Positions

Research Areas research areas

Overview

  • The MacManes lab tl;dr. We use physiology and genomics to study the coolest mammal on the planet! Who so cool? It lives it's entire life without ever needing to drink water, and may never urinate!

    We are interested in understanding how adaptive evolution has shaped animal (mostly in mammals) diversity. We are particularly interested in physiology and genomics, and use real-time metabolic phenotyping and high-throughput sequencing technologies to better understand this. We have several ongoing projects all related to how animals survive in exceptionally harsh environments, like deserts. Our experimental setup allows us to house animals in the lab in desert conditions (hot and dry), but to manipulate everything else (for instance diet, water availability) and measure things like blood electrolytes, metabolic rate, and rate of water loss. We can link those measurements to gene expression and other genomic processes! Sound cool? You should join us!!
  • Selected Publications

    Academic Article

    Year Title
    2023 White-nose syndrome restructures bat skin microbiomes.Microbiology spectrum.  11:e0271523. 2023
    2023 When the tap runs dry: the physiological effects of acute experimental dehydration in Peromyscus eremicus.The Journal of Experimental Biology.  226:jeb246386. 2023
    2022 Correction: Disentangling environmental drivers of circadian metabolism in desert-adapted mice.The Journal of Experimental Biology.  225:jeb244281. 2022
    2022 Chromosome size affects sequence divergence between species through the interplay of recombination and selection.Evolution.  76:782-798. 2022
    2022 High total water loss driven by low-fat diet in desert-adapted mice 2022
    2022 Prolactin and prolactin receptor expression in the HPG axis and crop during parental care in both sexes of a biparental bird (Columba livia).General and Comparative Endocrinology.  315:113940. 2022
    2021 Disentangling environmental drivers of circadian metabolism in desert-adapted mice.The Journal of Experimental Biology.  224:jeb242529. 2021
    2021 Feather Gene Expression Elucidates the Developmental Basis of Plumage Iridescence in African Starlings.Journal of Heredity.  112:417-429. 2021
    2021 The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system.Molecular Ecology.  30:4039-4061. 2021
    2021 Limited Evidence for Parallel Evolution Among Desert-Adapted Peromyscus Deer Mice.Journal of Heredity.  112:286-302. 2021
    2021 Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference.BMC Ecol Evol.  21:43. 2021
    2021 Lord of the Diptera (and Moths and a Spider): Molecular Diet Analyses and Foraging Ecology of Indiana Bats in IllinoisFrontiers in Ecology and Evolution.  9. 2021
    2020 The Genome of the Softshell Clam Mya arenaria and the Evolution of Apoptosis.Genome Biology and Evolution.  12:1681-1693. 2020
    2020 A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses.Ecology and Evolution.  10:9721-9739. 2020
    2020 A linked-read approach to museomics: Higher quality de novo genome assemblies from degraded tissues.Molecular Ecology Resources.  20:856-870. 2020
    2020 Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent.Molecular Ecology.  29:1300-1314. 2020
    2020 Stress-mediated convergence of splicing landscapes in male and female rock doves.BMC Genomics.  21:251. 2020
    2020 Disentangling environmental drivers of circadian metabolism in desert-adapted mice 2020
    2020 Isolating the role of corticosterone in the hypothalamic-pituitary-gonadal genomic stress response 2020
    2020 Limited evidence for parallel evolution among desert adaptedPeromyscusdeer mice 2020
    2020 Signal, bias, and the role of transcriptome assembly quality in phylogenomic inference 2020
    2019 Divergent selection and drift shape the genomes of two avian sister species spanning a saline-freshwater ecotone.Ecology and Evolution.  9:13477-13494. 2019
    2019 Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus.BMC Evolutionary Biology.  19:85. 2019
    2019 Dynamic pigmentary and structural coloration within cephalopod chromatophore organs.Nature Communications.  10:1004. 2019
    2019 A novel CRISPR/Cas9 associated technology for sequence-specific nucleic acid enrichment.PLoS ONE.  14:e0215441. 2019
    2019 Comparative and population genomics approaches reveal the basis of adaptation to deserts in a small rodent 2019
    2019 Stress-mediated convergence of splicing landscapes in male and female Rock Doves 2019
    2018 Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.Molecular Biology and Evolution.  35:2913-2927. 2018
    2018 Sex-biased transcriptomic response of the reproductive axis to stress.Hormones and Behaviour.  100:56-68. 2018
    2018 The Oyster River Protocol: a multi-assembler and kmer approach for de novo transcriptome assembly.PeerJ.  6:e5428. 2018
    2018 Transcriptomic analyses reveal tissue-specific selection on genes related to apoptotic processes in the subterranean rodent,Ctenomys sociabilisMolecular Biology and Evolution2018
    2017 Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia.Genome Biology and Evolution.  9:3312-3327. 2017
    2017 Comparative Genomics of Color Morphs In the Coral Montastraea cavernosa.Scientific Reports.  7:16039. 2017
    2017 Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury.American Journal of Physiology: Renal Physiology.  313:F262-F272. 2017
    2017 PALADIN: protein alignment for functional profiling whole metagenome shotgun data.Bioinformatics.  33:1473-1478. 2017
    2017 Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic-pituitary-gonadal (HPG) axis.Scientific Reports.  7:45125. 2017
    2017 Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse, Peromyscus eremicus.Physiological Reports.  5:e13218. 2017
    2017 Severe acute dehydration in a desert rodent elicits a transcriptional response that effectively prevents kidney injury 2017
    2017 Sex-biased transcriptomic response of the reproductive axis to stress 2017
    2017 The Oyster River Protocol: A Multi Assembler and Kmer Approach Forde novoTranscriptome Assembly 2017
    2016 TRANSCRIPTOMIC RESOURCES FOR THE ROCKY INTERTIDAL BLUE MUSSEL MYTILUS EDULIS FROM THE GULF OF MAINEThe Journal of Shellfish Research.  35:435-465. 2016
    2016 Comparative genomics explains the evolutionary success of reef-forming corals.eLife.  5:e13288. 2016
    2016 De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease 2016
    2016 De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease 2016
    2016 Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill Sunfish.PLoS ONE.  11:e0167509. 2016
    2016 Characterization of a Male Reproductive Transcriptome for Peromyscus eremicus (Cactus mouse) 2016
    2016 Characterization of a male reproductive transcriptome for Peromyscus eremicus (Cactus mouse).PeerJ.  4:e2617. 2016
    2016 Characterizing the adult and larval transcriptome of the multicolored Asian lady beetle, Harmonia axyridis.PeerJ.  4:e2098. 2016
    2016 Characterizing the reproductive transcriptomic correlates of acute dehydration in males in the desert-adapted rodent,Peromyscus eremicus 2016
    2016 Comparative genomics of beetle-vectored fungal pathogens reveals a reduction in genome size and independent evolution of pathogenicity of two tree pathogens 2016
    2016 De novo genome assembly of Geosmithia morbida, the causal agent of thousand cankers disease.PeerJ.  4:e1952. 2016
    2016 PALADIN:Protein Alignment for Functional Profiling Whole Metagenome Shotgun Data 2016
    2016 Physiological and biochemical changes associated with acute experimental dehydration in the desert adapted mouse,Peromyscus eremicus 2016
    2016 Widespread patterns of sexually dimorphic gene expression in an avian hypothalamic–pituitary–gonadal (HPG) axis 2016
    2015 RNAseq-ing a more integrative understanding of animal behaviorCurrent Opinion in Behavioral Sciences.  6:65-68. 2015
    2015 Characterizing the Adult and Larval Transcriptome of the Multicolored Asian Lady Beetle, Harmonia axyridis 2015
    2015 Establishing evidenced-based best practice for the de novo assembly and evaluation of transcriptomes from non-model organisms 2015
    2015 Optimizing error correction of RNAseq reads 2015
    2014 Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse Peromyscus eremicus.PeerJ.  2:e642. 2014
    2014 On the optimal trimming of high-throughput mRNA sequence data.Frontiers in Genetics.  5:13. 2014
    2013 De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.Nature Protocols.  8:1494-1512. 2013
    2013 Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.GigaScience.  2:10. 2013
    2013 Improving transcriptome assembly through error correction of high-throughput sequence reads.PeerJ.  1:e113. 2013
    2013 On the optimal trimming of high-throughput mRNA sequence data 2013
    2012 Is promiscuity associated with enhanced selection on MHC-DQα in mice (genus Peromyscus)?PLoS ONE.  7:e37562. 2012
    2012 The social brain: transcriptome assembly and characterization of the hippocampus from a social subterranean rodent, the colonial tuco-tuco (Ctenomys sociabilis).PLoS ONE.  7:e45524. 2012
    2011 Museum genomics: low-cost and high-accuracy genetic data from historical specimens.Molecular Ecology Resources.  11:1082-1092. 2011
    2011 Museum genomics: low‐cost and high‐accuracy genetic data from historical specimensMolecular Ecology Resources.  11:1082-1092. 2011
    2011 Promiscuity in mice is associated with increased vaginal bacterial diversity.Naturwissenschaften.  98:951-960. 2011
    2010 When non-coding is non-neutral: the role of CHD1 gene polymorphism in sexing, in phylogenetics and as a correlate of fitness in birdsIBIS: The International Journal of Avian Science.  152:223-225. 2010
    2009 Isolation and characterization of polymorphic microsatellite loci from Octodon degus.Molecular Ecology Resources.  9:999-1001. 2009
    Hostile genomic takeover by transposable elements in the Strawberry poison frogGenome Biology

    Article

    Year Title
    2024 When the tap runs dry: The multi-tissue gene expression and physiological responses of water deprived Peromyscus eremicus. 2024
    2023 When the tap runs dry: The physiological effects of acute experimental dehydration in Peromyscus eremicus. 2023

    Conference Paper

    Year Title
    2020 Brain transcriptional profiles of alternative reproductive tactics in bluegill sunfishIntegrative and Comparative Biology. E184-E184. 2020
    2015 Brain Transcriptional Profiles of Male Alternative Reproductive Tactics and Females in Bluegill SunfishIntegrative and Comparative Biology. E347-E347. 2015

    Patent

    Year Title
    METHODS FOR SEQUENCING NUCLEIC ACID MOLECULES

    Teaching Activities

  • Doctoral Thesis Taught course 2023
  • Doctoral Thesis Taught course 2022
  • Doctoral Thesis Taught course 2022
  • Human Anatomy & Physiology II Taught course 2022
  • Human Anatomy & Physiology II Taught course 2022
  • Human Anatomy & Physiology II Taught course 2022
  • Doctoral Thesis Taught course 2021
  • Population Genetics Taught course 2021
  • Population Genetics Lab Taught course 2021
  • Genomics and Bioinformatics Taught course 2021
  • Doctoral Thesis Taught course 2020
  • Population Genetics Taught course 2020
  • Population Genetics Taught course 2020
  • Population Genetics Lab Taught course 2020
  • Doctoral Thesis Taught course 2020
  • Honors Senior Thesis Taught course 2020
  • Adv Rsrch Exp/MCBS Taught course 2019
  • Doctoral Thesis Taught course 2019
  • Honors Senior Thesis Taught course 2019
  • Population Genetics Taught course 2019
  • Population Genetics Lab Taught course 2019
  • Adv Rsrch Exp/MCBS Taught course 2019
  • Applied Bioinformatics Taught course 2019
  • Doctoral Thesis Taught course 2019
  • Honors Senior Thesis Taught course 2019
  • Investigations in Genetics Taught course 2019
  • Rsrch Exp/MCBS Taught course 2019
  • Doctoral Thesis Taught course 2018
  • Genomics and Bioinformatics Taught course 2018
  • Genomics and Bioinformatics Taught course 2018
  • Genomics and Bioinformatics Taught course 2018
  • Honors Senior Thesis Taught course 2018
  • Investigations in Genetics Taught course 2018
  • Rsrch Exp/MCBS Taught course 2018
  • Doctoral Research Taught course 2018
  • Doctoral Research Taught course 2018
  • Principles of Genetics Taught course 2018
  • Principles of Genetics/Honors Taught course 2018
  • Rsrch Exp/MCBS Taught course 2018
  • Undergrad Teaching Experience Taught course 2018
  • Doctoral Research Taught course 2017
  • Doctoral Research Taught course 2017
  • Field Experience Taught course 2017
  • Genomics and Bioinformatics Taught course 2017
  • Genomics and Bioinformatics Taught course 2017
  • Genomics and Bioinformatics Taught course 2017
  • Honors Senior Thesis Taught course 2017
  • Doctoral Research Taught course 2017
  • Principles of Genetics Taught course 2017
  • Doctoral Research Taught course 2016
  • Genomics and Bioinformatics Taught course 2016
  • Genomics and Bioinformatics Taught course 2016
  • Genomics and Bioinformatics Taught course 2016
  • Doctoral Research Taught course 2016
  • Honors Senior Thesis Taught course 2016
  • Principles of Genetics Taught course 2016
  • Principles of Genetics Taught course 2016
  • Rsrch Exp/MCBS Taught course 2016
  • Rsrch Exp/MCBS Taught course 2016
  • Senior Honors Thesis Taught course 2016
  • Undergrad Teaching Experience Taught course 2016
  • Doctoral Research Taught course 2015
  • Genomics and Bioinformatics Taught course 2015
  • Genomics and Bioinformatics Taught course 2015
  • Honors Senior Thesis Taught course 2015
  • Rsrch Exp/MCBS Taught course 2015
  • Senior Honors Thesis Taught course 2015
  • Investigations Taught course 2015
  • Investigations Taught course 2015
  • Principles of Genetics Taught course 2015
  • Rsrch Exp/MCBS Taught course 2015
  • Adv Rsrch Exp/MCBS Taught course 2014
  • Genomics and Bioinformatics Taught course 2014
  • Principles of Genetics Taught course 2014
  • Rsrch Exp/MCBS Taught course 2014
  • Rsrch Exp/MCBS Taught course 2014
  • Education And Training

  • A.A.S. Nursing, Broome Comm College
  • B.S. Natural Resources, University of Michigan
  • Ph.D. Integrative Biology, University of California - Berkeley
  • Full Name

  • Matthew MacManes