Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree

It has proven remarkably difficult to obtain a well-resolved and strongly supported phylogeny for horned lizards (Phrynosoma) because of incongruence between morphological and mitochondrial DNA sequence data. We infer the phylogenetic relationships among all 17 extant Phrynosoma species using >5.1 kb of mtDNA (12S rRNA, 16S rRNA, ND1, ND2, ND4, Cyt b, and associated tRNA genes), and >2.2kb from three nuclear genes (RAG-1, BDNF, and GAPD) for most taxa. We conduct separate and combined phylogenetic analyses of these data using maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic relationships inferred from the mtDNA data are congruent with previous mtDNA analyses based on fewer characters and provide strong support for most branches. However, we detected strong incongruence between the mtDNA and nuclear data using comparisons of branch support and Shimodaira-Hasegawa tests, with the (P. platyrhinos+P. goodei) clade identified as the primary source of this conflict. Our analysis of a P. mcalliixP. goodei hybrid suggests that this incongruence is caused by reticulation via introgressive hybridization. Our preferred phylogeny based on an analysis of the combined data (excluding the introgressed mtDNA data) provides a new framework for interpreting character evolution and biogeography within Phrynosoma. In the context of this improved phylogeny we propose a phylogenetic taxonomy highlighting four clades: (1) Tapaja, containing the viviparous short-horned lizards P. ditmarsi, P. hernandesi, P. douglasii, and P. orbiculare; (2) Anota, containing species with prominent cranial horns (P. solare, P. mcallii, and the P. coronatum group); (3) Doliosaurus, containing three species lacking antipredator blood-squirting (P. modestum, P. platyrhinos, and P. goodei); and (4) Brevicauda, containing two viviparous species with extremely short tails that lack blood-squirting (P. braconnieri and P. taurus).     

Morphological correlates of ant eating in horned lizards (Phrynosoma)

The North American horned lizards ( Phrynosoma ) represent a morphologically specialized group of ant-eating lizards. Although variation in dietary fidelity is observed among the species, all appear to possess morphological specializations thought to be related to their ant-eating diets. Previous studies have examined morphological specialization in Phrynosoma , but they have not taken into account the phylogenetic relationships of its member species. In the present study, the morphological characteristics of the head, jaws and teeth that are thought to be important in prey capture and prey processing were examined to test whether variation in cranial morphology is associated with diet in lizards of the genus Phrynosoma . It is suggested that lizards of the genus Phrynosoma are indeed morphologically specialized and that ant-eating is associated with reduced dentition and an overall reduction in the robustness of morphological structures important in prey processing. Although this trend holds for the highly myrmecophagous species of Phrynosoma , a robust cranial morphology is apparent in the short-horned lizard clade ( Phrynosoma ditmarsi , Phrynosoma douglasii , Phrynosoma hernandesi , Phrynosoma orbiculare ), implying the ability to process a variety of dietary items. The present study suggests that additional feeding specializations exist within an already specialized clade (i.e. the short-horned lizard clade) and highlights the need for more detailed dietary and behavioural studies of feeding behaviour in this uniquely specialized group of lizards.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 89 , 13–24.     

Phylogenetic relationships of north American field crickets inferred from mitochondrial DNA data

A well-supported molecular phylogeny for North American Gryllus species based on a combined data set of mitochondrial (mt) DNA is presented. A total of 26 individuals representing 13 populations of 11 species of the genus Gryllus and 4 individuals of two outgroup species, Teleogryllus oceanicus and Acheta domestica, were sampled in this study. The complete cytochrome b gene (1036 bp) and a 500-bp fragment of the 16S rRNA gene were sequenced for each individual. Since results from separate analyses of the cytochrome b and 16S data sets, as well as a previously published mtDNA restriction-site data set, were not conflicting, all data were combined for phylogenetic analyses. The clade of European Gryllus was clearly separated from the North American clade. The amount of sequence divergence between these clades was significantly greater than within the clades, suggesting a basal drift-vicariant event in the genus. This is the first phylogenetic analysis of North American Gryllus that includes western species. Four well-supported groups were identified but their relationships showed no clear east-west structure. Our phylogeny supports the recent reassignment of G. integer Scudder 1901 from Texas to G. texensis Cade and Otte 2000. The evolution of cricket song and life cycle is discussed using the new phylogenetic framework.     

Attributes and congruence of three molecular data sets: inferring phylogenies among Septoria-related species from woody perennial plants

To improve our understanding of phylogenetic relationships within the anamorphic genus Septoria, three molecular data sets representing 2,417 bp of nuclear and mitochondrial genes were evaluated. Separate gene analyses and combined analyses were performed using first, the maximum parsimony criterion and second, a Bayesian framework. The homogeneity of data partitions was evaluated via a combination of homogeneity partition tests and tree topology incongruence tests before conducting combined analyses. A last incongruence re-evaluation using partitioned Bremer support was performed on the combined tree, which corroborated the previous estimates. After each separate data set attributes were examined, simple explanations were advocated as the causes of the significant incongruences detected. The analysis of multiple gene partitions showed unprecedented phylogenetic resolution within the genus Septoria that supported the results from previously published single gene phylogenies. Specifically, we have delimited distinct but closely related species representing monophyletic groups that frequently correlated with their respective host families. Conversely, the occurrence of well-supported groups including closely related but distinct molecular taxa sampled on unrelated host-plants allowed us to reject, in these particular cases, the co-evolutionary concept expected between a parasite and its host and to discuss alternative evolutionary models recently proposed for these pathogens.     

Molecular systematics of short-horned lizards: biogeography and taxonomy of a widespread species complex

We surveyed mitochondrial DNA (mtDNA) sequence variation in short-horned lizards (Phrynosoma douglasi) from throughout western North America and used these data to estimate an intraspecific phylogeny and to assess biogeographic scenarios underlying the geographic structure of lineages in this species. We sequenced 783 base pairs from 38 populations of P. douglasi and three putative outgroups (P. ditmarsi, P. orbiculare, P. platyrhinos). We detected high levels of nucleotide variation among populations and a spatial distribution of mtDNA lineages compatible with major geographic regions. The phylogenetic hypotheses best supported by the data suggest that P. douglasi, as currently described, is paraphyletic with respect to P. ditmarsi. Populations of P. douglasi from the Pacific Northwest (ID, CA, OR, WA) form a monophyletic group that is sister to the subsequent radiation of P. ditmarsi and other P. douglasi clades. These results suggest that divergences within this widespread species are fairly old. We focused on the genetic structure of populations of P. douglasi from a geographic perspective and interpreted the intraspecific phylogeny in light of geologic and climatic changes in western North America during the last 20 million years. The generally high levels of genetic variation found in these population comparisons are in accord with high levels of morphological variation in this species group; however, only in the Pacific Northwest region is there spatial congruence between these phylogenetic results and subspecific ranges based on previous morphological studies. We compared the evolutionary units delineated in this study with previously described subspecies of P. douglasi and evaluated the support (from morphology and mtDNA) for each population lineage in the phylogeny and the implications for the taxonomy of this group.     

A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach

Multi-gene phylogenetic analyses were conducted to address the evolution of Clavicipitaceae (Ascomycota). Data are presented here for approximately 5900 base pairs from portions of seven loci: the nuclear ribosomal small and large subunit DNA (nrSSU and nrLSU), beta-tubulin, elongation factor 1alpha (EF-1alpha), the largest and second largest subunits of RNA polymerase II (RPB1 and RPB2), and mitochondrial ATP Synthase subunit 6 (mtATP6). These data were analyzed in a complete 66-taxon matrix and 91-taxon supermatrix that included some missing data. Separate phylogenetic analyses, with data partitioned according to genes, produced some conflicting results. The results of separate analyses from RPB1 and RPB2 are in agreement with the combined analyses that resolve a paraphyletic Clavicipitaceae comprising three well-supported clades (i.e., Clavicipitaceae clade A, B, and C), whereas the tree obtained from mtATP6 is in strong conflict with the monophyly of Clavicipitaceae clade B and the sister-group relationship of Hypocreaceae and Clavicipitaceae clade C. The distribution of relative contribution of nodal support for each gene partition was assessed using both partitioned Bremer support (PBS) values and combinational bootstrap (CB) analyses, the latter of which analyzed bootstrap proportions from all possible combinations of the seven gene partitions. These results suggest that CB analyses provide a more consistent estimate of nodal support than PBS and that combining heterogeneous gene partitions, which individually support a limited number of nodes, results in increased support for overall tree topology. Analyses of the 91-taxa supermatrix data sets revealed that some nodes were more strongly supported by increased taxon sampling. Identifying the localized incongruence of mtATP6 and analyses of complete and supermatrix data sets strengthen the evidence for rejecting the monophyly of Clavicipitaceae and much of the current subfamilial classification of the family. Although the monophyly of the grass-associated subfamily Clavicipitoideae (e.g., Claviceps, Balansia, and Epichlo?) is strongly supported, the subfamily Cordycipitoideae (e.g., Cordyceps and Torrubiella) is not monophyletic. In particular, species of the genus Cordyceps, which are pathogens of arthropods and truffles, are found in all three clavicipitaceous clades. These results imply that most characters used in the current familial classification of Clavicipitaceae are not diagnostic of monophyly.     

The fulvettas (Alcippe, Timaliidae, Aves): a polyphyletic group

The phylogeny of fulvettas (Alcippe, Timaliidae) was investigated using molecular data. Fifteen species of the genus, other timaliids and Sylvioidea were used. ML and Bayesian analyses were done on separate and combined cyt -b and Nd2 DNA data sets. The polyphyly of the genus is confirmed. The clades correspond to the taxonomy of Wolters. We recommend that this polyphyly be taken into account when conducting phylogenetic analyses with incomplete taxonomic sampling.     

Assessing the phylogenetic utility of four mitochondrial genes and a nuclear intron in the asian pit viper genus,Trimeresurus: separate,simultaneous, and conditional data combination analyses

A number of methods have been proposed for addressing how to optimize the analysis of multiple data sets from diverse mitochondrial and nuclear gene partitions in the pursuit of robust organismal phylogenies. The present study used separate, simultaneous, and conditional data combination methods to analyze 3,135 bp of data from four mitochondrial partitions and the seventh intron of the beta fibrinogen gene in the Asian pit viper genus, Trimeresurus sensu stricto. The phylogenetic utility and homogeneity of all partitions were estimated via a combination of homogeneity partition tests, homoplasy indices, and partitioned Bremer support. Despite the detection of significant heterogeneity of phylogenetic signal between the mitochondrial and nuclear partitions, the simultaneous analysis represented the best-supported topology of all the data. The relatively slow rate (approximately one quarter of the rate of mtDNA) and functionally unconstrained molecular evolution of the intron resulted in much lower levels of homoplasy compared with the mitochondrial partitions. This was further shown via partitioned Bremer support, which, when considered throughout hierarchical clade levels, highlighted the phylogenetic strength and limitations of the intron at deeper and shallower phylogenetic levels, respectively. The simultaneous analysis helped to resolve the phylogenetic relationships of taxa that were unresolved throughout all individual gene trees and tentatively supports the existence of morphologically and genetically distinct clades within the genus. Topological appraisals of the mitochondrial gene partitions suggest that the cytochrome b and the NADH subunit 4 gene partitions are better estimators of phylogenetic relationships than are the 12S and 16S ribosomal RNA partitions at the taxonomic levels under consideration.     

Relationships among seed plants inferred from highly conserved genes: sorting conflicting phylogenetic signals among ancient lineages

Phylogenetic studies based on different types and treatment of data provide substantially conflicting hypotheses of relationships among seed plants. We conducted phylogenetic analyses of sequences of two highly conserved chloroplast genes, psaA and psbB, for a comprehensive taxonomic sample of seed plants and land plants. Parsimony analyses of two different codon position partitions resulted in well-supported, but significantly conflicting, phylogenetic trees. First and second codon positions place angiosperms and gymnosperms as sister clades and Gnetales as sister to Pinaceae. Third positions place Gnetales as sister to all other seed plants. Maximum likelihood trees for the two partitions are also in conflict. Relationships among the main seed plant clades according to first and second positions are similar to those found in parsimony analysis for the same data, but the third position maximum likelihood tree is substantially different from the corresponding parsimony tree, although it agrees partially with the first and second position trees in placing Gnetales as the sister group of Pinaceae. Our results document high rate heterogeneity among lineages, which, together with the greater average rate of substitution for third positions, may reduce phylogenetic signal due to long-branch attraction in parsimony reconstructions. Whereas resolution of relationships among major seed plant clades remains pending, this study provides increased support for relationships within major seed plant clades.     

A phylogenetic analysis of Coelopidae (Diptera) based on morphological and DNA sequence data

The phylogenetic relationships of 22 species of Coelopidae are reconstructed based on a data matrix consisting of morphological and DNA sequence characters (16S rDNA, EF-1alpha). Optimal gap and transversion costs are determined via a sensitivity analysis and both equal weighting and a transversion cost of 2 are found to perform best based on taxonomic congruence, character incongruence, and tree support. The preferred phylogenetic hypothesis is fully resolved and well-supported by jackknife, bootstrap, and Bremer support values, but it is in conflict with the cladogram based on morphological characters alone. Most notably, the Coelopidae and the genus Coelopa are not monophyletic. However, partitioned Bremer Support and an analysis of node stability under different gap and transversion costs reveal that the critical clades rendering these taxa non-monophyletic are poorly supported. Furthermore, the monophyly of Coelopidae and Coelopa is not rejected in analyses using 16S rDNA that was manually aligned. The resolution of the tree based on this reduced data sets is, however, lower than for the tree based on the full data sets. Partitioned Bremer support values reveal that 16S rDNA characters provide the largest amount of tree support, but the support values are heavily dependent on analysis conditions. Problems with direct comparison of branch support values for trees derived using fixed alignments with those obtained under optimization alignment are discussed. Biogeographic history and available behavioral and genetic data are also discussed in light of this first cladogram for Coelopidae based on a quantitative phylogenetic analysis.     

Amino acid vs. nucleotide characters: challenging preconceived notions

The 567-terminal analysis of atpB, rbcL, and 18S rDNA was used as an empirical example to test the use of amino acid vs. nucleotide characters for protein-coding genes at deeper taxonomic levels. Nucleotides for atpB and rbcL had 6.5 times the amount of possible synapomorphy as amino acids. Based on parsimony analyses with unordered character states, nucleotides outperformed amino acids for all three measures of phylogenetic signal used (resolution, branch support, and congruence with independent evidence). The nucleotide tree was much more resolved than the amino acid tree, for both large and small clades. Nearly twice the percentage of well-supported clades resolved in the 18S rDNA tree were resolved using nucleotides (91.8%) relative to amino acids (49.2%). The well-supported clades resolved by both character types were much better supported by nucleotides (98.7% vs. 83.8% average jackknife support). The faster evolving nucleotides with a smaller average character-state space outperformed the slower evolving amino acids with a larger average character-state space. Nucleotides outperformed amino acids even with 90% of the terminals deleted. The lack of resolution on the amino acid trees appears to be caused by a lack of congruence among the amino acids, not a lack of replacement substitutions.     

Phylogenetic relationships in the genus mus,based on paternally,maternally, and biparentally inherited characters

Several species in the rodent genus Mus are used as model research organisms, but comparative studies of these mice have been hampered by the lack of a well-supported phylogeny. We used DNA sequences from six genes representing paternally, maternally, and biparentally inherited regions of the genome to infer phylogenetic relationships among 10 species of Mus commonly used in laboratory research. Our sample included seven species from the subgenus Mus; one species each from the subgenera Pyromys, Coelomys, and Nannomys; and representatives from three additional murine genera, which served as outgroups in the phylogenetic analyses. Although each of the six genes yielded a unique phylogeny, several clades were supported by four or more gene trees. Nodes that conflicted between trees were generally characterized by weak support for one or both of the alternative topologies, thus providing no compelling evidence that any individual gene, or part of the genome, was misleading with respect to the evolutionary history of these mice. Analysis of the combined data resulted in a fully resolved tree that strongly supports monophyly of the genus Mus, monophyly of the subgenus Mus, division of the subgenus Mus into Palearctic (M. musculus, M. macedonicus, M. spicilegus, and M. spretus) and Asian (M. cervicolor, M. cookii, and M. caroli) clades, monophyly of the house mice (M. m. musculus, "M. m. molossinus," M. m. castaneus, and M. m. domesticus), and a sister-group relationship between M. macedonicus and M. spicilegus. Other clades that were strongly supported by one or more gene partitions were not strongly supported by the combined data. This appears to reflect a localized homoplasy in one partition obscuring the phylogenetic signal from another, rather than differences in gene or genome histories.     

Phylogenetic utility of indels within ribosomal DNA and beta-tubulin sequences from fungi in the Rhizoctonia solani species complex

The genus Rhizoctonia consists of a diverse assemblage of anamorphic fungi frequently associated with plants and soil throughout the world. Some anamorphs are related with teleomorphs (sexual stage) in different taxonomic classes, orders, and families. The fungus may exist as pathogen, saprophyte, or mycorrhizal symbiont and shows extensive variation in characteristics such as geographic location, morphology, host specificity, and pathogenicity. In this study, phylogenetic analyses were performed in the Rhizoctonia solani species complex with individual and combined data sets from three gene partitions (ITS, LSU rDNA, and beta-tubulin). To explore whether indels were a source of phylogenetically informative characters, single-site indels were treated as a new state, while indels greater than one contiguous nucleotide were analyzed by including them as ambiguous data (Coding A); excluding them from the analyses (Coding B), and with three distinct codes: multistate for different sequence (Coding C); multistate for different length (Coding D) and different characters for each distinct sequence (Coding E). Results suggest that indels in noncoding regions contain phylogenetic information and support the fact that the R. solani species complex is not monophyletic. Six clades within R. solani (teleomorph=Thanatephorus) representing distinct anastomosis groups and five clades within binucleate Rhizoctonia (teleomorph=Ceratobasidium) were well supported in all analyses. The data suggest that clades with representatives of R. solani fungi belonging to anastomosis groups 1, 4, 6, and 8 should be recognized as phylogenetic species.     

A total-evidence phylogeny of ticks provides insights into the evolution of life cycles and biogeography.

We inferred the phylogeny of 33 species of ticks from the subfamilies Rhipicephalinae and Hyalomminae from analyses of nuclear and mitochondrial DNA and morphology. We used nucleotide sequences from 12S rRNA, cytochrome c oxidase I, internal transcribed spacer 2 of the nuclear rRNA, and 18S rRNA. Nucleotide sequences and morphology were analyzed separately and together in a total-evidence analysis. Analyses of the five partitions together (3303 characters) gave the best-resolved and the best-supported hypothesis so far for the phylogeny of ticks in the Rhipicephalinae and Hyalomminae, despite the fact that some partitions did not have data for some taxa. However, most of the hidden conflict (lower support in the total-evidence analyses compared to that in the individual analyses) was found in those partitions that had taxa without data. The partitions with complete taxonomic sampling had more hidden support (higher support in the total-evidence analyses compared to that in the separate-partition analyses) than hidden conflict. Mapping of geographic origins of ticks onto our phylogeny indicates an African origin for the Rhipicephalinae sensu lato (i.e., including Hyalomma spp.), the Rhipicephalus-Boophilus lineage, the Dermacentor-Anocentor lineage, and the Rhipicephalus-Booophilus-Nosomma-Hyalomma-Rhipicentor lineage. The Nosomma-Hyalomma lineage appears to have evolved in Asia. Our total-evidence phylogeny indicates that (i) the genus Rhipicephalus is paraphyletic with respect to the genus Boophilus, (ii) the genus Dermacentor is paraphyletic with respect to the genus Anocentor, and (iii) some subgenera of the genera Hyalomma and Rhipicephalus are paraphyletic with respect to other subgenera in these genera. Study of the Rhipicephalinae and Hyalomminae over the last 7 years has shown that analyses of individual datasets (e.g., one gene or morphology) seldom resolve many phylogenetic relationships, but analyses of more than one dataset can generate well-resolved phylogenies for these ticks.     

Combined mitochondrial and nuclear sequences support the monophyly of forcipulatacean sea stars

Previous molecular phylogenetic analyses of forcipulatacean sea stars (Echinodermata: Asteroidea) have reconstructed a non-monophyletic order Forcipulatida, provided that two or more forcipulate families are included. This result could mean that one or more assumptions of the reconstruction method was violated, or else the traditional classification could be erroneous. The present molecular phylogenetic analysis included 12 non-forcipulatacean and 39 forcipulatacean sea stars, with multiple representatives of all but one of the forcipulate families and/or subfamilies. Bayesian analysis of approximately 4.2kb of sequence data representing seven partitions (nuclear 18S rRNA and 28S rRNA, mitochondrial 12S rRNA, 16S rRNA, 5 tRNAs and cytochrome oxidase I with first and second codon positions analyzed separately from third codon positions) recovered a consensus tree with three well-supported clades (78%-100% bootstrap support) that corresponded at least approximately to traditional taxonomic ranks: the superorder Forcipulatacea (Forcipulatida + Brisingida) + Pteraster, the Brisingida/Brisingidae and Asteriidae + Rathbunaster + Pycnopodia. When a molecular clock was enforced, the partitioned Bayesian analysis recovered the traditional Forcipulatacea. Five of six genera represented by two or more species were monophyletic with 100% bootstrap support. Most of the traditional subfamilial and familial groupings within the Forcipulatida were either unresolved or non-monophyletic. The separate partitions differed considerably in estimates of model parameters, mainly between nuclear sequences (with high GC content, low rates of sequence substitution and high transition/transversion rate ratios) and mitochondrial sequences.     

A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences

A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.     

African Dacus (Diptera: Tephritidae: Molecular data and host plant associations do not corroborate morphology based classifications

The genus Dacus Fabricius includes economically important pest fruit flies distributed in the Afrotropical and Indo-Australian regions. Two recent revisions based on morphological characters proposed new and partially discordant classifications synonymizing/revalidating several subgeneric names and forming species groups. Regardless these efforts, the phylogenetic relationships among Dacus species remained largely unresolved mainly because of the difficulties in assigning homologous character states. Therefore we investigated the phylogeny of African Dacus by sequencing 71 representatives of 32 species at two mitochondrial (COI, 16S) and one nuclear (period) gene fragments. Phylogenetic relationships were inferred through Bayesian and Maximum Parsimony methods and hypotheses about the monophyly of Dacus subgenera were tested by Shimodaira–Hasegawa tests. The congruence tests and the analyses of the single gene fragments revealed that the nuclear gene supports similar conclusions as the two mitochondrial genes. Levels of intra- and inter-specific differentiation of Dacus species were highly variable and, in some cases, largely overlapping. The analyses of the concatenated dataset resolved two major bootstrap-supported groups as well as a number of well-supported clades and subclades that often comprised representatives of different subgenera. Additionally, specimens of Dacus humeralis from Eastern and Western African localities formed separate clades, suggesting cryptic differentiation within this taxon. The comparisons between the molecular phylogeny and the morphological classification revealed a number of discrepancies and, in the vast majority of cases, the molecular data were not compatible with the monophyly of the currently recognised subgenera. Conversely, the molecular data showed that Apocynaceae feeders are a monophyletic sister group of species feeding on both Cucurbitaceae and Passifloraceae (these latter being also monophyletic). These results show a clear association between the molecular phylogeny of African Dacus and the evolution of host plant choice and provide a basis towards a more congruent taxonomy of this genus.     

Phylogeny of Anophelinae (Diptera: Culicidae) based on nuclear ribosomal and mitochondrial DNA sequences

Abstract Phylogenetic relationships among thirty-two species of mosquitoes in subfamily Anophelinae are inferred from portions of the mitochondrial genes COI and COII, the nuclear 18S small subunit rRNA gene and the expansion D2 region of the nuclear large subunit 28S rRNA gene. Sequences were obtained from the genera Anopheles , Bironella and Chagasia . Representatives of all six subgenera of Anopheles were included: Anopheles , Cellia , Kerteszia , Lophopodomyia , Nyssorhynchus and Stethomyia. Using parsimony and maximum likelihood methods, various combinations of these DNA sequence data were analysed separately: 18S, 28S, combined 18S and 28S, combined COI and COII, and combined 18S, 28S, COI and COII ('total evidence'). The combined rDNA data contain strong phylogenetic signal, moderately to strongly supporting most clades in MP and ML analyses; however, the mtDNA data (analysed as either nucleotide or amino acid sequences) contain little phylogenetic signal, except for relationships of very recently derived groups of species and, at the deepest level, for the monophyly of Anophelinae. The paraphyly of Anopheles relative to Bironella is confirmed by most analyses and statistical tests. Support for the monophyly of subgenera Anopheles , Cellia , Kerteszia and Nyssorhynchus is indicated by most analyses. Subgenus Lophopodomyia is reconstructed as the sister to Bironella , nested within a clade also containing Nyssorhynchus and Kerteszia . The most basal relationships within genus Anopheles are not well resolved by any of the data partitions, although the results of statistical analyses of the rDNA data (S-H-tests, likelihood ratio tests for monophyly and Bayesian MCMC analyses) suggest that the clade consisting of Bironella , Lophopodomyia , Nyssorhynchus and Kerteszia is the sister to the clade containing Cellia and Anopheles .     

Phylogeny-based delimitation of species boundaries and contact zones in the trilling chorus frogs (Pseudacris)

Although the trilling chorus frogs (subclade within Pseudacris: Hylidae) have been important in studies of speciation, continental patterns of genetic diversity within and among species have not been elucidated. As a result, this North American clade has been the subject of substantial taxonomic debate. In this study, we examined the phylogenetic relationships among the trilling Pseudacris and tested previously hypothesized scenarios for speciation using 2.4 kb of mitochondrial 12S and 16S rRNA genes from 253 populations. Bayesian phylogenetic analyses, in combination with published morphological and behavioral data, support recognition of at least nine species, including an undescribed species from the south-central United States. Evidence is presented for substantial geographic subdivision within P. brachyphona (northern and southern clades) and P. feriarum (coastal and inland clades). Discordance between morphology/behavior and molecular data in several individuals suggests occasional hybridization between sympatric species. These results require major revision of range limits for several taxa, in particular, P. maculata, P. triseriata, and P. feriarum. Hypothesis tests using parametric bootstrapping strongly reject previously proposed scenarios for speciation in the group. The tests also support recognition of the geographically restricted taxon P. kalmi as a distinct species. Results of this study provide both a firm phylogenetic basis for future studies of speciation in the trilling Pseudacris and a taxonomic framework for conservation efforts.