Ecological genomics of high altitude adaptation in Rufous-collared sparrows (Zonotrichia capensis)

Adaptation is among the most prominent subjects in evolutionary biology. Despite its ubiquity in nature, many details of how adaptation occurs in natural populations remain poorly understood. Of particular interest are the genes and biochemical pathways that underlie adaptive phenotypes and how plasticity in these systems contributes to adaptive evolution. In this dissertation, I address these questions by investigating the molecular genetic basis of high-altitude adaptation in the Rufous-collared Sparrow (Zonotrichia capensis), a species with a broad altitudinal distribution in the Andes. First, I examined the role that variable selection pressures along elevational gradients play in the population genetic structure of Z. capensis. I found that mitochondrial gene flow was severely reduced along elevational transects relative to latitudinal control transects. Nuclear gene flow, however, was not affected by the elevational gradient. These results suggest that natural selection constrains mitochondrial gene flow along elevational gradients. The mitonuclear discrepancy was consistent with local adaptation of mitochondrial haplotypes, highlighting the importance of metabolic pathways in high-altitude adaptation in Z. capensis. Second, I used a newly developed genomic tool, a zebra finch (Taeniopygia guttata) cDNA microarray, to measure variation in genome-wide patterns of gene expression between high- and low-elevation populations of Z. capensis. I found that nearly 200 genes, many of which were involved in metabolic processes, were differentially expressed when individuals were sampled at their native altitudes. A common garden experiment demonstrated substantial plasticity in gene expression, and these results suggest that plasticity in the biochemical pathways that underpin cold and hypoxia compensation in Z. capensis may mechanistically contribute to enabling its broad altitudinal distribution. Finally, I examined geographic variation in metabolic gene expression along an elevational gradient. Although metabolic adjustments are often involved in thermal stress response and temperature decreases linearly with elevation in the Andes, expression of metabolic genes was non-linearly related to elevation. These results suggest a decoupling of metabolic gene expression and local temperature regimes. This decoupling may have several explanations, but the most plausible seem to be related to either physiological tradeoffs between thermal stress and hypoxia compensation, or genetically encoded expression differences

Migration-selection balance and local adaptation of mitochondrial haplotypes in Rufous-Collared Sparrows (Zonotrichia Capensis) along an elevational gradient

Variable selection pressures across heterogeneous landscapes can lead to local adaptation of populations. The extent of local adaptation depends on the interplay between natural selection and gene flow, but the nature of this relationship is complex. Gene flow can constrain local adaptation by eroding differentiation driven by natural selection, or local adaptation can itself constrain gene flow through selection against maladapted immigrants. Here we test for evidence that natural selection constrains gene flow among populations of a widespread passerine bird (Zonotrichia capensis) that are distributed along an elevational gradient in the Peruvian Andes. Using multilocus sequences and microsatellites screened in 142 individuals collected along a series of replicate transects, we found that mitochondrial gene flow was significantly reduced along elevational transects relative to latitudinal control transects. Nuclear gene flow, however, was not similarly reduced. Clines in mitochondrial haplotype frequency were strongly associated with transitions in environmental variables along the elevational transects, but this association was not observed for the nuclear markers. These results suggest that natural selection constrains mitochondrial gene flow along elevational gradients and that the mitonuclear discrepancy may be due to local adaptation of mitochondrial haplotypes. © 2009 The Society for the Study of Evolution

Contributions of phenotypic plasticity to differences in thermogenic performance between highland and lowland deer mice

Small mammals face especially severe thermoregulatory challenges at high altitude because the reduced O2 availability constrains the capacity for aerobic thermogenesis. Adaptive enhancement of thermogenic performance under hypoxic conditions may be achieved via physiological adjustments that occur within the lifetime of individuals (phenotypic plasticity) and/or genetically based changes that occur across generations, but their relative contributions to performance differences between highland and lowland natives are unclear. Here, we examined potentially evolved differences in thermogenic performance between populations of deer mice (Peromyscus maniculatus) that are native to different altitudes. The purpose of the study was to assess the contribution of phenotypic plasticity to population differences in thermogenic performance under hypoxia. We used a common-garden deacclimation experiment to demonstrate that highland deer mice have enhanced thermogenic capacities under hypoxia, and that performance differences between highland and lowland mice persist when individuals are born and reared under common-garden conditions, suggesting that differences in thermogenic capacity have a genetic basis. Conversely, population differences in thermogenic endurance appear to be entirely attributable to physiological plasticity during adulthood. These combined results reveal distinct sources of phenotypic plasticity for different aspects of thermogenic performance, and suggest that thermogenic capacity and endurance may have different mechanistic underpinnings. Includes Supplementary material

Does adaptation to high altitude affect hypoxia-dependent structural plasticity of the placenta?

High altitude residence causes fetal growth restriction (FGR) during pregnancy in lowland mammals. Highland-adapted mammals do not experience this altitude-dependent FGR, suggesting that adaptation to altitude has produced some protective mechanisms. However, the specific mechanisms by which highland-adapted mammals preserve fetal growth at altitude remain unknown. We hypothesized that highland-adapted populations protect fetal growth through structural changes to the placenta that increase surface area for nutrient and gas exchange. We tested this hypothesis using deer mice (Peromyscus maniculatus), from populations native to low [400 m, Lincoln, NE] and high [4300 m, Mt. Evans, CO] altitudes. We predicted structural adaptation would occur via increases to the relative size of the labyrinth zone (LZ), the layer within the rodent placenta where nutrient and gas exchange occur. Placentas were collected from lowland and highland deer mice undergoing pregnancy under normoxia or hypoxia (60 kPa) to understand how hypoxia-dependent structural plasticity might interact with adaptive remodeling of the placenta (N = 5-7 per strain and treatment). Using immunohistochemistry, we quantified the size of each placenta zone. Our preliminary results show that highlanders have relatively larger placental arteries and LZs under both normoxia and hypoxia (P \u3c 0.05 in generalized linear mixed model), suggesting that blood delivery and area for exchange (as determined by the LZ size) may protect fetal growth in highlanders. Future work will pair histological characterization of placental structure with transcriptomics to guide a mechanistic understanding of how placentation constrains to fetal growth under hypoxia

Difference in Plumage Color Used in Species Recognition between Incipient Species Is Linked to a Single Amino Acid Substitution in the Melanocortin‐1 Receptor

This is the publisher's version, also available electronically from http://www.jstor.org/stable/10.1086/600084Many studies demonstrate that differences in mating signals are used by incipient species in recognizing potential mates or sexual competitors (i.e., species recognition). Little is known, however, about the genetic changes responsible for these differences in mating signals. Populations of the Monarcha castaneiventris flycatcher vary in plumage color across the Solomon Islands, with a subspecies on Makira Island having chestnut bellies and blue‐black upper parts (Monarcha castaneiventris megarhynchus) and a subspecies on neighboring satellite islands being entirely blue‐black (melanic; Monarcha castaneiventris ugiensis). Here we show that a single nonsynonymous point mutation in the melanocortin‐1 receptor (MC1R) gene is present in all melanic birds from one island (Santa Ana) but absent in all chestnut‐bellied birds from Makira Island, implicating this mutation in causing melanism. Birds from a second satellite island (Ugi) do not show the same perfect association between this MC1R variant and plumage color, suggesting an alternative mechanism for melanism on this island. Finally, taxidermic mount presentation experiments in Makira (chestnut) and Santa Ana (melanic) suggest that the plumage difference mediates species recognition. Assuming that the signals used in species recognition are also used in mutual mate choice, our results indicate that a single amino acid substitution contributes to speciation

Gene regulatory changes underlie developmental plasticity in respiration and aerobic performance in highland deer mice

Phenotypic plasticity can play an important role in the ability of animals to tolerate environmental stress, but the nature and magnitude of plastic responses are often specific to the developmental timing of exposure. Here, we examine changes in gene expression in the diaphragm of highland deer mice (Peromyscus maniculatus) in response to hypoxia exposure at different stages of development. In highland deer mice, developmental plasticity in diaphragm function may mediate changes in several respiratory traits that influence aerobic metabolism and performance under hypoxia. We generated RNAseq data from diaphragm tissue of adult deer mice exposed to (1) life-long hypoxia (before conception to adulthood), (2) post-natal hypoxia (birth to adulthood), (3) adult hypoxia (6–8 weeks only during adulthood) or (4) normoxia. We found five suites of co-regulated genes that are differentially expressed in response to hypoxia, but the patterns of differential expression depend on the developmental timing of exposure. We also identified four transcriptional modules that are associated with important respiratory traits. Many of the genes in these transcriptional modules bear signatures of altitude-related selection, providing an indirect line of evidence that observed changes in gene expression may be adaptive in hypoxic environments. Our results demonstrate the importance of developmental stage in determining the phenotypic response to environmental stressors. Includes supplementary materials

Contribution of a mutational hot spot to hemoglobin adaptation in high-altitude Andean house wrens

A key question in evolutionary genetics is why certain mutations or certain types of mutation make disproportionate contributions to adaptive phenotypic evolution. In principle, the preferential fixation of particular mutations could stem directly from variation in the underlying rate of mutation to function-altering alleles. However, the influence of mutation bias on the genetic architecture of phenotypic evolution is difficult to evaluate because data on rates of mutation to function-altering alleles are seldom available. Here, we report the discovery that a single point mutation at a highly mutable site in the βA-globin gene has contributed to an evolutionary change in hemoglobin (Hb) function in high-altitude Andean house wrens (Troglodytes aedon). Results of experiments on native Hb variants and engineered, recombinant Hb mutants demonstrate that a nonsynonymous mutation at a CpG dinucleotide in the βA-globin gene is responsible for an evolved difference in Hb–O2 affinity between high- and low-altitude house wren populations. Moreover, patterns of genomic differentiation between high- and low-altitude populations suggest that altitudinal differentiation in allele frequencies at the causal amino acid polymorphism reflects a history of spatially varying selection. The experimental results highlight the influence of mutation rate on the genetic basis of phenotypic evolution by demonstrating that a large-effect allele at a highly mutable CpG site has promoted physiological differentiation in blood O2 transport capacity between house wren populations that are native to different elevations