MacManes-LabWelcome to the MacManes Lab

The lab’s primary research interests involve understanding the genomic architecture of complex phenotypes, and the development of algorithms and analytical pipelines for high-throughput sequence data. We explore study in a wide variety of taxonomic groups including desert mice, rock doves, poison dart frogs, spiders, birds, and ladybug beetles using functional and population genomics.

To understand adaptation to extreme heat and aridity in the desert mouse Peromyscus eremicus, I have constructed an environmental chamber that will replicate desert conditions. Through careful manipulation of environmental conditions (heat, humidity, water availability) coupled with precise measurement of physiological state and high-throughput genome-wide sequencing we’ll begin to better understand how these animals survive despite never drinking water. I’m always looking for talented students to help with all aspects of the project, from animal care to molecular lab work, to work analyzing sequence data. Please contact me if interested!

In addition to this project, I’m also involved in several other projects — Understanding the genomic architecture of color polymorphism in Dendrobatid Frogs (Poison Dart Frogs) and the genomics of social behavior in the rock dove to name a couple. I also work on some purely computational projects including continued development of the de novo transcriptome assembler Trinity, and other projects developing pipelines for the optimal analysis of Illumina sequence data.

See my Curriculum vitae for detailed info about me and my work. I’d love to hear from you! Please contact me with inquiries!



April2016: Submitted the PALADIN paper ( and the P. eremicus physiology paper (

March2016: Taruna’s Geosmithia genome paper is accepted! See the preprint here:
January2016: Taruna submitted the 1st chapter (Geosmithia genome assembly) of her thesis for publication and to bioRxiv!

December2015: The Lab has release the Oyster River Protocol For Transcriptome Assembly. The protocol is here, and the preprint here, the blogpost here.

December2015: Lindsay submitted the Harmonia transcriptome paper, and posted it on bioRxiv.

December2015: The MacManes lab has graduated it 1st students, Congrats Lindsay Havens and good luck with the new job!!

Sept2015: a RNAseq-ing a more integrative understanding of animal behavior!

July2015: Full NSF proposal submitted to the NSF with Kyle Summers and Rasmus Nielsen in support of the Ranitomeya project.

May2015: a Optimizing error correction of RNAseq reads!

April2015: Matt gave a talk at the Institut de Biologie Intégrative et des Systèmes. Université Laval Quebec.

April2015: Chris, Jenny and Kaelina presented at the UNH Undergraduate Research Conference!

April2015: Kaelina was awarded a very fancy summertime REAP fellowship to do summertime research

March2015: Matt was awarded a small Sea Grant Award to finish up the Mya genome.

February2015: The MacManes and Calisi Labs (Barnard College) together have been awarded a $1.1M NSF grant to study the neuroendocrine|neurogenomics of parental care.

February2015: Matt was interviewed for a Nature piece on social media!

February2015: Matt is giving a talk at East Carolina University

January2015: Kaelina has been admitted into the UNH honors program!!!!

January2015: The MacManes lab talks to the Oyster River Parents and Preschoolers group about science stuff!

January2015: 3 pre-proposals submitted to the NSF.. Mouse pop. genomics and 2 colab. projects on frogs and clams!

January2015: The MacManes lab has been invited to join the Oxford Nanopore minION Access Program! We\’ll work on mRNA sequencing.

January2015: Lauren, Lindsay, Kae, Taruna, and Matt are off to NYC for the Inaugural population genomics meeting!

December2014: The Whitepaper: New Frontiers for the Integrative Study of Animal Behavior is out, with contributions from Matt

December2014: MacManes Lab celebrates christmas with good news from the NSF!!!

November2014: MacManes Lab hosts 5th graders from local middle school to do ladybug experiments!

October2014: PUBLISHED: Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus

October2014: Proposal to the Army has been submitted in support of the desert mouse project.

August2014: 2 full NSF proposals submitted. One in support of poison dart frog genomics, the other for rock dove neuro-social-genomics.

June2014: The lab travels to Evolution 2014! Lauren, Lindsay, and Matt all present!

May2014: Matt invited to be a Guest Lecturer at the MSU NGS course this summer.

May 2014: Matt is presenting twice at Evolution 2014 – desert mice and trimming mRNA seq reads.

May 2014: Grad Students Lindsay and Lauren are both presenting posters at Evolution 2014

May 20, 2014: Undergrad Researcher Jenny Dickson has been awarded 2014 Undergraduate Research Conference Award of Excellence

April 2014: Undergrad researcher Chris Carroll has been awarded a Undergraduate Research Award (URA).