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1
Introduction
WHAT IS GENOMICS?
Genomics, or genome science, is "the study of the structure, content,
and evolution of genomes," including the "analysis of the expression and
function of both gene and proteins" (Gibson and Muse, 2002~. In this
context, genomics encompasses functional genomics (gene and protein
expression and function), structural genomics (analysis of the three-
dimensional structures of proteins), metabolomics (analysis of the
metabolites produced and consumed by a population of cells), and many
other "-omics" (e.g., ecogenomics, metagenomics, pharmacogenomics,
toxicogenomics). Genome sciences make use of, and are integrated by,
the related disciplines of bioinformatics and computational biology. These
genomic approaches offer global or near-global overviews of gene lists,
and gene and protein expression. Furthermore, genomic profiles enable
the exploration of the genetic content of organisms that cannot be studied
by classical genetic methods. The definitions of these and other special-
ized terms will be introduced at first use and are summarized in Box 1-1.
The major goal of this report is to suggest how these new genomic tech-
nologies can foster increased understanding of polar biology by allowing
novel types of studies that heretofore were not possible to conduct in
polar settings.
15
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16
INS ~ FO[~R BlO[OGy ~ ~ GENERIC Egg
CEOLOCIC AND CLIMATIC TRENDS THAT INELOENCED
EVOLOTION IN THE POLAR REGIONS
Me distinct geologic and climatic histories of He Arctic and Antarctic
have created To unique polar ecosystems that share some atb~utes
~h11e differing greatly in others. The Antarctic is a glaciated continent
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INTRODUCTION
17
surrounded by a cold, often ice-covered ocean, while the Arctic is a cold,
ice-dominated ocean surrounded by large, continental landmasses. The
geologic and climatic histories that led to these different environments set
the stage for the evolution of their respective biotas and disparate eco-
systems (Figure 1-1~.
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18
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INTRODUCTION
19
Antarctica and the Southern Ocean
A globe of the Earth some 250 million years ago would show the
continent we know as Antarctica today in the center of the vast super-
continent Pangaea. Over time, major rifting events fragmented the super-
continent until Antarctica developed its present shape. The rifting opened
seaways between major oceans and changed the ocean circulation around
the Antarctic continent. Throughout this time, Antarctica has remained
in the low southern latitudes and has been in a near-polar position for
roughly 100 million years (Lawyer et al., 1992~. Despite this polar posi-
tion, the climate was initially quite warm. Seas around the continent had
bottom-water temperatures ranging from 12 to 16°C (Kennett, 1977, 1982)
and supported a complex fish fauna typical of contemporary temperate
oceans (Eastman, 1991, 1993), while temperate vegetation flourished on
land (Francis, 1999~. These temperate climatic conditions ended dramati-
cally when rifting opened crucial oceanic passages, including the Tas-
manian Seaway (~35 Ma) and the Drake Passage (~25 Ma), and declining
atmospheric carbon dioxide levels combined to trigger profound Antarctic
cooling and the onset of rapid glaciation (DeConto and Pollard, 2003~.
The East Antarctic continent was likely glaciated for the first time
about 34 million years ago (Zachos et al., 2001), but ice extent initially was
probably quite variable (Barrett et al., 1987; DeConto and Pollard, 2003~.
Further cooling shifted East Antarctica into a persistently cold mode
(Demon and Hall, 2000) and allowed growth of the more dynamic West
Antarctic ice sheet (Alley and Bindschadler, 2001~. The general cooling
trend over tens of millions of years has been interrupted by important
reversals (e.g., Scherer, 2002~. Still, overall, the present polar ocean sur-
rounding Antarctica is the most severely and consistently cold marine
environment on Earth (Dewitt, 1971; Littlepage, 1965~.
Today, the footprint of global change is variable across Antarctica.
The Dry Valleys of McMurdo Sound have cooled by 0.7 degree per de-
cade between 1986 and 2000 (Doran et al., 2002~. The peninsula also is
experiencing significant warming, and several ice shelves on the Antarc-
tic Peninsula have retreated, some reduced to fragments of their original
size (Turner et al., 2002~. Some of these changes have been dramatic: ice
shelves breaking off ice bergs the size of small states or simply disinte-
grating over the course of weeks, as was the case for the Larsen B ice shelf,
where 3,250 km2 of shelf area disintegrated over a 35-day period begin-
ning in lanuary 2002 . The
temperature trend for much of the continent remains unresolved due to
the paucity of data (Turner et al., 2001~.
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20
FRONTIERS IN POLAR BIOLOGY IN THE GENOMIC ERA
The Arctic Ocean and its Surrounding Landmasses
While the geologic framework has had a clear influence on the Ant-
arctic environmental conditions, the tectonic control and the interconnec-
tions of major ocean basins in the Arctic are less well defined. When
growth of terrestrial ice sheets drew down sea level during the Quaternary,
and perhaps earlier, the shallows of the Bering Straits became exposed as
a land bridge connecting Asia and North America (Kennett, 1982), block-
ing direct circulation between the Pacific and Arctic Oceans. Continental
motions across the Atlantic Ocean shifted Eurasia and North America
apart, contributing to improved communication between the Arctic Ocean
and the Atlantic Ocean, while squeezing the Bering Straits and restricting
Arctic Ocean communication with the Pacific. Although profound effects
on oceanic circulation have resulted, the exact history is still unresolved
(Kennett, 1982; NRC, 1991; Aagard et al., 1999~.
Extensive glaciation of the Northern Hemisphere post-dated the
Antarctic glaciation by over 30 million years. The first major glaciation
probably occurred in the late Pliocene (Kennett, 1982) and was certainly
occurring by the Pliocene-Pleistocene boundary, about 2.5 million years
ago (Shackleton et al., 1984~. Since then, multiple cycles of ice sheet accu-
mulation and melting have occurred, on 40,000 year and then 100,000
year cycles, each dramatically altering the biogeography of both terres-
trial and marine organisms. These ice-sheet cycles appear to be driven by
cycles in Earth's orbit that control the seasonal distribution of the sun's
radiation (Clark et al., 1999~. The accompanying dramatic shifts included
climatic zones displaced as many as 20-30 degrees of latitude and large
fluctuations in ocean circulation patterns, sometimes over timescales of
just hundreds of years. Dramatic changes in global atmospheric tempera-
ture (5-8°C), called Dansgaard-Oeschger cycles, occurred at intervals of
1,000-3,000 years at least within the most recent glacial cycle (Iohnsen et
al., 1992; GRIP Members; 1993; Grootes et al., 1993; Taylor et al., 1993;
Raymo et al., 1998~. Moreover, transitions between climatic regimes have
been very abrupt; for example, approximately 50 percent of the tempera-
ture change associated with the last glacial period occurred in less than a
decade (Severinghaus et al., 1998; NRC, 2002~.
Today, the sea ice cover of the Arctic Ocean is in transition, losing
3 percent of the area of total ice cover and 7 percent of the area of multiyear
ice per decade during recent decades (Johannessen et al., 1999; Kerr, l999~.
The decline in sea ice extent is much greater than can be accounted for by
natural climate variation (Vinnikov et al., 1999~. Recent surface warming
and ice thinning in the Arctic may be caused by changes in the state of the
Arctic Oscillation mode of atmospheric circulation (Moritz et al., 2002~.
Global warming due to accumulation of anthropogenic greenhouse gases
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INTRODUCTION
21
may also be driving the shrinkage, directly or by influencing the Arctic
Oscillation. Observations by people indigenous to the Arctic confirm that
changes to both the marine and terrestrial ecosystems are occurring more
rapidly now than in the past (Krupnik and Jolly, 2002~.
PHYSICAL PARAMETERS THAT SHAPE
BIOLOGICAL PROCESSES
The Antarctic and the Arctic present physical parameters that shape
their biotic communities and processes, but as a result of their distinct
histories some of these parameters are similar and some are quite different.
S· ·1 · ~
1mllarlhes
· Both regions are cold, isolated, and subject to pronounced seasonal
cycles of temperature and daylength.
· Glaciers, icebergs, and sea ice profoundly influence the biogeo-
graphic distribution of organisms in both regions and provide novel eco-
logical niches for colonization.
· Thermal conditions in both polar regions have served as an effec-
tive barrier to colonization by temperate species, although global warm-
ing is reducing this barrier.
· Both regions are highly sensitive to anthropogenic impacts, such as
chlorofluorocarbon (CFC)-induced ozone holes.
Differences
· The Southern Ocean has been remarkably cold and stable for at
least 8 million years, whereas the Arctic Ocean cooled much more recently
(~2.5 Ma). This difference in thermal history may have led to differences
in breadth of thermal tolerance by Arctic and Antarctic organisms.
· Arctic surface air temperatures are more variable than those of the
Antarctic in annual, seasonal and daily timeframes and often may change
by 40-50°C over a few days or on the same date between years. Tolerance
of such rapid temperature variability may have driven the adaptive evo-
lution of Arctic organisms in ways that are not experienced by Antarctic
species.
· Riverine freshwater and sediment discharge to the Arctic Ocean
are substantial, whereas they are virtually nonexistent in the Antarctic.
· Delivery of glacial icebergs, melt water, and till is of greater import
to the Southern Ocean.
· The continental shelves of the Arctic Ocean are broad and rela-
tively shallow, whereas those of the Southern Ocean are narrow and deep.
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22
FRONTIERS IN POLAR BIOLOGY IN THE GENOMIC ERA
Thus different types of benthic habitats are available in the two polar
oceans.
· Surface lakes and permafrost are prominent features of Arctic land-
masses, whereas the Antarctic continent is covered by a massive ice sheet
that has isolated subterranean lakes.
· Given the predominance of ice in the Antarctic environment, the
terrestrial flora and fauna of the Arctic are more diverse.
· The Arctic is home to indigenous human populations. These people
have a long and close relationship to the environment and associated
biological resources and are affected when these resources change,
whether because of natural variability or anthropogenic influences.
EVOLUTION IN POLAR REGIONS
The genetic structures of northern populations, communities, and
species whether terrestrial or marine are the "genetic legacy" of rapid
Quaternary climate changes (Hewitt, 2000), and the genomes of boreal
species are expected to bear the signature of these changes. In the Antarc-
tic, by contrast, the evolution of marine species has been driven by a long
period of stable, low temperatures; and the relatively limited terrestrial
ecosystems have been shaped by temperatures considerably more severe,
but less variable, than those of the north. Indeed, the McMurdo Dry
Valleys have been studied as an analogue for potential life on Mars, and
subglacial Lake Vostok has been studied as model for possible life on
Europa. The key to understanding the mechanisms of biotic evolution in
the distinct polar regimes of the north and south lies in analysis of the
genomes of organisms from major taxa at the individual, species, popula-
tion, and community levels of biological organization.
EXAMPLES OF RESEARCH AREAS THAT COULD BE
ADDRESSED WITH GENOMIC TOOLS
The development of sophisticated technologies for genome analysis,
as well as other enabling technologies (such as remote sensing, and
nanoscale biosensors), promises to revolutionize our understanding of
polar organisms, communities, and ecosystems. Areas of research
(explored in depth in Chapter 2) that offer potentially valuable opportu-
nities include:
· Polar ecosystems and global warming. Climate modeling and direct
experimental measurement indicate that environmental change, includ-
ing warming, will be most extreme in the polar regions. New genetic and
genomic technologies, such as transcriptional profiling using microarrays
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INTRODUCTION
23
and protein turnover studies via two-dimensional electrophoresis and
mass spectrometry, can be leveraged to understand the impact of such
change on individual species and on community structure.
· Ecological impact of ultraviolet radiation. Due to the anthropogenic
ozone hole that forms over Antarctica each austral spring, terrestrial and
marine organisms of the photosphere experience levels of ultraviolet
radiation that are much higher than those that were present during the
evolution of these species. What are the impacts of this exposure on
organismal fitness and community structure? Microarrays, proteomics,
and metabolomics can be brought to bear to yield quantitative indicators
of ecological impact.
· Evolutionary mechanisms of adaptation to extreme environmental condi-
tions. What molecular, biochemical, and physiological mechanisms enable
polar organisms to survive, grow, reproduce, and indeed thrive, under
extreme cold conditions? Because the Arctic and Antarctic regions under-
went glaciation during different geological epochs (Pleistocene and
Miocene, respectively), comparison of adaptations in ecotypically equiva-
lent boreal and austral taxa will provide important insights into conver-
gent and divergent evolutionary adaptation. Other major environmental
variables that have influenced evolution in polar regions include the
extreme variability of annual light cycles and the dry conditions of the
Antarctic continent.
· Systematics of polar organisms. In many instances, the phylogenetic
relationships of polar organisms are poorly understood. Total-evidence
phylogenetics, which incorporates molecular, cytological, and morpho-
logical character sets, can be applied to resolve evolutionary ambiguities
and enhance our understanding of the origin and radiation of key taxo-
nomic groups. Analysis of whole genomes will greatly facilitate system-
atic studies of polar organisms.
· Gene flow. Measurement of gene flow between populations is criti-
cal to understanding evolutionary speciation. Allele-specific microarray
technology can be employed to determine the effect of gene flow between
populations on the rates and patterns of speciation in polar regions.
· Polar regions as extraterrestrial analogues. The cryptoendolithic and
lake-dwelling organisms of the McMurdo Dry Valleys have long been
recognized as potential analogues of life (if any) on Mars, just as perma-
frost formations in the Arctic provide useful frozen habitat analogues.
Similarly, the long-isolated (~20 million years), microbial communities of
Lake Vostok in Antarctica and the severely chilled microorganisms in
winter Arctic sea ice might serve as models for evaluating the potential
for life on Europa. Genome analyses of these organisms will provide us
with an understanding of their origins and of genetic traits that might be
expected in extraterrestrial life.
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24
FRONTIERS IN POLAR BIOLOGY IN THE GENOMIC ERA
· Polar biotechnology. The uniquely cold-adapted enzymes of polar
organisms provide numerous opportunities for biotechnological devel-
opment. Proteases that function at temperatures near 0°C are already
important for food processing and for cold-water detergent formulations.
One can envision that enzymes from polar organisms will have numerous
commercial applications where maintenance of low temperature is
required. Molecules that protect polar organisms against damage from
freezing also have important biotechnological applications.
Representative terms from entire chapter:
polar regions
