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Traditional earthworm taxonomy is hindered due to their anatomical simplicity and the plasticity of the characteristics often used for diagnosing species. Making phylogenetic inferences based on these characters is more than difficult. In this study we use molecular tools to unravel the phylogeny of the clitellate family Hormogastridae. The family includes species of large to mid-sized earthworms distributed almost exclusively in the western Mediterranean region where they play an important ecological role. We analyzed individuals from 46 locations spanning the Iberian Peninsula to Corsica and Sardinia, representing the four described genera in the family and 20 species. Molecular markers include mitochondrial regions of the cytochrome c oxidase subunit I gene (COI), 16S rRNA and tRNAs for Leu, Ala, and Ser, two nuclear ribosomal genes (nearly complete 18S rRNA and a fragment of 28S rRNA) and two nuclear protein-encoding genes (histones H3 and H4). Analyses of the data using different approaches corroborates monophyly of Hormogastridae, but the genus Hormogaster is paraphyletic and Hormogaster pretiosa appears polyphyletic, stressing the need for taxonomic revisionary work in the family. The genus Vignysa could represent an early offshoot in the family, although the relationships with other genera are uncertain. The genus Hemigastrodrilus is related to the Hormogaster elisae complex and both are found in the Atlantic drainage of the Iberian Peninsula and France. From a biogeographic perspective Corsica and Sardinia include members of two separate hormogastrid lineages. The species located in Corsica and Northern Sardinia are related to Vignysa, whereas Hormogaster pretiosa pretiosa, from Southern Sardinia, is closely related to the Hormogaster species from the NE Iberian Peninsula. A molecular dating of the tree using the separation of the Sardinian microplate as a calibration point (at 33 MY) and assuming a model of vicariance indicates that the diversification of Hormogastridae may be ancient, ranging from 97 to 67 Ma., (Copyright © 2011 Elsevier Inc. All rights reserved.)

Natural hybridization among recently diverged species has traditionally been viewed as a homogenizing force, but recent research has revealed a possible role for interspecific gene flow in facilitating species radiations. Natural hybridization can actually contribute to radiations by introducing novel genes or reshuffling existing genetic variation among diverging species. Species that have been affected by natural hybridization often demonstrate patterns of discordance between phylogenies generated using nuclear and mitochondrial markers. We used Amplified Fragment Length Polymorphism (AFLP) data in conjunction with mitochondrial DNA in order to examine patterns of gene flow and nuclear-mitochondrial discordance in the Anaxyrus americanus group, a recent radiation of North American toads. We found high levels of gene flow between putative species, particularly in species pairs sharing similar male advertisement calls that occur in close geographic proximity, suggesting that prezygotic reproductive isolating mechanisms and isolation by distance are the primary determinants of gene flow and genetic differentiation among these species. Additionally, phylogenies generated using AFLP and mitochondrial data were markedly discordant, likely due to recent and/or ongoing natural hybridization events between sympatric populations. Our results indicate that the putative species in the A. americanus group have experienced high levels of gene flow, and suggest that their North American radiation could have been facilitated by the introduction of beneficial genetic variation from admixture between divergent populations coming into secondary contact after glacial retreats., (Copyright © 2011 Elsevier Inc. All rights reserved.)

The aim of this study was to estimate the influence of the palaeogeographic and climatic history of the Aegean region on the diversity of freshwater crabs of the genus Potamon and to test whether this area served as source or reservoir in species diversity. Necessary species delimitation was accomplished by phylogenetic analyses of the mitochondrial markers COX1 and ND1, partial 16S rRNA gene and the tRNALeu gene. We found 14 genetic lineages of which nine could be assigned to previously recognised species. Temporal estimates of the splitting pattern in the phylogeny of Potamon indicated that a combination of geological and climatic events influenced their diversification. Within Potamon, the lineages separated into a western group and an eastern group. This first split in the genus occurred approximately 8.3-5.5 Mya, thus possibly correlated with the Messinian salinity crisis. A likelihood approach to geographic range evolution suggested for most species, occurring in the Aegean area, an origin in the Middle East. Moreover, there were no insular endemics in the central Aegean archipelago, therefore low sea-levels during the Pleistocene glacial periods possibly enabled dispersal to these islands, but subsequent rise in sea-level did not cause speciation. Nevertheless, the diversification of most lineages occurred during the Pleistocene epoch thus coinciding with Quaternary fluctuations of the climate., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Cucurbitaceae contain c. 800 species in 130 genera and are among the economically most important families of plants. We inferred their phylogeny based on chloroplast DNA sequences from two genes, one intron, and two spacers (rbcL, matK, trnL, trnL-trnF, rpl20-rps12) obtained for 171 species in 123 genera. Molecular data weakly support the traditional subfamilies Cucurbitoideae (111 genera) and Nhandiroboideae (19 genera, 60 species), and recover most of the eleven tribes, but almost none of the subtribes. Indofevillea khasiana is sister to all other Cucurbitoideae, and the genera of Joliffieae plus a few Trichosantheae form a grade near the base of Cucurbitoideae. A newly discovered large clade consists of the ancestrally Asian genera Nothoalsomitra, Luffa, Gymnopetalum, Hodgsonia, Trichosanthes, and the New World tribe Sicyeae. Genera that are poly- or paraphyletic include Ampelosicyos, Cucumis, Ibervillea, Neoachmandra, Psiguria, Trichosanthes, and Xerosicyos. Flower characters, especially number of free styles, fusion of filaments and/or anthers, tendril type, and pollen size, exine, and aperture number correlate well with the chloroplast phylogeny, while petal and fruit characters as well as karyotype exhibit much evolutionary flexibility.

Hotspot archipelagoes provide exceptional models for the study of the evolutionary process, due to the effects of isolation and topographical diversity in inducing the formation of unique biotic assemblages. In this paper, we examine the evolutionary patterns exhibited by the jumping spider genus Havaika Prószyński, 2001 in the Polynesian islands of the Hawaiian and Marquesas chains. To date, systematic research on Havaika has been seriously limited by the poor taxonomic knowledge on the group, which was based on a handful of specimens that showed continuous variability and lacked clear-cut diagnostic characters. Here, we circumvent this problem by inferring a phylogeny based on DNA sequences of several fragments including both mitochondrial (protein coding cytochrome oxidase I, NAD1 dehydrogenase, ribosomal 16S, and tRNA leu) and nuclear (internal transcribed spacer 2) genes, and a statistical morphological analyses of a large sample of specimens. Results suggest that the Marquesan and Hawaiian Havaika may be the result of independent colonizations. Furthermore, data provide little support for the standard "progression rule" (evolution in the direction of older to younger islands) in Hawaiian Islands. This may be explained by a recent arrival of the group: age estimates of the different lineages suggest that Havaika colonized the Hawaiian Islands after most of the extant islands were already formed. The lack of clear-cut diagnostic characters among species may also be explained by the recent origin of the group since molecular data do not provide any evidence of hybridization among lineages. Quantitative morphological data coupled with the phylogenetic information allow us to reevaluate the current limitation of Havaika taxonomy. Molecular data support the existence of at least four different evolutionary lineages that are further morphologically diagnosable. However, genealogical relationships are better predicted by geographical affinity (i.e. island) than by morphological characters used in the original descriptions of the species. A pattern of size segregation linked to largely overlapping distributions of some of the species hints at a potential involvement of competition in generating morphological diversity. This study contributes to our understanding on the origin and shaping of the biodiversity of oceanic islands and sets the stage for more detailed studies on particular aspects of these previously overlooked spiders.

We examine phylogenetic relationships among salamanders of the family Salamandridae using approximately 2700 bases of new mtDNA sequence data (the tRNALeu, ND1, tRNAIle, tRNAGln, tRNAMet, ND2, tRNATrp, tRNAAla, tRNAAsn, tRNACys, tRNATyr, and COI genes and the origin for light-strand replication) collected from 96 individuals representing 61 of the 66 recognized salamandrid species and outgroups. Phylogenetic analyses using maximum parsimony and Bayesian analysis are performed on the new data alone and combined with previously reported sequences from other parts of the mitochondrial genome. The basal phylogenetic split is a polytomy of lineages ancestral to (1) the Italian newt Salamandrina terdigitata, (2) a strongly supported clade comprising the "true" salamanders (genera Chioglossa, Mertensiella, Lyciasalamandra, and Salamandra), and (3) a strongly supported clade comprising all newts except S. terdigitata. Strongly supported clades within the true salamanders include monophyly of each genus and grouping Chioglossa and Mertensiella as the sister taxon to a clade comprising Lyciasalamandra and Salamandra. Among newts, genera Echinotriton, Pleurodeles, and Tylototriton form a strongly supported clade whose sister taxon comprises the genera Calotriton, Cynops, Euproctus, Neurergus, Notophthalmus, Pachytriton, Paramesotriton, Taricha, and Triturus. Our results strongly support monophyly of all polytypic newt genera except Paramesotriton and Triturus, which appear paraphyletic, and Calotriton, for which only one of the two species is sampled. Other well-supported clades within newts include (1) Asian genera Cynops, Pachytriton, and Paramesotriton, (2) North American genera Notophthalmus and Taricha, (3) the Triturus vulgaris species group, and (4) the Triturus cristatus species group; some additional groupings appear strong in Bayesian but not parsimony analyses. Rates of lineage accumulation through time are evaluated using this nearly comprehensive sampling of salamandrid species-level lineages. Rate of lineage accumulation appears constant throughout salamandrid evolutionary history with no obvious fluctuations associated with origins of morphological or ecological novelties.

Complete DNA sequences have been determined for the mitochondrial genomes of the crinoids Phanogenia gracilis (15892 bp) and Gymnocrinus richeri (15966 bp). The mitochondrial genetic map of the stalkless feather star P. gracilis is identical to that of the comatulid feather star Florometra serratissima (Scouras, A., Smith, M.J., 2001. Mol. Biol. Evol. 18, 61-73). The mitochondrial gene order of the stalked crinoid G. richeri differs from that of F. serratissima and P. gracilis by the transposition of the nad4L protein gene. The G. richeri nad4L mitochondrial map position is unique among metazoa and is likely a derived feature in this stalked crinoid. Nucleotide compositional analyses of protein genes encoded on the major sense strand confirm earlier conclusions regarding a crinoid-distinctive T over C bias. All three crinoids exhibit high T levels in third codon positions, whereas other echinoderm classes favor A or C in the third codon position. The nucleotide bias is reflected in the relative synonymous codon usage patterns of crinoids versus other echinoderms. We suggest that the nucleotide bias of crinoids, in comparison to other echinoderms, indicates that a physical inversion of the origin of replication has occurred in the crinoid lineage. Evolutionary rate tests support the use of the cytochrome b (cob) gene in molecular phylogenetic analyses of echinoderms. A consensus echinoderm tree was generated based on cytochrome b nucleotide alignments that placed the asteroids as a sister group to a clade containing the ophiuroids and the (echinoids+holothuroids) with the crinoids basal to the rest of the echinoderm classes: [Crinoid,(Asteroid,(Ophiuroid,(Echinoid,Holothuroid)))].

Structure, variability, and molecular evolution of the trnL(UAA) intron in bryophytes (mosses and liverworts) is analyzed based on more than 1000 sequences representing all classes, including comparisons of lengths and GC-contents, sequence similarities, evolutionary rates and ti/tv ratios of the major lineages and selected genera. Secondary structure analyses of the more variable stem-loop regions facilitated recognition of sequence repeats and minute inversions that often occurred independently in non-related lineages, thus supporting alignment construction and homology assessment. The most length-variable stem-loop region P8 does not share a common evolutionary history across all major bryophyte lineages. Independent nucleotide additions such as internally repeated sequence segments resulted in non-homologous P8 sequences that cannot be folded into a common P8 secondary structure, neither for all bryophytes nor for liverworts or mosses. To address evolutionary patterns, separate analyses of P6/P8 and the remaining intron (core) have to be performed, as overall values of the complete intron are misleading. It is argued that a transition bias observed above the genus level in the core structure is caused by structural constraints, not by its higher GC-content in comparison to the more AT-rich P6 and P8. Compensating base pair changes detected in highly conserved elements are often characteristic of the major bryophyte lineages (classes). Sequence divergence and evolutionary rates are generally higher in liverworts than in mosses, resulting in ambiguous alignments of P6 and P8 even within classes. In mosses, trends towards length reduction of P8 and lower evolutionary rates of the intron are observed. Average intraspecific variation is less than 1%, corresponding to 2-3 mutations in the complete intron.

While Anartia butterflies have served as model organisms for research on the genetics of speciation, no phylogeny has been published to describe interspecific relationships. Here, we present a molecular phylogenetic analysis of Anartia species relationships, using both mitochondrial and nuclear genes. Analyses of both data sets confirm earlier predictions of sister species pairings based primarily on genital morphology. Yet both the mitochondrial and nuclear gene phylogenies demonstrate that Anartia jatrophae is not sister to all other Anartia species, but rather that it is sister to the Anartia fatima-Anartia amathea lineage. Traditional biogeographic explanations for speciation across the genus relied on A. jatrophae being sister to its congeners. These explanations invoked allopatric divergence of sister species pairs and multiple sympatric speciation events to explain why A. jatrophae flies alongside all its congeners. The molecular phylogenies are more consistent with lineage divergence due to vicariance, and range expansion of A. jatrophae to explain its sympatry with congeners. Further interpretations of the tree topologies also suggest how morphological evolution and eco-geographic adaptation may have set species range boundaries.

There are two evolutionary lineages in the genus Brassica: the rapa/oleracea lineage and the nigra lineage. Using nuclear DNA sequences such as the intergenic spacer between 5S rRNA genes and the internal transcribed spacer between 18S and 25S rRNA genes, we and others had previously demonstrated that Raphanus sativus is closely related to the nigra lineage. In the present study, we sequenced the chloroplast noncoding region between trnT and trnF and that between trnD and trnT in seven species and showed that R. sativus is more closely related to the rapa/oleracea lineage than to the nigra lineage. The conflicting results from nuclear DNA and chloroplast DNA support the hypothesis that Raphanus was derived from a hybridization between the rapa/oleracea and the nigra lineages. We estimated the date of this hybridization event to be 60% of the divergence time between the two Brassica lineages. In addition, the pattern and rate of nucleotide substitution were studied. There were more transversions than transitions in these noncoding regions, which have a high AT content. Furthermore, the proportion of transversions among the substitutions at a site increases with increasing A + T content of its two adjacent nucleotides. An influence of immediate 5(') pyrimidine on substitution pattern is also observed when both adjacent bases in the two DNA strands are A or T. The rate of nucleotide substitution in the trnL group I intron is only about one third of the rate in the nearby intergenic spacers in the trnT-trnF fragment. The rate of nucleotide substitution in the rapa/oleracea lineage is at least 1.5 times that in the nigra lineage., (2002 Elsevier Science (USA).)

A conspicuous biogeographic pattern of the Northern Hemisphere is the disjunct occurrence of related taxa on different continents. Perhaps best studied in plants, this pattern includes disjunct distributions of genera in eastern Asia and eastern North America. Such continental disjunctions are thought to be the remnants of a mostly continuously distributed, mixed mesophytic forest dating to the Miocene, which subsequently became fragmented by geological and climatic changes. Some highly host-specific insects, namely aphids, live on descendants of the mixed mesophytic forest taxa and exhibit the same disjunct distributions as that of their host plants. We estimated the phylogeny of Hormaphidini aphids, which host-alternate between witch-hazel (Hamamelis; an eastern Asian-eastern North American disjunct genus) and birch (Betula). Based on partial nuclear elongation factor 1alpha and mitochondrial tRNA leucine/cytochrome oxidase II sequences, trees inferred from maximum-parsimony and maximum-likelihood showed strong support for two monophyletic genera (Hamamelistes and Hormaphis), each containing a clade of Japanese and a clade of North American species. The estimated divergence dates of Asian and North American clades in both genera was 20-30 million years ago, consistent with the idea that aphids may have experienced the same vicariance events as those of their host plants., (2002 Elsevier Science (USA).)

The 10 extant species of emydine turtles represent an array of morphological and ecological forms recognizable and popular among scientists and hobbyists. Nevertheless, the phylogenetic affinities of most emydines remain contentious. Here, we examine the evolutionary relationships of emydine turtles using 2092 bp of DNA encoding the mitochondrial genes cyt b, ND4, and adjacent tRNAs. These data contain 339 parsimony informative characters that we use to erect hypotheses of relationships for the Emydinae. Both maximum parsimony and maximum likelihood methods yield a monophyletic Emydinae in which all but three nodes are well resolved. Emys orbicularis, Emydoidea blandingii, and Clemmys marmorata form a monophyletic clade, as do the species of Terrapene. Clemmys muhlenbergii and Clemmys insculpta form a third monophyletic group that may be sister to all other emydines. Clemmys guttata is problematic and probably related to Terrapene. Based on this phylogeny, and previous molecular work on the group, we suggest the following taxonomic revisions: (1) Clemmys should be restricted to a single species, C. guttata. (2) Calemys should be resurrected for C. muhlenbergii and C. insculpta. (3) Emys should be expanded to include three species: E. orbicularis, E. blandingii, and E. marmorata. Furthermore, our analyses show that neither kinetic-shelled nor akinetic-shelled emydines form monophyletic groups. Therefore, shell kinesis was either independently gained in Emys and Terrapene or secondarily lost in E. marmorata and C. guttata. Parsimony, paleontological evidence, and the multiple origins of shell kinesis in related turtle lineages (especially geoemydines) support the independent origin of plastral kinesis.

We estimated phylogenetic relationships among species of the bee genus Diadasia, a group of new world, specialist bees. We sequenced approximately 2 kb of the mitochondrial genes cytochrome oxidase subunit I and II and tRNA leucine and approximately 1 kb of the nuclear gene elongation factor 1-alpha for 24 North American Diadasia species, 4 South American species, and five outgroup genera. Parsimony analyses of the two data sets were highly congruent. A combined analysis produced a well-resolved phylogenetic hypothesis that supported the monophyly of Diadasia, but not that of traditional subgenera: Diadasia s. str. was paraphyletic in all analyses. With one exception, the North and South American species formed separate clades, supporting previous hypotheses that two lineages of Diadasia have dispersed from South to North America: a more recent dispersal of D. ochracea and an older dispersal of the ancestor to all other North American species. Different species of Diadasia specialize on pollen from at least five different plant families; the phylogeny presented here, along with known host affinities, indicates that host-switching has been rare., (Copyright 2001 Academic Press.)

Four gene regions were sequenced for 30 species of jumping spiders, most from the subfamily Dendryphantinae, to investigate their molecular phylogeny and evolution. These are three regions from the mitochondria (ca. 560 bp of 16S plus adjacent tRNA, 1047 bp of cytochrome oxidase 1 (CO1), and 414 bp of NADH1 (ND1) and one region from the nuclear genome (ca. 750 bp of 28S). Parsimony and likelihood analyses of these gene regions separately and together support the monophyly of the dendryphantines as delimited previously by morphological characters. A group of elongate-bodied genera are placed as basal among the dendryphantines, and previously proposed relationships of Poultonella, Paraphidippus, and Sassacus vitis are confirmed. Comparison of overall rates of molecular evolution indicates striking differences across the gene regions, with highest divergence in ND1, CO1, 16S, and 28S in decreasing order. All four regions are characterized by both within- and among-site rate variation. Phylogenetic results from CO1 conflict conspicuously with phylogenetic results from the other genes and morphological data. Attempts to account for potential sources of this conflict (e.g., accommodating biased base composition, high homoplasy, within- and among-site rate variation, etc.) are largely unsuccessful., (Copyright 2001 Academic Press.)

A molecular phylogenetic analysis was conducted to determine relationships and to investigate character evolution in the Phytomyza ilicis group of leafmining flies on hollies (Aquifoliaceae: Ilex). A total of 2207 bp of the mitochondrial cytochrome oxidase I and II genes were sequenced for all known holly leafminers, as well as for several undescribed members of this group. Maximum-parsimony analysis of the sequence data indicates that these leafminers form a monophyletic group with the inclusion of an undescribed leafminer that feeds on the distantly related plant Gelsemium sempevirens (Loganiaceae). Species boundaries of previously known and of undescribed holly leafmining species were confirmed with the molecular data, with one exception. Optimization of variable ecological and morphological characters onto the most parsimonious phylogeny suggests that these traits are evolutionarily labile, requiring multiple instances of convergence and/or reversal to explain their evolutionary history. Speciation in holly leafminers is associated with host shifts and appears to involve colonization of new hosts more often than cospeciation as the hosts diverge. Monophagy is the most common feeding pattern in holly leafminers, and more generalized feeding is inferred to have evolved at least two separate times, possibly as a prelude to speciation., (Copyright 2000 Academic Press.)

The Caribbean rock iguana, Cyclura, has had an unstable intrageneric taxonomy and an unclear phylogenetic position within the family Iguanidae. We use mtDNA sequence data to address these issues and explore the phylogeographic history of the genus. ND4 to leucine tRNA sequence data were collected from multiple individuals of each of the eight species of Cyclura (including 15 of 16 subspecies) and from four localities of Iguana iguana (representative of this species' broad geographic range). This data set was combined with sequence data from Sites et al. (1996, Mol. Biol. Evol. 13, 1087-1105) and analyzed under maximum-parsimony and maximum-likelihood optimization criteria. The ND4 region provided good resolution for the majority of nodes, as indicated by high bootstrap support. In agreement with several recent molecular studies, Cyclura is recovered as monophyletic and is not closely related to any other genus, whereas Iguana is strongly supported as the sister taxon to Sauromalus. This result is statistically more likely than other published hypotheses of Iguanid relationships. Cyclura shows a southeast to northwest speciation sequence in the Caribbean, with the most ancient lineage on the Puerto Rican Bank. The amount of interspecific sequence divergence within Cyclura (maximum 11.4%) is very high in comparison to data from other iguanid taxa at this locus, suggesting that this group either has been in the Caribbean for a very long time or has gone through a very rapid rate of evolution at this locus. Using dates from other published studies, we calculate a molecular clock that suggests that Cyclura colonized the Caribbean between 15 and 35 mya. Several questions regarding subspecific taxonomy are raised in the analysis and await further investigation using a more rapidly evolving marker such as nuclear microsatellites., (Copyright 2000 Academic Press.)

The genus Calathus Bonelli comprises 24 species on the Canary Islands. Sequences of 927 and 687 bp of the mitochondrial cytochrome oxidase I and II genes, respectively, as well as the intervening tRNA leu gene in 21 of the 24 species, have identified three genetically divergent and unequivocally monophyletic groupings. A phylogeographic analysis is presented for the major monophyletic group comprising all the species of Gran Canaria, La Gomera, and El Hierro, and two Tenerifean species. A distance-based phylogenetic analysis and maximum parsimony analysis have clearly shown that this clade is composed of four distinct lineages. DNA sequence data suggest a recent origin for this clade and that lineages have not evolved at the same rate. Compared with diversification patterns observed in other Coleoptera on the Canary Islands, diversification has been recent relative to the time of colonization within the islands of Gran Canaria and La Gomera. Calathus diversification on La Gomera has been greater than on Gran Canaria. The influences of geological and ecological history are discussed in relation to Calathus diversification., (Copyright 1999 Academic Press.)

Butterflies of the genus Papilio have served as the basis for numerous studies in insect physiology, genetics, and ecology. However, phylogenetic work on relationships among major lineages in the genus has been limited and inconclusive. We have sequenced 2.3 kb of DNA from the mitochondrial cytochrome oxidase I and II genes (COI and COII) for 23 Papilio taxa and two outgroups, Pachliopta neptunus and Eurytides marcellus, in order to assess the potential of these genes for use in Papilio phylogenetics and to examine patterns of gene evolution across a broad taxonomic range. Nucleotide and amino acid variation is distributed heterogeneously, both within and between genes. Structural features of the proteins are not always reliable predictors of variation. In a combined analysis, these sequences support a nearly fully resolved topology within subgenera and species groups, though higher level relationships among species groups require additional study. The most noteworthy findings are that neither Papilio alexanor nor P. xuthus belongs in the machaon group and that the subgenus Pterourus is paraphyletic with respect to the subgenus Pyrrhosticta. We leave relationships among members of the phorcas species group as a trichotomy. These two protein coding genes, particularly COI, show excellent performance in resolving relationships at the level of species and species groups among Papilionidae. We strongly endorse a similar approach for future studies aimed at these levels., (Copyright 1999 Academic Press.)

The trnL-trnF intergenic spacer of cpDNA has been sequenced from 38 tree samples representing 23 Coffea taxa and the related genus Psilanthus. These sequences were used for phylogenetic reconstruction using parsimony analyses. The results suggest a radial mode of speciation and a recent origin in Africa for the genus Coffea. Phylogenetic relationships inferred from the cpDNA analysis suggest several major clades, which present a strong geographical correspondence (i.e., west Africa, central Africa, east Africa, and Madagascar). The overall results agree well with the phylogeny previously inferred from nuclear genome data. However, several inconsistencies are observed among taxa endemic to west Africa, suggesting the occurrence of introgressive hybridization. Evidence is also obtained for the genetic origin of the allotetraploid species C. arabica.

We examined the phylogenetic relationships among taxa of attine or "fungus-growing" ants (Tribe Attini) using parsimony analyses of molecular and morphological data. We sequenced a region of mitochondrial DNA from 13 taxa of attines and from one closely related outgroup species, Wasmannia auropunctata. Our study sequence included the 3' end of the cytochrome c oxidase subunit I (CO I) locus (183 to 198 total sites; 91 informative sites), an intergenic spacer region of variable size (0 to 152 sites), the tRNA leucine locus (65 to 74 sites), and the 5' end of the cytochrome c oxidase subunit II (co II) locus (292 total sites; 140 informative sites). The inferred relationships among the attine taxa based on an unweighted analysis of the nucleotide sequence data closely matched the relationships inferred from an analysis of larval morphological characters from 11 of the taxa. In fact, the inferred relationships were completely congruent among the protein parsimony analysis of amino acid data, the morphology analysis, and "total evidence" analysis combining the amino acid and morphology data. The congruent conclusions we obtained from two independent data sets increases our confidence in the reliability of our analyses.

Despite a considerable literature describing the biology of flies in the tephritid genus Rhagoletis, the phylogenetic relationships of the more than 60 species classified within the genus are not well resolved. Knowledge of these relationships is important, not only in terms of obtaining information that will be useful for the control of Rhagoletis where it is an agricultural pest, but also in determining what role host plant shifts have played in the generation of Rhagoletis species diversity, a focal point in debate over the role of sympatric speciation in the evolutionary process. In this paper, the phylogenetic history of 28 Rhagoletis species and 6 species in related tephritid genera is inferred from nucleotide sequences of subunit II of the mitochondrial cytochrome oxidase (COII) gene and the adjacent tRNALeu/COII intergenic region. Analyses of the data using distance and character-state approaches suggest the following: (i) the genus Rhagoletis as currently defined is not monophyletic; (ii) the 5 predominantly North American Rhagoletis species groups do constitute a monophyletic assemblage; (iii) the North American species groups form 2 clades, 1 consisting of taxa in the R. pomonella and R. tabellaria species groups (plus R. fausta), and the other consisting of taxa in the R. ribicola, R. cingulata, and R. suavis species groups; and (iv) the origin(s) of the North American species groups is obscure, as evidenced by the recovery of clades containing both Palearctic and Neotropical taxa. Areas of congruence and conflict with published phylogenies of Rhagoletis are examined and, while many areas of conflict may be due to an insufficient number of characters or incomplete taxon sampling, we cannot discount the possibility that real differences exist between the Rhagoletis mitochondrial DNA gene tree and the Rhagoletis species tree.

Marine turtles are divided into two families, the Dermochelyidae and the Cheloniidae. The majority of species are currently placed within the two tribes of the Cheloniidae, the Chelonini and the Carettini, but debate continues over generic and tribal affinities as well as species boundaries. We used nucleotide sequences (907 bp) from the ND4-LEU tRNA region and the control region (526 bp) of mitochondrial DNA to resolve areas of uncertainty in marine turtle (Chelonioidae) systematics. The ND4-LEU tRNA fragment was more conserved than the fragment from the control region, with sequence divergences ranging from 0.026 to 0.148 and 0.067 to 0.267, respectively. Parsimony analysis based only on the ND4-LEU tRNA data suggests that the hawksbill, Eretmochelys imbricata, lies within the tribe Carettni and is closely related to the genus Caretta, but could not resolve the position of the flatback, Natator depressus. A similar analysis based only on the control region sequence data suggested that N. depressus is affiliated with the Chelonini, but failed to resolve the position of E. imbricata and the loggerhead, Caretta caretta. In contrast to these results, the combination of both data sets with published cytochrome b data produced a phylogeny based on 1924 bp of sequence data which resolves the position of E. imbricata relative to Caretta and Lepidochelys and joins N. depressus as sister to the Carettini. Based on the molecular data, the Chelonini contains the Chelonia species, while the Carettini contains the remaining species of Cheloniidae. The control region sequence divergence between Pacific and Atlantic populations of the leatherback, Dermochelys coriacea, was relatively low (0.0081) when compared with the green turtle, Chelonia mydas (0.071-0.074). Atlantic and Pacific populations of Ch. mydas were found to be paraphyletic with respect to the black turtle, Ch. agassizi, suggesting that the current taxonomic designations within the Pacific Chelonia are questionable. This analysis shows the utility of combining sequence data for different regions of mtDNA that by themselves are insufficient to obtain robust phylogenies.

Despite the prominence of the Azteca-Cecropia interaction as the focus of extensive ecological investigation, a reliable phylogeny of the Azteca ants has been lacking, primarily because many of the morphological and behavioral characters are phylogenetically uninformative or conflicting. A phylogenetic analysis of a select set of Azteca ants, including six Cecropia inhabitants and two non-Cecropia inhabitants, plus an outgroup taxon, is presented on the basis of mitochondrial DNA sequences. The evolutionary relationships deduced from the molecular data are analyzed with reference to ecological and morphological studies, specifically addressing the phylogenetic relationship of structurally an behaviorally ambiguous taxa, species complex groupings, and the colonization of Cecropia trees. According to the molecular phylogeny, the Cecropia-inhabiting Azteca do not form a monophyletic clade, indicating multiple independent colonization or abandonment of Cecropia trees by the Azteca.