The Future of Systematics: Tree-Thinking Without the Tree

Phylogenetic trees are meant to represent the genealogical history of life and apparently derive their justification from the existence of the tree of life and the fact that evolutionary processes are tree-like. However, there are a number of problems for these assumptions. Here it is argued that once we understand the important role that phylogenetic trees play as models which contain idealizations, we can accept these criticisms and deny the reality of the tree while justifying the continued use of trees in phylogenetic theory and preserving nearly all of what defenders of trees have called “the importance of tree-thinking.

Axiomatic opportunities and obstacles for inferring a species tree from gene trees

The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all taxa are present in every gene tree. Here, we list four apparently desirable properties that a method for estimating a species tree from gene trees could have (the strongest property states that building a species tree from input gene trees and then pruning leaves gives a tree that is the same as, or more resolved than, the tree obtained by first removing the taxa from the input trees and then building the species tree). We show that while it is technically possible to simultaneously satisfy these properties when taxon coverage is complete, they cannot all be satisfied in the more general supertree setting. In part two, we discuss a concordance-based consensus method based on Baum's `plurality clusters', and an extension to concordance supertrees.Comment: 19 pages, 2 figure

Phylogeny as population history

The construction and use of phylogenetic trees is central to modern systematics. But it is unclear exactly what phylogenies and phylogenetic trees represent. They are sometimes said to represent genealogical relationships between taxa, between species, or simply between “groups of organisms.” But these are incompatible representational claims. This paper focuses on how trees are used to make inferences and then argues that this focus requires that phylogenies represent the histories of populations

Updating on the Credences of Others: Disagreement, Agreement, and Synergy

We introduce a family of rules for adjusting one’s credences in response to learning the credences of others. These rules have a number of desirable features. 1. They yield the posterior credences that would result from updating by standard Bayesian conditionalization on one’s peers’ reported credences if one’s likelihood function takes a particular simple form. 2. In the simplest form, they are symmetric among the agents in the group. 3. They map neatly onto the familiar Condorcet voting results. 4. They preserve shared agreement about independence in a wide range of cases. 5. They commute with conditionalization and with multiple peer updates. Importantly, these rules have a surprising property that we call synergy — peer testimony of credences can provide mutually supporting evidence raising an individual’s credence higher than any peer’s initial prior report. At first, this may seem to be a strike against them. We argue, however, that synergy is actually a desirable feature and the failure of other updating rules to yield synergy is a strike against them

Updating on the Credences of Others: Disagreement, Agreement, and Synergy

We introduce a family of rules for adjusting one’s credences in response to learning the credences of others. These rules have a number of desirable features. 1. They yield the posterior credences that would result from updating by standard Bayesian conditionalization on one’s peers’ reported credences if one’s likelihood function takes a particular simple form. 2. In the simplest form, they are symmetric among the agents in the group. 3. They map neatly onto the familiar Condorcet voting results. 4. They preserve shared agreement about independence in a wide range of cases. 5. They commute with conditionalization and with multiple peer updates. Importantly, these rules have a surprising property that we call synergy — peer testimony of credences can provide mutually supporting evidence raising an individual’s credence higher than any peer’s initial prior report. At first, this may seem to be a strike against them. We argue, however, that synergy is actually a desirable feature and the failure of other updating rules to yield synergy is a strike against them

Discordant antibiotic therapy and length of stay in children hospitalized for urinary tract infection

BACKGROUND: Urinary tract infections (UTIs) are a common reason for pediatric hospitalizations. OBJECTIVE: To determine the effect of discordant antibiotic therapy (in vitro nonsusceptibility of the uropathogen to initial antibiotic) on clinical outcomes for children hospitalized for UTI. DESIGN/SETTING: Multicenter retrospective cohort study in children aged 3 days to 18 years, hospitalized at 5 children's hospitals with a laboratory‐confirmed UTI. Data were obtained from medical records and the Pediatric Hospital Information System (PHIS) database. PARTICIPANTS: Patients with laboratory‐confirmed UTI. MAIN EXPOSURE: Discordant antibiotic therapy. MEASUREMENTS: Length of stay and fever duration. Covariates included age, sex, insurance, race, vesicoureteral reflux, antibiotic prophylaxis, genitourinary abnormality, and chronic care conditions. RESULTS: The median age of the 216 patients was 2.46 years (interquartile range [IQR]: 0.27, 8.89) and 25% were male. The most common causative organisms were E. coli and Klebsiella species. Discordant therapy occurred in 10% of cases and most commonly in cultures positive for Klebsiella species, Enterobacter species, and mixed organisms. In adjusted analyses, discordant therapy was associated with a 1.8 day (95% confidence interval [CI]: 1.5, 2.1) longer length of stay [LOS], but not with fever duration. CONCLUSIONS: Discordant antibiotic therapy for UTI is common and associated with longer hospitalizations. Further research is needed to understand the clinical factors contributing to the increased LOS and to inform decisions for empiric antibiotic selection in children with UTIs. Journal of Hospital Medicine 2012; © 2012 Society of Hospital MedicinePeer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/94298/1/1960_ftp.pd

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes