On the number of ranked species trees producing anomalous ranked gene trees

Analysis of probability distributions conditional on species trees has demonstrated the existence of anomalous ranked gene trees (ARGTs), ranked gene trees that are more probable than the ranked gene tree that accords with the ranked species tree. Here, to improve the characterization of ARGTs, we study enumerative and probabilistic properties of two classes of ranked labeled species trees, focusing on the presence or avoidance of certain subtree patterns associated with the production of ARGTs. We provide exact enumerations and asymptotic estimates for cardinalities of these sets of trees, showing that as the number of species increases without bound, the fraction of all ranked labeled species trees that are ARGT-producing approaches 1. This result extends beyond earlier existence results to provide a probabilistic claim about the frequency of ARGTs

Maximum likelihood estimation of species trees and anomaly zone detection using ranked gene trees

A phylogenetic tree represents the evolutionary relationships among a set of organisms. Gene trees can be used to reconstruct phylogenetic trees. The methods in this dissertation focus on the gene tree topologies with emphasis on ranked gene tree topologies. A ranked tree depicts the order in which nodes appear in the tree together with topological relationships among gene lineages. One challenge that arises during phylogenetic inference is the existence of the anomaly zones, the regions of branch-length space in the species tree that can produce gene trees that have topologies differing from the species tree topology but are more probable than the gene tree matching the species tree. In this work, we show how the parameters of a constant-rate birth-death process used to simulate species trees affect the probability that the species tree lies in the anomaly zone. We prove that the probability that a species tree is in an anomaly zone approaches 1 as the number of species and the birth rate go to infinity in a pure birth process. We propose a heuristic approach to infer whether species trees lie in the different types of anomaly zones trees when it is intractable to compute the entire distribution of gene tree topologies. In this dissertation, we develop the first maximum likelihood (ML) method that infers a species tree from the ranked gene trees. We introduce the software PRANC, which can compute the probabilities of ranked gene trees under the coalescent process and infer an ML species tree. We propose methods to estimate a starting tree to be able to locate the ML species tree quickly. To illustrate the methods proposed, we analyze two experimental studies of skinks and gibbons

Increased stress in Asiatic black bears relates to food limitation, crop raiding, and foraging beyond nature reserve boundaries in China

AbstractAsiatic black bears (Ursus thibetanus) are declining throughout much of their range. In China they are partially protected by a nature reserve system and rely heavily on hard mast as a food source prior to winter denning. Bears may compensate for mast shortages by raiding agricultural crops and killing livestock, mainly outside reserves where they are exposed to increased threats of poaching. We hypothesized that stress would vary with availability of high-quality refugia and fluctuations in mast abundance. We collected fecal samples from free-ranging bears in and around nature reserves in southwestern China, recorded habitat characteristics at each fecal sample location, and quantified abundance of hard mast. We used feces for genetic and endocrine analysis and identified 106 individuals. Feces collected outside reserves, or in agricultural fields within reserves, contained elevated concentrations of glucocorticoid metabolites compared to samples collected in intact, mast-producing forests within reserves. Relationships with habitat variables indicated that the hypothalamic–pituitary–adrenal (HPA) axis of the Asiatic black bear is responsive to human activity, abundance of hard mast, extent of forest cover, and quality of diet. Our findings demonstrate biological reactions of a large mammal to variable forest quality, human threats, and foraging relative to boundaries of protected areas

Dinoflagellate Genomic Organization and Phylogenetic Marker Discovery Utilizing Deep Sequencing Data

Dinoflagellates possess large genomes in which most genes are present in many copies. This has made studies of their genomic organization and phylogenetics challenging. Recent advances in sequencing technology have made deep sequencing of dinoflagellate transcriptomes feasible. This dissertation investigates the genomic organization of dinoflagellates to better understand the challenges of assembling dinoflagellate transcriptomic and genomic data from short read sequencing methods, and develops new techniques that utilize deep sequencing data to identify orthologous genes across a diverse set of taxa. To better understand the genomic organization of dinoflagellates, a genomic cosmid clone of the tandemly repeated gene Alchohol Dehydrogenase (AHD) was sequenced and analyzed. The organization of this clone was found to be counter to prevailing hypotheses of genomic organization in dinoflagellates. Further, a new non-canonical splicing motif was described that could greatly improve the automated modeling and annotation of genomic data. A custom phylogenetic marker discovery pipeline, incorporating methods that leverage the statistical power of large data sets was written. A case study on Stramenopiles was undertaken to test the utility in resolving relationships between known groups as well as the phylogenetic affinity of seven unknown taxa. The pipeline generated a set of 373 genes useful as phylogenetic markers that successfully resolved relationships among the major groups of Stramenopiles, and placed all unknown taxa on the tree with strong bootstrap support. This pipeline was then used to discover 668 genes useful as phylogenetic markers in dinoflagellates. Phylogenetic analysis of 58 dinoflagellates, using this set of markers, produced a phylogeny with good support of all branches. The Suessiales were found to be sister to the Peridinales. The Prorocentrales formed a monophyletic group with the Dinophysiales that was sister to the Gonyaulacales. The Gymnodinales was found to be paraphyletic, forming three monophyletic groups. While this pipeline was used to find phylogenetic markers, it will likely also be useful for finding orthologs of interest for other purposes, for the discovery of horizontally transferred genes, and for the separation of sequences in metagenomic data sets

What, if anything, are species?

This book is an extended argument for abandoning the species rank. Instead, the author proposes that the rank of "species" be replaced by a pluralistic and multi-level view. In such a view, all clades including the smallest identifiable one would be named and studied within a phylogenetic context. What are currently called "species" represent different sorts of things depending on the sort of organisms and processes being considered. This is already the case, but is not formally recognized by those scientists using the species rank in their work. Adopting a rankless taxonomy at all levels would enhance academic studies of evolution and ecology and yield practical benefits in areas of public concern such as conservation. The Open Access version of this book, available at www.taylorfrancis.com, has been made available under a Creative Commons Attribution-Non Commercial-No Derivatives 4.0 license. KEY FEATURES • Proposes the replacement of restrictive species concepts with a pluralistic view • Suggests abandoning the formal taxonomic rank of "species" • Considers zoological, botanical, and microbiological aspects of the species level • Deals with practical issues such as conservation, inventories, and field guide

Cross-contamination explains "inter- and intraspecific horizontal genetic transfers" between asexual bdelloid rotifers

A few metazoan lineages are thought to have persisted for millions of years without sexual reproduction. If so, they would offer important clues to the evolutionary paradox of sex itself [1, 2]. Most "ancient asexuals" are subject to ongoing doubt because extant populations continue to invest 17 in males [3–9]. However, males are famously unknown in bdelloid rotifers, a class of microscopic invertebrates comprising hundreds of species [10–12]. Bdelloid genomes have acquired an unusually high proportion of genes from non-metazoans via horizontal transfer [13–17]. This well-substantiated finding has invited speculation [13] that homologous horizontal transfer between bdelloid individuals also may occur, perhaps even "replacing" sex [14]. In 2016, Current Biology published an Article claiming to supply evidence for this idea. Debortoli et al. [18] sampled rotifers from natural populations and sequenced one mitochondrial and four nuclear loci. Species assignments were incongruent among loci for several samples, which was interpreted as evidence of "interspecific horizontal genetic transfers". Here, we use sequencing chromatograms supplied by the authors to demonstrate that samples treated as individuals actually contained two or more highly divergent mitoc hondrial and ribosomal sequences, revealing cross-contamination with DNA from multiple animals of different species. Other chromatograms indicate contamination with DNA from conspecific animals, explaining genetic and genomic evidence for "intraspecific horizontal exchanges" reported in the same study. Given the clear evidence of contamination, the data and findings of Debortoli et al. [18] provide no reliable support for their conclusions that DNA is transferred horizontally between or within bdelloid species

An integrated study of earth resources in the State of California based on ERTS-1 and supporting aircraft data, volume 1

There are no author-identified significant results in this report