Scalable Species Tree Inference with External Constraints

Species tree inference under the multi-species coalescent (MSC) model is a basic step in biological discovery. Despite the developments in recent years of methods that are proven statistically consistent and that have high accuracy, large datasets create computational challenges. Although there is gener- ally some information available about the species trees that could be used to speed up the estimation, only one method, ASTRAL-J, a recent development in the ASTRAL family of methods, is able to use this information. Here we describe two new methods, NJst-J and FASTRAL-J, that can estimate the species tree given partial knowledge of the species tree in the form of a non-binary unrooted constraint tree.. We show that both NJst-J and FASTRAL-J are much faster than ASTRAL-J and we prove that all three methods are statistically consistent under the multi-species coalescent model subject to this constraint. Our extensive simulation study shows that both FASTRAL-J and NJst-J provide advantages over ASTRAL-J: both are faster (and NJst-J is particularly fast), and FASTRAL-J is generally at least as accurate as ASTRAL-J. An analysis of the Avian Phylogenomics project dataset with 48 species and 14,446 genes presents additional evidence of the value of FASTRAL-J over ASTRAL-J (and both over ASTRAL), with dramatic reductions in running time (20 hours for default ASTRAL, and minutes or seconds for ASTRAL-J and FASTRAL-J, respectively). Availability: FASTRAL-J and NJst-J are available in open source form at https://github.com/ RuneBlaze/FASTRAL-constrained and https://github.com/RuneBlaze/NJst-constrained. Locations of the datasets used in this study and detailed commands needed to reproduce the study are provided in the supplementary materials at http://tandy.cs.illinois.edu/baqiao-suppl.pdf.

Supertrees and the Tree of Life: generating a metaphylogeny for a diverse invertebrate family (Insecta:Diptera:Therevidae) using constraint trees and the parsimony ratchet to overcome low taxon overlap

The dipteran family Therevidae (stiletto flies) is cosmopolitan and has been the focus of many taxonomic and phylogenetic studies over the last 25 years. Despite this work, questions remain concerning the relationships between subfamilies, genera and generic groups and membership of those groups. We use the supertree method to produce an inclusive phylogeny for the family Therevidae from 24 phylogenetic studies using matrix representation with parsimony (MRP) analysis. The supertree method, one of the most common approaches to calculating globally inclusive phylogenies from smaller more exclusive analyses, produced the therevid metaphylogeny despite only 34% of the terminal taxa being found in more than one source tree. We describe a method for handling low taxon overlap in supertree analyses, in combination with the parsimony ratchet and constraint tree techniques. The supertree presented here is an overarching phylogenetic hypothesis of the Therevidae, incorporating extensive sampling of major lineages and summarising past phylogenetic work on the family. The inclusive metaphylogeny for 362 therevid taxa robustly retrieves the subfamilies Agapophytinae, Phycinae, Therevinae and Xestomyzinae, and the tribes Cyclotelini and Therevini. The Phycinae and Xestomyzinae form a clade, sister to the remaining Therevidae. The Australasian and South American Taenogera Kröber genus-group is monophyletic and sister to a clade of Therevinae and the Australian endemic Agapophytinae. The Therevinae consists of the Anabarhynchus Macquart genus-group of Australian, South American, New Caledonian and New Zealand taxa as sister to the non-Australasian ‘higher Therevinae’, which contains the tribes Cyclotelini and Therevini. The Therevini includes the Hoplosathe Lyneborg & Zaitzev, Litolinga Irwin & Lyneborg, Baryphora Loew, Pandivirilia Irwin & Lyneborg and Thereva Latreille generic-groups. MRP supertree methods can be used to produce inclusive metaphylogenies in situations where source trees have poor data overlap and low taxon overlap, and are therefore valuable in species-rich groups such as arthropods. These methods may be necessary for constructing the ‘Tree of Life’, representing phylogenetic relationships among the millions of known species. However, our analyses show that in situations of source tree conflict, MRP supertree analyses present only the majority signal. We also show that conflict between source trees can be hidden in MRP supertrees, thus our results emphasise the need to evaluate the resulting clades with reference to the source trees.

The ultrastructure of the spermatozoa of the worm lizard Amphisbaena alba (Squamata, Amphisbaenidae) and the phylogenetic relationships of amphisbaenians

We describe the ultrastructure of epididymal spermatozoa of Amphisbaena alba and make comparisons with spermatozoa of other squamates. The mature spermatozoon of A. alba is filiform and characterized by the following features: the acrosome is depressed in transverse section; the perforatorial base plate is absent; the perforatorial tip is pointed; the perforatorium is single; the epinuclear lucent zone is well developed; the midpiece is moderately long; the mitochondria are columnar, forming regular circlets interrupted by dense bodies in transverse section; the dense bodies are solid, arranged in regular rings and linear series; the nuclear shoulders are rounded; the nucleus is elongate; the endonuclear canal is absent; fibers 3 and 8 are enlarged; multilaminar membranes are absent; and the fibrous sheath is in the midpiece. A phylogenetic analysis of squamates using spermatozoon-ultrastructure characters resulted in 2415 equally parsimonious, largely unresolved trees. The use of a constraint tree derived from gross anatomical characters suggested that the Amphisbaenia is the sister-group of the Autarchoglossa. We conclude that to improve the resolution of phylogenetic hypotheses derived from spermatozoon-ultrastructure characters, the number of characters ought to be increased, and more investigations are necessary to ascertain the degree of intrafamilial variability.