Abstract：
:Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Murray GG,Weinert LA,Rhule EL,Welch JJdoi
10.1093/sysbio/syv084subject
Has Abstractpub_date
2016-03-01 00:00:00pages
265-79issue
2eissn
1063-5157issn
1076-836Xpii
syv084journal_volume
65pub_type
杂志文章abstract：:Ants (Hymenoptera: Formicidae) are conspicuous organisms in most terrestrial ecosystems, often attaining high levels of abundance and diversity. In this study, we investigate the evolutionary history of a major clade of ants, the subfamily Dolichoderinae, whose species frequently achieve ecological dominance in ant co...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syq012
更新日期：2010-05-01 00:00:00
abstract：:The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and reso...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syv031
更新日期：2015-11-01 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：:Conifer-feeding sawflies in the genus Neodiprion provide an excellent opportunity to investigate the origin and maintenance of barriers to reproduction, but obtaining a phylogenetic estimate for comparative studies of Neodiprion speciation has proved difficult. Specifically, nonmonophyly within and discordance between...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150802580949
更新日期：2008-12-01 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：:Targeted sequence capture is becoming a widespread tool for generating large phylogenomic data sets to address difficult phylogenetic problems. However, this methodology often generates data sets in which increasing the number of taxa and loci increases amounts of missing data. Thus, a fundamental (but still unresolve...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syv058
更新日期：2016-01-01 00:00:00
abstract：:It is common for studies that employ the comparative method for the study of adaptation, i.e. documentation of potentially adaptive across-species patterns of trait-environment or trait-trait correlation, to be designated as "macroevolutionary." Authors are justified in using "macroevolution" in this way by appeal to ...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa086
更新日期：2021-01-07 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：: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：:Platyrrhine primates and caviomorph rodents are clades of mammals that colonized South America during its period of isolation from the other continents, between 100 and 3 million years ago (Mya). Until now, no molecular study investigated the timing of the South American colonization by these two lineages with the sam...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150500481390
更新日期：2006-04-01 00:00:00
abstract：:The spatial distribution of biomes has changed considerably over deep time, so the geographical opportunity for an evolutionary lineage to shift into a new biome may depend on how the availability and connectivity of biomes has varied temporally. To better understand how lineages shift between biomes in space and time...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa045
更新日期：2021-01-01 00:00:00
abstract：:Horizontal gene transfer (HGT) is one of the main mechanisms driving the evolution of microorganisms. Its accurate identification is one of the major challenges posed by reticulate evolution. In this article, we describe a new polynomial-time algorithm for inferring HGT events and compare 3 existing and 1 new tree com...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syp103
更新日期：2010-03-01 00:00:00
abstract：:Several methods have been proposed to infer the states at the ancestral nodes on a phylogeny. These methods assume a specific tree and set of branch lengths when estimating the ancestral character state. Inferences of the ancestral states, then, are conditioned on the tree and branch lengths being true. We develop a h...
journal_title：Systematic biology
pub_type： 杂志文章
doi：
更新日期：2001-06-01 00:00:00
abstract：:This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species....
journal_title：Systematic biology
pub_type： 杂志文章,评审
doi：10.1093/sysbio/syu048
更新日期：2015-01-01 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：: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：:Species delimitation and species tree inference are difficult problems in cases of recent divergence, especially when different loci have different histories. This paper quantifies the difficulty of jointly finding the division of samples to species and estimating a species tree without constraining the possible assig...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syp077
更新日期：2010-01-01 00:00:00
abstract：:Lineage sorting and introgression can lead to incongruence among gene phylogenies, complicating the inference of species trees for large groups of taxa that have recently and rapidly radiated. In addition, it can be difficult to determine which of these processes is responsible for this incongruence. We explore these ...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150600697283
更新日期：2006-06-01 00:00:00
abstract：:Using different data sets mainly from the plant family Rubiaceae, but in parts also from the Apocynaceae, Asteraceae, Lardizabalaceae, Saxifragaceae, and Solanaceae, we have investigated the effect of number of characters, number of taxa, and kind of data on bootstrap values within phylogenetic trees. The percentage o...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/106351599260085
更新日期：1999-09-01 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：:Whereas examples of insular speciation within the endemic-rich Macaronesian hotspot flora have been documented, the phylogeography of recently evolved plants in the region has received little attention. The Macaronesian red fescues constitute a narrow and recent radiation of four closely related diploid species distri...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150802302450
更新日期：2008-10-01 00:00:00
abstract：:We collected ~29 kb of sequence data using Roche 454 pyrosequencing in order to estimate the timing and pattern of diversification in the carnivorous pitcher plant Sarracenia alata. Utilizing modified protocols for reduced representation library construction, we generated sequence data from 86 individuals across 10 po...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/sys048
更新日期：2012-10-01 00:00:00
abstract：:Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of ...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syr052
更新日期：2011-10-01 00:00:00
abstract：:Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key proces...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syz005
更新日期：2019-09-01 00:00:00
abstract：:Species are the starting point for most studies of ecology and evolution, but the proper circumscription of species can be extremely difficult in morphologically variable lineages, and there are still few convincing examples of molecularly informed species delimitation in plants. Here, we focus on the Viburnum nudum c...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syy084
更新日期：2019-03-01 00:00:00
abstract：:Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclea...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syt101
更新日期：2014-03-01 00:00:00
abstract：:We explored the efficacy of species tree methods at the family level in birds, using the Australo-Papuan Fairy-wrens (Passeriformes: Maluridae) as a model system. Fairy-wrens of the genus Malurus are known for high intensities of sexual selection, resulting in some cases in rapid speciation. This history suggests that...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syr101
更新日期：2012-03-01 00:00:00
abstract：:We present a phylogenetic hypothesis and novel, rank-free classification for all extant species of softshell turtles (Testudines:Trionychidae). Our data set included DNA sequence data from two mitochondrial protein-coding genes and a approximately 1-kb nuclear intron for 23 of 26 recognized species, and 59 previously ...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150490503053
更新日期：2004-10-01 00:00:00
abstract：:Tropical forests of Central and South America represent hotspots of biological diversity. Tree squirrels of the tribe Sciurini are an excellent model system for the study of tropical biodiversity as these squirrels disperse exceptional distances, and after colonizing the tropics of the Central and South America, they ...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syv054
更新日期：2015-11-01 00:00:00
abstract：:Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting m...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syr100
更新日期：2012-01-01 00:00:00
