Phylogenetic relationships of the genera Arthroderma and Nannizzia inferred from mitochondrial DNA analysis

The phylogenetic relationship of the genera Arthroderma and Nannizzia, was investigated by mitochondrial DNA analysis based on the restriction-fragment-length polymorphisms. Phylogenetic trees made on ten species. A. benhamiae, A. insingulare, A. quadrifidum, A. simii, A. vanbreuseghemii, N. fulva, N. grubyia, N. gypsea, N. incurvata and N. otae showed no definite distinctions between the genera Arthroderma and Nannizzia. These results support the conclusion of Weitzman et al. that the genera Arthroderma and Nannizzia are congeneric.     

Phylogenetic relationships of elopomorph fishes inferred from mitochondrial ribosomal DNA sequences

The superorder Elopomorpha, a grouping which includes all teleost fishes that possess a specialized leptocephalous larva [true eels (Anguilliformes), gulpers and bobtail snipe eels (Saccopharyngiformes), bonefishes, spiny eels, and halosaurs (Albuliformes, including Notacanthiformes), ladyfishes and tarpons (Elopiformes, including Megalopiformes)] comprises >800 species for which phylogenetic relationships are poorly understood. In the present study, we analyzed mitochondrial DNA sequences in segments of the 12S and 16S rRNA genes in 33 elopomorph taxa encompassing all of the previously proposed orders, and 9 of the 15 currently recognized families of the Anguilliformes, as well as outgroup representatives from the superorders Osteoglossomorpha (nine species) and Clupeomorpha (three species), to develop phylogenetic hypotheses based on distance and parsimony methods. Both methods failed to support the monophyly of the Elopomorpha, casting doubt on the validity of the leptocephalus as an elopomorph synapomorphy. The orders Elopiformes, Albuliformes, and Anguilliformes, however, were resolved as monophyletic assemblages. Parsimony analysis supported the separation of the Anguilliformes into two groups (primitive and advanced) based on the presence of divided versus fused frontal bones. In addition, the molecular data indicated a close affinity of the anguilliform Thalassenchelys coheni (incertae sedis), known only from the leptocephalus, with the family Serrivomeridae. The implications of these data as regards the evolution of the elopomorph assemblage are discussed.     

Phylogenetic relationships and biogeography of the genus Chondrostoma inferred from mitochondrial DNA sequences

A phylogeny of the species of the nase genus Chondrostoma was constructed from a complete mitochondrial cytochrome b gene (1140 bp). Molecular phylogeny was used to revise the current systematics of this group, and to infer a biogeographical model of the Mediterranean area during the Cenozoic period. We confirmed the monophyly of the genus Chondrostoma, and defined seven different lineages within it: Polylepis, Arcasii, Lemmingii, Toxostoma, Nasus, C. genei, and C. soetta. The separation of main lineages within Chondrostoma occurred in the Middle-Upper Miocene, approximately 11 million years ago, while the greatest species radiation took place in the Pliocene close to the time the current drainages system were created. It is unlikely that this genus experienced an extensive dispersal during the Messinian, in the Lago-Mare Phase. Given the level of current knowledge, a biogeographical model constructed on the basis of vicariant events seems more realistic than does a dispersalist model.     

Phylogenetic relationships of neopterygian fishes, inferred from mitochondrial DNA sequences.

To investigate the relationships among the three main groups of extant neopterygian fishes--Amiidae, Lepisosteidae, and Teleostei--we sequenced fragments of three mitochondrial genes from 12 different actinopterygian fishes and translated the nucleotide sequences into amino acid sequences. When all three regions are considered together, Amiidae clusters with Lepisosteidae in the most parsimonious cladograms, but other clades, such as Neopterygii and Teleostei, that are well supported by morphological evidence fail to emerge as monophyletic. When the cytochrome b sequences are analyzed together with previously published sequences for other taxa, the majority-rule consensus tree is consistent with the monophyly of Teleostei and Neopterygii and marginally supports the Amiidae + Lepisosteidae clade. In either analysis, when Neopterygii and Teleostei are constrained to monophyly, all the most-parsimonious cladograms support the Amiidae + Lepisosteidae topology. Where molecules and morphology disagree, provisional morphology-based constraints on the analysis of molecular data offer a practical means of integrating the two types of data.     

Phylogenetic relationships of Pestalotiopsis and allied genera inferred from ribosomal DNA sequences and morphological characters

The taxonomy of the coelomycetous fungus Pestalotiopsis and other closely related genera based on morphological characters has been equivocal. To gain insight in the phylogenetic relationships of Pestalotiopsis and its allies, part of the large subunit (28S) ribosomal DNA region was examined and compared with existing morphological information. Phylogenetic analyses were conducted using parsimony, distance, and likelihood criteria. Results of the analyses showed that Bartalinia, Pestalotiopsis, Seimatosporium, and Seiridium represent distinct monophyletic groups with high bootstrap support. However, Truncatella species are paraphyletic with Bartalinia, sharing a common ancestor. Pestalotia species sequenced clustered together with Pestalotiopsis. These genera should be recognized as distinct natural groups except for Monochaetia and Discosia, which need to be further resolved. Tree topologies are generally in concordance with previous morphological hypotheses, most notably the placement of all Pestalotia species, except the type P. pezizoides, in Pestalotiopsis. Well-supported clades corresponding to groupings based on conidial morphology were resolved and the relative importance of morphological characters for generic delimitation is discussed. Molecular data also provide further evidence to support the association of these coelomycetes with the Amphisphaeriaceae.     

Phylogenetic relationships in European Ceriporiopsis species inferred from nuclear and mitochondrial ribosomal DNA sequences

The aim of this work was to clarify taxonomy and examine evolutionary relationships within European Ceriporiopsis species using a combined analysis of the large subunit (nLSU) nuclear rRNA and small subunit (mtSSU) mitochondrial rRNA gene sequences. Data from the ITS region were applied to enhance the view of the phylogenetic relationships among different species. The studied samples grouped into four complex clades, suggesting that the genus Ceriporiopsis is polyphyletic. The generic type Ceriporiopsis gilvescens formed a separate group together with Ceriporiopsis guidella and Phlebia spp. in the phlebioid clade. In this clade, the closely related species Ceriporiopsis resinascens and Ceriporiopsis pseudogilvescens grouped together with Ceriporiopsis aneirina. C. resinascens and C. pseudogilvescens have identical LSU and SSU sequences but differ in ITS. Ceriporiopsis pannocincta also fell in the phlebioid clade, but showed closer proximity to Gloeoporus dichrous than to C. gilvescens or C. aneirina–C. pseudogilvescens–C. resinascens group. Another clade was composed of a Ceriporiopsis balaenae–Ceriporiopsis consobrina group and was found to be closely related to Antrodiella and Frantisekia, with the overall clade highly reminiscent of the residual polyporoid clade. The monotypic genus Pouzaroporia, erected in the past for Ceriporiopsis subrufa due to its remarkable morphological differences, also fell within the residual polyporoid clade. Ceriporiopsis subvermispora held an isolated position from the other species of the genus. Therefore, the previously proposed name Gelatoporia subvermispora has been adopted for this species. Physisporinus rivulosus appeared unrelated to two other European Physisporinus species. Moreover, Ceriporiopsis (=Skeletocutis) jelicii grouped in a separate clade, distinct from Ceriporiopsis species. Finally, the ITS data demonstrated the proximity of some Ceriporiopsis species (Ceriporiopsis portcrosensis and Ceriporiopsis subsphaerospora) to Skeletocutis amorpha.     

Classification and phylogenetic relationships of African tilapiine fishes inferred from mitochondrial DNA sequences

African cichlid fishes are composed of two major lineages, the haplochromines and the tilapiines. Whereas the phylogenetic relationships of the haplochromines have been studied extensively, primarily because of their spectacular adaptive radiations in the Great Lakes of East Africa, little is known about the relationships among the tilapiine species, despite the fact that they have become an important component of African, indeed world, aquaculture. To remedy this situation, molecular phylogenetic analysis of tilapiine fishes was undertaken. A segment of mitochondrial DNA encompassing the terminal part of the tRNA(Pro) gene and the most variable part of the control region was amplified by the polymerase chain reaction with DNA samples isolated from 42 tilapiine species, and the amplification products were subjected to heteroduplex analysis and sequencing. Phylogenetic trees based on 68 sequences revealed the existence of 11 sequence groups and 11 single-sequence branches. The groups, designated Ti1 through Ti11, were distinguished by specific combinations of diagnostic substitutions, formation of monophyletic clusters, and separation by genetic distances in excess of 0.04. Although the relationships among the groups could not be resolved, the sequences separated Oreochromis and Sarotherodon from Tilapia, as defined by Trewavas. The Oreochromis sequences clustered with the Sarotherodon sequences and thus supported the hypothesis that the mouthbrooding behavior of the tilapiine fishes evolved only once from the substrate-spawning behavior. Since on phylogenetic trees the O. alcalicus (sub)species were always separated from O. amphimelas by other Oreochromis species, it was concluded that the adaptation to life in water with a high salt concentration and high pH values evolved independently at least twice in the tilapiine fishes. The tilapiines diverged from the haplochromines more than 8 million years ago; most of the intragroup divergences among the tilapiines took place an estimated 1.1 to 6 million years ago.     

Phylogenetic relationships and biogeography of xantusiid lizards, inferred from mitochondrial DNA sequences.

Portions of two mitochondrial genes (12S ribosomal RNA and cytochrome b) were sequenced in seven species to examine phylogenetic relationships within the lizard family Xantusiidae. Phylogenies derived from these sequences (709 total bp) are concordant and indicate that the Cuban species Cricosaura typica is the sister group to all other xantusiids. The Middle American genus Lepidophyma is the closest relative of Xantusia, and X. riversiana (California Islands) the closest relative of X. vigilis (mainland). These findings are not in agreement either with the results of a recent morphological analysis that united Cricosaura and Lepidophyma as closest relatives or with past studies that have recognized X. riversiana as a separate genus. Levels of sequence divergence, as well as the age and affinities of some mainland fossil taxa, suggest that the origin of Cricosaura was associated with the tectonic evolution of the Greater Antilles in the late Cretaceous. These results further demonstrate that significant resolution of phylogenies can be obtained with relatively short DNA sequences and that these mitochondrial genes are concordant in their estimation of phylogeny.     

Phylogenetic relationships of African microhylid frogs inferred from DNA sequences of mitochondrial 12S and 16S rRNA genes

The phylogenetic relationships of microhylid frogs are poorly understood. The first molecular phylogeny for continental African microhylids is presented, including representatives of all subfamilies, six of the eight genera, and the enigmatic hemisotid Hemisus. Mitochondrial 12S and 16S rRNA sequence data were analysed using parsimony, likelihood and Bayesian methods. Analyses of the data are consistent with the monophyly of all sampled subfamilies and genera. Hemisus does not nest within either brevicipitines or non-brevicipitines. It is possibly the sister group to brevicipitines, in which case brevicipitines might not be microhylids. Phrynomantis and Hoplophryne potentially group with non-African, non-brevicipitine microhylids, in agreement with recent morphological and molecular data. Within brevicipitines, Breviceps is recovered as the sister group to a clade of Callulina+Spelaeophryne+Probreviceps. The relationships among the genera within this latter clade are unclear, being sensitive to the method of analysis. Optimal trees suggest the Probreviceps macrodactylus subspecies complex might be paraphyletic with respect to P. uluguruensis, corroborating preliminary morphological studies indicating that P. m. rungwensis may be a distinct species. P. m. loveridgei may be paraphyletic with respect to P. m. macrodactylus, though this is not strongly supported. Some biogeographic hypotheses are examined in light of these findings.     

从细胞色素b基因序列探讨笛鲷属的分子系统发生关系

测定了9种中国南海的笛鲷属鱼类的细胞色素b基因的部分序列,结合来自GenBank中1种分布于菲律宾和9种分布于美国大西洋的笛鲷属鱼类的相应同源序列,用邻接法和最大简约法构建分子系统树。结果显示:红鳍笛鲷(Lutjanuserythropterus)与红笛鲷(L.sanguineus)之间的同源序列碱基差异百分率只有0.32%,支持二者是同种异名的观点;中国南海的笛鲷属鱼类间的平均碱基差异要高于美国大西洋笛鲷属鱼类。在MP和NJ树中,美国大西洋笛鲷表现为亲缘关系较近,来源于中国南海的笛鲷鱼类相对集中在树的基部,分歧较大。这与所研究的笛鲷地理分布和地理隔离基本相一致,同时也说明中国南海笛鲷分化较早并且分歧较大。     

Phylogenetic relationships of Sparassis inferred from nuclear and mitochondrial ribosomal DNA and RNA polymerase sequences

Sparassis species show extensive morphological variation, especially when materials from eastern Asia and Australia are compared with collections from North America and Europe. We have been studying the taxonomy of Sparassis from eastern Asia, North America, Australia and Europe, using both morphological and molecular data. DNA was extracted from 32 recent collections of Sparassis from Australia, Canada, China, Finland, France, Germany, Japan, Switzerland, Thailand, the United Kingdom and the United States. The report of a Sparassis taxon from Australia is the first report of this genus from the Southern Hemisphere. Sequences of nuclear and mitochondrial rDNA and the gene encoding RNA polymerase subunit II (RPB2) were used to examine relationships both within the genus Sparassis and between Sparassis species and other members of the polyporoid clade. Equally weighted parsimony analyses and Bayesian analyses were performed using independent datasets and combined datasets of sequences from different regions. Our results suggest that: (i) Polyporoid fungi producing a brown rot may form a clade; (ii) as suggested in a previous study, Sparassis and Phaeolus form a monophyletic group, which is united by the production of a brown rot, the presence of a bipolar mating system and the frequent habit of growing as a root and butt rot on living trees; (iii) at least seven lineages are within Sparassis, represented by S. spathulata, S. brevipes, S. crispa, S. radicata and three taxa that have not been described, which can be distinguished on the basis of fruiting body structure, presence or absence of clamp connections, presence or absence of cystidia and spore size.     

Phylogenetic relationships among Syndermata inferred from nuclear and mitochondrial gene sequences

Phylogenetic relationships among Syndermata have been extensively debated, mainly because the sister-group of the Acanthocephala has not yet been clearly identified from analyses of morphological and molecular data. Here we conduct phylogenetic analyses on samples from the 4 classes of Acanthocephala (Archiacanthocephala, Eoacanthocephala, Polyacanthocephala, and Palaeacanthocephala) and the 3 Rotifera classes (Bdelloidea, Monogononta, and Seisonidea). We do so using small-subunit (SSU) and large-subunit (LSU) ribosomal DNA and cytochrome c oxidase subunit 1 (cox 1) sequences. These nuclear and mitochondrial DNA sequences were obtained for 27 acanthocephalans, 9 rotifers, and representatives of 6 phyla that were used as outgroups. Maximum parsimony (MP), maximum likelihood (ML), and Bayesian analyses were conducted on the nuclear rDNA(SSU+LSU) and the combined sequence dataset(SSU+LSU+cox 1 genes). Phylogenetic analyses of the combined rDNA and cox 1 data uniformly provided strong support for a clade including rotifers plus acanthocephalans (Syndermata). Strong support was also found for monophyly of Acanthocephala in analyses of the combined dataset or rDNA sequences alone. Within the Acanthocephala the monophyletic grouping of the representatives of each class was strongly supported. Our results depicted Archiacanthocephala as the sister-group to the remaining acanthocephalans. Analyses of the combined dataset recovered a sister-group relationship between Acanthocephala and Bdelloidea by parsimony, likelihood, and Bayesian methods. Support for this clade was generally strong. Alternative topologies that depicted a different rotifer sister-group of Acanthocephala (or monophyly of Rotifera) were significantly worse. In this paraphyletic assemblage of rotifers, the relative positions of Seisonidea and Monogononta to the clade Bdelloidea+Acanthocephala were inconsistent among trees based on different inference methods. These results indicate that Bdelloidea is the free-living sister-group to acanthocephalans, which should prove key for comparative investigations of the morphological, molecular, and ecological changes accompanying the evolution of parasitism.     

Phylogenetic relationships among Pneumocystis from Asian macaques inferred from mitochondrial rRNA sequences

The presence of Pneumocystis organisms was detected by nested-PCR at mitochondrial large subunit (mtLSU) rRNA gene in 23 respiratory samples from Asian macaques representing two species: Macaca mulatta and M. fascicularis. A very high level of sequence heterogeneity was detected with 18 original sequence types. Two genetic groups of Pneumocystis could be distinguished from the samples. Within each group, the extent of genetic divergence was low (2.5+/-1.4% in group 1 and 2.3+/-1.7% in group 2). Genetic divergences were systematically higher when macaque-derived sequence types were compared with Pneumocystis mtLSU sequences from other primate species (from 5.3+/-2.7% to 19.3+/-3.0%). The two macaque-derived groups may be considered as distinct Pneumocystis species. Surprisingly, these Pneumocystis species were recovered from both M. mulatta and M. fascicularis suggesting that host-species restriction may not systematically occur in the genus Pneumocystis. Alternatively, these observations question about the species concept in macaques.     

Phylogenetic relationships ofPolemoniaceae inferred from 18S ribosomal DNA sequences

Cladistic analyses of chloroplast DNA disagree with current classifications by placingPolemoniaceae near sympetalous families with two staminal whorls, includingFouquieriaceae andDiapensiaceae, rather than near sympetalous families with a single staminal whorl, such asHydrophyllaceae andConvolvulaceae. To explore further the affinities ofPolemoniaceae, we sequenced 18S ribosomal DNA for eight genera ofPolemoniaceae and 31 families representing a broadly definedAsteridae. The distribution of variation in these sequences suggest some sites are hypervariable and multiple hits at these sites have obscured much of the hierarchical structure present in the data. Nevertheless, parsimony, least-squares minimum evolution, and maximum likelihood methods all support a monophyleticPolemoniaceae that is placed nearFouquieriaceae, Diapensiaceae and related ericalean families.     

Phylogenetic relationships among Bactrocera species (Diptera: Tephritidae) inferred from mitochondrial DNA sequences

Several members of the dipteran family Tephritdae are serious pests because females lay eggs in ripening fruit. The genus Bactrocera is one of the largest within the family with over 500 described species arranged in 28 subgenera. The phylogenetic relationships among the various species and subgenera, and the monophyly of specific groups have not been examined using a rigorous phylogenetic analysis. Therefore, phylogenetic relationships among 24 Bactrocera species belonging to 9 subgenera were inferred from DNA sequence of portions of the mitochondrial 16S rRNA, cytochrome oxidase II, tRNA(Lys), and tRNA(Asp) genes. Two morphological characters that traditionally have been used to define the four groups within the subgenus Bactrocera were evaluated in a phylogenetic context by mapping the character states onto the parsimony tree. In addition, the evolutionary trend in male-lure response was evaluated in a phylogenetic context. Maximum parsimony analyses suggested the following relationships: (1) the genus Bactrocera is monophyletic, (2) the subgenus B. (Zeugodacus) is paraphyletic, (3) the subgenus B. (Daculus) is a sister group to subgenus B. (Bactrocera), and (4) the subgenus B. (Bactrocera) is monophyletic. The mapping analyses suggested that the morphological characters exhibit a simple evolutionary transition from one character state to another. Male-lure response was identified as being a labile behavior that has been lost on multiple occasions. Cue-lure response was plesiomorphic to methyl-eugenol response, and the latter has evolved independently within the Bactrocera and Zeugodacus groups of subgenera. The implications of our results for devising a coherent, consolidated classification for Bactrocera is discussed.     

Phylogenetic relationships of the Acanthocephala inferred from 18S ribosomal DNA sequences

Phylogenetic relationships within the Acanthocephala have remained unresolved. Past systematic efforts have focused on creating classifications with little consideration of phylogenetic methods. The Acanthocephala are currently divided into three major taxonomic groups: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These groups are characterized by structural features in addition to the taxonomy and habitat of hosts parasitized. In this study the phylogenetic relationships of 11 acanthocephalan species are examined with 18S rDNA sequences. Maximum parsimony, minimum evolution, and maximum likelihood methods are used to estimate phylogenetic relationships. Within the context of sampled taxa, all phylogenetic analyses are consistent with monophyly of the major taxonomic groups of the Acanthocephala, suggesting that the current higher order classification is natural. The molecular phylogeny is used to examine patterns of character evolution for various structural and ecological characteristics of the Acanthocephala. Arthropod intermediate host distributions, when mapped on the phylogeny, are consistent with monophyletic groups of acanthocephalans. Vertebrate definitive host distributions among the Acanthocephala display independent radiations into similar hosts. Levels of uncorrected sequence divergence among acanthocephalans are high; however, relative-rate tests indicate significant departure from rate uniformity among acanthocephalans, arthropods, and vertebrates. This precludes comparison of 18S divergence levels to assess the relative age of the Acanthocephala. However, other evidence suggests an ancient origin of the acanthocephalan-arthropod parasitic association.     

Phylogenetic relationships of freshwater bryozoans (Ectoprocta, Phylactolaemata) inferred from mitochondrial ribosomal DNA sequences

Most species of freshwater bryozoans (Ectoprocta: Phylactolaemata) have few morphological distinctions, and within phylactolaemates, the morphology of the statoblast has been used to determine evolutionary relationships. Here, two controversial phylogenies have been proposed for phylactolaemates with regard to the relationship of Lophopodidae to other families. Two plumatellid genera, Gelatinella and Hyalinella , are candidates for the ancestral type of lophopodids. In addition, the coexistence of spines on the surfaces of the statoblast has led to the suggestion that lophopodids are closely related to the family Cristatellidae. In this study, we analysed mitochondrial DNA sequences of the 12S and 16S rDNA genes of 10 phylactolaemate species. Our results suggest that plumatellids may not be a direct ancestral group of lophopodids and that cristatellids are not a sister group of lophopodids. Fredericella , which was previously thought to be an ancestral group, was revealed to be derived. In addition, our results suggest that Stephanella is the most basal phylactolaemate. Mapping morphological characteristics onto the sequence-based phylogenetic tree revealed convergent evolution of statoblast characters.     

Phylogenetic relationships of Chalara and allied species inferred from ribosomal DNA sequences

The phylogenetic relationships of Chalara and allied taxa are studied based on ribosomal DAN sequences. Partial 28S rDNA and 18S rDNA regions from 26 strains were sequenced in this study. These and related sequences from GenBank were analyzed using parsimony and Bayesian analyses. Most of the Chalara species clustered in a strongly supported monophyletic lineage representing Helotiales. However, a few Chalara species appeared closely related to Xylariales. The phylogenetic significance of morphological characters observed in Chalara species are evaluated based on our sequence analyses. Conidial septation, conidial width and conidiophore pigmentation are thought to be indicative in understanding their evolutionary relationships. Sterile setae, which traditionally have been used to delimitate Chaetochalara from Chalara, are phylogenetically insignificant.     

基于线粒体和核基因序列的蜜蜂属系统发育分析

文章测定了中国分布的蜜蜂属(Apis)5种蜜蜂22个样本的线粒体基因ND2、CO2、16S rRNA以及核基因ITPR的序列,对序列的碱基组成和蜜蜂种间的遗传距离进行了分析。结合下载的蜜蜂属其他4个种的相关序列,采用最大简约法、邻接法和最大似然法重建了蜜蜂属系统发育关系。系统发育分析结果支持蜜蜂属划分为3个类群,即小蜜蜂类群(包括小蜜蜂和黑小蜜蜂)、大蜜蜂类群(包括大蜜蜂和黑大蜜蜂)和穴居蜜蜂类群(西方蜜蜂、东方蜜蜂、沙巴蜂、苏拉威西蜂、绿努蜂),且小蜜蜂类群较早分化。结果还显示,我国海南岛的大蜜蜂和大陆的大蜜蜂之间可能存在较大的遗传分歧。     

Phylogenetic relationships among the phrynosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes

Nucleotide sequences of the mitochondrial protein coding cytochrome b (cyt b; 650 bp) and small-subunit 12S ribosomal RNA (approximately 350 bp) genes were used in analyses of phylogenetic relationships among extant phrynosomatid sand lizards, including an examination of competing hypotheses regarding the evolution of "earlessness." Sequences were obtained from all currently recognized species of sand lizards as well as representatives of the first and second outgroups and analyzed using both parsimony and likelihood methods. The cyt b data offer strong support for relationships that correspond with relatively recent divergences and moderate to low support for relationships reflecting more ancient divergences within the clade. These data support monophyly of the "earless" taxa, the placement of Uma as the sister taxon to the other sand lizards, and monophyly of all four taxa traditionally ranked as genera. All well-supported relationships in the 12S phylogeny are completely congruent with well-supported relationships in the cyt b phylogeny; however, the 12S data alone provide very little support for deeper divergences. Phylogenetic relationships within species are concordant with geography and suggest patterns of phylogeographic differentiation, including the conclusion that at least one currently recognized species (Holbrookia maculata) actually consists of more than one species. By independently optimizing likelihood model parameters for various subsets of the data, we found that nucleotide substitution processes vary widely between genes and among the structural and functional regions or classes of sites within each gene. Therefore, we compared competing phylogenetic hypotheses, using parameter estimates specific to those subsets, analyzing the subsets separately and in various combinations. The hypothesis supported by the cyt b data was favored over rival hypotheses in all but one of the five comparisons made with the entire data set, including the set of partitions that best explained the data, although we were unable to confidently reject (P < 0.05) alternative hypotheses. Our results highlight the importance of optimizing models and parameter estimates for different genes or parts thereof--a strategy that takes advantages of the strengths of both combining and partitioning data.