SNP Data Processing Tools Online

We recently released a new software package (shinyPhrynomics) for single nucleotide polymorphism (SNP) data analysis. The software package is a collection of R codes for transforming your SNP data matrix into various popular phylogenetic program formats, including RAxML, MrBayes, and SNAPP. Options for plotting data include summaries of genetic  variation and missing data.

These tools are available for download and via a friendly online graphical user interface.

Check out our new Software page for links to this and other data analysis tools and methods.

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2014 JMIH “Herp” Meetings, Chattanooga Tennessee

The annual JMIH “herp” meetings were held last week in Chattanooga Tennessee. JMIH2014 The meetings were great, and there were plenty of great talks by UW researchers. Jared Grummer won 1st runner-up in the HL Graduate Research Award competition for best student presentation. During the genomics session, Charles Linkem took his audience on a tour of the “anomaly zone” (a mythical place in phylogeny land where everything you do is wrong). Matt McElroy charmed everyone with his talk on thermal adaptation in Anolis lizards – the conclusion is that they’re hot.   Rachel Arnold’s talk on frog fish phylogeny (her dissertation work) was amazing. For those of  you who don’t know, I should have mentioned that fish people present at the herp meetings too.

The meetings ended on a high note late Monday night with the always entertaining SSAR auction. In case you missed the auction, you can watch me get outbid on a really expensive snake hemipene t-shirt. The t-shirt sold for $270!


We’re all looking forward to future herp meetings in Reno & KU in 2015, and New Orleans in 2016.

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Visiting Professor Dr. Caleb Ofori-Boateng


Dr. Ofori-Boateng at the University of Washington

The Leaché lab is hosting visiting professor Dr. Caleb Ofori-Boateng from Ghana. I first met Caleb in 2006 during a Conservation International Rapid Assessment Program survey of some forested regions in Ghana, and we’ve been collaborating ever since. Caleb recently won the prestigious Future for Nature Award for his conservation efforts to protect the last remaining populations of the critically endangered Togo slippery frog in Ghana. He is visiting the lab with funding from the  Zoological Society of London EDGE Fellowship Program.

There are only two isolated populations of this frog remaining in Ghana (the Atewa Hills and the Togo-Volta region), and Caleb is collecting molecular genetic data from samples that he collected from these populations to investigate their genetic diversity. In Ghana, Caleb has developed an outreach program dubbed “conservation evangelism,” in which he educates locals about the merits of conservation biology while they are congregated at church. He integrates his conservation message into a “sermon”, and because local people generally trust information provided by religious centers they are accepting of the conservation message.

Caleb conservation work has been quite successful. He lobbied to stop mining in the Atewa Hills, and his conservation evangelism outreach programs has helped reduce hunting pressure and human consumption of the Togo slippery frog. His current efforts are aimed at designating the Atewa Hills as a National Park, which would help protect the Togo slippery frog in the long-term, as well as other threatened species, including chimpanzees, the long-tailed pangolin, Geoffroy’s pied colobus, and the Nimba flycatcher.

Selected publications from Dr. Ofori-Boateng:
Ofori‐Boateng, Oduro, Hillers, Norris, Oppong, Adum, & Rödel. 2013. Differences in the effects of selective logging on amphibian assemblages in three West African forest types. Biotropica 45:94-101.

Adum, Eichhorn, Oduro, Ofori-Boateng, & Rödel. 2013. Two‐stage recovery of amphibian assemblages following selective logging of tropical forests. Conservation Biology 27:354-363.

Adum, Ofori-Boateng, Oduro, & Rödel. 2011. Re-discovery of the Giant West African Squeaker, Arthroleptis krokosua Ernst, Agyei & Rödel, 2008 (Amphibia: Anura: Arthroleptidae) in two forests of south-western Ghana with observations on the species’ variability and habitat preferences. Zootaxa 2744:34-38.

Hillers, Ofori-Boateng, Segniagbeto, Agyei, & Rödel. 2009. Assessment of the amphibians in the forests of southern Ghana and western Togo. Zoosystematics and evolution 85:127-141.

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New Lab Publications

The graduate and postdoctoral researchers in the lab have published some interesting papers this year:

Banbury BL, O’Meara BC. 2014. Reol: R interface to the Encyclopedia of Life. Ecology and Evolution DOI:10.1002/ece3.1109.

Oaks J. 2014. An Improved Approximate-Bayesian Model-choice Method for Estimating Shared Evolutionary History. BMC Evolutionary Biology 14:150.

Bryson Jr RW, Linkem CW, Dorcas ME, Lathrop A. 2014. Multilocus species delimitation in the Crotalus triseriatus species group (Serpentes: Viperidae: Crotalinae), with the description of two new species. Zootaxa 3826:475-496.

McElroy MT. 2014. Countergradient Variation in Locomotor Performance of Two Sympatric Polynesian Skinks (Emoia impar, Emoia cyanura). Physiological and Biochemical Zoology 87:222-230.

Harris RB, Birks SM, Leaché AD. 2014. Incubator birds: biogeographical origins and evolution of underground nesting in megapodes (Galliformes: Megapodiidae). Journal of Biogeography DOI:10.1111/jbi.12357.

Chavez AS, Maher SP, Arbogast BS, Kenagy GJ. 2014. Diversification and Gene Flow in Nascent Lineages of Island and Mainland North American Tree Squirrels (Tamiasciurus). Evolution 68:1094-1109.

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A new species of spiny lizard

sceloporus_newJared Grummer and Rob Bryson have described a new species, Sceloporus aurantius.  Their paper is published in Zootaxa. You can read an article on the discovery of the new species in the UW Daily.
Grummer & Bryson. 2014. A new species of bunchgrass lizard (Squamata: Phrynosomatidae) from the southern sky islands of the Sierra Madre Occidental, Mexico. Zootaxa 3790(3): 439–450.

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