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
Christine L. Lambkin A B N , John W. H. Trueman C , David K. Yeates A , Kevin C. Holston D E , Donald W. Webb F , Martin Hauser D G , Mark A. Metz D H , Hilary N. Hill I J , Jeffrey H. Skevington K , Longlong Yang I L , Michael E. Irwin D M and Brian M. Wiegmann IA CSIRO Entomology, PO Box 1700, Canberra, ACT 2601, Australia.
B Queensland Museum, PO Box 3300, South Bank, Brisbane, Qld 4101, Australia.
C School of Botany and Zoology, Australian National University, Canberra, ACT 0200, Australia.
D Department of Natural Resources & Environmental Sciences, University of Illinois, 901 West Illinois Street, Urbana, IL 61801, USA.
E Research Division, Entomology, Swedish Museum of Natural History, PO Box 50007, SE-104 05 Stockholm, Sweden.
F Illinois Natural History Survey, Institute of Natural Resource Sustainability, University of Illinois, 1816 South Oak Street, MC-652, Champaign, IL 61820, USA.
G Department of Food and Agriculture, Plant Pest Diagnostics Branch, 3294 Meadowview Road, Sacramento, CA 95832-1448, USA.
H United States National Museum of Natural History, 10th and Constitution Avenue NW, Washington, DC 20013, USA.
I Department of Entomology, North Carolina State University, Raleigh, NC 27695-7613, USA.
J 16 N. Belle Grove Road, Catonsville, MD 21228, USA.
K Canadian National Collection of Insects, Agriculture and Agri-Food Canada, 960 Carling Avenue, K.W. Neatby Building Ottawa, ON K1A 0C6, Canada.
L The Hamner Institute for Health Sciences, 6 Davis Drive, PO Box 12137, Research Triangle Park, NC 27709-2137, USA.
M 15634 E. Wandering Creek Place,Vail, AZ 85641, USA.
N Corresponding author. Email: christine.lambkin@qm.qld.gov.au
Invertebrate Systematics 23(2) 171-191 https://doi.org/10.1071/IS08035
Submitted: 2 September 2008 Accepted: 9 April 2009 Published: 4 June 2009
Abstract
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.
Acknowledgements
We thank Olaf Bininda-Emonds (Carl von Ossietzky Universität, Oldenburg) for his assistance. We acknowledge the comments of Shaun Winterton (Queensland Department of Primary Industries and Fisheries, Brisbane) and Steve Gaimari (Californian Department of Forestry and Agriculture, Sacramento) on an early version of the manuscript. We thank two anonymous reviewers for useful and considered comments, Torsten Dikow (Field Museum of Natural History, Chicago) for suggesting TNT, and Claudia Arango (Queensland Museum, Brisbane) for guidance in use of the program. TNT was made available through sponsorship of the Willi Hennig Society. We are extremely grateful for permission to reproduce the excellent photographs taken by J. N. Dell, Georgia, USA; Peter Krogh, Kensington, MD; Nicole Lartigau, Tom Murray, Massachusetts, USA; Dr C. Riley Nelson, Brigham Young University, Utah, USA; Shaun Winterton, QDPIF, Australia; Cor Zonneveld, Netherlands; and the amazing digital illustration prepared by J. Marie Metz through funding from Therevid PEET and Schlinger Foundation. Support for this study was provided by CSIRO Entomology, the National Science Foundation’s Partnerships for Enhancing Expertise in Taxonomy project ‘Therevid PEET, Towards a World Monograph of the Therevidae (Insecta: Diptera) under award numbers NSF DEB 95-21925 and NSF DEB 99-77958’, the National Science Foundation’s Assembling the Tree of Life Project ‘Building the Dipteran Tree of Life: Cooperative Research in Phylogenetics and Bioinformatics of True Flies (Insecta: Diptera)’ award no. EF-0334948, the Schlinger Foundation, and the Queensland Museum. Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of the National Science Foundation or the Schlinger Foundation.
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