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Filogenia Molecular e Biogeografia das Espécies e Subespécies do Gênero Ramphastos (Piciformes: Ramphastidae); Molecular Phylogenetics and Biogeography of the Species and Subspecies of the Genus Ramphastos (Piciformes: Ramphastidae)

Patané, José Salvatore Leister
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 20/04/2007 PT
Relevância na Pesquisa
37.01%
Esta tese de doutorado versa sobre relações filogenéticas, evolução e biogeografia das espécies do gênero Ramphastos, representado pelos tucanos.; This PhD thesis is about phylogenetics, evolution and biogeography of the species of the genus Ramphastos (toucans).

Filogenética de Pilocarpinae (Rutaceae); Phylogenetic of Pilocarpinae (Rutaceae)

Oliveira, Pedro Dias de
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 10/07/2008 PT
Relevância na Pesquisa
27.41%
Esta tese está dividida em três partes: I Filogenética Básica, II Filogenia de Pilocarpinae e III Novidades Taxonômicas em Esenbeckiinae. Parte I Filogenética Básica - fornece uma rápida revisão de alguns dos métodos básicos atualmente em uso na filogenética, envolvendo aspectos teóricos e operacionais, assim como algumas de suas possíveis implicações. O Capítulo 1 discute dois conceitos importantes (grupo e caráter) e interrelacionados, mostra como pode ser construído um modelo estocástico para o tratamento de caractres, enfatizando sua adequação e demonstranto como homologia e, por conseqüência grupos, podem ser adequadamente tratados sob ótica probabilística. O Capítulo 2 apresenta os métodos de construção e otimização de árvores uzando máxima verossimilhnaça e análise bayesiana. Parte II Filogenia de Pilocarpinae - apresenta a filogenia de Pilocarpinae baseada em dados moleculares (espaçadores ITS1, ITS2 e gene 5.8 S do DNA nuclear e espaçador trnG-S do DNA platidial) e a filogenia de Pilocarpus Vahl baseada em dados moleculares (mesmas regiões usadas anteriormente) e morfológicos. O Capítulo 3 apresenta a filogenia em nível genérico da subtribo Pilocarpinae e de gêneros relacionados (Helietta e Balfourodendron )...

A preliminary analysis of the population genetics and molecular phylogenetics of Onchocerca volvulus (Nematoda: Filarioidea) using nuclear ribosomal second internal transcribed spacer sequences

Morales-Hojas,Ramiro; Cheke,Robert A; Post,Rory J
Fonte: Instituto Oswaldo Cruz, Ministério da Saúde Publicador: Instituto Oswaldo Cruz, Ministério da Saúde
Tipo: Artigo de Revista Científica Formato: text/html
Publicado em 01/11/2007 EN
Relevância na Pesquisa
37.01%
Nuclear internal transcribed spacer 2 (ITS2) rDNA sequences were used for a molecular phylogenetics analysis of five Onchocerca species. The sister species of the human parasite O. volvulus was found to be the cattle parasite O. ochengi and not O. gibsoni, contrary to chromosomal evidence. The genetic differentiation of two African populations (representing the two African strains) and a Brazilian population of O. volvulus was also studied. Phylogenetic and network reconstruction did not show any clustering of ITS2 alleles on geographic or strain grounds. Furthermore, population genetics tests showed no indication of population differentiation but suggested gene flow among the three populations.

Relaxed Phylogenetics and Dating with Confidence

Drummond, Alexei J; Ho, Simon Y. W; Phillips, Matthew J; Rambaut, Andrew
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
27.01%
In phylogenetics, the unrooted model of phylogeny and the strict molecular clock model are two extremes of a continuum. Despite their dominance in phylogenetic inference, it is evident that both are biologically unrealistic and that the real evolutionary process lies between these two extremes. Fortunately, intermediate models employing relaxed molecular clocks have been described. These models open the gate to a new field of “relaxed phylogenetics.” Here we introduce a new approach to performing relaxed phylogenetic analysis. We describe how it can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times. Our approach also provides a means for measuring the clocklikeness of datasets and comparing this measure between different genes and phylogenies. We find no significant rate autocorrelation among branches in three large datasets, suggesting that autocorrelated models are not necessarily suitable for these data. In addition, we place these datasets on the continuum of clocklikeness between a strict molecular clock and the alternative unrooted extreme. Finally, we present analyses of 102 bacterial, 106 yeast, 61 plant, 99 metazoan, and 500 primate alignments. From these we conclude that our method is phylogenetically more accurate and precise than the traditional unrooted model while adding the ability to infer a timescale to evolution.

Phylogenetics of modern birds in the era of genomics

Edwards, Scott V; Bryan Jennings, W; Shedlock, Andrew M
Fonte: The Royal Society Publicador: The Royal Society
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
27.41%
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...

Evolution of proteins and proteomes: a phylogenetics approach

Gabaldón, Toni
Fonte: Libertas Academica Publicador: Libertas Academica
Tipo: Artigo de Revista Científica
Publicado em 24/02/2007 EN
Relevância na Pesquisa
27.17%
The study of evolutionary relationships among protein sequences was one of the first applications of bioinformatics. Since then, and accompanying the wealth of biological data produced by genome sequencing and other high-throughput techniques, the use of bioinformatics in general and phylogenetics in particular has been gaining ground in the study of protein and proteome evolution. Nowadays, the use of phylogenetics is instrumental not only to infer the evolutionary relationships among species and their genome sequences, but also to reconstruct ancestral states of proteins and proteomes and hence trace the paths followed by evolution. Here I survey recent progress in the elucidation of mechanisms of protein and proteome evolution in which phylogenetics has played a determinant role.

Choosing and Using Introns in Molecular Phylogenetics

Creer, Simon
Fonte: Libertas Academica Publicador: Libertas Academica
Tipo: Artigo de Revista Científica
Publicado em 14/06/2007 EN
Relevância na Pesquisa
27.01%
Introns are now commonly used in molecular phylogenetics in an attempt to recover gene trees that are concordant with species trees, but there are a range of genomic, logistical and analytical considerations that are infrequently discussed in empirical studies that utilize intron data. This review outlines expedient approaches for locus selection, overcoming paralogy problems, recombination detection methods and the identification and incorporation of LVHs in molecular systematics. A range of parsimony and Bayesian analytical approaches are also described in order to highlight the methods that can currently be employed to align sequences and treat indels in subsequent analyses. By covering the main points associated with the generation and analysis of intron data, this review aims to provide a comprehensive introduction to using introns (or any non-coding nuclear data partition) in contemporary phylogenetics.

New primers for promising single-copy genes in fungal phylogenetics and systematics

Schmitt, I.; Crespo, A.; Divakar, P.K.; Fankhauser, J.D.; Herman-Sackett, E.; Kalb, K.; Nelsen, M.P.; Nelson, N.A.; Rivas-Plata, E.; Shimp, A.D.; Widhelm, T.; Lumbsch, H.T.
Fonte: Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures Publicador: Nationaal Herbarium Nederland & Centraallbureau voor Schimmelcultures
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
27.01%
Developing powerful phylogenetic markers is a key concern in fungal phylogenetics. Here we report degenerate primers that amplify the single-copy genes Mcm7 (MS456) and Tsr1 (MS277) across a wide range of Pezizomycotina (Ascomycota). Phylogenetic analyses of 59 taxa belonging to the Eurotiomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes and Sordariomycetes, indicate the utility of these loci for fungal phylogenetics at taxonomic levels ranging from genus to class. We also tested the new primers in silico using sequences of Saccharomycotina, Taphrinomycotina and Basidiomycota to predict their potential of amplifying widely across the Fungi. The analyses suggest that the new primers will need no, or only minor sequence modifications to amplify Saccharomycotina, Taphrinomycotina and Basidiomycota.

Hippo Pathway Phylogenetics Predicts Monoubiquitylation of Salvador and Merlin/Nf2

Wisotzkey, Robert G.; Konikoff, Charlotte E.; Newfeld, Stuart J.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 14/12/2012 EN
Relevância na Pesquisa
27.01%
Recently we employed phylogenetics to predict that the cellular interpretation of TGF-β signals is modulated by monoubiquitylation cycles affecting the Smad4 signal transducer/tumor suppressor. This prediction was subsequently validated by experiments in flies, frogs and mammalian cells. Here we apply a phylogenetic approach to the Hippo pathway and predict that two of its signal transducers, Salvador and Merlin/Nf2 (also a tumor suppressor) are regulated by monoubiquitylation. This regulatory mechanism does not lead to protein degradation but instead serves as a highly efficient “off/on” switch when the protein is subsequently deubiquitylated. Overall, our study shows that the creative application of phylogenetics can predict new roles for pathway components and new mechanisms for regulating intercellular signaling pathways.

Molecular phylogenetics before sequences: Oligonucleotide catalogs as k-mer spectra

Ragan, Mark A; Bernard, Guillaume; Chan, Cheong Xin
Fonte: Landes Bioscience Publicador: Landes Bioscience
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
27.01%
From 1971 to 1985, Carl Woese and colleagues generated oligonucleotide catalogs of 16S/18S rRNAs from more than 400 organisms. Using these incomplete and imperfect data, Carl and his colleagues developed unprecedented insights into the structure, function, and evolution of the large RNA components of the translational apparatus. They recognized a third domain of life, revealed the phylogenetic backbone of bacteria (and its limitations), delineated taxa, and explored the tempo and mode of microbial evolution. For these discoveries to have stood the test of time, oligonucleotide catalogs must carry significant phylogenetic signal; they thus bear re-examination in view of the current interest in alignment-free phylogenetics based on k-mers. Here we consider the aims, successes, and limitations of this early phase of molecular phylogenetics. We computationally generate oligonucleotide sets (e-catalogs) from 16S/18S rRNA sequences, calculate pairwise distances between them based on D2 statistics, compute distance trees, and compare their performance against alignment-based and k-mer trees. Although the catalogs themselves were superseded by full-length sequences, this stage in the development of computational molecular biology remains instructive for us today.

Molecular Phylogenetics and Systematics of the Bivalve Family Ostreidae Based on rRNA Sequence-Structure Models and Multilocus Species Tree

Salvi, Daniele; Macali, Armando; Mariottini, Paolo
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 24/09/2014 EN
Relevância na Pesquisa
27.17%
The bivalve family Ostreidae has a worldwide distribution and includes species of high economic importance. Phylogenetics and systematic of oysters based on morphology have proved difficult because of their high phenotypic plasticity. In this study we explore the phylogenetic information of the DNA sequence and secondary structure of the nuclear, fast-evolving, ITS2 rRNA and the mitochondrial 16S rRNA genes from the Ostreidae and we implemented a multi-locus framework based on four loci for oyster phylogenetics and systematics. Sequence-structure rRNA models aid sequence alignment and improved accuracy and nodal support of phylogenetic trees. In agreement with previous molecular studies, our phylogenetic results indicate that none of the currently recognized subfamilies, Crassostreinae, Ostreinae, and Lophinae, is monophyletic. Single gene trees based on Maximum likelihood (ML) and Bayesian (BA) methods and on sequence-structure ML were congruent with multilocus trees based on a concatenated (ML and BA) and coalescent based (BA) approaches and consistently supported three main clades: (i) Crassostrea, (ii) Saccostrea, and (iii) an Ostreinae-Lophinae lineage. Therefore, the subfamily Crassotreinae (including Crassostrea), Saccostreinae subfam. nov. (including Saccostrea and tentatively Striostrea) and Ostreinae (including Ostreinae and Lophinae taxa) are recognized. Based on phylogenetic and biogeographical evidence the Asian species of Crassostrea from the Pacific Ocean are assigned to Magallana gen. nov....

Probabilistic Graphical Model Representation in Phylogenetics

Höhna, Sebastian; Heath, Tracy A.; Boussau, Bastien; Landis, Michael J.; Ronquist, Fredrik; Huelsenbeck, John P.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
27.17%
Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation of the chosen model is crucial for: (i) reproducibility of an analysis, (ii) model development, and (iii) software design. Moreover, a unified, clear and understandable framework for model representation lowers the barrier for beginners and nonspecialists to grasp complex phylogenetic models, including their assumptions and parameter/variable dependencies. Graphical modeling is a unifying framework that has gained in popularity in the statistical literature in recent years. The core idea is to break complex models into conditionally independent distributions. The strength lies in the comprehensibility, flexibility, and adaptability of this formalism, and the large body of computational work based on it. Graphical models are well-suited to teach statistical models, to facilitate communication among phylogeneticists and in the development of generic software for simulation and statistical inference. Here, we provide an introduction to graphical models for phylogeneticists and extend the standard graphical model representation to the realm of phylogenetics. We introduce a new graphical model component...

Phylogenetics and the Human Microbiome

Matsen, Frederick A.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
27.17%
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this article, I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.

Selection for High Oridonin Yield in the Chinese Medicinal Plant Isodon (Lamiaceae) Using a Combined Phylogenetics and Population Genetics Approach

Schoville, Sean D.; Dong, Chengming; Wang, Wenquan; Jian, Zaiyou; Zhao, Zhongzhen; Cao, Shugeng; Eisenberg, David Miles; Clardy, Jon C.; Harris, Eric S. J.
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
EN_US
Relevância na Pesquisa
27.01%
Oridonin is a diterpenoid with anti-cancer activity that occurs in the Chinese medicinal plant Isodon rubescens and some related species. While the bioactivity of oridonin has been well studied, the extent of natural variation in the production of this compound is poorly known. This study characterizes natural variation in oridonin production in order to guide selection of populations of Isodon with highest oridonin yield. Different populations of I. rubescens and related species were collected in China, and their offspring were grown in a greenhouse. Samples were examined for oridonin content, genotyped using 11 microsatellites, and representatives were sequenced for three phylogenetic markers (ITS, rps16, trnL-trnF). Oridonin production was mapped on a molecular phylogeny of the genus Isodon using samples from each population as well as previously published Genbank sequences. Oridonin has been reported in 12 out of 74 species of Isodon examined for diterpenoids, and the phylogeny indicates that oridonin production has arisen at least three times in the genus. Oridonin production was surprisingly consistent between wild-collected parents and greenhouse-grown offspring, despite evidence of gene flow between oridonin-producing and non-producing populations of Isodon. Additionally...

Determination of microsatellite DNA mutation rates , mutation models and mutation bias in four main felidae lineages (european wild cat , felis silvestris ; ocelot , leopardus pardalis ; puma , puma concolor ; jaguar , panthera onca); Molecular Population Genetics, Evolutionary Biology and Biological Conservation of Neotropical Carnivores

Ruiz García, Manuel; García Perea, Rosa; Corrales, Carolina; Murillo, Andrea; Alvarez, Diana; Pinedo Castro, Myreya; Shostell, Joseph Mark
Fonte: Nova Science Pub Inc Publicador: Nova Science Pub Inc
Formato: 1-720
Relevância na Pesquisa
27.35%
We analyzed for 12 nuclear DNA microsatellites in 4 wild cat species (European wild cat, ocelot, puma, and jaguar) representing four different phylogenetics felid lineages. The objective of our study, using these species and molecular markers, was to obtain more data about the molecular evolution of microsatellites. The main findings of this study are: 1- From the measurements of diverse genetics variables and statistics in the four species, we determined that the ocelot showed the highest number of alleles, number of repeats, allele range and levels of heterozygosity. However, no significant differences were observed among the average microsatellite mutation rates observed in the four species of felids studied. 2- We estimated two independent average mutation rates (3.116 x 10-5 and 5.353 x 10-5) using two different phylogenetics strategies. However, there was no significant difference between these two estimates. 3- We found the observed mutation model to be basically a uni-step mutation model or a two-phase mutation model. The four felid species showed an average stepwise mutation model for 92-94 % of the uni-step mutations. 4- The regression models we applied among different genetic diversity statistics, samples sizes and other variables showed: a- the allele range was clearly more correlated with the allele number at the microsatellites studied than to the allele dispersion...

Determination of Microsatellite DNA Mutation Rates, Mutation Models and Mutation Bias in four main Felidae Lineages (European wild cat , Felis silvestris; Ocelot, Leopardus pardalis; Puma, Puma concolor; Jaguar, Panthera onca); Molecular Population Genetics, Evolutionary Biology, and Biological Conservation of Neotropical Carnivores

Ruiz-García, Manuel; García-Perea, Rosa; Corrales, Carolina; Murillo, Andrea; Alvarez, Diana; Pinedo-Castro, Myreya; Shostell, Joseph Mark
Fonte: Nova Science Publishers, Inc. Publicador: Nova Science Publishers, Inc.
Formato: 1-79
Relevância na Pesquisa
27.27%
We analyzed for 12 nuclear DNA microsatellites in 4 wild cat species (European wild cat, ocelot, puma, and jaguar) representing four different phylogenetics felid lineages. The objective of our study, using these species and molecular markers, was to obtain more data about the molecular evolution of microsatellites. The main findings of this study are: 1- From the measurements of diverse genetics variables and statistics in the four species, we determined that the ocelot showed the highest number of alleles, number of repeats, allele range and levels of heterozygosity. However, no significant differences were observed among the average microsatellite mutation rates observed in the four species of felids studied. 2- We estimated two independent average mutation rates (3.116 x 10-5 and 5.353 x 10-5) using two different phylogenetics strategies. However, there was no significant difference between these two estimates. 3- We found the observed mutation model to be basically a uni -step mutation model or a two-phase mutation model. The four felid species showed an average stepwise mutation model for 92-94 % of the uni-step mutations. 4- The regression models we applied among different genetic diversity statistics...

Population Genetics and Phylogeographic Analyses of the Jaguarundi (Puma yagouaroundi) by Means of Three Mitochondrial Markers: The First Molecular Population Study of This Species.; Molecular population genetics, phylogenetics, evolutionary biology and conservation of the neotropical carnivores

Ruiz-García, Manuel; Pinedo-Castro, Myreya
Fonte: Nova Science Publishers, Inc. Publicador: Nova Science Publishers, Inc.
Formato: 245–288
Relevância na Pesquisa
37.01%
A total of 44 wild jaguarundis were sampled throughout Mexico, Guatemala, Costa Rica, Colombia, Venezuela, Ecuador, Peru, Bolivia and Brazil and sequenced for three mitochondrial genes (ATP8, 16S rRNA, NADH5). This is the first molecular population genetics and phylogenetic study of this species and the most relevant results were as follows: 1- The gene diversity levels for the jaguarundi at the three mitochondrial genes sequenced were very elevated as it was found for other Neotropical wild cats such as the jaguar, ocelot, margay and the Pampas cat; 2 - The levels of gene heterogeneity among putative subspecies or among countries was extremely small, although this species has a broad distribution from southern USA to Argentina; 3- Additionally, the phylogenetics trees (genetic distances, maximum likelihood, maximum parsi mony and Bayesian) showed that no molecular subspecies were defined in contradiction with the morphological classifications of Allen (1919), Cabrera (1957) and de Oliveira (1998); 4-Bayesian and network procedures showed that the first haplotype divergence process in the jaguarundi began around 2.0-1.6 MYA, with a second haplotype divergence event around 1.1-0.8 MYA...

Molecular systematics of selected Australian brown algae.

Soisup, Nuttanun
Fonte: Universidade de Adelaide Publicador: Universidade de Adelaide
Tipo: Tese de Doutorado
Publicado em //2014
Relevância na Pesquisa
27.27%
This thesis focuses on the molecular systematics of four selected Australian brown algal genera (Phaeophyceae); Acrocarpia, Caulocystis, Cystophora (Fucales) and Lobophora (Dictyotales). The thesis consists of five chapters. Chapter 1: General introduction; Chapter 2: The phylogenetics, DNA barcoding and phylogeographic discrimination of Caulocystis and Acrocarpia species; Chapter 3: The molecular phylogenetics of Cystophora; Chapter 4: An assessment of species diversity within Australian Lobophora based on rbcL and cox1 DNA sequence analyses, and Chapter 5: General discussion. The first chapter describes the marine floral biodiversity of Australia, the ecological importance of benthic brown algae, the development of taxonomic studies in macroalgae, and the aims and significance of this study. The second chapter is the first molecular taxonomic study specifically targeting two endemic Australian Fucales genera, Acrocarpia and Caulocystis, based on cox1, rbcL and ITS2 DNA sequence analyses. Results from molecular and morphological data suggest that two known Caulocystis species are conspecific, and hence should be merged into a single taxon. The third chapter aims to clarify taxonomic problems originating from the phenotypic plasticity of the Australian and New Zealand endemic genus Cystophora. Traditionally...

Phylogenetics and the human microbiome

Matsen IV, Frederick A
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 07/07/2014
Relevância na Pesquisa
27.17%
The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this paper I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.; Comment: to appear in Systematic Biology

Bayesian Structural Phylogenetics

Challis, Christopher
Fonte: Universidade Duke Publicador: Universidade Duke
Tipo: Dissertação
Publicado em //2013
Relevância na Pesquisa
37.01%

This thesis concerns the use of protein structure to improve phylogenetic inference. There has been growing interest in phylogenetics as the number of available DNA and protein sequences continues to grow rapidly and demand from other scientific fields increases. It is now well understood that phylogenies should be inferred jointly with alignment through use of stochastic evolutionary models. It has not been possible, however, to incorporate protein structure in this framework. Protein structure is more strongly conserved than sequence over long distances, so an important source of information, particularly for alignment, has been left out of analyses.

I present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model and mutations follow a standard substitution matrix, while backbone atoms diffuse in three-dimensional space according to an Ornstein-Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables pairwise evolutionary distance estimation on time scales not previously attainable with sequence evolution models. Ideally inference should not be performed in a pairwise fashion between proteins...