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The phylogenetic relationships among the southern African freshwater crab species were examined using partial sequence data from three mitochondrial genes (12S rRNA, 16S rRNA, and mtDNA COI) 26 morphological characters and 14 allozyme loci. The aims of the present study were firstly to determine whether freshwater crab species that live in the same geographic region share a close phylogenetic relationship. Secondly, to investigate whether hybridizing species are genetically closely related and thirdly, to test for the validity of subgenera based on the genetic data sets. Phylogenetic analysis based on sequence data revealed largely congruent tree topologies and some associations had consistently high bootstrap support, and these data did not support Bott's subgeneric divisions. The morphological data were less informative for phylogenetic reconstruction while the allozyme data generally supported patterns recovered by the sequence data. A combined analysis of all the data recovered two monophyletic clades, one comprised of small-bodied mountain stream species and the other clade consisting of large-bodied riverine species. The combined analyses reflected clear biogeographic patterning for these river crabs. In addition, there was a clear correlation between genetic distance values and the ability of sympatric species to hybridize.
Mol Phylogenet Evol 2002 Dec
PMID:Phylogenetic relationships of the southern African freshwater crab fauna (Decapoda: Potamonautidae: Potamonautes) derived from multiple data sets reveal biogeographic patterning. 1245 Jul 55

Little is known about what determines patterns of host association of horizontally transmitted parasites over evolutionary timescales. We examine the evolution of associations between mushroom-feeding Drosophila flies (Diptera: Drosophilidae), particularly in the quinaria and testacea species groups, and their horizontally transmitted Howardula nematode parasites (Tylenchida: Allantonematidae). Howardula species were identified by molecular characterization of nematodes collected from wild-caught flies. In addition, DNA sequence data is used to infer the phylogenetic relationships of both host Drosophila (mtDNA: COI, II, III) and their Howardula parasites (rDNA: 18S, ITS1; mtDNA: COI). Host and parasite phylogenies are not congruent, with patterns of host association resulting from frequent and sometimes rapid host colonizations. Drosophila-parasitic Howardula are not monophyletic, and host switches have occurred between Drosophila and distantly related mycophagous sphaerocerid flies. There is evidence for some phylogenetic association between parasites and hosts, with some nematode clades associated with certain host lineages. Overall, these host associations are highly dynamic, and appear to be driven by a combination of repeated opportunities for host colonization due to shared breeding sites and large potential host ranges of the nematodes.
Mol Ecol 2003 Jan
PMID:Associations between mycophagous Drosophila and their Howardula nematode parasites: a worldwide phylogenetic shuffle. 1249 92

Determining the geographical origin of an introduced organism can be critical to understanding or managing a non-native species, but is often difficult when the organism is small or inconspicuous. We used a phylogeographical approach to identify the region of endemism and determine the geographical origin of world populations of the seed-feeding wasp Megastigmus transvaalensis (Hussey). This wasp feeds on African Rhus species and South American Schinus species in various locations around the world. Because it is present both in Africa and in South America, it is unclear whether the wasp was originally an African Rhus-feeder that has begun feeding on Schinus or a South American Schinus-feeder that has started feeding on Rhus. Phylogenetic analysis of 800 bp of mitochondrial cytochrome oxidase I sequence data found extensive variation and phylogeographical structure within African M. transvaalensis. Specimens from other locations around the world were all identical in COI sequence and were phylogenetically nested within the African samples. We conclude that M. transvaalensis was originally an African Rhus-feeder that readily attacks Schinus. We evaluate potential pathways of introduction of this wasp to the New World, and we discuss implications of our results for biocontrol efforts against invasive Schinus populations.
Mol Ecol 2003 Feb
PMID:Tracing the geographical origin of Megastigmus transvaalensis (Hymenoptera: Torymidae): an African wasp feeding on a South American plant in North America. 1253 92

Few estimates of relative substitution rates, and the underlying mutation rates, exist between mitochondrial and nuclear genes in insects. Previous estimates for insects indicate a 2-9 times faster substitution rate in mitochondrial genes relative to nuclear genes. Here we use novel methods for estimating relative rates of substitution, which incorporate multiple substitutions, and apply these methods to a group of insects (lice, Order: Phthiraptera). First, we use a modification of copath analysis (branch length regression) to construct independent comparisons of rates, consisting of each branch in a phylogenetic tree. The branch length comparisons use maximum likelihood models to correct for multiple substitution. In addition, we estimate codon-specific rates under maximum likelihood for the different genes and compare these values. Estimates of the relative synonymous substitution rates between a mitochondrial (COI) and nuclear (EF-1alpha) gene in lice indicate a relative rate of several 100 to 1. This rapid relative mitochondrial rate (>100 times) is at least an order of magnitude faster than previous estimates for any group of organisms. Comparisons using the same methods for another group of insects (aphids) reveals that this extreme relative rate estimate is not simply attributable to the methods we used, because estimates from aphids are substantially lower. Taxon sampling affects the relative rate estimate, with comparisons involving more closely related taxa resulting in a higher estimate. Relative rate estimates also increase with model complexity, indicating that methods accounting for more multiple substitution estimate higher relative rates.
Mol Phylogenet Evol 2003 Feb
PMID:Dramatically elevated rate of mitochondrial substitution in lice (Insecta: Phthiraptera). 1256 34

The phylogeny of groups within Gobioidei is examined with molecular sequence data. Gobioidei is a speciose, morphologically diverse group of teleost fishes, most of which are small, benthic, and marine. Efforts to hypothesize relationships among the gobioid groups have been hampered by the prevalence of reductive evolution among goby species; such reduction can make identification of informative morphological characters particularly difficult. Gobies have been variously grouped into two to nine families, several with included subfamilies, but most existing taxonomies are not phylogenetic and few cladistic hypotheses of relationships among goby groups have been advanced. In this study, representatives of eight of the nine gobioid familes (Eleotridae, Odontobutidae, Xenisthmidae, Gobiidae, Kraemeriidae, Schindleriidae, Microdesmidae, and Ptereleotridae), selected to sample broadly from the range of goby diversity, were examined. Complete sequence from the mitochondrial ND1, ND2, and COI genes (3573 bp) was used in a cladistic parsimony analysis to hypothesize relationships among the gobioid groups. A single most parsimonious topology was obtained, with decay indices indicating strong support for most nodes. Major phylogenetic conclusions include that Xenisthmidae is part of Eleotridae, and Eleotridae is paraphyletic with respect to a clade composed of Gobiidae, Microdesmidae, Ptereleotridae, Kraemeriidae, and Schindleriidae. Within this five-family clade, two clades are recovered. One includes Gobionellinae, which is paraphyletic with respect to Kraemeriidae, Sicydiinae, Oxudercinae, and Amblyopinae. The other contains Gobiinae, also paraphyletic, and including Microdesmidae, Ptereleotridae, and Schindleriidae. Previous morphological evidence for goby groupings is discussed; the phylogenetic hypothesis indicates that the morphological reduction observed in many goby species has been derived several times independently.
Mol Phylogenet Evol 2003 Mar
PMID:Molecular phylogeny of the gobioid fishes (Teleostei: Perciformes: Gobioidei). 1264 97

The phylogenetic relationships and the origin of two groups of rissooid freshwater snails endemic to Lake Baikal were investigated using partial mitochondrial COI, 12S rDNA, and 16S rDNA sequences. The Baikalian Benedictiinae proved to be closely related to the Lithoglyphinae. According to a molecular clock estimate the two groups diverged in the Paleogene. The Benedictiinae might have evolved autochthonously in precursors of Lake Baikal. The Baikalian Baicaliidae are probably most closely related to the Amnicolidae and the Bithyniidae. These groups diverged at the latest during the Cretaceous. Thus the origin of the Baicaliidae predates the origin of the Baikal rift zone. The Baicaliidae evolved probably in other Central Asian freshwater reservoirs. However, the radiation of the extant Baicaliidae only started in the Neogene and might have occurred autochthonously in Lake Baikal. The conchological similarity of the Baicaliidae and the Pyrgulidae is due to convergence. The Pyrgulidae diverged from the common stem lineage of the other hydrobiid families at the latest in the Jurassic. The Bithyniidae is derived from hydrobiids and is related to the Amnicolidae.
Mol Phylogenet Evol 2003 Mar
PMID:Relationships and origin of endemic Lake Baikal gastropods (Caenogastropoda: Rissooidea) based on mitochondrial DNA sequences. 1501 62

Allodapine bees are most diverse in Africa but are distributed throughout the Old World tropical and Austral regions. They are considered useful for studies into the evolution of social behaviour since they exhibit the full range of social organisation from solitary to highly eusocial (sensu; ). Five genera are found in Australia, namely Braunsapis, Exoneurella, Exoneura, Brevineura, and Inquilina. Sociality and life histories are well documented for the exoneurine genera (review in ) and Inquilina is an obligate social parasite of species of Exoneura (). In this paper, maximum parsimony and maximum likelihood methods using molecular sequence data from two mitochondrial gene regions (cyt b and COI) and a single nuclear gene region (EF-1alpha) are used to reconstruct phylogenetic relationships of the Australian allodapine genera. Results suggest that the exoneurine group (Brevineura, Exoneurella, and Exoneura+Inquilina) diverged very rapidly and are monophyletic to the exclusion of other (primarily African) allodapine genera. A clade containing Australian species of Braunsapis is also monophyletic to the exclusion of African congeners. Braunsapis is not phylogenetically close to, and is a more derived group than the exoneurine group and probably came to occupy the Australian plate via a later dispersal through the southern Asian region. It is unclear at this point how the exoneurine group came to occupy the Australian plate and possible scenarios are discussed.
Mol Phylogenet Evol 2003 May
PMID:Phylogenetic divergence of the Australian allodapine bees (Hymenoptera: Apidae). 1269 86

Respiration, mitochondrial (mt)DNA content, and mitochondrial-specific RNA expression in fat body cells from active and cold-adapted larvae of the goldenrod gall fly, Eurosta solidaginis, and the Arctic woolly bear caterpillar, Gynaephora groenlandica, were compared. Reduced amounts of mtDNA were observed in cold-adapted larvae of both E. solidaginis and G. groenlandica collected in fall or winter, compared with summer-collected larvae. mtDNA increased to levels similar to those of summer-collected larvae after incubation at 10 degrees C or 15 degrees C for 5 h. Mitochondrial-specific RNAs (COI and 16S) were observed in fat body cells of both active and cold-adapted E. solidaginis larvae. Our results suggest that mitochondrial proteins required for respiration may be restored rapidly from stable RNAs present in overwintering larvae.
Insect Mol Biol 2003 Jun
PMID:Variations in mitochondrial DNA and gene transcription in freezing-tolerant larvae of Eurosta solidaginis (Diptera: Tephritidae) and Gynaephora groenlandica (Lepidoptera: Lymantriidae). 1275 62

Sea urchins of the family Strongylocentrotidae have been important model systems in many fields of basic biology, yet knowledge of their evolutionary identities such as the phylogenetic relationships and divergence times remains limited. Here, I inferred molecular phylogenies of seven Strongylocentrotid species (Strongylocentrotus franciscanus, S. nudus, S. purpuratus, S. intermedius, S. droebachiensis, S. pallidus, and Hemicentrotus pulcherrimus) from the analyses of mitochondrial DNA sequences of 12SrDNA (349 nt), 12SrDNA-tRNA(gln) region (862 nt), and a combined sequence of cytochrome oxidase subunit I (COI, 1080 nt) and NADH dehydrogenase subunit I (NDI, 742 nt). The rate of sequence evolution and divergence times for each species were then estimated from the trees with reference to the time of separation between Strongylocentrotidae and Parechinidae, 35 to 50 MYA. The three trees agree well with each other, and the phylogeny is summarized by ((S. franciscanus, S. nudus), (H. pulcherrimus (S. purpuratus, S. intermedius (S. droebachiensis, S. pallidus)))). It is notable that the genus Strongylocentrotus consists of two distinct clades and that H. pulcherrimus branches off within Strongylocentrotus, implying assignment of a separate, monospecific genus to this species inappropriate. The rate of sequence evolution is calibrated to be 0.24%-0.34%/Myr in 12SrDNA, 0.25%-0.36%/Myr in 12SrDNA-tRNA(gln), and 0.65%-0.93%/Myr in COI-NDI combined sequences. S. purpuratus, in particular, shows the significantly higher rate of evolution in the 12SrDNA and 12SrDNA-tRNA(gln) regions compared to other species, suggesting careful use of its sequences in comparative studies. The two clades of Strongylocentrotidae seem to have split 13-19 MYA, and H. pulcherrimus branched off 7.2-14 MYA. In the former clade, S. franciscanus and S. nudus separated 5.7-8.1 MYA. In the latter clade, S. purpuratus, S. intermedius, and the clade of S. droebachiensis and S. pallidus diverged approximately 4.6-12 MYA, and the last two closest species separated 2.1-3.1 MYA.
Mol Biol Evol 2003 Aug
PMID:Molecular phylogenies and divergence times of sea urchin species of Strongylocentrotidae, Echinoida. 1277 24

The phylogenetic relationship between Buthus occitanus populations across the Strait of Gibraltar was investigated using nuclear 18S/ITS-1 DNA sequences and mitochondrial 16S and COI DNA sequences. All analyses showed that the European samples are highly separated from North African samples, and also suggest the existence of three main groups within this species complex, i.e., an European, an Atlas (=Moroccan samples) and a Tell-Atlas group (=Tunisian samples). The European clade was subdivided into three distinct subclades. The application of a previous calibration of the molecular clock of another buthid species suggested that most of the detected mitochondrial DNA lineages including the European lineages are about three times older than the re-opening of the Gibraltar Strait, and consequently, that other and older vicariant events are responsible for the observed phylogeographic structure of this species complex. Concerning the Moroccan samples, a discordance between nuclear and mitochondrial gene markers was observed. The 18S/ITS-1 gene tree could not resolve the phylogenetic relationships among the Moroccan B. occitanus subspecies and the closely related species B. atlantis, whereas mitochondrial genes suggested the co-existence of several old phylogenetic lineages in Morocco. We hypothesized that this difference may be explained by male-biased gene flow and gene conversion at the tandemly repeated 18S/ITS-1 gene regions.
Mol Phylogenet Evol 2003 Jul
PMID:The phylogeographic importance of the Strait of Gibraltar as a gene flow barrier in terrestrial arthropods: a case study with the scorpion Buthus occitanus as model organism. 1280 75


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