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PubMed2005

On the phylogenetic placement of human T cell leukemia virus type 1 sequences associated with an Andean mummy.

Recently, the putative finding of ancient human T cell leukemia virus type 1 (HTLV-1) long terminal repeat (LTR) DNA sequences in association with a 1500-year-old Chilean mummy has stirred vigorous debate. The debate is based partly on the inherent uncertainties associated with phylogenetic reconstruction when only short sequences of closely related genotypes are available. However, a full analysis of what phylogenetic information is present in the mummy data has not previously been published, leaving open the question of what precisely is the range of admissible interpretation. To fulfill this need, we re-analyzed the mummy data in a new way. We first performed phylogenetic analysis of 188 published LTR DNA sequences from extant strains belonging to the HTLV-1 Cosmopolitan clade, using the method of statistical parsimony which is designed both to optimize phylogenetic resolution among sequences with little evolutionary divergence, and to permit precise mapping of individual sequence mutations onto branches of a divergence network. We then deduced possible phylogenetic positions for the two main categories of published Chilean mummy sequences, based on their published 157-nucleotide LTR sequences. The possible phylogenetic placements for one of the mummy sequence categories are consistent with a modern origin. However, one of these placements for the other mummy sequence category falls very close to the root of the Cosmopolitan clade, consistent with an ancient origin for both this mummy sequence and the Cosmopolitan clade.

Asian People↗

PubMed2005

Diversity of non-reducing polyketide synthase genes in the Pertusariales (lichenized Ascomycota): a phylogenetic perspective.

Lichenized fungi synthesize a great variety of secondary metabolites. These are typically crystalline compounds, which are deposited extracellularly on the fungal hyphae. While we know a lot about the chemical properties and structures of these substances, we have very little information on the molecular background of their biosynthesis. In the current study we analyze the diversity of non-reducing polyketide synthase (PKS) genes in members of the lichenized Pertusariales. This order primarily contains fully oxidized secondary metabolites from different substance classes, and is chemically and phylogenetically well studied. Using a degenerate primer approach with subsequent cloning we detected up to five non-reducing PKS sequences in a single PCR product. Eighty-five new KS sequence fragments were obtained for this study. Analysis of the 157 currently available fungal KS sequence fragments in a Bayesian phylogenetic framework revealed 18 highly supported clades that included only lichenized taxa, only non-lichenized taxa, or both. Some Pertusarialean groupings of PKS sequences corresponded partly to phylogenetic groupings based on ribosomal DNA. This is reasonable, because a correlation between well-supported phylogenetic lineages and the occurrence of secondary metabolites in the Pertusariales has been observed before. However, no clear linkage was found between the PKS genes analyzed and the ability to produce a particular secondary substance. Several PKS clades did not reveal obvious patterns of secondary compound distribution or phylogenetic association. Compared with earlier phylogenetic analyses of KS sequences the increased sampling in the current study allowed us to detect many new groupings within the fungal non-reducing PKSs.

Ascomycota↗

PubMed2006

The impact of intragenic recombination on phylogenetic reconstruction at the sectional level in Eucalyptus when using a single copy nuclear gene (cinnamoyl CoA reductase).

Low copy number nuclear genes have been found to be useful for phylogenetic reconstruction at different taxonomic levels. This study investigated the utility of a single copy gene, cinnamoyl CoA reductase (CCR), for resolving phylogenetic relationships at the sectional level within Eucalyptus. The monophyly of sections Exsertaria and Latoangulatae was explored, using section Maidenaria as an outgroup, and the impact of intragenic recombination on phylogenetic reconstruction examined. Phylogenetic analysis did not resolve monophyletic groups. Latoangulatae and Maidenaria were polyphyletic or paraphyletic. Exsertaria species formed a clade but included a single Latoangulatae species (E. major). Recombination analysis identified two intragenic recombination events that involved species from different sections, which have probably been facilitated by inter-sectional hybridisation. One of the events most likely occurred prior to speciation, with several Latoangulatae species having the recombinant allele. The other event may have occurred after speciation, since only one of two E. globulus samples possessed the recombinant allele. This is the first detailed report of intragenic recombination in both CCR and Eucalyptus, and between species of different sections of a plant genus. The occurrence of intragenic recombination may explain the anomalous positions of some species within the phylogenetic tree, and indicates that phylogenetic analysis of Eucalyptus using nuclear genes will be problematic unless recombination is taken into account.

Aldehyde Oxidoreductases↗

PubMed2006

Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F, and rbcL in basal angiosperms.

The prevailing view in molecular systematics is that relationships among distantly related taxa should be inferred using DNA segments with low rates of evolution. However, recent analyses of sequences from the rapidly evolving matK and trnT-trnF regions yielded well resolved and highly supported trees for early diverging angiosperms. We compare here the phylogenetic structure in matK, trnT-F, and rbcL datasets for the same 42, primarily basal angiosperm taxa. Phylogenetic trees based on matK or trnT-F are far more robust than those based on rbcL. Combined analysis of the rapidly evolving regions provides support for higher-level relationships stronger than that derived from analyses of multi-gene datasets of up to several fold the number of characters analyzed here. In addition to displaying a higher percentage of parsimony-informative characters, the average phylogenetic signal per informative character is significantly higher in the datasets from rapidly evolving DNA than in the more slowly evolving rbcL, as detected using resampling of identical numbers of parsimony-informative characters from the data matrices and subjecting different statistics for overall tree robustness and phylogenetic signal to significance tests. Automated via a set of scripts, the method used here should be easily extendable to comparisons of a broader range of genomic regions for varying taxon samplings. The relative performance of markers correlates not only with a lower mean homoplasy in matK and trnT-trnF compared to rbcL, but in particular correlates negatively with the percentage of sites exhibiting maximum or close to maximum homoplasy. A likelihood ratio test confirms that the rapidly evolving gene matK evolves significantly closer to neutrality, which may be one of the underlying factors for lower levels of overall homoplasy. Our results are in line with evidence from simulation studies suggesting that the deleterious effect of multiple hits in using rapidly evolving DNA at rather deep phylogenetic levels may have been overestimated, and thus promote extending the use of rapidly evolving DNA to deeper phylogenetic levels.

Codon↗

PubMed2002

Structure, molecular evolution, and phylogenetic utility of the 5(') region of the external transcribed spacer of 18S-26S rDNA in Lessingia (Compositae, Astereae).

The 18S-26S nuclear rDNA external transcribed spacer (ETS) has recently gained attention as a region that is valuable in phylogenetic analyses of angiosperms primarily because it can supplement nucleotide variation from the widely used and generally shorter internal transcribed spacers (ITS-1 and ITS-2) and thereby improve phylogenetic resolution and clade support in rDNA trees. Subrepeated ETS sequences (often occurring in the 5(') region) can, however, create a challenge for systematists interested in using ETS sequence data for phylogeny reconstruction. We sequenced the 5(')ETS for members of Lessingia (Compositae, Astereae) and close relatives (26 taxa total) to characterize the subrepeat variation across a group of closely related plant lineages and to gain improved understanding of the structure, molecular evolution, and phylogenetic utility of the region. The 5(')ETS region of Lessingia and relatives varied in length from approximately 245 to 1009 bp due to the presence of a variable number of subrepeats (one to eight). We assessed homology of the subrepeats using phylogenetic analysis and concluded that only two of the subrepeats and a portion of a third ( approximately 282 bp in total) were orthologous across Lessingia and could be aligned with confidence and included in further analyses. When the partial 5(')ETS data were combined with 3(')ETS and ITS data in phylogenetic analyses, no additional resolution of relationships among taxa was obtained beyond that found from analysis of 3(')ETS + ITS sequences. Inferred patterns of concerted evolution indicate that homogenization is occurring at a faster rate in the 3(')ETS and ITS regions than in the 5(')ETS region. Additionally, homogenization appears to be acting within but not among subrepeats of the same rDNA array. We conclude that challenges in assessing subrepeat orthology across taxa greatly limit the utility of the 5(')ETS region for phylogenetic analyses among species of Lessingia.

Asteraceae↗

PubMed2003

Molecular phylogenetics and evolution of the endemic Hawaiian genus Adenophorus (Grammitidaceae).

Recent studies of the phylogeny of several groups of native Hawaiian vascular plants have led to significant insights into the origin and evolution of important elements of the Hawaiian flora. No groups of Hawaiian pteridophytes have been subjected previously to rigorous phylogenetic analysis. We conducted a molecular phylogenetic analysis of the endemic Hawaiian fern genus Adenophorus employing DNA sequence variation from three cpDNA fragments: rbcL, atpbeta, and the trnL-trnF intergenic spacer (IGS). In the phylogenetic analyses we employed maximum parsimony and Bayesian inference. Bayesian phylogenetic inference often provided stronger support for hypothetical relationships than did nonparametric bootstrap analyses. Although phylogenetic analyses of individual DNA fragments resulted in different patterns of relationships among species and varying levels of support for various clades, a combined analysis of all three sets of sequences produced one, strongly supported phylogenetic hypothesis. The primary features of that hypothesis are: (1) Adenophorus is monophyletic; (2) subgenus Oligadenus is paraphyletic; (3) the enigmatic endemic Hawaiian species Grammitis tenella is strongly supported as the sister taxon to Adenophorus; (4) highly divided leaf blades are evolutionarily derived in the group and simple leaves are ancestral; and, (5) the biogeographical origin of the common ancestor of the Adenophorus-G. tenella clade remains unresolved, although a neotropical origin seems most likely.

Base Sequence↗

PubMedDate not supplied

Conflicting phylogenetic signals at the base of the metazoan tree.

A phylogenetic framework is essential for under-standing the origin and evolution of metazoan development. Despite a number of recent molecular studies and a rich fossil record of sponges and cnidarians, the evolutionary relationships of the early branching metazoan groups to each other and to a putative outgroup, the choanoflagellates, remain uncertain. This situation may be the result of the limited amount of phylogenetic information found in single genes and the small number of relevant taxa surveyed. To alleviate the effect of these analytical factors in the phylogenetic recons-truction of early branching metazoan lineages, we cloned multiple protein-coding genes from two choanoflagellates and diverse sponges, cnidarians, and a ctenophore. Comparisons of sequences for alpha-tubulin, beta-tubulin, elongation factor 2, HSP90, and HSP70 robustly support the hypothesis that choanoflagellates are closely affiliated with animals. However, analyses of single and concatenated amino acid sequences fail to resolve the relationships either between early branching metazoan groups or between Metazoa and choano-flagellates. We demonstrate that variable rates of evolution among lineages, sensitivity of the analyses to taxon selection, and conflicts in the phylogenetic signal contained in different amino acid sequences obscure the phylogenetic associations among the early branching Metazoa. These factors raise concerns about the ability to resolve the phylogenetic history of animals with molecular sequences. A consensus view of animal evolution may require investigations of genome-scale characters.

Animals↗

PubMed2000

Localizing proteins in the cell from their phylogenetic profiles.

We introduce a computational method for identifying subcellular locations of proteins from the phylogenetic distribution of the homologs of organellar proteins. This method is based on the observation that proteins localized to a given organelle by experiments tend to share a characteristic phylogenetic distribution of their homologs-a phylogenetic profile. Therefore any other protein can be localized by its phylogenetic profile. Application of this method to mitochondrial proteins reveals that nucleus-encoded proteins previously known to be destined for mitochondria fall into three groups: prokaryote-derived, eukaryote-derived, and organism-specific (i.e., found only in the organism under study). Prokaryote-derived mitochondrial proteins can be identified effectively by their phylogenetic profiles. In the yeast Saccharomyces cerevisiae, 361 nucleus-encoded mitochondrial proteins can be identified at 50% accuracy with 58% coverage. From these values and the proportion of conserved mitochondrial genes, it can be inferred that approximately 630 genes, or 10% of the nuclear genome, is devoted to mitochondrial function. In the worm Caenorhabditis elegans, we estimate that there are approximately 660 nucleus-encoded mitochondrial genes, or 4% of its genome, with approximately 400 of these genes contributed from the prokaryotic mitochondrial ancestor. The large fraction of organism-specific and eukaryote-derived genes suggests that mitochondria perform specialized roles absent from prokaryotic mitochondrial ancestors. We observe measurably distinct phylogenetic profiles among proteins from different subcellular compartments, allowing the general use of prokaryotic genomes in learning features of eukaryotic proteins.

Algorithms↗

PubMed2002

A molecular phylogenetic study of the Palmae (Arecaceae) based on atpB, rbcL, and 18S nrDNA sequences.

Notoriously slow rates of molecular evolution and convergent evolution among some morphological characters have limited phylogenetic resolution for the palm family (Arecaceae). This study adds nuclear DNA (18S SSU rRNA) and chloroplast DNA (cpDNA; atpB and rbcL) sequence data for 65 genera of palms and characterizes molecular variation for each molecule. Phylogenetic relationships were estimated with maximum likelihood and maximum parsimony techniques for the new data and for previously published molecular data for 45 palm genera. Maximum parsimony analysis was also used to compare molecular and morphological data for 33 palm genera. Incongruence among datasets was detected between cpDNA and 18S data and between molecular and morphological data. Most conflict between nuclear and cpDNA data was associated with the genus Nypa. Several taxa showed relatively long branches with 18S data, but phylogenetic resolution of these taxa was essentially the same for 18S and cpDNA data. Base composition bias for 18S that contributed to erroneous phylogenetic resolution in other taxa did not seem to be present in Palmae. Morphological data were incongruent with all molecular data due to apparent morphological homoplasy for Caryoteae, Ceroxyloideae, Iriarteae, and Thrinacinae. Both cpDNA and nuclear 18S data firmly resolved Caryoteae with Borasseae of Coryphoideae, suggesting that at least some morphological characters used to place Caryoteae in Arecoideae are homoplastic. In this study, increased character sampling seems to be more important than increased taxon sampling; a comparison of the full (65-taxon) and reduced (45- and 33-taxon) datasets suggests little difference in core topology but considerably more nodal support with the increased character sample sizes. These results indicate a general trend toward a stable estimate of phylogenetic relationships for the Palmae. Although the 33-taxon topologies are even better resolved, they lack several critical taxa and are affected by incongruence between molecular and morphological data. As such, a comparison of results from the 45- and 33-taxon trees offers the best available reference for phylogenetic inference on palms.

Arecaceae↗

PubMed2006

Molecular phylogenetics and evolutionary diversification of labyrinth fishes (Perciformes: Anabantoidei).

Labyrinth fishes (Perciformes: Anabantoidei) are primary freshwater fishes with a disjunct African-Asian distribution that exhibit a wide variety of morphological and behavioral traits. These intrinsic features make them particularly well suited for studying patterns and processes of evolutionary diversification. We reconstructed the first molecular-based phylogenetic hypothesis of anabantoid intrarelationships using both mitochondrial and nuclear nucleotide sequence data to address anabantoid evolution. The mitochondrial data set included the complete cytochrome b, partial 12S rRNA, complete tRNA Val, and partial 16S rRNA genes (3332 bp) of 57 species representing all 19 anabantoid genera. The nuclear data set included the partial RAG1 gene (1494 bp) of 21 representative species. The phylogenetic analyses of a combined (mitochondrial+nuclear) data set recovered almost fully resolved trees at the intrafamily level with different methods of phylogenetic inference. Phylogenetic relationships at this taxonomic level were compared with previous morphology-based hypotheses. In particular, the enigmatic pike-head (Luciocephalus) was confidently placed within the "spiral egg" clade, thus resolving the long-standing controversy on its relative phylogenetic position. The molecular phylogeny was used to study the evolution of the different forms of parental care within the suborder. Our results suggest that the evolution of breeding behavior in anabantoids is highly correlated with phylogeny, and that brood care evolved three times independently from an ancestral free spawning condition without parental care. Ancestral character state reconstructions under maximum parsimony and maximum likelihood further indicated that both bubble nesting and mouthbrooding have evolved recurrently during anabantoid evolution. The new phylogenetic framework was also used to test alternative biogeographic hypotheses that account for the disjunct African-Asian distribution. Molecular divergence time estimates support either a drift vicariance linked to the breakup of Gondwana or Late Mesozoic Early Tertiary dispersal from Africa to Asia or vice versa.

Animals↗

PubMed2001

Remarkable conservation of translation initiation factors: IF1/eIF1A and IF2/eIF5B are universally distributed phylogenetic markers.

Initiation of protein biosynthesis is an essential process occurring in cells throughout the three phylogenetic domains, Bacteria, Archaea, and Eucarya. IF1/eIF1A and IF2/eIF5B, two conserved translation initiation factors are involved in this important step of protein biosynthesis. The essentiality, universal distribution, conservation, and interspecies functional homology of both factors are a unique combination of properties ideal for molecular phylogenetic studies as demonstrated by the extensively compared SSU rRNAs. Here, we assess the use of IF1/eIF1A and IF2/eIF5B in universal and partial phylogenetic studies by comparison of sequence information from species within all three phylogenetic domains and among closely related strains of Haemophilus parainfluenzae. We conclude that the amino acid sequence of IF1/eIF1A-IF2/eIF5B is a universal phylogenetic marker and that the nucleotide sequence of the IF2/eIF5B G-domain is more credible than SSU rRNA for the construction of partial phylogenies among closely related species and strains. Because of these two application levels, IF1/eIF1A-IF2/eIF5B is a phylogenetic "dual level" marker.

Amino Acid Sequence↗

PubMed2006

Phylogenetic relatedness limits co-occurrence at fine spatial scales: evidence from the schoenoid sedges (Cyperaceae: Schoeneae) of the Cape Floristic Region, South Africa.

Species co-occurrence at fine spatial scales is expected to be nonrandom with respect to phylogeny because of the joint effects of evolutionary (trait convergence and conservatism) and ecological (competitive exclusion and habitat filtering) processes. We use data from 11 existing vegetation surveys to test whether co-occurrence in schoenoid sedge assemblages in the Cape Floristic Region shows significant phylogenetic structuring and to examine whether this changes with the phylogenetic scale of the analysis. We provide evidence for phylogenetic overdispersion in an alliance of closely related species (the reticulate-sheathed Tetraria clade) using both quantile regression analysis and a comparison between the mean observed and expected phylogenetic distances between co-occurring species. Similar patterns are not evident when the analyses are performed at a broader phylogenetic scale. Examination of six functional traits suggests a general pattern of trait conservatism within the reticulate-sheathed Tetraria clade, suggesting a potential role for interspecific competition in structuring co-occurrence within this group. We suggest that phylogenetic overdispersion of communities may be common throughout many of the Cape lineages, since interspecific interactions are likely intensified in lineages with large numbers of species restricted to a small geographic area, and we discuss the potential implications for patterns of diversity in the Cape.

Cyperaceae↗

PubMed2006

Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).

In the eight years since phylogenomics was introduced as the intersection of genomics and phylogenetics, the field has provided fundamental insights into gene function, genome history and organismal relationships. The utility of phylogenomics is growing with the increase in the number and diversity of taxa for which whole genome and large transcriptome sequence sets are being generated. We assert that the synergy between genomic and phylogenetic perspectives in comparative biology would be enhanced by the development and refinement of minimal reporting standards for phylogenetic analyses. Encouraged by the development of the Minimum Information About a Microarray Experiment (MIAME) standard, we propose a similar roadmap for the development of a Minimal Information About a Phylogenetic Analysis (MIAPA) standard. Key in the successful development and implementation of such a standard will be broad participation by developers of phylogenetic analysis software, phylogenetic database developers, practitioners of phylogenomics, and journal editors.

Genomics↗

PubMed2002

A tree kernel to analyse phylogenetic profiles.

MOTIVATION: The phylogenetic profile of a protein is a string that encodes the presence or absence of the protein in every fully sequenced genome. Because proteins that participate in a common structural complex or metabolic pathway are likely to evolve in a correlated fashion, the phylogenetic profiles of such proteins are often 'similar' or at least 'related' to each other. The question we address in this paper is the following: how to measure the 'similarity' between two profiles, in an evolutionarily relevant way, in order to develop efficient function prediction methods? RESULTS: We show how the profiles can be mapped to a high-dimensional vector space which incorporates evolutionarily relevant information, and we provide an algorithm to compute efficiently the inner product in that space, which we call the tree kernel. The tree kernel can be used by any kernel-based analysis method for classification or data mining of phylogenetic profiles. As an application a Support Vector Machine (SVM) trained to predict the functional class of a gene from its phylogenetic profile is shown to perform better with the tree kernel than with a naive kernel that does not include any information about the phylogenetic relationships among species. Moreover a kernel principal component analysis (KPCA) of the phylogenetic profiles illustrates the sensitivity of the tree kernel to evolutionarily relevant variations.

Algorithms↗

PubMed2003

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.

Animals↗

PubMedDate not supplied

Signal, noise, and reliability in molecular phylogenetic analyses.

DNA sequences and other molecular data compared among organisms may contain phylogenetic signal, or they may be randomized with respect to phylogenetic history. Some method is needed to distinguish phylogenetic signal from random noise to avoid analysis of data that have been randomized with respect to the historical relationships of the taxa being compared. We analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases. Analysis of random data often yields a single most-parsimonious tree, especially if the number of characters examined is large and the number of taxa examined is small (both often true in molecular studies). The most-parsimonious tree inferred from random data may also be considerably shorter than the second-best alternative. The distribution of tree lengths of all tree topologies (or a random sample thereof) provides a sensitive measure of phylogenetic signal: data matrices with phylogenetic signal produce tree-length distributions that are strongly skewed to the left, whereas those composed of random noise are closer to symmetrical. In simulations of phylogeny with varying rates of mutation (up to levels that produce random variation among taxa), the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny. Tables of critical values of a skewness test statistic, g1, are provided for binary and four-state characters for 10-500 characters and 5-25 taxa. These tables can be used in a rapid and efficient test for significant structure in data matrices for phylogenetic analysis.

Animals↗

PubMed1998

Granule-bound starch synthase: structure, function, and phylogenetic utility.

Interest in the use of low-copy nuclear genes for phylogenetic analyses of plants has grown rapidly, because highly repetitive genes such as those commonly used are limited in number. Furthermore, because low-copy genes are subject to different evolutionary processes than are plastid genes or highly repetitive nuclear markers, they provide a valuable source of independent phylogenetic evidence. The gene for granule-bound starch synthase (GBSSI or waxy) exists in a single copy in nearly all plants examined so far. Our study of GBSSI had three parts: (1) Amino acid sequences were compared across a broad taxonomic range, including grasses, four dicotyledons, and the microbial homologs of GBSSI. Inferred structural information was used to aid in the alignment of these very divergent sequences. The informed alignments highlight amino acids that are conserved across all sequences, and demonstrate that structural motifs can be highly conserved in spite of marked divergence in amino acid sequence. (2) Maximum-likelihood (ML) analyses were used to examine exon sequence evolution throughout grasses. Differences in probabilities among substitution types and marked among-site rate variation contributed to the observed pattern of variation. Of the parameters examined in our set of likelihood models, the inclusion of among-site rate variation following a gamma distribution caused the greatest improvement in likelihood score. (3) We performed cladistic parsimony analyses of GBSSI sequences throughout grasses, within tribes, and within genera to examine the phylogenetic utility of the gene. Introns provide useful information among very closely related species, but quickly become difficult to align among more divergent taxa. Exons are variable enough to provide extensive resolution within the family, but with low bootstrap support. The combined results of amino acid sequence comparisons, maximum-likelihood analyses, and phylogenetic studies underscore factors that might affect phylogenetic reconstruction. In this case, accommodation of the variable rate of evolution among sites might be the first step in maximizing the phylogenetic utility of GBSSI.

Amino Acid Sequence↗

PubMed2005

Phylogenetics of modern birds in the era of genomics.

In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics. In this review, we summarize current approaches and data characteristics of recent higher-level bird studies and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the systematic use of retroposon insertions and other rare genomic changes all promise an integrated phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing ground for such approaches because of the more balanced representation of single-copy and repetitive DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian phylogenetics, its application to large numbers of taxa poses a number of methodological and infrastructural challenges, and can be greatly facilitated by a 'community genomics' approach in which the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the comparative genomics era-with its ability to vastly increase the number and type of molecular characters and to provide a genomic context for these characters-will usher in a host of new perspectives and opportunities for integrating genome evolution and avian phylogenetics.

Animals↗