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Molecular Evolution of Cytochrome B in High- and Low-Altitude Deer Mice (Genus Peromyscus)

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Molecular Evolution of Cytochrome B in High- and Low-Altitude Deer Mice (Genus Peromyscus) Heredity (2009) 102, 226–235 & 2009 Macmillan Publishers Limited All rights reserved 0018-067X/09 $32.00 www.nature.com/hdy ORIGINAL ARTICLE Molecular evolution of cytochrome b in high- and low-altitude deer mice (genus Peromyscus) EJ Gering1, JC Opazo2 and JF Storz School of Biological Sciences, University of Nebraska, Lincoln, NE, USA Patterns of amino-acid polymorphism in human mitochon- of synonymous and nonsynonymous substitution rates to drial genes have been interpreted as evidence for divergent test for evidence of divergent selection between high- and selection among populations that inhabit climatically distinct low-altitude haplogroups of the deer mouse, Peromyscus environments. If similar patterns are mirrored in other broadly maniculatus. We also tested for evidence of divergent distributed mammalian species, then adaptive modifications selection among different species of Peromyscus that inhabit of mitochondrial protein function may be detected in different thermal environments. In contrast to the purported comparisons among locally adapted populations of a single evidence for positive selection on mitochondrial proteins in wide-ranging species, or among closely related species that humans and other nonhuman mammals, results of our tests have adapted to different environments. Here, we test for suggest that the evolution of cytochrome b in Peromyscus is evidence of positive selection on cytochrome b variation chiefly governed by purifying selection. within and among species of the ecologically diverse rodent Heredity (2009) 102, 226–235; doi:10.1038/hdy.2008.124; genus Peromyscus. We used likelihood-based comparisons published online 24 December 2008 Keywords: adaptation; cytochrome b; deer mouse; McDonald–Kreitman test; positive selection; Peromyscus Introduction This pattern is consistent with positive selection or a relaxation of purifying selection in the high-latitude The mitochondrial cytochrome b gene encodes an populations (Elson et al., 2004; Kivisild et al., 2006). A integral membrane protein component of the cytochrome second pattern that has emerged from phylogenetic bc1 complex, which catalyzes the redox transfer of analysis of human mtDNA variation is that physico- electrons from ubiquinone to cytochrome c in the chemically radical amino-acid substitutions are generally mitochondrial electron transport chain. As the efficiency more common in terminal branches of the haplotype of the electron transport chain governs key aspects of genealogies than in the older, internal branches (Moila- aerobic energy metabolism (reviewed by Rolfe and nen and Majamaa, 2003). This pattern further suggests a Brown, 1997), several investigators have suggested that history of purifying selection against mildly deleterious functional modifications of redox proteins, such as amino-acid variants and is consistent with a commonly cytochrome b, may be involved in physiological adapta- observed excess of low-frequency amino-acid poly- tion to different thermal environments (Mishmar et al., morphisms in mitochondrial genes of humans and other 2003; Ruiz-Pesini et al., 2004; Fontanillas et al., 2005). For animals (Nachman et al., 1996; Hasegawa et al., 1998; example, Mishmar et al. (2003) and Ruiz-Pesini et al. Nachman, 1998; Rand and Kann, 1996, 1998; Fry, 1999). (2004) argued that patterns of amino-acid polymorphism However, in human mtDNA haplogroups that are in human mitochondrial genes reflect a history of local characteristic of temperate and Arctic regions, a sig- adaptation to different climatic regimes. Global surveys nificantly disproportionate number of physicochemically of nucleotide variation in human mitochondrial genes radical amino-acid substitutions were concentrated in show that ratios of nonsynonymous to synonymous the internal branches of the haplotype genealogies, a substitution rates are significantly higher in European/ pattern consistent with a history of lineage-specific temperate and Asian (Siberian)/Arctic haplogroups than positive selection (Ruiz-Pesini et al., 2004). In cytochrome b in the African/tropical haplogroups (Mishmar et al., haplogroups characteristic of north-temperate Eurasia, 2003; Ruiz-Pesini et al., 2004; but see also Sun et al., 2007). Ruiz-Pesini et al. (2004) identified physicochemically radical substitutions in highly conserved coenzyme Q Correspondence: EJ Gering, Section of Integrative Biology, The University (CoQ)-binding sites. As the CoQ-binding sites of of Texas at Austin, 1 University Station C0930, Austin, cytochrome b play a critical role in the complex III Q TX 78712, USA. cycle, these substitutions may influence the allocation of E-mail: [email protected] energy derived from oxidative phosphorylation to 1Current address: Section of Integrative Biology, University of Texas, metabolic heat production. 1 University Station C0930, Austin, TX 78712, USA. If patterns of amino-acid polymorphism in human 2Current address: Instituto de Ecologia y Evolucion, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile. mitochondrial genes reflect a history of divergent Received 19 March 2008; revised 11 November 2008; accepted 21 selection among populations that inhabit climatically November 2008; published online 24 December 2008 distinct environments, as suggested by Mishmar et al. Cytochrome b evolution in Peromyscus EJ Gering et al 227 (2003) and Ruiz-Pesini et al. (2004), then it stands to lineages that are at present regarded as subspecies reason that parallel patterns of adaptive variation may be of P. maniculatus (Carleton, 1989; Hogan et al., 1993; observed in other broadly distributed mammalian Dragoo et al., 2006). species that inhabit a similar diversity of thermal For analyses of cytochrome b variation among different environments. Modifications of mitochondrial protein species of Peromyscus, we used a total of 38 sequences function may be evident in comparisons between locally representing 26 nominal species with diverse altitudinal adapted populations of a wide-ranging species, or and latitudinal ranges (Table S2, Supplementary material between closely related species that have adapted to online). This set of species was selected with the goal of different environments. maximizing phylogenetic coverage, while maintaining a Here, we test for evidence of positive selection on relatively even distribution of branch lengths in the cytochrome b variation within and among species of the reconstructed tree. In the cases of P. betae, P. boylii, ecologically diverse rodent genus, Peromyscus. Mice in P. maniculatus and P. truei, we included specimens that the genus Peromyscus inhabit an extremely diverse range were representative of multiple, genetically distinct of habitat types, ranging from alpine and subarctic subspecies because physiological traits that may be environments to subtropical cloud forests in Central influenced by efficiency of the electron transport chain America (Hall, 1981; Carleton, 1989). An appreciable are known to vary at the intraspecific level (Cook and fraction of this environmental heterogeneity is also Hannon, 1954; Chappell and Snyder, 1984; MacMillen contained within the range of the most widely distrib- and Garland, 1989; Storz, 2007). uted species in the genus, Peromyscus maniculatus (Hall, As explained below (see Results), the species-level and 1981). As might be expected, this ecological variation genus-level phylogeny reconstructions both showed that within and among Peromyscus species is mirrored by P. melanotis was basal to a monophyletic group that extensive variation in basal metabolic rates and thermal comprised the entire P. maniculatus species complex. We tolerances (MacMillen and Garland, 1989). therefore sequenced cytochrome b from 13 additional If the highly conserved functions of the electron P. melanotis specimens (Table S1, Supplementary material transport chain have undergone adaptive modifications online) for the purpose of making outgroup comparisons in human populations that have colonized cold, high- with P. maniculatus in McDonald–Kreitman tests latitude environments within the last 10 000–50 000 years, (McDonald and Kreitman, 1991). then similar modifications of redox proteins, such as cytochrome b, may be evident in Peromyscus species or PCR and sequencing subspecies that have inhabited high altitude or high Genomic DNA was isolated from tissue samples with latitude environments for much longer periods of the DNeasy Tissue Kit (Qiagen Inc., Valencia, CA, USA) evolutionary time. In addition to differences in the likely according to the manufacturer’s specifications. We timescale of environmental adaptation, species like amplified the cytochrome b gene using the primers P. maniculatus are characterized by much larger effective Cytochrome-b 15334L (50-CTTCATTTTTGGTTTACAA population sizes than humans, so weak selection on GAC-30) and L14724 (50-TGATATGAAAAACCATCG amino-acid variation is more likely to dominate drift. TTG-30) with a 5 min denaturing period (95 1C) followed To test for evidence of divergent selection on cyto- by 30 cycles of denaturing (94 1C Â 30 s), annealing chrome b variation in deer mice, we compared ratios of (55 1C Â 30 s) and extension (72 1C Â 60 s). PCRs were synonymous and nonsynonymous substitution among performed using 2.5 mlof10Â Buffer II (Applied the branches of species- and genus-level cytochrome b Biosystems, Foster City, CA, USA), 2.5 mlof25mM phylogenies. To test for evidence of divergent selection MgCl , 2.5 mlof10mM dNTPs (2.5 mM each, dATP, within P. maniculatus, we also made
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