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Over 200 described endemic species make up the adaptive radiation of cichlids in Lake Tanganyika. This species assemblage has been viewed as both an evolutionary reservoir of old cichlid lineages and an evolutionary hotspot from which the modern cichlid lineages arose, seeding the adaptive radiations in Lakes Victoria and Malawi. Here we report on a phylogenetic analysis of Lake Tanganyika cichlids combining the previously determined sequences of the mitochondrial ND2 gene (1047 bp) with newly derived sequences of the nuclear RAG1 gene (approximately 700 bp of intron 2 and approximately 1100 bp of exon 3). The nuclear data-in agreement with mitochondrial DNA-suggest that Lake Tanganyika harbors several ancient lineages that did not undergo rampant speciation (e.g., Bathybatini, Trematocarini). We find strong support for the monophyly of the most species-rich Tanganyikan group, the Lamprologini, and we propose a new taxonomic group that we term the C-lineage. The Haplochromini and Tropheini both have an 11-bp deletion in the intron of RAG1, strongly supporting the monophyly of this clade and its derived position. Mapping the phylogenetically informative positions revealed that, for certain branches, there are six times fewer apomorphies in RAG1. However, the consistency index of these positions is higher compared to the mitochondrial ND2 gene. Nuclear data therefore provide, on a per-base pair basis, less but more reliable phylogenetic information. Even if in our case RAG1 has not provided as much phylogenetic information as we expected, we suggest that this marker might be useful in the resolution of the phylogeny of older groups.
J Mol Evol 2005 Nov
PMID:Comparative phylogenetic analyses of the adaptive radiation of Lake Tanganyika cichlid fish: nuclear sequences are less homoplasious but also less informative than mitochondrial DNA. 1622 15

Systematic relationships among monarch flycatchers (genus Monarcha) are poorly understood despite dramatic patterns of morphological differentiation that have long attracted the attention of evolutionary biologists. With sequence data from the mitochondrial ND2 gene and Control Region, we produced a phylogenetic hypothesis for evolutionary relationships within Monarcha and among the biogeographically complex Solomon Island endemics. Outgroup analyses contradicted monophyly of the genus by imbedding a representative of the genus Clytorhynchus within one of two major clades recovered within Monarcha. These two monarch clades generally correspond with ecological and morphological distinctions, suggesting the genus may warrant revision pending the inclusion of taxa currently allied with Clytorhynchus (e.g., Neolalage spp.). Maximum likelihood reconstructions support monophyletic groupings of the two endemic Solomon Island monarch radiations, however, two currently recognized superspecies (Monarcha manadensis and M. melanopsis) were polyphyletic and paraphyletic, respectively. Interestingly, molecular and morphological differentiation were strikingly decoupled among several Solomon Island endemics and between migratory and non-migratory forms of Monarcha trivirgatus in eastern Australia, suggesting morphological evolution has masked the true history of speciation in these groups. This initial phylogeny provides a novel platform for ongoing exploration of the history underlying dramatic patterns of geographic variation among tropical Pacific flycatchers.
Mol Phylogenet Evol 2005 Dec
PMID:Molecular phylogenetics of monarch flycatchers (genus Monarcha) with emphasis on Solomon Island endemics. 1629 Oct 94

We used sequence variation in the mtDNA control-region and ND2 and cyt b genes to assess the systematics and biogeography of the five species of pupfish (Cyprinodon) on Hispaniola. These include four endemics, the relatively large-bodied Cyprinodon bondi, Cyprinodon nichollsi, and Cyprinodon sp., each from a separate lake in southwestern Hispaniola, and Cyprinodon higuey from a coastal lake in eastern Hispaniola. The fifth species consists of coastal populations referable to Cyprinodon variegatus riverendi. The results indicate that Hispaniola has been invaded by at least two forms, first by a late Pliocene progenitor of Cyprinodon variegatus ovinus and the large-bodied Hispaniolan species, and, more recently, by one or more ancestral forms allied with Cyprinodon variegatus variegatus and C. v. riverendi. Levels of divergence indicate that large expanses of open sea have not acted as long-term barriers to inter-island dispersal of cyprinodontiform fishes. This study, together with the molecular systematics of other insular Caribbean fishes, indicates that most insular groups originated from late Neogene dispersal from the mainland. The patterns of mtDNA variation in Cyprinodon showed little congruence with the species/subspecies taxonomy.
Mol Phylogenet Evol 2006 Jun
PMID:Molecular systematics of Hispaniolan pupfishes (Cyprinodontidae: Cyprinodon): implications for the biogeography of insular Caribbean fishes. 1644 12

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).
Mol Phylogenet Evol 2006 Jun
PMID:Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree. 1648 60

The southern African landscape appears to have experienced frequent shifts in vegetation associated with climatic change through the mid-Miocene and Plio-Pleistocene. One group whose historical biogeography may have been affected by these fluctuations are the dwarf chameleons (Bradypodion), due to their associations with distinct vegetation types. Thus, this group provides an opportunity to investigate historical biogeography in light of climatic fluctuations. A total of 138 dwarf chameleons from the Cape Floristic Region of South Africa were sequenced for two mitochondrial genes (ND2 and 16S), and resulting phylogenetic analyses showed two well-supported clades that are distributed allopatrically. Within clades, diversity among some lineages was low, and haplotype networks showed patterns of reticulate evolution and incomplete lineage sorting, suggesting relatively recent origins for some of these lineages. A dispersal-vicariance analysis and a relaxed Bayesian clock suggest that vicariance between the two main clades occurred in the mid-Miocene, and that both dispersal and vicariance have played a role in shaping present-day distributions. These analyses also suggest that the most recent series of lineage diversification events probably occurred within the last 3-6 million years. This suggests that the origins of many present-day lineages were founded in the Plio-Pleistocene, a time period that corresponds to the reduction of forests in the region and the establishment of the fynbos biome.
Mol Ecol 2006 Mar
PMID:Biogeographic patterns and phylogeography of dwarf chameleons (Bradypodion) in an African biodiversity hotspot. 1649 2

Anoles of the Anolis onca series represent a dramatic case of retrograde evolution, exhibiting great reduction (A. annectens) and loss (A. onca) of the subdigital pads considered a key innovation for the evolutionary radiation of anoles in arboreal environments. We present a molecular phylogenetic analysis of these anoles and their closest known relatives (A. auratus, A. lineatus, A. meridionalis, and A. nitens) using new mitochondrial DNA sequence data from the ND2 gene, five tRNA genes (tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr)), the origin of light-strand replication, and a portion of the CO1 gene (1,446 aligned base positions, 612 parsimony informative). Our results confirm monophyly of the A. onca series and suggest an evolutionary separation of approximately 10 million years between A. annectens and A. onca. Evolution of subdigital structure in this series illustrates ectopic expression of developmental programs that replace flexible subdigital lamellae of the toepad with rigid, keeled scales resembling dorsal digital scales. Our phylogenetic results indicate that narrowing of the toepad in A. auratus evolved separately from toepad reduction in the A. onca series. Expansion of the subdigital lamellae along the phalanges in A. auratus appears to compensate constriction of lamellae by digital narrowing, maintaining greater climbing capability in this species. Toepad evolution in the lineage ancestral to A. auratus features changes of the same developmental modules as the A. onca series but in the opposite direction. Large molecular distances between geographic populations of A. auratus indicate that its derived toepad structure is at least 9 million years old.
J Exp Zool B Mol Dev Evol 2006 Sep 15
PMID:Molecular phylogenetics of the Anolis onca series: a case history in retrograde evolution revisited. 1650 31

Because of the difficulties of constructing a robust phylogeny for Charadriiform birds using morphological characters, recent studies have turned to DNA sequences to resolve the systematic uncertainties of family-level relationships in this group. However, trees constructed using nuclear genes or the mitochondrial Cytochrome b gene suggest deep-level relationships of shorebirds that differ from previous studies based on morphology or DNA-DNA hybridization distances. To test phylogenetic hypotheses based on nuclear genes (RAG-1, myoglobin intron-2) and single mitochondrial genes (Cytochrome b), approximately 13,000 bp of mitochondrial sequence was collected for one exemplar species of 17 families of Charadriiformes plus potential outgroups. Maximum likelihood and Bayesian analyses show that trees constructed from long mitochondrial sequences are congruent with the nuclear gene topologies [Chardrii (Lari, Scolopaci)]. Unlike short mitochondrial sequences (such as Cytochrome b alone), longer sequences yield a well-supported phylogeny for shorebirds across various taxonomic levels. Examination of substitution patterns among mitochondrial genes reveals specific genes (especially ND5, ND4, ND2, and COI) that are better suited for phylogenetic analyses among shorebird families because of their relatively homogeneous nucleotide composition among lineages, slower accumulation of substitutions at third codon positions, and phylogenetic utility in both closely and distantly related lineages. For systematic studies of birds in which family and generic levels are examined simultaneously, we recommend the use of both nuclear and mitochondrial sequences as the best strategy to recover relationships that most likely reflect the phylogenetic history of these lineages.
Mol Phylogenet Evol 2006 Jun
PMID:Sequences from 14 mitochondrial genes provide a well-supported phylogeny of the Charadriiform birds congruent with the nuclear RAG-1 tree. 1653 Oct 74

We analyzed 2995 base pairs of nucleotide sequence data (nuclear beta-fibrinogen intron 7 and mitochondrial cytochrome b and ND2 genes), using parsimony and model-based approaches to infer phylogenetic relationships of the woodpeckers and allies, yielding novel hypotheses for several critical gaps in the knowledge of picid phylogeny. We tested the monophyly of sub-families within the Picidae, and sampled from widely distributed and diverse genera (Celeus, Colaptes, Dryocopus, Melanerpes, Picoides, Picumnus, Sasia, Piculus, and Picus). Relationships of three poorly known Southeast Asian genera (Dinopium, Reinwardtipicus, and Blythipicus) were also examined, revealing unexpected sister relationships. All phylogenetic approaches recovered largely congruent topologies, supporting a monophyletic Picinae and paraphyletic Picumninae, with the monotypic piculet, Nesoctites micromegas, as sister to the Picinae. We report paraphyly for Celeus and Piculus, whereas the broadly distributed genera Picumnus and Dryocopus were supported as monophyletic. Our phylogenetic results indicate a complex geographic history for the Picidae, with multiple disjunct sister lineages distributed between the New World and Asia. The relationships and geographic distribution of basal picid lineages indicates an Old World origin of the Picidae; however, the geographic origin of the Picinae remains equivocal, as the sister relationship between the Caribbean N. micromegas and the true woodpeckers presents the possibility of a New World origin for the Picinae.
Mol Phylogenet Evol 2006 Aug
PMID:Evolutionary history of woodpeckers and allies (Aves: Picidae): placing key taxa on the phylogenetic tree. 1663 80

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.
Mol Phylogenet Evol 2006 Aug
PMID:Molecular phylogeny of the Drosophila virilis section (Diptera: Drosophilidae) based on mitochondrial and nuclear sequences. 1667 48

Variation and geographic differentiation in mitochondrial DNA (mtDNA) was studied in the widespread and phenotypically variable Eurasian nuthatch (Sitta europaea). To assess whether sequences were evolving in a selectively neutral fashion, we used McDonald-Kreitman [Nature 351 (1991) 652] tests and a tree-based method, which suggested that although ND2 sequences are affected by natural selection against slightly deleterious alleles, the effects do not compromise phylogeographic inferences. Three phylogenetic species-level clades of nuthatches were discovered, corresponding to the Caucasus, southern Europe, and northern Europe plus Asia. Unimodal mismatch distributions within each clade suggest that populations have undergone recent growth. A westward range expansion was inferred from the geographic pattern in nucleotide diversity. Although samples were insufficient, it is possible that nuthatches in England and Japan are recently differentiated. Two specimens of the subspecies S. e. arctica formed a sister group to all other S. europaea, differing by ca. 10% uncorrected sequence divergence, pointing the need for additional study of this phenotypically distinct taxon. As with other species, mtDNA data support major phenotypic distinctions, but not subspecies.
Mol Phylogenet Evol 2006 Sep
PMID:Selective neutrality of mitochondrial ND2 sequences, phylogeography and species limits in Sitta europaea. 1671 3


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