Abstract：
:The phylogenetic comparative method uses estimates of evolutionary relationships to explicitly model the covariance structure of interspecific data. By accounting for common ancestry, the coevolution between 2 or more traits, as a response to one another or to environmental variables, can be studied without confounding similarities due to identity by descent. Because the true phylogeny is unknowable, an estimate must be used, introducing a source of error into phylogenetic comparative analysis that can be difficult to quantify. This manuscript aims to elucidate how tree misspecification is propagated through a comparative analysis. I focus on the phylogenetic regression under a Brownian motion model of evolution and consider the effect of local phylogenetic perturbations on the regression fit. Motivated by Felsenstein's method of independent contrasts, I derive a matrix square root of the phylogenetic covariance matrix that has an obvious phylogenetic interpretation. I use this result to transform the perturbed phylogenetic regression model into an ordinary linear regression in which one interpretable point has been affected. The simplicity of this formulation allows the contributions of data and phylogeny to be disentangled when studying the effect of tree misspecification. Consequentially, I find that branch length misspecification can be easily explained in terms of the reweighting of contrast scores between subtrees. An analytical consideration of this and other perturbations helps to explain why the phylogenetic regression appears generally to be robust to tree misspecification, and I am able to identify conditions under which the regression may not yield robust results. I discuss why soft polytomies do not meet these problematic conditions, leading to the conclusion that unresolved bifurcations should have only modest effects on the regression fit.
journal_name
Syst Bioljournal_title
Systematic biologyauthors
Stone EAdoi
10.1093/sysbio/syq098subject
Has Abstractpub_date
2011-05-01 00:00:00pages
245-60issue
3eissn
1063-5157issn
1076-836Xpii
syq098journal_volume
60pub_type
杂志文章abstract：:Young polyploid events are easily diagnosed by various methods, but older polyploid events become increasingly difficult to identify as chromosomal rearrangements, tandem gene or partial chromosome duplications, changes in substitution rates among duplicated genes, pseudogenization or locus loss, and interlocus intera...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150590945359
更新日期：2005-06-01 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：:Population structure influences genealogical patterns, however, data pertaining to how populations are structured are often unavailable or not directly observable. Inference of population structure is highly important in molecular epidemiology where pathogen phylogenetics is increasingly used to infer transmission pat...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa009
更新日期：2020-09-01 00:00:00
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 ...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syv084
更新日期：2016-03-01 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：:All methods proposed to date for mapping landmark configurations on a phylogenetic tree start from an alignment generated by methods that make no use of phylogenetic information, usually by superimposing all configurations against a consensus configuration. In order to properly interpret differences between landmark c...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syr119
更新日期：2012-05-01 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：: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：:All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/106351599260319
更新日期：1999-06-01 00:00:00
abstract：:Understanding how gene flow affects population divergence and speciation remains challenging. Differentiating one evolutionary process from another can be difficult because multiple processes can produce similar patterns, and more than one process can occur simultaneously. While simple population models produce predic...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa071
更新日期：2020-09-17 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：:Lice in the genus Pectinopygus parasitize a single order of birds (Pelecaniformes). To examine the degree of congruence between the phylogenies of 17 Pectinopygus species and their pelecaniform hosts, sequences from mitochondrial 12S rRNA, 16S rRNA, COI, and nuclear wingless and EF1-alpha genes (2290 nucleotides) and ...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150701311370
更新日期：2007-04-01 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：:When doing a bootstrap analysis with a single tree saved per pseudoreplicate, biased search algorithms may influence support values more than actual properties of the data set. Two methods commonly used for finding phylogenetic trees consist of randomizing the input order of species in multiple addition sequences foll...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syu051
更新日期：2014-11-01 00:00:00
abstract：:Mouse lemurs (Microcebus) are a radiation of morphologically cryptic primates distributed throughout Madagascar for which the number of recognized species has exploded in the past two decades. This taxonomic revision has prompted understandable concern that there has been substantial oversplitting in the mouse lemur c...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa053
更新日期：2020-07-08 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：: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：:How should characters and taxa be sampled to resolve efficiently the phylogeny of ancient and highly speciose groups? We addressed this question empirically in the treefrog family Hylidae, which contains > 800 species and may be nonmonophyletic with respect to other anuran families. We sampled 81 species (54 hylids an...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150500234625
更新日期：2005-10-01 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：: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：: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 the...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1093/sysbio/syaa061
更新日期：2020-07-29 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：: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：: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：: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：: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：:Bacteria are profoundly different from eukaryotes in their patterns of genetic exchange. Nevertheless, ecological diversity is organized in the same way across all of life: individual organisms fall into more less discrete clusters on the basis of their phenotypic, ecological, and DNA sequence characteristics. Each se...
journal_title：Systematic biology
pub_type： 杂志文章,评审
doi：10.1080/10635150118398
更新日期：2001-08-01 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：:The mitochondrial genome is one of the most frequently used loci in phylogenetic and phylogeographic analyses, and it is becoming increasingly possible to sequence and analyze this genome in its entirety from diverse taxa. However, sequencing the entire genome is not always desirable or feasible. Which genes should be...
journal_title：Systematic biology
pub_type： 杂志文章
doi：10.1080/10635150500541672
更新日期：2006-04-01 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
