Molecular and Phylogenetics, Phylogeography and Conservation Genetics. My bread and butter research is molecular phylogenetics and all that that entails. Virtually all of my ARC funded research is to develop big molecular phylogenies and then use these phylogenies to answer cool evolutionary questions. My interests span higher level phylogenetics, species level phylogeography and also phylogenetic approaches to comparative biology and conservation genetics. At the moment I am involved in several large ARC funded projects on elapid snakes, myobatrachid frogs and phylogeography of Australian herps. I also am involved in two major "team" grants with international links: The ARC Network: Discovering the Past and Present to Shape the Future and the National Science Foundation Tree of Life Grant: AmphibiaTree.

Current and ongoing projects:

Molecular phylogenetics of Australian and African elapid snakes

Much of my recent phylogenetic work has been done on the venomous elapid snakes of the world, a group which includes virtually all of Australia's venomous terrestrial species, as well as the sea snakes, Afro-Asian cobras and the American and Asian coral snakes. This is a major project for which I received ARC funding. The project now involves a number of collaborators including Ian Scott, Mike Lee, John Scanlon, Wolfgang Wuster, Vimoksalehi Lukoschek, Ulrich Kuch, Ulrich Joger, Hans-Werner Herrmann. The venomous proteroglyphous or "elapid" snakes are a large and diverse component of the modern snake fauna. Comprised of 61 genera and more than 300 species, they represent approximately 10% of the world's living snake species and more than 50% of the world's taxa of venomous snakes. Largely because of their medical importance, elapid snakes have received considerable systematic attention. Diverse data sets have been employed to elucidate relationships among these snakes but despite this array of evidence, elapid relationships have been the subject of much disagreement at all taxonomic levels. I have been working on the phylogenetic relationships of elapid snakes of the world for almost 10 years and published a number of papers on the subject. Over the past few years we have been generating a huge mtDNA data set comprising approximately 4000 base pairs of data for about 120 species of elapid snakes - about 2/3 of the genera and about 1/3 of all elapid species. This data set helps address the origin of elapids, the relationships among the major clades, the origin of sea snakes and the phylogenetic relationships within the African elapids, the true sea snakes and Australo-Papuan elapids. I'm busy trying to write up all that work now.....Several of my students also are working on aspects of this project. My PhD student Vimoksalehi Lukoschek is about to submit a molecular phylogeny of sea snakes. Ulrich Kuch is nearing completion of a phylogeny of black snakes (genus Pseudechis) and Matt Morgan is working on a phylogeny for the genera Rhinoplocephalus and Suta.

Lukoschek, V, JS Keogh. 2006. Molecular phylogeny of sea snakes reveals a rapidly diverged adaptive radiation. Biological Journal of the Linnean Society 89: 523-539.

Keogh, JS, IAW Scott, C Hayes. 2005. Rapid and repeated origin of insular gigantism and dwarfism in Australian tiger snakes. Evolution 59:226-233.

Keogh, JS, IAW Scott, JD Scanlon. 2000. Molecular phylogeny of viviparous Australian elapid snakes: Affinities of 'Echiopsis' atriceps (Storr, 1980) and 'Drysdalia' coronata (Schlegel, 1837), with description of a new genus. Journal of Zoology (London) 252:317-326. PDF

Slowinski, J, JS Keogh. 2000. Phylogenetic relationships of elapid snakes based on cytochrome b mtDNA sequences. Molecular Phylogenetics and Evolution 15:157-164. PDF

Keogh, JS. 1999. Evolutionary implications of hemipenial morphology in the terrestrial Australian elapid snakes. Zoological Journal of the Linnean Society 125:239-278. PDF

Keogh, JS. 1998. Molecular phylogeny of elapid snakes and a consideration of their biogeographic history. Biological Journal of the Linnean Society 63:177-203. PDF

Keogh, JS, R Shine, S Donnellan. 1998. Phylogenetic relationships of terrestrial Australo-Papuan elapid snakes based on cytochrome b and 16S rRNA sequences. Molecular Phylogenetics and Evolution 10:67-81. PDF

Keogh, JS & SA Smith. 1996. Taxonomy and natural history of the Australian bandy-bandy snakes (Elapidae: Vermicella) with the description of two new species. Journal of Zoology (London) 240: 677-701.

"Popular" elapid stuff.....

Keogh, JS. 2003. Cobras, kraits, seasnakes, death adders, and allies (Elapidae). Grzimek's Animal Life Encyclopedia, 2nd Edition. Vol. 7, Reptiles, edited by M Hutchins, JB Murphy, N Schleger. Farmington Hills, MI: Gale Group. Pp. 483-499

Keogh, JS. 2002. Where did sea snakes come from? Nature Australia 27(5): 62-71.

Keogh, JS. 2000. Snake Penises. Nature Australia 26(9): 42-49.

Other snake stuff......

Keogh, JS, D Barker, R Shine. 2001. Heavily exploited but poorly known: Systematics and biogeography of commercially harvested pythons (Python curtus group) in Southeast Asia. Biological Journal of the Linnean Society 73:113-129. PDF

Wuster, W, B Bush, JS Keogh. M O'Shea, R Shine. 2001. Taxonomic contributions in the "amateur" literature: comments on recent descriptions of new genera and species by Raymond Hoser. Litteratura Serpentium 21:67-91.

Keogh, JS. 1996. Origin of the hemipenis retractor penis magnus muscles: Evidence for utility in snake systematics. The Snake 27:114-119.

Keogh, JS. 1996. Evolution of the colubrid snake tribe Lampropeltini, a morphological perspective. Herpetologica 52:406-416.

Molecular phylogenetics and biogeography of Australian Myobatrachid frogs

This is a major project for which I, Dale Roberts (UWA) and Phil Byrne received ARC funding. The project now involves several collaborators including Christine Hayes, Nicki Mitchell and Paul Doughty. The Family Myobatrachidae (22 genera, 120+ species), or "southern frogs" is wholly endemic to the Australo-Papuan region, represents 57% of the Australian frog fauna and displays more diversity in reproductive strategies than any other frog family. They display incredible diversity in egg deposition strategies, degree and nature of parental care, call structure, body size, clutch and egg size, metamorph size, egg physiology, and habitat use. We are in the process of building a robust molecular phylogeny for all species in this Family and in so doing provide the most comprehensive molecular phylogeny available for any group of frogs. Over the past couple of years Christine Hayes has been assemblying a mtDNA data set of approximately 5000bp for all species and about 170 individuals. This work is nearing completion and we then will start generating data from several nuclear genes. Once the phylogenetic work is done we will use this phylogeny to exploit existing ecological and behavioural data sets to provide powerful phylogenetic tests of hypotheses on the evolution of diverse reproductive strategies, call structure, sexual size dimorphism and sexual conflict (Phil Byrne), egg size and number (Nicki Mitchell) and larval morphology (Paul Doughty). In addition to this, Matt Morgan, one of my PhD students, is working on a detailed phylogeny for the frog genus Helioporus and using this data set to address broad biogeographic questions. I am linked in with a major National Science Foundation Tree of Life Grant called AmphibiaTree run by David Cannatella, David Hillis, David Wake, Marvalee Wake, James Hanken, Linda Trueb and Rafe Brown.

Read, K, JS Keogh, IAW Scott, JD Roberts, P Doughty. 2001. Molecular phylogeny of the Australian frog genera Crinia, Geocrinia and allied taxa (Anura: Myobatrachidae). Molecular Phylogenetics and Evolution 21:294-308. PDF

Molecular phylogeography and applications (conservation genetics, population genetics)

We are now doing a lot of phylogeography projects on a variety of animals, and this is the focus of another ARC Discovery grant. We are trying to move away from generating more "phylogeography of xxxx" papers and instead we are addressing specific biogeographic and evolutionary questions with phylogenetic data. We also are bridging the gap between population genetics and phylogeography by using both mtDNA and microsat data to look at very fine scale genetic structure. We also use phylogenetic techniques to address issues of conservation concern. We are working on lots of different things, so it's easier just to list them:

• Molecular phylogeny and phylogeography of the Australian water skinks, Eulamprus quoyi group - There are several projects under way here involving lots of people (Kate Hodges, former honours student, Lin Schwartzkoph, Ian Scott, Garry Peterson, Glenn Shea and Ross Sadlier). We have sequenced over 250 individuals from throughout the range and are continue to obtain more samples. The ultimate goal is to use this data to test alternative hypotheses for eastern Australian biogeography.
• Comparative phylogeography of southwestern Australian frogs - Danielle Edwards, one of my PhD students, co-supervised by Dale Roberts, is doing a huge project looking at several species of SW WA frogs using both mtDNA and microsatellite techniques.
• Fine scale phylogeography and conservation genetics of the endandred Corroborree Frog - Matt Morgan, one of my PhD students, is developing and using loads of microsats for this project and will use these data to look at micro-scale dispersal and gene flow and to inform the captive breeding program.
• Phylogeography and the evolution of mimicry in the eastern froglet, Crinia signifera - Beckie Symula, a PhD student of David Cannatella and David Hillis, is linked with our lab doing this work for her PhD.
• Molecular phylogeography and population genetics of broadheaded snakes, Hoplocephalus bungaroides and the sympatric small-eyed snake, Rhinoplocephalus nigrescens. In collaboration with Jonno Webb at the University of Sydney, we are developing microsats and using mtDNA to do a comparative study of gene-flow and paternity in these sympatric snakes.

Morgan, MJ, PG Byrne, C Hayes, JS Keogh. Microsatellite markers in the endangered Australian northern corroboree frog, Pseudophryne pengilleyi (Anura: Myobatrachidae) and amplification in other Pseudophryne species. Conservation Genetics. In Press.

Edwards, D., JD Roberts, JS Keogh. Impact of Plio-Pleistocene arid cycling on the population history of a southwestern Australian frog. Molecular Ecology. In Press.

Hodges, K, DM Rowell, JS Keogh. 2007. Remarkably different phylogeographic structure in two closely related lizard species in a zone of sympatry in south eastern Australia. Journal of Zoology, London. In Press.

Smith, W, IAW Scott, JS Keogh. Molecular phylogeography Varanus rosenbergi (Reptilia: Varanidae) and its conservation status in New South Wales. Systematics and Biodiversity. In Press.

Melville, J., S.Goebel, C Starr, JS Keogh, JJ Austin. 2007. Conservation genetics and species status of an endangered Australian dragon, Tympanocryptis pinguicolla (Reptilia: Agamidae). Conservation Genetics 8:185-195.

Pepper, M, P Doughty, JS Keogh. 2006. Molecular phylogeny and phylogeography of the Australian Diplodactylus stenodactylus (Gekkota; Reptilia) species-group based on mitochondrial and nuclear genes reveals an ancient split between Pilbara and non-Pilbara D. stenodactylus. Molecular Phylogenetics and Evolution 41:539-555.

Kuch, U, JS Keogh, J Weigel, LA Smith, D Mebs. 2005. Phylogeography of Australia's king brown snake (Pseudechis australis) reveals Pliocene divergence and Pleistocene dispersal of a top predator. Naturwissenschaften 92:121-127.

Chapple, DG, JS Keogh, MN Hutchinson. 2005. Substantial genetic substructuring in southeastern and alpine Australia revealed by molecular phylogeography of the Egernia whitii (Lacertilia: Scincidae) species group. Molecular Ecology 14:1279-1292.

Chapple, DG, JS Keogh, MN Hutchinson. 2004. Molecular phylogeography and systematics of the arid-zone members of the Egernia whitii (Lacertilia: Scincidae) species group. Molecular Phylogenetics and Evolution 33:549-561. PDF.

Keogh, JS, IAW Scott, C Hayes. 2005. Rapid and repeated origin of insular gigantism and dwarfism in Australian tiger snakes. Evolution 59:226-233.

Chapple, DG, JS Keogh. 2004. Parallel adaptive radiations in arid and temperate Australia: molecular phylogeography and systematics of the Egernia whitii (Lacertilia: Scincidae) species group. Biological Journal of the Linnean Society 83:157-173. PDF.

Wong, BMB, JS Keogh, DJ McGlashan. 2004. Current and historical patterns of drainage connectivity in eastern Australia inferred from population genetic structuring in a widespread freshwater fish Pseudomugil signifer (Pseudomugilidae). Molecular Ecology 13:391-401. PDF.

Keogh, JS, IAW Scott, M Fitzgerald, R Shine. 2003. Molecular phylogeny of the Australian venomous snake genus Hoplocephalus and conservation genetics of the threatened H. stephensii. Conservation Genetics 4:57-65. PDF

Scott, IAW, JS Keogh. 2000. Conservation genetics of the endangered grassland earless dragon Tympanocryptis pinguicolla (Reptilia: Agamidae) in Southeastern Australia. Conservation Genetics 1:357-363. PDF

Other phylogenetic projects on the horizon....

There are two other major projects that I am in the initial stages of developing. For a number of years I have been working with Martin Whiting on African flat lizards, genus Platysaurus. We have published one small phylogeny and are now looking for cash to do field work in Mozambique, Malawi and Tanzania to collect the remaining taxa. We will use this phylogeny to address various biogeographic issues in southern Africa and also the evolution of colour and signalling structure (see the behavioural ecology page). I am also about to embark on something totally new - a phylogeny of fiddler crabs with Pat Backwell! We are only getting going on this, but we intend to use it to take over the world. With Peter Harlow from the Toronga Zoo, I am also doing some phylogenetic work on inter-island relationships in the Fijian iguana, Brachylophus vitiensis to evaluate levles of divergence and possibilities for captive breeding.

Scott, IAW, JS Keogh, MJ Whiting. 2004. Shifting sands and shifty lizards: Molecular phylogeny and biogeography of African flat lizards (Platysaurus). Molecular Phylogenetics and Evolution 31:618-629. PDF.