Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny

Page, Roderic

doi:10.1006/mpev.1999.0676

Cited by 145 publications

(72 citation statements)

References 57 publications

(58 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The nuclear gene encoding the visual pigment rhodopsin is useful for phylogenetic analyses (Bossuyt & Milinkovitch 2000;Page 2000;Birks & Edwards 2002;Chen et al 2003;Veith et al 2003) and occurs as a single copy in A. carolinensis, a close relative of A. porcatus and A. allisoni (Kawamura & Yokoyama 1994). Here, we examine the third intron and portions of the flanking exon sequence for this gene.…”

Section: Materials and Methods (A) Specimens Examined And Species Idenmentioning

confidence: 99%

Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles

Glor

Gifford

Larson

et al. 2004

Proc. R. Soc. Lond. B

101

104

View full text Add to dashboard Cite

Sympatric speciation is often proposed to account for species-rich adaptive radiations within lakes or islands, where barriers to gene flow or dispersal may be lacking. However, allopatric speciation may also occur in such situations, especially when ranges are fragmented by fluctuating water levels. We test the hypothesis that Miocene fragmentation of Cuba into three palaeo-archipelagos accompanied species-level divergence in the adaptive radiation of West Indian Anolis lizards. Analysis of morphology, mitochondrial DNA (mt DNA) and nuclear DNA in the Cuban green anoles (carolinensis subgroup) strongly supports three predictions made by this hypothesis. First, three geographical sets of populations, whose ranges correspond with palaeo-archipelago boundaries, are distinct and warrant recognition as independent evolutionary lineages or species. Coalescence of nuclear sequence fragments sampled from these species and the large divergences observed between their mtDNA haplotypes suggest separation prior to the subsequent unification of Cuba ca. 5 Myr ago. Second, molecular phylogenetic relationships among these species reflect historical geographical relationships rather than morphological similarity. Third, all three species remain distinct despite extensive geographical contact subsequent to island unification, occasional hybridization and introgression of mtDNA haplotypes. Allopatric speciation initiated during partial island submergence may play an important role in speciation during the adaptive radiation of Anolis lizards.

show abstract

Section: Materials and Methods (A) Specimens Examined And Species Idenmentioning

confidence: 99%

Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles

Glor

Gifford

Larson

et al. 2004

Proc. R. Soc. Lond. B

101

104

View full text Add to dashboard Cite

show abstract

“…The evolution of the vertebrates represents an ideal case for testing the utility of reconciled tree methods (Page 2000). Vertebrate classi cation has been of interest since antiquity, and a great deal of morphological data from both extant and fossil taxa have produced a well-supported outline of vertebrate phylogeny ( gure 2).…”

Section: Introductionmentioning

confidence: 99%

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

Cotton

Page

2002

Proc. R. Soc. Lond. B

View full text Add to dashboard Cite

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenetic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view. Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny.

show abstract

“…Lwoff (1944) long ago stressed the importance of losses in biochemical evolution and decades ago it was the standard explanation for the highly variable enzymic capabilities of many bacteria. Gene duplication and differential loss of paralogues is very common in vertebrates (Page, 2000). It is probably also common in bacteria, as Martin (e.g.…”

mentioning

confidence: 99%

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Cavalier‐Smith¹

2002

International Journal of Systematic and Evolutionary Microbiology

418

590

View full text Add to dashboard Cite

Prokaryotes constitute a single kingdom, Bacteria, here divided into two new subkingdoms : Negibacteria, with a cell envelope of two distinct genetic membranes, and Unibacteria, comprising the new phyla Archaebacteria and Posibacteria, with only one. Other new bacterial taxa are established in a revised higher-level classification that recognizes only eight phyla and 29 classes. Morphological, palaeontological and molecular data are integrated into a unified picture of large-scale bacterial cell evolution despite occasional lateral gene transfers. Archaebacteria and eukaryotes comprise the clade neomura, with many common characters, notably obligately co-translational secretion of N-linked glycoproteins, signal recognition particle with 7S RNA and translationarrest domain, protein-spliced tRNA introns, eight-subunit chaperonin, prefoldin, core histones, small nucleolar ribonucleoproteins (snoRNPs), exosomes and similar replication, repair, transcription and translation machinery. Eubacteria (posibacteria and negibacteria) are paraphyletic, neomura having arisen from Posibacteria within the new subphylum Actinobacteria (possibly from the new class Arabobacteria, from which eukaryotic cholesterol biosynthesis probably came). Replacement of eubacterial peptidoglycan by glycoproteins and adaptation to thermophily are the keys to neomuran origins. All 19 common neomuran character suites probably arose essentially simultaneously during the radical modification of an actinobacterium. At least 11 were arguably adaptations to thermophily. Most unique archaebacterial characters (prenyl ether lipids ; flagellar shaft of glycoprotein, not flagellin ; DNA-binding protein 10b ; specially modified tRNA ; absence of Hsp90) were subsequent secondary adaptations to hyperthermophily and/or hyperacidity. The insertional origin of protein-spliced tRNA introns and an insertion in proton-pumping ATPase also support the origin of neomura from eubacteria. Molecular co-evolution between histones and DNA-handling proteins, and in novel protein initiation and secretion machineries, caused quantum evolutionary shifts in their properties in stem neomura. Proteasomes probably arose in the immediate common ancestor of neomura and Actinobacteria. Major gene losses (e.g. peptidoglycan synthesis, hsp90, secA) and genomic reduction were central to the origin of archaebacteria. Ancestral archaebacteria were probably heterotrophic, anaerobic, sulphur-dependent hyperthermoacidophiles ; methanogenesis and halophily are secondarily derived. Multiple lateral gene transfers from eubacteria helped secondary archaebacterial adaptations to mesophily and genome re-expansion. The origin from a drastically altered actinobacterium of neomura, and the immediately subsequent simultaneous origins of archaebacteria and eukaryotes, are the most extreme and important cases of T. Cavalier-Smith quantum evolution since cells began. All three strikingly exemplify De Beer's principle of mosaic evolution : the fact that, during major evolutionary transformations, some org...

show abstract

Extracting Species Trees From Complex Gene Trees: Reconciled Trees And Vertebrate Phylogeny

Cited by 145 publications

References 57 publications

Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles

Partial island submergence and speciation in an adaptive radiation: a multilocus analysis of the Cuban green anoles

Going nuclear: gene family evolution and vertebrate phylogeny reconciled

The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification.

Contact Info

Product

Resources

About