Transcriptomic Variation and Plasticity in Rufous-collaredSparrows (Zonotrichia capensis) Along an Altitudinal

Gradient

Zachary A. Cheviron, Andrew Whitehead and Robb T. Brumfield

Introduction• High elevation is metabolically challenging• Constant energy production maintained

despite: • Reduced oxygen availability • Increased thermal stress

• Genetic changes that alter transcript abundance are a possible route for adaptive evolution

•Adaptive role of transcriptional variation in high- altitude environments is largely unexplored.

Rufous-collared Sparrow (Zonotrichia capensis)

• Very broad, continuous distribution along Pacific slope of Peruvian Andes on altitudinal gradient • Sea level to > 4600 m

• Gene flow reduced along altitudinal gradient• Individuals at 4500 m have lower critical

temperatures (temp at which metabolic resources must be used to maintain body temperature)

• Consistent with adaptation to cold, high-altitude habitats

Digital range map created by Ridgely et al. 2003 and downloaded from InfoNatura (2005).

Species Distribution and Sampling Sites

- Higher altitudes indicated with darker colors. - T, L, and H refer to Transplant, Low altitude, and High altitude sampling sites, respectively.

Left: Agricultural fields along the coast (100 m elev.). Middle: Arid montane scrub (2,000 m).

Right: Puna grassland (4,200 m).

Typical habitats along an elevational gradient on the western slope of the Andes in Peru

• Acclimation to stressful environments often associated with up-regulation of hormones and proteins. –Correlated with changes at transcription

level –Variation in protein expression accounts for

many acclimation mechanisms on physiological timescales.– Similar regulatory changes may also

contribute to adaptation over evolutionary timescales

Introduction

• Identify genes and biochemical pathways important for high-altitude stress compensation– Test for differences in gene expression between

populations in native high- and low-altitude environments

• Distinguish expression differences that are plastic in response to environment, fixed between populations, or interact between population and environment– ‘common garden’ experiment: High- and low-altitude

individuals transplanted to a single low-altitude site– Plastic transcriptional variation likely important in

acclimation responses – Fixed transcriptional variation may be heritable

and important in evolutionary adaptation

Objectives

Sample Site Selection

• High-altitude site ~ 4150 m a.s.l• Low-altitude site ~ 2000 m a.s.l.• Below alt. where physiological acclimation begins

• High- and low-altitude populations genetically differentiated

• Population sampled at 2000 m genetically indistinguishable from populations sampled near sea level

• Phylo-geographic break between high- and low-altitude populations at ~ 3800 m a.s.l.

Left: Outside La Oroya, Peru (4,100 m) in June. Right: Near Lircay, Peru (4,300 m) in February.

Rufous-collared Sparrows are non-migratory in this portion of their range, so seasonality adds physiological stress for high elevation individuals.

Two high-elevation field sampling sites in the central Andes during different seasons

• 4 treatment groups with 4 individuals in each – High-altitude native and High-altitude transplant – Low-altitude native and Low-altitude transplant

• Native treatments– Individuals captured, housed at ambient temp 1 - 4

days– Tissues sampled at native altitude

• Transplanted high-altitude treatment– individuals captured at high altitude– transplanted to low altitude– housed at ambient temp for 7 days– tissues sampled

Sample Collection and Experimental Design

Methods• Microarrays – sample gene expression of

many genes simultaneously– Used microarray chip from Zebra Finch– Achieved good binding with Rufous-collared

Sparrow tissues• Data Analysis – compared expression levels

among native groups and altitudinal transplants

• 259 cDNAs represent 188 unique annotated transcripts exhibited significant main effects of population of origin– Almost all up-regulated in high-altitude individuals

Results: Differential gene expression among treatment groups

Expression levels of 8 cDNAs exhibited significant main effects of sampling locality (native alt vs. transplanted alt)

333 cDNAs exhibited significant linear model main effects of population of origin without an interaction effect. (74 unannotated or did not generate significant sequence matches in database searches)

77 cDNAs had significant interactions between population of origin and sampling locality of these 77 cDNAs, 51 had significant population main effects

Results: Hierarchical Clustering Analysis• cDNAs cluster into 4 main groups based on

transcription patterns• Gene clusters 1 and 4 best defined high- and

low-altitude sample clusters– Primarily genes involved in metabolic processes, esp.

oxidative phosphorylation• Gene clusters 2 and 3– Genes relatively under-transcribed – Involved in protein synthesis

Hierarchical Clustering Analysis333 genes in 4 clusters

Gene ontology categories

Warmer colors = higher transcription

Results: Plasticity in expression of cDNAs with population effects

• None differentially expressed in the common garden• Suggests plasticity largely governs variation in

transcriptomic profiles among populations native to different altitudes

Plasticity patterns in gene expression for cDNAs with significant population of origin effectsPlasticity pattern No. of cDNAs Percentage

Group means not significantafter multiple test correction

61 18.3

1. Convergence towardsintermediate expression

184 55.3

2. Convergence towardsnative high altitude

86 25.8

3. Convergence towardsnative low altitude

2 0.6

• cDNAs divided into plasticity patterns based on Tukey HSD results• 99.2% cDNAs significantly different between native high- and native low-altitude groups

Plasticity patterns• Pattern 1 (convergence towards intermediate expression)– Native high- and low-altitude individuals different– Transplanted birds not different from each other or either

native group – Genes involved in metabolic processes• oxidative phosphorylation• citrate cycle• pyruvate metabolism

• Pattern 2: (convergence toward native high-alt. expression levels in transplanted birds)– Included several transcripts involved in immune response

signaling pathways– May be due to transplant-induced stress response

Discussion• 188 unique annotated transcripts differentially expressed between

populations at high and low altitude• Almost all up-regulated in high-altitude birds • These genes belong to relatively few gene ontology categories

– oxidative phosphorylation – oxidative stress response– protein biosynthesis – signal transduction

• Many of these genes involved in cold and hypoxic stress response or are targets of natural selection at high altitude in a wide range of other vertebrates

• Expression levels of differentially expressed genes were highly plastic

• No transcripts that were differentially expressed between individuals sampled at their native altitudes remained different in common environment

• Remarkable given short 1-week acclimation period• Results suggest great deal of plasticity in

transcriptomic profiles

Discussion

Gene ontology categories (determined using gene databases)

Gene ontology category Percentage of differentiallyexpressed transcripts

Metabolism 27.7

Protein synthesis 20.6

Signal transduction 9.4

Growth 7.3

Protein transport 6.1

Cell cycle 5.6

Oxidative stress response 3.9

Immune response 2.8

Protein catabolism 2.9

Hormone regulation 1.1

Stress response 1.1

Other 11.5

Differential gene expression between high- and low-altitude populations

• When challenged with cold stress, endotherms must increase metabolic heat production to maintain constant body temperature

• This response often mediated by an increase in metabolic rate, and thermogenic capacity has been shown to be under natural selection in high-altitude deer mice

• High-altitude rufous-collared sparrows have significantly greater cold tolerance than those from coastal populations

• Suggests cold adaptation could be mediated through increased metabolic thermogenic capacity

• Mean minimum temperature at high-altitude site in Feb ~ 1 °C (~ 10 °C colder than low altitude site)

• Genes up-regulated in high-altitude birds involved in – ATP production (ADP, ATP translocases and ATP synthases) – Citric acid cycle (malate dehydrogenase and isocitrate dehydrogenase)– Oxidative phosphorylation– 5 major complexes of electron transport chain

• Complex I — NADH dehydrogenase a 4, b 2, b 8, Fe-S• Complex II — succinate dehydrogenase• Complex III — cytochrome c• Complex IV — cytochrome c oxidase V1a • Complex 5 — F0 ATP synthase subunits d, f, and o, and F1 ATP synthase d

• Consistent with other examples of adaptation in fish, birds and rodents

Differential gene expression between high- and low-altitude populations

• Other genes upregulated with altitude– Two glycolytic enzymes – Several enzymes involved in minimizing ROS– 37 genes involved with protein synthesis – Several genes involved in ubiquitin-dependant

protein catabolism

Differential gene expression between high- and low-altitude populations

• Transcriptomic profiles of high-altitude birds more similar to those in response to cold exposure than to hypoxia – Suggests that for rufous-collared sparrows, cold may impose a

more severe physiological demand than hypoxia at high altitude• Consistent with physiological studies suggesting increased

cold resistance but not hypoxia resistance in high-altitude birds

• Number of genes involved in hypoxia response differentially expressed between high- and low-altitude individuals– a-globin producing genes– Preprocathepsin-D producing genes– Several other genes involved in nitric oxide – Suggests compensation for hypoxic stress as well

Differential gene expression between high- and low-altitude populations

Flexibility of transcriptomic response to environmental stressors in rufous-collared

sparrows may play a role in explaining its exceptionally broad altitudinal distribution.

Take home message

Additional Resources

Zachary Cheviron‘s Website: http://www.environment.ucla.edu/ctr/news/article.asp?parentID=3137

Database websites: • NCBI Gene database

http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene

• AmiGOhttp://amigo.geneontology.org