets vary based on the genetic region analyzed and method of analysis suggesting all possible cladistic relationships. These results are more consistent with investigations of morphology and behavior among these primates. The primary cause of discrepancy between this study and previous genetic studies is postulated to reside in increased sampling in the present study of genetic variation among members of the Atelinae, specifically Ateles. The present study utilized samples of Ateles from all postulated species for this genetically variable primate, while previous studies used only one or two species of Ateles. This paper demonstrates that shifting relationships are produced when different species of Ateles are used to reconstruct phylogenies. This research concludes that a trichotomy should still be supported between members of tribe Atelini until further analyses, which include additional Atelinae haplotypes are conducted.

Animals↗
PubMed2004

Chiral response of Oryzeae and Paniceae plants in alpha-methylbenzyl-3-p-tolyl urea agar medium.

The results presented here support the hypothesis that plants of the tribe Oryzeae respond enantioselectively and homogeneously to optically active 1-alpha-methylbenzyl-3-p-tolylurea (MBTU) in root growth inhibition, in contrast to Echinochloa species. The Oryzeae plants tested in this study belong to different genera (Oryza, Leersia, Chikusichloa and Zizania), to different species (O sativa, O glaberrima, O alta, O coarctata, O latifolia, O minuta, O rufipogon), to various ecospecies of Oryza (japonica, indica, japonica x indica, javanica) and to different levels of evolution [cultivated rice (O sativa and O glaberrima) and ancestral wild rice species]. In spite of their different phylogenic status and diverse sensitivity, the root growth of all members of the genus Oryza was inhibited more by R-MBTU than by S-MBTU. Zizania palustris, Z latifolia, Leersia oryzoides and Chikusichloa aquatica belonging to the tribe Oryzeae exhibited similar chiral recognition to the Oryza plants, suggesting that Oryzeae have a common chiral recognition mechanism in their response to optically active MBTUs. In contrast, Echinochloa plants (E crus-galli (L) Beauv var crus-galli and E colonum (L) Link), belonging into subfamily Panicoideae tribe Paniceae, responded in a different way, where their root growth was more sensitive to S-MBTU than to the antipodal R-MBTU. A reverse chiral response between the tribe Oryzeae and the genus Echinochloa was clearly indicated in this study. This diverse response may be relevant to Gramineae classification.

Agar↗
PubMed1996

Private polymorphisms: how many? How old? How useful for genetic taxonomies?

The data on the distribution and frequencies of private polymorphisms in the tribal populations of Central and South America are used to address the question of the extent to which such data can be used to address questions of phylogenetic history. It is shown that due to the great increases in population number that accompanied agricultural development, most private polymorphisms have arisen since population settlement and tribal differentiation. Conversely, the absence of Amerindian variants of wide distribution confirms the small size of the hemispheric population until relatively recent times. Patterns of recent population decline and recovery that accompanied European contact since 1492 have also had a strong impact on the age distribution of extant variants, eliminating many that were relatively young in 1492. The majority of surviving variants that have achieved polymorphic frequencies in a tribe or group of tribes are from 100 to 400 generations old (2500 to 10,000 years). Such genetic variants thus characterize tribes, or groups of closely related tribes, but do not provide a greater time depth of phylogenetic history.

Alleles↗
PubMed2000

The complete external transcribed spacer of 18S-26S rDNA: amplification and phylogenetic utility at low taxonomic levels in asteraceae and closely allied families.

For molecular phylogenetic reconstruction of some intrageneric groups of plants, a DNA region is needed that evolves more rapidly than the internal transcribed spacer (ITS) of the 18S-26S nuclear ribosomal DNA (nrDNA) repeat. If the region identified is nuclear, it would also be desirable for it to undergo rapid concerted evolution to eliminate problems with coalescence. The external transcribed spacer (ETS) of the nrDNA repeat has shown promise for intrageneric phylogenetic reconstruction, but only the 3' end of the region has been utilized for phylogenetic reconstruction and "universal" primers for PCR amplification have been elusive. We present a method for reliably amplifying and sequencing the entire ETS throughout Asteraceae and some closely allied families. We also show that the ETS is more variable and phylogenetically informative than the ITS in three disparate genera of Asteraceae-Argyranthemum (tribe Anthemideae), Asteriscus (tribe Inuleae), and Helianthus (tribe Heliantheae). The full ETS was amplified using a primer (ETS1f) within the intergenic spacer in combination with a primer (18S-2L) in the 5' end of the highly conserved 18S gene. ETS1f was designed to correspond to a highly conserved region found in Helianthus and Crepis, which are in separate subfamilies of Asteraceae. ETS1f/18S-2L primed in all of the tribes of Asteraceae as well as exemplar taxa from Campanulaceae, Goodeniaceae, and Calyceraceae. For both Argyranthemum and Asteriscus, we were able to directly sequence the ETS PCR products when a single band was produced. When multiple bands were produced, we gel-purified and occasionally cloned the band of interest before sequencing. Although PCR produced single bands for Helianthus species, it was necessary to clone Helianthus amplifications prior to sequencing due to multiple intragenomic ETS repeat types. Alignment of ETS sequences for Argyranthemum and Asteriscus was straightforward and unambiguous despite some subrepeat structure in the 5' end. For Helianthus, different numbers of large tandem subrepeats in different species required analysis of the orthology of the subrepeats prior to alignment. In all three genera, the ETS provided more informative variation for phylogenetic reconstruction and allowed better resolution of relationships than the ITS. Although cloned sequences from Helianthus differed, intragenomic clones consistently formed clades. This result indicated that concerted evolution was proceeding rapidly enough in ETS that species-specific phylogenetic signal was retained. It should be now be possible to use the entire ETS for phylogenetic reconstruction of recently diverged lineages in Asteraceae and at least three other families (approximately 26,000 species or about 8% of all angiosperms).

Asteraceae↗
PubMed2001

Phylogenetic relationships of major clades of Catostomidae (Teleostei: Cypriniformes) as inferred from mitochondrial SSU and LSU rDNA sequences.

Suckers (Family Catostomidae) are holarctic in distribution and include 76 recent species in 14 genera, with 13 genera and 75 species occurring in North and Central America and Siberia. Although this group constitutes a significant component of many aquatic ecosystems, most historic systematic effort has been either alpha- or limited beta-level studies focusing on the two largest tribes within the family, the Catostomini and the Moxostomatini. A recent phylogenetic study based on morphological, biochemical, and early life history characters has advanced current understanding of relationships among catostomid fishes. To further examine phylogenetic relationships among basal lineages of catostomids, we sequenced the entire mitochondrial (mt) SSU and LSU rRNA genes from genera representing all subfamilies and tribes within Catostomidae. Phylogenetic analysis of gene sequences yielded monophyletic Catostomidae, Ictiobinae, and Catostominae and para- or polyphyletic Cycleptinae, with Myxocyprinus as the basal-most taxon and Cycleptus as either the next most-basal taxon or the taxon basal to the Catostominae. Relationships within the Catostominae were generally consistent with those proposed in the above-noted recent phylogenetic study although Thoburnia and Hypentelium were either a clade sister to or a grade group relative to Moxostoma and Scartomyzon. In all trees, Scartomyzon was paraphyletic and embedded within Moxostoma. Phylogenetic affinities of Erimyzon and Minytrema varied depending on data set and character weighting scheme employed. To better reflect phylogenetic relationships resolved in this extensive analysis, we propose the following changes to the classification of catostomids: formation of the new subfamily Myxocyprininae, containing Myxocyprinus from China; restriction of the Cycleptinae to the two species of Cycleptus from North America; restriction of the tribe Moxostomatini to Moxostoma and Scartomyzon; Erimyzon and Minytrema are incertae sedis within Catostominae; and resurrection of the tribe Thoburniini, containing Thoburnia and expanded to include Hypentelium.

Animals↗