Abstract:
:The insect order Psocodea is a diverse lineage comprising both parasitic (Phthiraptera) and non-parasitic members (Psocoptera). The extreme age and ecological diversity of the group may be associated with major genomic changes, such as base compositional biases expected to affect phylogenetic inference. Divergent morphology between parasitic and non-parasitic members has also obscured the origins of parasitism within the order. We conducted a phylogenomic analysis on the order Psocodea utilizing both transcriptome and genome sequencing to obtain a data set of 2,370 orthologous genes. All phylogenomic analyses, including both concatenated and coalescent methods suggest a single origin of parasitism within the order Psocodea, resolving conflicting results from previous studies. This phylogeny allows us to propose a stable ordinal level classification scheme that retains significant taxonomic names present in historical scientific literature and reflects the evolution of the group as a whole. A dating analysis, with internal nodes calibrated by fossil evidence, suggests an origin of parasitism that predates the K-Pg boundary. Nucleotide compositional biases are detected in third and first codon positions and result in the anomalous placement of the Amphientometae as sister to Psocomorpha when all nucleotide sites are analyzed. Likelihood-mapping and quartet sampling methods demonstrate that base compositional biases can also have an effect on quartet-based methods.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
de Moya RS,Yoshizawa K,Walden KKO,Sweet AD,Dietrich CH,Johnson KPdoi
10.1093/sysbio/syaa075subject
Has Abstractpub_date
2020-09-26 00:00:00eissn
1063-5157issn
1076-836Xpii
5912026pub_type
杂志文章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::We prove that the slope parameter of the ordinary least squares regression of phylogenetically independent contrasts (PICs) conducted through the origin is identical to the slope parameter of the method of generalized least squares (GLSs) regression under a Brownian motion model of evolution. This equivalence has seve...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr118
更新日期:2012-05-01 00:00:00
abstract::Correct rooting of the angiosperm radiation is both challenging and necessary for understanding the origins and evolution of physiological and phenotypic traits in flowering plants. The problem is known to be difficult due to the large genetic distance separating flowering plants from other seed plants and the sparse ...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys070
更新日期:2013-01-01 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::The Southern Hemisphere has traditionally been considered as having a fundamentally vicariant history. The common trans-Pacific disjunctions are usually explained by the sequential breakup of the supercontinent Gondwana during the last 165 million years, causing successive division of an ancestral biota. However, rece...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490423430
更新日期:2004-04-01 00:00:00
abstract::The recent development of Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary models. At the same time, stochastic models have become more realistic (and complex) and have been extended to new types of data, such as morphology....
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490264699
更新日期:2004-02-01 00:00:00
abstract::The treehopper subfamily Membracinae (Insecta: Hemiptera: Membracidae) comprises the majority of genera and species diversity in the New World tropics. These treehoppers exhibit a wide range of social behaviors, making them an excellent group for studying patterns of social evolution in insects. However, to date the t...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490445869
更新日期:2004-06-01 00:00:00
abstract::Issues concerning transformational and taxic comparisons are central to understanding the impact of the recent proliferation of molecular developmental data on evolutionary biology. More importantly, an understanding of taxism and transformationalism in comparative biology is critical to assessing the impact of the re...
journal_title:Systematic biology
pub_type: 杂志文章,评审
doi:10.1080/10635150050207366
更新日期:2000-03-01 00:00:00
abstract::Sampling across tree space is one of the major challenges in Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) algorithms. Standard MCMC tree moves consider small random perturbations of the topology, and select from candidate trees at random or based on the distance between the old and new topolog...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syaa002
更新日期:2020-09-01 00:00:00
abstract::Evolutionary events co-occurring along phylogenetic trees usually point to complex adaptive phenomena, sometimes implicating epistasis. While a number of methods have been developed to account for co-occurrence of events on the same internal or external branch of an evolutionary tree, there is a need to account for th...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw004
更新日期:2016-09-01 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::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::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::Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 spec...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490888840
更新日期:2004-12-01 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::The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil di...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150290102465
更新日期:2002-10-01 00:00:00
abstract::We develop a maximum likelihood (ML) method for estimating migration rates between species using genomic sequence data. A species tree is used to accommodate the phylogenetic relationships among three species, allowing for migration between the two sister species, while the third species is used as an out-group. A Mar...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw063
更新日期:2017-05-01 00:00:00
abstract::Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated netw...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150701424553
更新日期:2007-06-01 00:00:00
abstract::We found that trends in the rate of description of 580,000 marine and terrestrial species, in the taxonomically authoritative World Register of Marine Species and Catalogue of Life databases, were similar until the 1950s. Since then, the relative number of marine to terrestrial species described per year has increased...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syr080
更新日期:2012-10-01 00:00:00
abstract::The genomics revolution offers great promise for resolving the phylogeny of living taxa, but does it offer any benefits for reconstructing relationships among extinct (fossil) taxa? Superficially, the answer would seem to be "no," given that molecular data cannot be obtained for most fossil taxa. However, because foss...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syp012
更新日期:2009-02-01 00:00:00
abstract::Conserved genes have found their way into the mainstream of molecular systematics. Many of these genes are members of multigene families. A difficulty with using single genes of multigene families for phylogenetic inference is that genes from one species may be paralogous to those from another taxon. We focus attentio...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150290069995
更新日期:2002-08-01 00:00:00
abstract::Investigations of biodiversity, biogeography, and ecological processes rely on the identification of "species" as biologically significant, natural units of evolution. In this context, morphotaxonomy only provides an adequate level of resolution if reproductive isolation matches morphological divergence. In many group...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syw031
更新日期:2016-09-01 00:00:00
abstract::Systematists expect their hypotheses to be asymptotically precise. As the number of phylogenetically informative characters for a set of taxa increases, the relationships implied should stabilize on some topology. If true, this increasing stability should clearly manifest itself if an index of congruence is plotted ag...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150390132731
更新日期:2003-02-01 00:00:00
abstract::We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the fami...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/syz043
更新日期:2020-03-01 00:00:00
abstract::Nucleotide transitions are frequently down-weighted relative to transversions in phylogenetic analysis. This is based on the assumption that transitions, by virtue of their greater evolutionary rate, exhibit relatively more homoplasy and are therefore less reliable phylogenetic characters. Relative amounts of homoplas...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/106351500750049734
更新日期:2000-12-01 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::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
abstract::Among models of nucleotide evolution, the Barry and Hartigan (BH) model (also known as the General Markov Model) is very flexible as it allows separate arbitrary substitution matrices along edges. For a given tree, the estimates of the BH model are a set of joint probability matrices, each giving the pairwise frequenc...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1093/sysbio/sys046
更新日期:2012-12-01 00:00:00
abstract::Matrix representation with parsimony (MRP) supertree construction has been criticized because the supertree may specify clades that are contradicted by every source tree contributing to it. Such unsupported clades may also occur using other supertree methods; however, their incidence is largely unknown. In this study,...
journal_title:Systematic biology
pub_type: 杂志文章
doi:
更新日期:2003-12-01 00:00:00
abstract::Alignments of nucleotide or amino acid sequences may contain a variety of different signals, one of which is the historical signal that we often try to recover by phylogenetic analysis. Other signals, such as those arising due to compositional heterogeneities, among-lineage and among-site rate heterogeneities, invaria...
journal_title:Systematic biology
pub_type: 杂志文章
doi:10.1080/10635150490503035
更新日期:2004-08-01 00:00:00