Mitochondrial 16S rRNA Sequences Research Articles

Intraspecific diversity of mitochondrial DNA in the land snail Euhadra peliomphala (Bradybaenidae)

Exceptionally high levels of intraspecific variation of mitochondrial DNA (mtDNA) sequences encoding 16S ribosomal RNA (16SrRNA) were detected in populations of the land snail Euhadra peliomphala from the eastern part of Japan. Geographical isolation has occurred within small areas and has created many genetically distinct local populations. These are morphologically segregated into two groups: the first consists of populations from the southern part of the Izu Peninsula, and the second of populations from other areas within the peninsula. They are separated by mountains in the middle of the peninsula. Sequence divergences between these two groups were 7.6–9.5%. The sequence divergences and geological ages of the Izu peninsula and its mountains suggest that the divergence rate of mitochondrial 16SrRNA sequences of this species is extremely rapid, approximately 10% per million years. This rapid evolutionary rate of mtDNA and vicariance events due to tectonic events and sea level changes has also contributed to creating exceptional geographical variation in the mtDNA of this species.

Intraspecific diversity of mitochondrial DNA in the land snail Euhadra peliomphala (Bradybaenidae)

Exceptionally high levels of intraspecific variation of mitochondrial DNA (mtDNA) sequences encoding 16S ribosomal RNA (16SrRNA) were detected in populations of the land snail Euhadra peliomphala from the eastern part of Japan. Geographical isolation has occurred within small areas and has created many genetically distinct local populations. These are morphologically segregated into two groups: the first consists of populations from the southern part of the Izu Peninsula, and the second of populations from other areas within the peninsula. They are separated by mountains in the middle of the peninsula. Sequence divergences between these two groups were 7.6–9.5%. The sequence divergences and geological ages of the Izu peninsula and its mountains suggest that the divergence rate of mitochondrial 16SrRNA sequences of this species is extremely rapid, approximately 10% per million years. This rapid evolutionary rate of mtDNA and vicariance events due to tectonic events and sea level changes has also contributed to creating exceptional geographical variation in the mtDNA of this species.

Total evidence: Molecules, morphology, and the phylogenetics of cichlid fishes

We present a most comprehensive phylogenetic analysis of the family Cichlidae. New data analyzed include mitochondrial 16S rRNA sequences and two nuclear loci (Tmo-M27 and Tmo-4C4) for a large taxonomic sampling with emphasis on South American species. We also incorporate a published morphological data set for a total evidence analysis. Character congruence among mitochondrial (74 taxa) and nuclear data (50 taxa) was high. However, partition-homogeneity tests suggest significant heterogeneity among molecular and morphological data. In agreement with results obtained from molecular data alone, total evidence analysis (1,460 characters for 34 taxa) supports a robust phylogenetic hypothesis for the family Cichlidae that is congruent with drift-vicariance events associated with the fragmentation of Gondwana. Our analyses confirm the placement of Malagasy/Indian cichlids as the most basal lineages, with a sister-group relationship to the monophyletic African and Neotropical clades. Total evidence suggests that the controversial African genus Heterochromis is at the base of the African radiation. Among more than 50 Neotropical genera analyzed, Retroculus is identified as the basal taxon, with successive branching of Cichla, Astronotus, geophagines (including crenicichlines) + chaetobranchines, and cichlasomines + heroines. Relative rate tests applied to mitochondrial DNA suggest significantly higher rates of genetic variation in Neotropical than in African taxa, and both mitochondrial and nuclear sequences show that rate heterogeneity among Neotropical lineages is confined to the geophagine cichlids. J. Exp. Zool. (Mol. Dev. Evol.) 288:76–92, 2000. © 2000 Wiley-Liss, Inc

Total evidence: Molecules, morphology, and the phylogenetics of cichlid fishes

We present a most comprehensive phylogenetic analysis of the family Cichlidae. New data analyzed include mitochondrial 16S rRNA sequences and two nuclear loci (Tmo-M27 and Tmo-4C4) for a large taxonomic sampling with emphasis on South American species. We also incorporate a published morphological data set for a total evidence analysis. Character congruence among mitochondrial (74 taxa) and nuclear data (50 taxa) was high. However, partition-homogeneity tests suggest significant heterogeneity among molecular and morphological data. In agreement with results obtained from molecular data alone, total evidence analysis (1,460 characters for 34 taxa) supports a robust phylogenetic hypothesis for the family Cichlidae that is congruent with drift-vicariance events associated with the fragmentation of Gondwana. Our analyses confirm the placement of Malagasy/Indian cichlids as the most basal lineages, with a sister-group relationship to the monophyletic African and Neotropical clades. Total evidence suggests that the controversial African genus Heterochromis is at the base of the African radiation. Among more than 50 Neotropical genera analyzed, Retroculus is identified as the basal taxon, with successive branching of Cichla, Astronotus, geophagines (including crenicichlines) + chaetobranchines, and cichlasomines + heroines. Relative rate tests applied to mitochondrial DNA suggest significantly higher rates of genetic variation in Neotropical than in African taxa, and both mitochondrial and nuclear sequences show that rate heterogeneity among Neotropical lineages is confined to the geophagine cichlids.

Extreme Intraspecific Mitochondrial DNA Sequence Divergence inGalaxias maculatus(Osteichthys: Galaxiidae), One of the World's Most Widespread Freshwater Fish

Biogeographic controversies surrounding the widespread freshwater fish,Galaxias maculatus,were addressed with DNA sequence data. Mitochondrial cytochromeband 16S rRNA sequences were obtained from representatives of six populations of this species. Substantial levels of cytochromeb(maximum 14.6%) and 16S rRNA sequence divergence (maximum 6.0%) were detected between western Pacific (Tasmania–New Zealand) and South American (Chile–Falkland Islands) haplotypes. A considerable level of divergence was also detected between Tasmanian and New Zealand haplotypes (maximum 5.1%) and within and among Chilean and Falkland Island G. maculatus (maximum 3.8%). The phylogenetic structure of haplotypes conflicts with the accepted pattern of continental fragmentation. Molecular clock calibrations suggest that haplotype divergences postdate the fragmentation of Gondwana. These findings point to marine dispersal rather than ancient vicariance as an explanation for the wide distribution. The phylogenetic structure of South American haplotypes was not consistent with their geographic distribution. We consider factors such as population divergence, population size, dispersal, secondary contact, and philopatry as potential causes of the high level of mtDNA nucleotide diversity in this species.

Molecular Relationships of the Extinct Pig-Footed Bandicoot Chaeropus ecaudatus (Marsupialia: Perameloidea) Using 12S rRNA Sequences

The pig-footed bandicoot, Chaeropus ecaudatus, is presumed to be extinct as no specimens have been collected or seen since early this century. Usually classified as a specialized member of the family Peramelidae, there is nevertheless still some doubt as to its taxonomic affinities, because this animal is highly specialized and shows several uniquely derived characters. We report here the first attempt to determine the molecular relationships of this animal using mitochondrial 12S rRNA sequences derived from spirit-preserved museum specimens. Phylogenetic analysis shows that the sequence derived from the Chaeropus sample is clearly that of a bandicoot. Within the bandicoot clade, the pig-footed bandicoot is quite distinct from all other taxa. Divergence-time estimates from the 12S rRNA sequences suggest that Chaeropus diverged from the other bandicoot genera in the late Oligocene or early Miocene and that bandicoots diverged from other Australian families in the late Paleocene–early Eocene.

Phylogenetic Relationships of the Western North American Phoxinins (Actinopterygii: Cyprinidae) as Inferred from Mitochondrial 12S and 16S Ribosomal RNA Sequences

Parsimony analysis of the mitochondrial 12S and 16S rRNA sequences of North American phoxinin taxa indicated the existence of three major clades, the Western Clade, the Creek Chub Clade, and the Open Posterior Myodome Clade. The monophyletic Western Clade identified in this paper contained fewer taxa than that identified by previous authors. This clade contained species restricted to drainages west of the Continental Divide, such asGila, Acrocheilus, Relictus, Eremichthys, Siphateles, Ptychocheilus, Lavinia,andOrthodon,and the wide-ranging genusPhoxinusfound in eastern North America and Eurasia. Within this Western CladePhoxinuswas the basal sister group.Gilawas recognized as a monophyletic group exclusive ofSiphatelesandSnyderichthys,clades traditionally recognized as subgenera ofGila.The genusGilawas most closely related to the genusAcrocheilusand together these formed the sister group to the genusRelictus.These relationships were supported independent of weighting schemes used in analyses. Identification ofPhoxinusas the basal sister taxon of the Western clade implies that other major clades of North American Phoxinins likely have Asian or European relatives.

Interordinal Mammalian Relationships: Evidence for Paenungulate Monophyly Is Provided by Complete Mitochondrial 12S rRNA Sequences

The complete mitochondrial 12S rRNA sequences of 5 placental mammals belonging to the 3 orders Sirenia, Proboscidea, and Hyracoidea are reported together with phylogenetic analyses (distance and parsimony) of a total of 51 mammalian orthologues. This 12S rRNA database now includes the 2 extant proboscideans (the African and Asiatic elephantsLoxodonta africanaandElephas maximus), 2 of the 3 extant sirenian genera (the sea cowDugong dugonand the West Indian manateeTrichechus manatus), and 2 of the 3 extant hyracoid genera (the rock and tree hyraxesProcavia capensisandDendrohyrax dorsalis). The monophyly of the 3 orders Sirenia, Proboscidea, and Hyracoidea is supported by all kinds of analysis. There are 23 and 3 diagnostic subsitutions shared by the 2 proboscideans and the 2 hyracoids, respectively, but none by the 2 sirenians. The 2 proboscideans exhibit the fastest rates of 12S rRNA evolution among the 11 placental orders studied. Based on various taxonomic sampling methods among eutherian orders and marsupial outgroups, the most strongly supported clade in our comparisons clusters together the 3 orders Sirenia, Proboscidea, and Hyracoidea in the superorder Paenungulata. Within paenungulates, the grouping of sirenians and proboscideans within the mirorder Tethytheria is observed. This branching pattern is supported by all analyses by high bootstrap percentages (BPs) and decay indices. When only one species is selected per order or suborder, the taxonomic sampling leads to a relative variation in bootstrap support of 53% for Tethytheria (BPs ranging from 44 to 93%) and 7% for Paernungulata (92–99%). When each order or suborder is represented by two species, this relative variation decreased to 10% for Tethytheria (78–87%) and 3% for Paenungulata (96–99%). Two nearly exclusive synapomorphies for paenungulates are identified in the form of one transitional compensatory change, but none were detected for tethytherians. Such a robust and reliable resolution of the paenungulate node implies a long history of the common ancestors, allowing time for synapomorphies to accumulate. This observation suggests a Late Cretaceous/Early Paleocene origin for the Paenungulata.

Geographic and bathymetric patterns of mitochondrial 16S rRNA sequence divergence among deep-sea amphipods, Eurythenes gryllus

The physical uniformity of the deep sea suggests a lack of absolute barriers to faunal dispersal, and thus genetic homogeneity in broadly distributed species is expected. The deep-sea amphipod Eurythenes gryllus Lichtenstein (Crustacea: Lysianassoidea) is considered a panoceanic, cold-water stenotherm, with a vertical depth distribution from 184 to 6500 m. We surveyed mtDNA sequence diversity in E. gryllus to assess genetic diversity and population structure in different oceans and across traditionally defined bathyal and abyssal zones. DNA sequences (437 nucleotides length) from the mitochondrial large-subunit ribosomal RNA gene (16S rRNA) of 95 individuals, collected between 1982 and 1990 from 14 locations in the central North Pacific (including multiple samples on the slope of a seamount), castern and western North Atlantic, and the Arctic Ocean, were obtained. Our analysis of DNA sequence diversity indicates (1) genetic homogeneity among sites within the same depth zone at the scale of ocean basins; and (2) genetically divergent, cryptic taxa distributed at different depths, with the greatest diversity in the bathyal zone. These observations suggest that ecological and physical conditions are important isolating mechanisms that may lead to speciation in this group.

A Phylogeny for the African Treefrog Family Hyperoliidae Based on Mitochondrial rDNA

Mitochondrial 12S rRNA sequences were used to construct a phylogeny for the African treefrog family, Hyperoliidae. The sequences were aligned using the well-established mt 12S rRNA secondary structure as a map to designate stem and loop positions. Conservation of secondary structure permits a more accurate basis for assessing homologies than does primary sequence alone. The molecular trees showed many similarities to the morphological trees constructed previously. Species within a genus always grouped together. The generaHyperolius, Heterixalus, Afrixalus,andKassinawere resolved, but not with statistical significance.Leptopeliswas the basal group. The analysis shows clearly thatPhlyctimantisgroups withKassinaas it did in Drewes' morphological tree and thatTachycnemisgroups closely withHeterixalus,a relationship not suggested by the morphological data. Character weighting (including compensatory base changes), mitochondrial trees vs gene trees, and the biogeography of the group are discussed.

Nuclear counterparts of the cytoplasmic mitochondrial 12S rRNA gene: A problem of ancient DNA and molecular phylogenies

Monkey mummy bones and teeth originating from the North Saqqara Baboon Galleries (Egypt), soft tissue from a mummified baboon in a museum collection, and nineteenth/twentieth-century skin fragments from mangabeys were used for DNA extraction and PCR amplification of part of the mitochondrial 12S rRNA gene. Sequences aligning with the 12S rRNA gene were recovered but were only distantly related to contemporary monkey mitochondrial 12S rRNA sequences. However, many of these sequences were identical or closely related to human nuclear DNA sequences resembling mitochondrial 12S rRNA (isolated from a cell line depleted in mitochondria) and therefore have to be considered contamination. Subsequently in a separate study we were able to recover genuine mitochondrial 12S rRNA sequences from many extant species of nonhuman Old World primates and sequences closely resembling the human nuclear integrations. Analysis of all sequences by the neighbor-joining (NJ) method indicated that mitochondrial DNA sequences and their nuclear counterparts can be divided into two distinct clusters. One cluster contained all temporary cytoplasmic mitochondrial DNA sequences and approximately half of the monkey nuclear mitochondriallike sequences. A second cluster contained most human nuclear sequences and the other half of monkey nuclear sequences with a separate branch leading to human and gorilla mitochondrial and nuclear sequences. Sequences recovered from ancient materials were equally divided between the two clusters. These results constitute a warning for when working with ancient DNA or performing phylogenetic analysis using mitochondrial DNA as a target sequence: Nuclear counterparts of mitochondrial genes may lead to faulty interpretation of results.

Phylogeny of African monkeys based upon mitochondrial 12S rRNA sequences.

The suborder Anthropoidea of the primates has traditionally been divided in three superfamilies: the Hominoidea (apes and humans) and the Cercopithecoidea (Old World monkeys), together comprising the infraorder Catarrhini, and the Ceboidea (New World monkeys) belonging to the infraorder Platyrrhini. We have sequenced an approximately 390-base-pair part of the mitochondrial 12S rRNA gene for 26 species of the major groups of African monkeys and apes and constructed an extensive phylogeny based upon DNA evidence. Not only is this phylogeny of great importance in classification of African guenons, but it also suggests rearrangements in traditional monkey taxonomy and evolution. Baboons and mandrills were found to be not directly related, while we could confirm that the known four superspecies of mangabeys do not form a monophyletic group, but should be separated into two genera, one clustering with baboons and the other with mandrills. Patas monkeys are clearly related to members of the genus Cercopithecus despite their divergence in build and habitat, while the talapoin falls outside the Cercopithecus clade (including the patas monkey).

Isolation of cDNA clones coding for mitochondrial 16S ribosomal RNA from the crustacean Artemia

cDNA clones coding for Artemia mitochondrial 16S ribosomal RNA (rRNA) have been isolated. The clones cover from nucleotide 650 of the RNA molecule to its 3' end. The comparison of Artemia sequence with both vertebrate and invertebrate mitochondrial 16S rRNA sequences has shown the existence of regions of high similarity between them. A model for the secondary structure of the 3' half of Artemia mitochondrial 16S rRNA is proposed. The size of the rRNA molecule has been estimated at 1.35 kb. Despite the similarity of the Artemia gene to insect rRNA in size, sequence and secondary structure, the G + C content of the Artemia gene (42%) is closer to that of mammals than to the insect genes. The number of mitochondria in Artemia has been estimated at 1500 per diploid genome in the cyst and 4000 in the nauplius. In contrast, the amount of mt 16S rRNA is constant at all stages of Artemia development.

A new species of Arthroleptella Hewitt, 1926 (Anura: Ranidae) from the Groot Winterhoek mountains of the Western Cape province, South Africa

A new species of Arthroleptella (moss frog), is described from the Groot Winterhoek Mountains in the Western Cape Province, South Africa. The new species is allopatric to other Arthroleptella species. It is distinguished from other Arthroleptella species by its advertisement call, which is a chirp followed by three to seven clicks, blotched patterning on the posterior dorsum and very small size. Combined mitochondrial 12S and 16S rRNA sequences differ from 1.4% to 4.6% from the other species. The new species has fewer notes per call than Arthroleptella landdrosia and fewer pulses per call than Arthroleptella bicolor. The new species is the sister species to A. bicolor.