Abstract:
:The analysis of time-resolved phylogenies (timetrees) and geographic location data allows estimation of dispersal rates, for example for invasive species and infectious diseases. Many estimation methods are based on the Brownian Motion model for diffusive dispersal on a 2-dimensional plane, however the accuracy of these methods deteriorates substantially when dispersal occurs at global scales because Spherical Brownian Motion (SBM) differs from planar Brownian Motion. No statistical method exists for estimating SBM diffusion coefficients from a given timetree and tip coordinates, and no method exists for simulating SBM along a given timetree. Here I present new methods for simulating SBM along a given timetree, and for estimating SBM diffusivity from a given timetree and tip coordinates using a modification of Felsenstein's independent contrasts and maximum-likelihood. My simulation and fitting methods can accommodate arbitrary time-dependent diffusivities and scale efficiently to trees with millions of tips, thus enabling new analyses even in cases where planar BM would be a sufficient approximation. I demonstrate these methods using a timetree of marine and terrestrial Cyanobacterial genomes, as well as timetrees of two globally circulating Influenza B clades. My methods are implemented in the R package "castor".
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Louca Sdoi
10.1093/sysbio/syaa061subject
Has Abstractpub_date
2020-07-29 00:00:00eissn
1063-5157issn
1076-836Xpii
5877953pub_type
杂志文章abstract::Although most often used to represent phylogenetic uncertainty, network methods are also potentially useful for describing the phylogenetic complexity expected to characterize recent species radiations. One network method with particular advantages in this context is split decomposition. However, in its standard imple...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150590906046
更新日期:2005-02-01 00:00:00
abstract::The dominance of angiosperms has played a direct role in the diversification of insects, especially Coleoptera. The shift to angiosperm feeding from other diets is likely to have increased the rate of speciation in Phytophaga. However, Phytophaga is only one of many hyperdiverse lineages of beetles and studies of host...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701211844
更新日期:2007-02-01 00:00:00
abstract::We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of indiv...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150390197019
更新日期:2003-08-01 00:00:00
abstract::Tree reconstruction methods are often judged by their accuracy, measured by how close they get to the true tree. Yet, most reconstruction methods like maximum likelihood (ML) do not explicitly maximize this accuracy. To address this problem, we propose a Bayesian solution. Given tree samples, we propose finding the tr...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr021
更新日期:2011-07-01 00:00:00
abstract::Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr073
更新日期:2011-12-01 00:00:00
abstract::Significant phylogenetic codivergence between plant or animal hosts (H) and their symbionts or parasites (P) indicates the importance of their interactions on evolutionary time scales. However, valid and realistic methods to test for codivergence are not fully developed. One of the systems where possible codivergence ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802172184
更新日期:2008-06-01 00:00:00
abstract::Although concerns are being raised about a potential shortage of taxonomists and systematists, recent analyses suggest instead that the number of researchers involved in taxonomic descriptions is higher than ever and that the average number of new species described annually per taxonomist has declined in recent decade...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw053
更新日期:2016-11-01 00:00:00
abstract::Genomic data have had a profound impact on nearly every biological discipline. In systematics and phylogenetics, the thousands of loci that are now being sequenced can be analyzed under the multispecies coalescent model (MSC) to explicitly account for gene tree discordance due to incomplete lineage sorting (ILS). Howe...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syz056
更新日期:2020-05-01 00:00:00
abstract::As we collect range-wide genetic data for morphologically-defined species, we increasingly unearth evidence for cryptic diversity. Delimiting this cryptic diversity is challenging, both because the divergences span a continuum and because the lack of overt morphological differentiation suggests divergence has proceede...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syy026
更新日期:2018-11-01 00:00:00
abstract::There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syx039
更新日期:2017-09-01 00:00:00
abstract::A controversial topic that underlies much of phylogenetic experimental design is the relative utility of increased taxonomic versus character sampling. Conclusions about the relative utility of adding characters or taxa to a current phylogenetic study have subtly hinged upon the appropriateness of the rate of evolutio...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syq025
更新日期:2010-07-01 00:00:00
abstract::The Cracidae is one of the most endangered and distinctive bird families in the Neotropics, yet the higher relationships among taxa remain uncertain. The molecular phylogeny of its 11 genera was inferred using 10,678 analyzable sites (5,412 from seven different mitochondrial segments and 5,266 sites from four nuclear ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150290102519
更新日期:2002-12-01 00:00:00
abstract::Gene trees record the combination of gene-level events, such as duplication, transfer and loss (DTL), and species-level events, such as speciation and extinction. Gene tree-species tree reconciliation methods model these processes by drawing gene trees into the species tree using a series of gene and species-level eve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syt054
更新日期:2013-11-01 00:00:00
abstract::Substitution rates are known to be variable among genes, chromosomes, species, and lineages due to multifarious biological processes. Here, we consider another source of substitution rate variation due to a technical bias associated with gene tree discordance. Discordance has been found to be rampant in genome-wide da...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw018
更新日期:2016-07-01 00:00:00
abstract::Penelope-like elements (PLEs) are a relatively little studied class of eukaryotic retroelements, distinguished by the presence of the GIY-YIG endonuclease domain, the ability of some representatives to retain introns, and the similarity of PLE-encoded reverse transcriptases to telomerases. Although these retrotranspos...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150601077683
更新日期:2006-12-01 00:00:00
abstract::Historically, comparisons of host and parasite phylogenies have concentrated on cospeciation. However, many of these comparisons have demonstrated that the phylogenies of hosts and parasites are seldom completely congruent, suggesting that phenomena other than cospeciation play an important role in the evolution of ho...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490265085
更新日期:2004-02-01 00:00:00
abstract::Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, an...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701656378
更新日期:2007-12-01 00:00:00
abstract::The remarkable fossil record of whales and dolphins (Cetacea) has made them an exemplar of macroevolution. Although their overall adaptive transition from terrestrial to fully aquatic organisms is well known, this is not true for the radiation of modern whales. Here, we explore the diversification of extant cetaceans ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp060
更新日期:2009-12-01 00:00:00
abstract::We modified the phylogenetic program MrBayes 3.1.2 to incorporate the compound Dirichlet priors for branch lengths proposed recently by Rannala, Zhu, and Yang (2012. Tail paradox, partial identifiability and influential priors in Bayesian branch length inference. Mol. Biol. Evol. 29:325-335.) as a solution to the prob...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys030
更新日期:2012-10-01 00:00:00
abstract::Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynami...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syy048
更新日期:2019-03-01 00:00:00
abstract::Phylogenetic relationships inferred from multilocus organellar and nuclear DNA data are often difficult to resolve because of evolutionary conflicts among gene trees. However, conflicting or "outlier" associations (i.e., linked pairs of "operational terminal units" in two phylogenies) among these data sets often provi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv070
更新日期:2016-01-01 00:00:00
abstract::The evolutionary history of gains and losses of vegetative reproductive propagules (soredia) in Porpidia s.l., a group of lichen-forming ascomycetes, was clarified using Bayesian Markov chain Monte Carlo (MCMC) approaches to monophyly tests and a combined MCMC and maximum likelihood approach to ancestral character sta...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150600697465
更新日期:2006-06-01 00:00:00
abstract::Evolutionary biologists have adopted simple likelihood models for purposes of estimating ancestral states and evaluating character independence on specified phylogenies; however, for purposes of estimating phylogenies by using discrete morphological data, maximum parsimony remains the only option. This paper explores ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351501753462876
更新日期:2001-11-01 00:00:00
abstract::Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov ch...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150600812544
更新日期:2006-08-01 00:00:00
abstract::Polyploidization is an important speciation mechanism in the barley genus Hordeum. To analyze evolutionary changes after allopolyploidization, knowledge of parental relationships is essential. One chloroplast and 12 nuclear single-copy loci were amplified by polymerase chain reaction (PCR) in all Hordeum plus six out-...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syv035
更新日期:2015-09-01 00:00:00
abstract::Siparunaceae comprise Glossocalyx with one species in West Africa and Siparuna with 65 species in the neotropics; all have unisexual flowers, and 15 species are monoecious, 50 dioecious. Parsimony and maximum likelihood analyses of combined nuclear ribosomal ITS and chloroplast trnL-trnF intergenic spacer sequences yi...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351501753328820
更新日期:2001-09-01 00:00:00
abstract::As an archive of sequence data for over 165,000 species, GenBank is an indispensable resource for phylogenetic inference. Here we describe an informatics processing pipeline and online database, the PhyLoTA Browser (http://loco.biosci.arizona.edu/pb), which offers a view of GenBank tailored for molecular phylogenetics...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150802158688
更新日期:2008-06-01 00:00:00
abstract::Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49), we present a phylo...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/49.2.306
更新日期:2000-06-01 00:00:00
abstract::We investigate the impact of past climates on plant diversification by tracking the "footprint" of climate change on a phylogenetic tree. Diversity within the cosmopolitan carnivorous plant genus Drosera (Droseraceae) is focused within Mediterranean climate regions. We explore whether this diversity is temporally link...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/1063515060081570
更新日期:2006-10-01 00:00:00
abstract::Phylogenomic analyses have helped resolve many recalcitrant relationships in the angiosperm tree of life, yet phylogenetic resolution of the backbone of the Leguminosae, one of the largest and most economically and ecologically important families, remains poor due to generally limited molecular data and incomplete tax...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa013
更新日期:2020-07-01 00:00:00