Phylogenetic Relationships among Members of the Coregoninae Inferred from Direct Sequencing of PCR-Amplified Mitochondrial DNA

1993 ◽  
Vol 50 (10) ◽  
pp. 2112-2118 ◽  
Author(s):  
S. Fournier Lockwood ◽  
Robert E. Dillinger Jr. ◽  
Tim P. Birt ◽  
John M. Green ◽  
Thomas P. Snyder
Keyword(s):  
Mitochondrial Dna ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Direct Sequencing ◽  
Cladistic Analysis ◽  
Sequence Divergence ◽  
Amino Acid Replacement ◽  
Mitochondrial Cytochrome B ◽  
Mtdna Sequence ◽  
Polymerase Chain

We determined the DNA sequence of a portion of the mitochondrial cytochrome b gene for eight members of the Coregoninae (Salmonidae) from North America in an effort to elucidate phylogenetic relationships in the subfamily. DNA was prepared for sequencing by the polymerase chain reaction (PCR). Direct estimates of mitochondrial DNA (mtDNA) sequence divergence among taxa ranged from 0.0% between Arctic cisco (Coregonus autumnalis) from the Mackenzie River, Canada, and cisco (C. artedi) from the Laurentian Great Lakes to 5.8% between the inconnu (Stenodus leucichthys) and the round whitefish (Prosopium cylindraceum). As has been noted in other fish species and vertebrates in general, third position silent substitutions predominated over any other type of nucleotide change. No amino acid replacement substitutions were found among any of the eight taxa examined. Comparison of mtDNA sequence divergence estimates from this and other studies suggests that the radiation of the genera within the Coregoninae occurred relatively recently (2–6 million yr B.P.). Cladistic analysis of the mtDNA sequence data yields a hypothesis of relationships that supports previous genetic and morphological classifications of coregonines.

Genetic divergence and geographic diversification in Nautilus

Paleobiology ◽  
1995 ◽  
Vol 21 (2) ◽  
pp. 220-228 ◽  
Author(s):  
Charles G. Wray ◽  
Neil H. Landman ◽  
W. Bruce Saunders ◽  
James Bonacum
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Distinct Species ◽  
Morphological Characters ◽  
Geographic Diversification ◽  
Isolated Populations ◽  
Systematic Analysis

Despite exhaustive investigation of present-day Nautilus, the phylogenetic relationships of the five or six recognized species within this genus remain unclear. Mitochondrial and nuclear DNA sequence data plus a suite of morphological characters are used to investigate phylogenetic relationships. Systematic analysis of the morphological variation fails to characterize described species as independent lineages. However, DNA sequence analysis indicates that there are three geographically distinct clades consisting of western Pacific, eastern Australian/Papua-New Guinean, and western Australian/Indonesian forms. The morphologically and genetically distinct species Nautilus scrobiculatus falls outside the three geographically recognized assemblages. Members of the genus Nautilus also exhibit low levels of sequence divergence. All these data suggest that Nautilus is currently undergoing diversification, which may have begun only several million years ago. These data also suggest that some of the morphological features used to define Nautilus species may simply represent fixed variations in isolated populations within the same species.

Molecular evolution of freshwater snail intermediate hosts within the Bulinus forskalii group

Parasitology ◽  
2001 ◽  
Vol 123 (7) ◽  
pp. 277-292 ◽  
Author(s):  
C. S. JONES ◽  
D. ROLLINSON ◽  
R. MIMPFOUNDI ◽  
J. OUMA ◽  
H. C. KARIUKI ◽  
...  
Keyword(s):  
Sequence Data ◽  
Random Amplified Polymorphic Dna ◽  
Sequence Divergence ◽  
Freshwater Snail ◽  
Coi Gene ◽  
Species Differentiation ◽  
Intermediate Hosts ◽  
East African ◽  
Species Complexes ◽  
Mtdna Sequence

Freshwater snails of the Bulinus forskalii group are one of four Bulinus species complexes responsible for the transmission of schistosomes in Africa and adjacent regions. The species status of these conchologically variable and widely distributed planorbids remains unclear, and parasite compatibility varies considerably amongst the eleven taxa defined, making unambiguous identification and differentiation important prerequisites for determining their distributions and evolutionary relationships. Random Amplified Polymorphic DNA (RAPD) analyses were used to investigate relationships between taxa, with particular emphasis on Central and West African representatives. RAPD-derived phylogenies were compared with those from other independent molecular markers, including partial sequences of mitochondrial cytochrome oxidase subunit I (COI) gene, and the nuclear ribosomal RNA internal transcribed spacer 1 region (ITS1). The phylogenetic reconstructions from the three approaches were essentially congruent, in that all methods of analysis gave unstable tree topologies or largely unresolved branches. There were large sequence divergence estimates between species, with few characters useful for determining relationships between species and limited within species differentiation. Nuclear and mtDNA sequence data from Central and East African representatives of the pan-African B. forskalii showed little evidence of geographical structuring. Despite the unresolved structure within the phylogenies, specimens from the same species clustered together indicating that all methods were capable of differentiating taxa but could not establish the inter-specific relationships with confidence. The limited genetic variation displayed by B. forskalii, and the evolution and speciose nature of the group, are discussed in the context of the increasingly arid climate of the late Miocene and early Pliocene of Africa.

scholarly journals Phylogenetic Relationships of Micronesian White-Eyes Based on Mitochondrial Sequence Data

The Auk ◽  
2000 ◽  
Vol 117 (2) ◽  
pp. 355-365 ◽  
Author(s):  
Beth Slikas ◽  
Isaac B. Jones ◽  
Scott R. Derrickson ◽  
Robert C. Fleischer
Keyword(s):  
Genetic Divergence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Single Species ◽  
Additional Species ◽  
Data Set ◽  
Mitochondrial Sequence ◽  
Sister Relationships ◽  
Optimal Trees

Abstract Using mitochondrial sequence data, we estimated phylogenetic relationships and genetic divergence among selected species of white-eyes (Zosteropidae). We focused on taxa endemic to islands in Micronesia, specifically Zosterops conspicillatus, Z. semperi, Z. hypolais, Rukia oleaginea, and Cleptornis marchei. We also included in our data set five additional species of Zosterops from the Indo-Australian region and three species from Africa, as well as additional passerine outgroups. Our mitochondrial sequence data revealed substantial genetic divergence (5.7 to 7.3%) among Z. conspicillatus, Z. semperi, and Z. hypolais, three taxa that formerly were treated as a single species. In addition, a sequence divergence of 6.5 ± SE of 1.7% was found between the population of Z. conspicillatus from Rota and “conspecific” populations on Guam, Tinian, and Saipan. The distinctiveness of the Rota population suggests that this taxon should be recognized as a distinct species, a result that bears on the conservation of this population because it has been declining dramatically in recent years. All optimal trees based on analysis of the mitochondrial sequence data place Rukia oleaginea within the genus Zosterops. In all optimal trees, Cleptornis marchei positions as the sister taxon to a clade including all other zosteropids included in this study. The trees based on our data strongly contradict the traditional classification of Cleptornis as a honeyeater (family Meliphagidae). Our data cannot resolve with any confidence the sister relationships of the insular endemic white-eyes, although the optimal trees suggest multiple colonizations of Micronesia by more than one white-eye lineage.

scholarly journals Mitochondrial DNA variation and the evolution of Robertsonian chromosomal races of house mice, Mus domesticus.

Genetics ◽  
1994 ◽  
Vol 136 (3) ◽  
pp. 1105-1120 ◽  
Author(s):  
M W Nachman ◽  
S N Boyer ◽  
J B Searle ◽  
C F Aquadro
Keyword(s):  
Mitochondrial Dna ◽  
Western Europe ◽  
Sequence Divergence ◽  
Mus Domesticus ◽  
Sequence Evolution ◽  
Ancestral Polymorphism ◽  
Chromosomal Races ◽  
Mtdna Sequence ◽  
Average Sequence Divergence ◽  
Standard Karyotype

Abstract The house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races with diploid numbers from 2n = 22 to 2n = 38. Although these races are highly differentiated karyotypically, they are otherwise indistinguishable from standard karyotype (i.e., 2n = 40) mice, and consequently their evolutionary histories are not well understood. We have examined mitochondrial DNA (mtDNA) sequence variation from the control region and the ND3 gene region among 56 M. domesticus from Western Europe, including 15 Rb populations and 13 standard karyotype populations, and two individuals of the sister species, Mus musculus. mtDNA exhibited an average sequence divergence of 0.84% within M. domesticus and 3.4% between M. domesticus and M. musculus. The transition/transversion bias for the regions sequenced is 5.7:1, and the overall rate of sequence evolution is approximately 10% divergence per million years. The amount of mtDNA variation was as great among different Rb races as among different populations of standard karyotype mice, suggesting that different Rb races do not derive from a single recent maternal lineage. Phylogenetic analysis of the mtDNA sequences resulted in a parsimony tree which contained six major clades. Each of these clades contained both Rb and standard karyotype mice, consistent with the hypothesis that Rb races have arisen independently multiple times. Discordance between phylogeny and geography was attributable to ancestral polymorphism as a consequence of the recent colonization of Western Europe by mice. Two major mtDNA lineages were geographically localized and contained both Rb and standard karyotype mice. The age of these lineages suggests that mice have moved into Europe only within the last 10,000 years and that Rb populations in different geographic regions arose during this time.

scholarly journals Phylogenetic relationships in the genus Apis inferred from mitochondrial DNA sequence data

Apidologie ◽  
1991 ◽  
Vol 22 (1) ◽  
pp. 87-92 ◽  
Author(s):  
L. Garnery ◽  
D. Vautrin ◽  
J. M. Cornuet ◽  
M. Solignac
Keyword(s):  
Mitochondrial Dna ◽  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Dna Sequence Data ◽  
Mitochondrial Dna Sequence
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