Cold Antarctic Waters Research Articles

Vertical Convergence of Turbulent and Double-Diffusive Heat Flux Drives Warming and Erosion of Antarctic Winter Water in Summer

Abstract The seasonal warming of Antarctic Winter Water (WW) is a key process that occurs along the path of deep water transformation to intermediate waters. These intermediate waters then enter the upper branch of the circumpolar overturning circulation. Despite its importance, the driving mechanisms that mediate the warming of Antarctic WW remain unknown, and their quantitative evaluation is lacking. Using 38 days of glider measurements of microstructure shear, we characterize the rate of turbulent dissipation and its drivers over a summer season in the northern Weddell Sea. Observed dissipation rates in the surface layer are mainly forced by winds and explained by the stress scaling (r2 = 0.84). However, mixing to the base of the mixed layer during strong wind events is suppressed by vertical stratification from sea ice melt. Between the WW layer and the warm and saline circumpolar deep water, a subsurface layer of enhanced dissipation is maintained by double-diffusive convection (DDC). We develop a WW layer temperature budget and show that a warming trend (0.2°C over 28 days) is driven by a convergence of heat flux through mechanically driven mixing at the base of the mixed layer and DDC at the base of the WW layer. Notably, excluding the contribution from DDC results in an underestimation of WW warming by 23%, highlighting the importance of adequately representing DDC in ocean models. These results further suggest that an increase in storm intensity and frequency during summer could increase the rate of warming of WW with implications for rates of upper-ocean water mass transformation. Significance Statement Around Antarctica, the summer warming of the subsurface cold Antarctic Winter Water feeds the upper layer of the overturning circulation. This study aims to quantify the mechanisms that mediate the warming of Antarctic Winter Water. Our results reveal that the observed warming of this layer can be explained by both surface wind-driven mixing processes as well as double-diffusive convection occurring beneath the Winter Water layer. Understanding the role of these mechanisms is important for understanding the regions upper-ocean heat distribution, the rates of water mass transformation and how they might respond to changes in sea ice, stratification, and the overlying large-scale winds.

Distribution, hosts and long-term decline in abundance of the Patagonian lamprey inferred from diet assessment of albatrosses

Knowledge of lampreys during their marine phase is limited, and for the southern hemisphere species was gleaned from their predators (albatrosses) in the 1970s. Taking advantage of new methodologies and long-term data on predator diet and distributions, we infer diverse aspects of lamprey distribution and ecology. DNA analyses indicated that albatrosses at South Georgia prey on Patagonian lamprey Geotria macrostoma, originating from Argentina. Their core pelagic distribution when free swimming appears to be the Antarctic Polar Frontal zone (APFZ), and not South Georgia waters as assumed previously. If so, the APFZ would be the first known hotspot in abundance of an anadromous lamprey in oceanic waters. We could not identify a teleost fish that would be a likely host. Instead, we infer that the lamprey may prey on baleen whales, based on comparison of stable isotope ratios in lamprey with candidate host species, timing of appearance in albatross diets coincident with whale migrations, and circumstantial evidence (unexplained scarring recorded during the whaling era). We suggest that the lamprey do not tolerate cold Antarctic waters, and detach from southerly-migrating whales at the thermal boundary of the APFZ, where they become accessible to albatrosses in surface waters. Given strong evidence that relative importance of prey in seabird diets reflects availability in foraging areas, the steep decrease in the annual consumption of lamprey by albatrosses at South Georgia from > 550 tonnes in 1975–1976 and 1986, to very low levels in most years since 2012, is likely to indicate a major population decrease. Despite our unconventional means of assessing the population trend, there is a compelling case for listing of Patagonian lamprey at least as Near threatened by the International Union for the Conservation of Nature, and an urgent need to better understand anthropogenic threats in Argentina.

Living in the Extreme: Fatty Acid Profiles and Their Specificity in Certain Tissues of Dominant Antarctic Silverfish, Pleuragramma antarcticum, from the Antarctic Sound (Southern Ocean) Collected during the Austral Summer

The fatty acid profile of seven different organs (brain, gills, heart, muscles, gonads, liver, and gall bladder) of the lipid-rich Antarctic silverfish, Pleuragramma antarcticum, from the Antarctic Sound was studied. Qualitative and quantitative analyses of fatty acids were performed using gas chromatography with mass-selective and flame ionization detectors. It was seen that the muscles and gills differed from the other organs with the prevalence of saturated fatty acids, mainly due to 16:0 and 14:0 that may reveal their additional metabolic role in these organs for adaptation of the fish to the cold Antarctic waters. Monounsaturated fatty acids 18:1(n − 9) and 16:1(n − 7) were prevalent in the other organs of silverfish, especially their high content in the liver, reflecting the carnivorous feeding type (mainly adult ice krill) of the species and their dietary preferences in the austral summer. The high content of essential fatty acids, 22:6(n − 3) (14% of total fatty acids) found in the brain and 20:5(n − 3) (12% of total fatty acids) found in the muscles, highlights the functional significance of these lipid components in the studied tissues of fish. The results will improve the understanding of the functional value of individual fatty acids in terms of their organ specificity and the adaptation of the Antarctic silverfish to life in the frigid ice waters of the Antarctic pelagic ecosystem.

Recent Freshening, Warming, and Contraction of the Antarctic Bottom Water in the Indian Sector of the Southern Ocean

High saline and cold Antarctic Bottom Water (AABW) forms around the continental margin of Antarctica that ventilates into the global ocean. To study the recent changes in AABW, we have analyzed the in situ observations collected from Indian Ocean expeditions to the Southern Ocean during 2010, 2011, 2017, 2018, and 2020. A comprehensive analysis of these observations indicated recent freshening, warming, and contraction in the layer thickness of the AABW. Even though the AABW depicted inter-annual variability, it changed to moderately fresher and lighter water mass at the end of the recent decade. The characteristics of AABW exhibited a contraction in its layer thickness (∼50–120 m) during recent years. The water mass showed its freshening (∼0.002) and warming (∼0.04°C) tendency from 2018 to 2020. The recent warming (∼0.3°C) of Circumpolar Deep Water (CDW) near the Prydz Bay suggests enhanced melting of ice shelves. It is hypothesized that the combined influences of onshore intrusion of warm CDW, upper ocean warming, sea ice decline, wind forcing, polynya, and calving events possibly caused the freshening and reduction in the thickness of AABW. The continued changes in the ocean-atmospheric environmental conditions and the subsequent changes in the bottom water characteristics likely influence the global climate, overturning circulation, and the biogeochemical cycle.

Role of Chemosynthetic Thermophilic Communities on the Biogeochemical Cycles of Minerals in the Orca Seamount Area, Antarctica

The Orca Seamount is a submarine volcanic structure, located in a tectonic area of the Bransfield Strait, characterized by cortical extension and roll back-type subduction. Recent investigations have described the presence of hydrothermal activity and thermophilic microorganisms in this submarine volcano, raising questions regarding the role these microorganisms might play in the environment. The presence of hydrothermal activity interacting with cold Antarctic marine waters has probably exerted a great impact on the chemistry of the Orca Seamount area, providing different types of substrates capable to support complex microbial communities. In this work, we further study the Orca Seamount area with respect to the mineralogy present in this environment and the role microorganisms might play in the biogeochemical cycles. Here we show that the assemblage of minerals detected in the Orca Seamount area is like those commonly found in other hydrothermal environments, consistent with previous investigations reporting hydrothermal activity in this zone. Sulfur- and iron-bearing minerals in addition to inorganic soluble compounds are able to support chemosynthetic microbial communities inhabiting the Orca Seamount. The role of these microorganisms on the sulfur, iron, and carbon cycle is discussed and analyzed in the context of the mineralogy and conditions of the environment.

Historical abundance and distributions of Salpa thompsoni hot spots in the Southern Ocean and projections for further ocean warming

Abstract In contrast to Antarctic krill Euphausia superba, Antarctic salps (Salpa thompsoni) respond positively to warmer water temperatures and have the ability to create massive blooms under favourable conditions. Therefore, they can compete with krill for primary production. Over the last three decades, significant variability in S. thompsoni occurrence has been observed as a response to the environmental fluctuations of the Southern Ocean ecosystem (e.g. changes in sea surface temperature and ice‐cover shrinkage around the cold Antarctic waters). This study presents historical abundance data of salps from the south‐west Atlantic Sector of the Southern Ocean, covering a time span of 26 years. These data allow tracking of fluctuations in Antarctic salp abundance and their distribution with bottom depth, temperature, and ice conditions, aiming to reveal salp hot spots and to predict the future range of S. thompsoni distribution with upcoming climate warming in the next 50 years. Results showed the highest salp density in shallow shelf waters with ice cover and low temperatures between 1 and −1°C. In the studied area, S. thompsoni hot spots were located mostly around Elephant Island, but also the islands around Brensfield and Gerlache Straits, as well as to the south near the Bellingshausen Sea. Inferences made of future salp distribution suggest that the range of S. thompsoni will move southwards, enlarging their habitat area by nearly 500,000 km2, which may have significant implications on the whole Antarctic food web. The information presented herein may be used for Antarctic ecosystem management, protection, and conservation.

14C and 10Be dated Late Holocene fluctuations of Patagonian glaciers in Torres del Paine (Chile, 51°S) and connections to Antarctic climate change

Southern Hemisphere Holocene glacier chronologies are important for unraveling past climate change, mid-to-high latitude teleconnections, and regional to global climate forcing. At present, a significant number of glacier chronologies for Patagonia are based on 14C dating, which may afford only maximum- or minimum-limiting dates. Here, we combine geomorphology and stratigraphy with radiocarbon (14C) and beryllium-10 (10Be) surface exposure-age dating at three outlet glaciers, Zapata, Tyndall, and Pingo. These glaciers drain the southernmost tip of the Southern Patagonian Ice Field at Torres del Paine National Park, Chile (51°S). After an expansion that we date at 3200 yr. B.P., the Torres del Paine glaciers expanded to their last major Late Holocene maxima at 600 and 340 yr. B.P., with the final dated readvance after 190 yr. B.P. We use these data, together with other Patagonian glacier records, to define the early, mid and final glacial stages of the last millennium. These cold events were separated by warm conditions that allowed the Nothofagus forest to colonize deglaciated land. The presence of near-concurrent glacier fluctuations in Patagonia and Antarctic Peninsula indicates widespread cooling punctuated the Late Holocene, including the last millennium, across much of the extratropical Southern Hemisphere. We link this cooling to cold oceanographic-atmospheric conditions forced by a northern shift or intensification of the Southern Westerly Winds. Such scenario increased northward advection of cold Antarctic circumpolar water along western Patagonia and favored decreased upwelling of warm circumpolar deep water together with expanded sea ice around the Antarctic Peninsula.

Genome-wide analyses reveal drivers of penguin diversification.

Penguins are the only extant family of flightless diving birds. They currently comprise at least 18 species, distributed from polar to tropical environments in the Southern Hemisphere. The history of their diversification and adaptation to these diverse environments remains controversial. We used 22 new genomes from 18 penguin species to reconstruct the order, timing, and location of their diversification, to track changes in their thermal niches through time, and to test for associated adaptation across the genome. Our results indicate that the penguin crown-group originated during the Miocene in New Zealand and Australia, not in Antarctica as previously thought, and that Aptenodytes is the sister group to all other extant penguin species. We show that lineage diversification in penguins was largely driven by changing climatic conditions and by the opening of the Drake Passage and associated intensification of the Antarctic Circumpolar Current (ACC). Penguin species have introgressed throughout much of their evolutionary history, following the direction of the ACC, which might have promoted dispersal and admixture. Changes in thermal niches were accompanied by adaptations in genes that govern thermoregulation and oxygen metabolism. Estimates of ancestral effective population sizes (Ne ) confirm that penguins are sensitive to climate shifts, as represented by three different demographic trajectories in deeper time, the most common (in 11 of 18 penguin species) being an increased Ne between 40 and 70 kya, followed by a precipitous decline during the Last Glacial Maximum. The latter effect is most likely a consequence of the overall decline in marine productivity following the last glaciation.

Дослідження фронтальної структури поверхневих вод Південної Атлантики за даними попутних спостережень в листопаді – грудні 2018 р.

The purpose was identification the oceanic structures of the surface layer, which were crossed by the ship “More Sodruzhestva”, based on observations of temperature and salinity with high resolution, both in time and in space, during the transatlantic cruise in November-December 2018. Furthermore, the aim was to determine the geographical position of these structures, their ranges of variability and spatial gradients of the observed oceanographic characteristics. The research method consisted in a comparative analysis of the information obtained with the help one of the standard measuring systems used for continuous passing observations at the height of the summer of 2018 and information on the same areas obtained in previous years and reflected in the scientific literature. As a result, such oceanic structures as the Bengal Current, the Southern Subtropical Front, the Sub-Antarctic Front, and the zone of its confluence with the Antarctic Polar Front were identified. Spatial gradients characteristic of fronts were 6—10 times greater than gradients in the spaces between fronts. In areas of the transatlantic section in the western hemisphere, ranging in length from one and a half to two thousand nautical miles, there is a very great similarity between the variability of temperature and salinity, which are not physically interconnected. The correlation coefficient between them on one of the segments with a length of 1600 miles was 0.96. An explanation is given for this phenomenon. One of the conclusions is the assumption that this is not a rare event. It should be quite common in large areas of mixing warm, high-salt subtropical waters and much less salty, in cold Antarctic waters. This assumption must be verified. We show a good coincidenceof the results of our contact observations and satellite data.

Antarctic blackfin icefish genome reveals adaptations to extreme environments

Icefishes (suborder Notothenioidei; family Channichthyidae) are the only vertebrates that lack functional haemoglobin genes and red blood cells. Here, we report a high-quality genome assembly and linkage map for the Antarctic blackfin icefish Chaenocephalus aceratus, highlighting evolved genomic features for its unique physiology. Phylogenomic analysis revealed that Antarctic fish of the teleost suborder Notothenioidei, including icefishes, diverged from the stickleback lineage about 77 million years ago and subsequently evolved cold-adapted phenotypes as the Southern Ocean cooled to sub-zero temperatures. Our results show that genes involved in protection from ice damage, including genes encoding antifreeze glycoprotein and zona pellucida proteins, are highly expanded in the icefish genome. Furthermore, genes that encode enzymes that help to control cellular redox state, including members of the sod3 and nqo1 gene families, are expanded, probably as evolutionary adaptations to the relatively high concentration of oxygen dissolved in cold Antarctic waters. In contrast, some crucial regulators of circadian homeostasis (cry and per genes) are absent from the icefish genome, suggesting compromised control of biological rhythms in the polar light environment. The availability of the icefish genome sequence will accelerate our understanding of adaptation to extreme Antarctic environments.

Wind‐driven ocean dynamics impact on the contrasting sea‐ice trends around West Antarctica

AbstractSince late 1978, Antarctic sea‐ice extent in the East Pacific has retreated persistently over the Amundsen and Bellingshausen Seas in warm seasons, but expanded over the Ross and Amundsen Seas in cold seasons, while almost opposite seasonal trends have occurred in the Atlantic over the Weddell Sea. By using a surface‐forced ocean and sea‐ice coupled model, we show that regional wind‐driven ocean dynamics played a key role in driving these trends. In the East Pacific, the strengthening Southern Hemisphere (SH) westerlies in the region enhanced the Ekman upwelling of warm upper Circumpolar Deep Water and increased the northward Ekman transport of cold Antarctic surface water. The associated surface ocean warming south of 68°S and the cooling north of 68°S directly contributed to the retreat of sea‐ice in warm seasons and the expansion in cold seasons, respectively. In the Atlantic, the poleward shifting SH westerlies in the region strengthened the northern branch of the Weddell Gyre, which in turn increased the meridional thermal gradient across it as constrained by the thermal wind balance. Ocean heat budget analysis further suggests that the strengthened northern branch of the Weddell Gyre acted as a barrier against the poleward ocean heat transport, and thus produced anomalous heat divergence within the Weddell Gyre and anomalous heat convergence north of the gyre. The associated cooling within the Weddell Gyre and the warming north of the gyre contributed to the expansion of sea‐ice in warm seasons and the retreat in cold seasons, respectively.

Bottom contact behaviour by humpback whales in Brazilian waters: first underwater observations at Trindade Island

Few records of humpback whales (Megaptera novaeangliae) have been made in Brazilian oceanic waters. This article reports the first record of bottom contact behaviour by humpback whales in Brazilian waters and adds four new sightings of the species to Trindade, an island located 1160 km from the Brazilian coast. The bottom contact behaviour has been associated with moult and hygienic functions for some cetaceans. The change of water temperature, triggered by the migration from cold Antarctic waters to the warm tropical Trindade coast, could have accelerated the turnover of skin superficial layers and the moulting process to this humpback whale here reported. Despite such uncertain reason of the behaviour, this novel record comes to increase the behavioural repertoire for the humpback whales in Brazilian waters, may be possibly an additional cleaning strategy.

Intrusive layering of the Antarctic slope front

Cascading of cold Antarctic shelf water (ASW) initiates compensatory isopycnic upwelling of the warm Circumpolar Deep Water (CDW). The baroclinic/thermoclinic Antarctic slope front (ASF) is formed, and a mesoscale intrusive structure develops on the shelf edge and slope. Mesoscale processes when the ASF peaks are periodically accompanied by local baroclinic instability, which forms a smaller-scale intrusive structure. Therefore, the ASF is naturally subdivided into two layers according to the intrusion scales (vertical δН and horizontal L) and the horizontal parameters of the front (thermoclinity (T L)ρ and baroclinity γρ). Analysis of ASF intrusive layering due to the baroclinic factor supports the following conclusion: the higher the (T L)ρ of the ASF, the greater the intrusion intensity |δθ| (temperature anomaly amplitude), while an increase in γρ of the ASF leads to a decrease in intrusion scales δН and L. Frontal intrusions can be distinguished by a development degree. Regardless of the degree of development, all warm intrusions are characterized by vertical density stratification, while cold intrusions are characterized by density quasihomogeneity. According to field data, the ASF instability process is subdivided into four stages. When theASF is baroclinically unstable, the local baroclinic deformation radius Rd L of the front is close in magnitude to the horizontal scale L of the intrusions that form, and their characteristic vertical scale δH is close to the typical vertical scale of front instability.

Combination of At-Sea Activity, Geolocation and Feather Stable Isotopes Documents Where and When Seabirds Molt

Key facets of the foraging ecology of seabirds during the inter-breeding period still remain poorly understood because of the difficulty of studying them at sea, including during the energy-demanding moulting stage. Here, the extent to which three sympatric petrels (Antarctic and thin-billed prions, and blue petrel) from the subantarctic Kerguelen Islands modify their foraging ecology during moult was investigated using a combination of complementary tools, namely miniaturized saltwater immersion geolocators (GLS) and the isotopic method. Firstly, moulting behaviour was first characterized in the blue petrel, a reference species that is known to renew its plumage in autumn. GLS and feather stable isotopes (13C as a proxy of the birds’ foraging habitat) indicated that the post-breeding moult of blue petrel occurred in Antarctic waters. Importantly, activity recorders showed that moult was marked by a strong peak in time spent daily sitting on water, which thereafter declined to lower values during the remaining winter months. Secondly, the peak in time spent sitting on water was used as a proxy to characterize the contrasted moult strategies of the two prion species. As blue petrels demonstrated, thin-billed prions moulted during the post-breeding period in cold Antarctic waters where they fed primarily on low trophic level prey, most likely Antarctic krill (15N as a proxy of the birds’ diet). By contrast, Antarctic prions presented an unexpected pre-breeding moult of longer duration that took place further north, in warm subtropical waters. Interestingly, the two Antarctic moulting species, the blue petrel and thin-billed prion, renewed their plumage at the same time and within the same oceanic zone that is likely to be a previously undescribed hot spot of seabird diversity during the Austral autumn. The study contributes to a growing body of evidence that closely-related species exhibit various foraging strategies allowing ecological segregation and sheds new light on the poorly known critical moulting stage of seabirds.

Colonial life under the Humboldt Current System: deep sea corals from O Higgins I seamount

A benthic community constituted by an assemblage of at least four species of deep-sea corals collected in only one trawl carried-out on the summit of the O'Higgins I seamount, central Chile. The corals were collected in only one trawl carried-out during a Chilean-Japanese cruise onboard the R/V Koyo Maru in December 29, 2004. Presence of oxygenated and cold Antarctic Intermediate Water (>400 m depth) on the plateau was recorded under of the Equatorial Subsurface Water associated to the oxygen-minimum zone (OMZ, <1 mL O2 L -1 ). The biogeographic origin of the fauna evidenced a mix of Subantarctic and central Chile continental margin species. The assemblage is represented by two species of anthipatarians (Leiopathes sp. and Chrysopathes sp.), one unidentified species of Paragorgiidae and one species of Isididae (Acanella chilensis). The study demonstrated that deep-water corals of the O'Higgins seamount provide crucial habitat for commercially important crustacean exploited along continental margin off central Chile such as nylon shrimp (Heterocarpus reedi). This resource as well as some fishes such as alfonsino (Beryx splendens) and orange roughy (Hoplostethus atlanticus) could drawing the commercial fishing industry to these fragile areas poorly known Chilean marine benthic communities. Due to a strong economic pressure, fast actions for marine conservation of seamounts are required in Chile.

Miocene to Pliocene development of surface and subsurface temperatures in the Benguela Current system

The initiation of the Benguela upwelling has been dated to the late Miocene, but estimates of its sea surface temperature evolution are not available. This study presents data from Ocean Drilling Program (ODP) Site 1085 recovered from the southern Cape Basin. Samples of the middle Miocene to Pliocene were analyzed for alkenone‐based (U37K′, SSTUK) and glycerol dialkyl glycerol tetraether (GDGT) based (TEX86, TempTEX) water temperature proxies. In concordance with global cooling during the Miocene, SSTUKand TempTEXexhibit a decline of about 8°C and 16°C, respectively. The temperature trends suggest an inflow of cold Antarctic waters triggered by Antarctic ice sheet expansion and intensification of Southern Hemisphere southeasterly winds. A temperature offset between both proxies developed with the onset of upwelling, which can be explained by differences in habitat: alkenone‐producing phytoplankton live in the euphotic zone and record sea surface temperatures, while GDGT‐producing Thaumarchaeota are displaced to colder subsurface waters in upwelling‐influenced areas and record subsurface water temperatures. We suggest that variations in subsurface water temperatures were driven by advection of cold Antarctic waters and thermocline adjustments that were due to changes in North Atlantic deep water formation. A decline in surface temperatures, an increased offset between temperature proxies, and an increase in primary productivity suggest the establishment of the Benguela upwelling at 10 Ma. During the Messinian Salinity Crisis, between 7 and 5 Ma, surface and subsurface temperature estimates became similar, likely because of a strong reduction in Atlantic overturning circulation, while high total organic carbon contents suggest a “biogenic bloom.” In the Pliocene the offset between the temperature estimates and the cooling trend was reestablished.

Research Spotlight: Climate response to melting of the West Antarctic Ice Sheet

The West Antarctic Ice Sheet (WAIS) could collapse in the future as the rising sea level and warming climate destabilize the sheet. Previous studies have shown that melting of WAIS could contribute to several meters of global sea level rise over the next few centuries. Some studies have pointed to evidence that WAIS has collapsed in the past during previous interglacial periods, which could give clues to what might happen in the future. To gain additional insight into how the Earth's climate would respond to a collapse of WAIS, Menviel et al. simulated the effects on global climate and the carbon cycle of a massive meltwater discharge from the collapse of the ice sheet. They found that a large meltwater discharge into the Southern Ocean would lead to a substantial cooling of the Southern Ocean, causing a northward expansion of the sea ice margin. Southern Hemisphere westerly winds would intensify. Furthermore, the formation of cold Antarctic Bottom Water would be suppressed, and subsurface warming would take place in areas where Antarctic Bottom Water is formed under present‐day conditions. This subsurface warming would lead to positive feedback that would accelerate the melting of the ice sheet. (Paleoceanography, doi:10.1029/2009PA001892, 2010)

Observations of the Antarctic Slope Undercurrent in the southeastern Weddell Sea

The Antarctic Slope Front presents a dynamical barrier between the cold Antarctic shelf waters in contact with ice shelves and the warmer subsurface waters offshore. Two hydrographic sections with full‐depth current measurements were undertaken in January and February 2009 across the slope and shelf in the southeastern Weddell Sea. Southwestward surface‐intensified currents of ∼30 cm s−1, and northeastward undercurrents of 6–9 cm s−1, were in thermal‐wind balance with the sloping isopycnals across the front, which migrated offshore by 30 km in the time interval between the two sections. A mid‐depth undercurrent on February 23 was associated with a 130‐m uplift of the main pycnocline, bringing Warm Deep Water closer to the shelf break. This vertical displacement, comparable to that caused by seasonal variations in wind speed, implies that undercurrents may affect the exchanges between coastal and deep waters near the Antarctic continental margins.

A gene family-based method for interspecies comparisons of sequencing-based transcriptomes and its use in environmental adaptation analysis

We describe a new method for sequencing-based cross-species transcriptome comparisons and define a new metric for evaluating gene expression across species using protein-coding families as units of comparison. Using this measure transcriptomes from different species were evaluated by mapping them to gene families and integrating the mapping results with expression data. Statistical tests were applied to the transcriptome evaluation results to identify differentially expressed families. A Perl program named Pro-Diff was compiled to implement this method. To evaluate the method and provide an example of its use, two liver EST transcriptomes from two closely related fish that live in different temperature zones were compared. One EST library was from a recent sequencing project of Dissosticus mawsoni, a fish that lives in cold Antarctic sea waters, while the other was newly sequenced data (available at: http://www.fishgenome.org/polarbank/) from Notothenia angustata, a species that lives in temperate near-shore water of southern New Zealand. Results from the comparison were consistent with results inferred from phenotype differences and also with our previously published Gene Ontology-based method. The Pro-Diff program and operation manual can be downloaded from: http://www.fishgenome.org/download/Prodiff.rar.

Copious copies keep out the cold

ife in the sub-zero temperatures of the Southern Ocean requires special adaptation to extreme cold, and the notothenioid fish radiation—which dominates the biomass and species diversity of Antarctic fish—has provided textbook examples of molecular evolution and adaptation to thermal challenge. Previous studies have typically investigated single genes or phenotypes, such as antifreeze proteins, but in an exciting new survey, Chen et al. (2008) take a novel approach to characterizing the genome-wide changes in gene duplication and transcription, relating these to adaptation to the cold Antarctic waters. The broad implications and excitement generated by this research are because of its tripartite approach. First, the authors investigated the transcriptome of the cold-adapted fish Dissostichus mawsoni by sequencing cDNA libraries made from multiple tissues. Chen et al. (2008) used unnormalized libraries in order to quantify EST (expressed sequence tag) abundance, and this revealed a highly biased transcription pattern, beyond ordinary expectations for simple tissue specificity. They identified a small number of dominant transcripts in each tissue, and a transcriptional shift towards a functional theme that suggests an elevated stress response. Second, the frequency of recovery of gene transcripts was compared with published high-volume EST data sets for similar tissues in five model fish species (zebrafish, salmon, stickleback, mummichog and medaka). Over the 11 possible comparisons, 177 genes were found to be upregulated in D. mawsoni, of which 85 (48%) were already known to be upregulated with cold response in carp (Gracey et al., 2004). This result suggests that, not surprisingly, evolutionary adaptation to the Southern Ocean has co-opted some of the mechanisms that underlie typical physiological response to cold. Third, and importantly, the authors investigated the contribution of gene duplication to transcriptional upregulation, using a D. mawsoni cDNA microarray based on the EST data. They employed array comparative genomic hybridizations (aCGH) to compare gene copy number at 10 700 loci in three Antarctic and two non-Antarctic notothenioid fishes. Using a hybridization threshold ratio set for a single, known, gene duplication event between two of these species, Chen et al. (2008) identified 101 protein-coding genes for which the average hybridization ratio across the cold-adapted species was above this threshold—indicating likely gene duplication. These candidate loci include 15 with potential activity in cold response, and many that were also among those upregulated in D. mawsoni relative to temperate species according to the EST analysis (Figure 1). It is perhaps unusual to apply a threshold analysis technique to this experiment, as Chen et al. (2008) do, rather than a statistical analysis that is more appropriate to the hybridization design. A more rigorous statistical analysis of aCGH results would help to quantify hybridization variation within and between species and ecotypes (for example, Emerson et al., 2008). Even so, successful identification of copy number variation (CNV) here supports the microarray technique as a rapid, sensitive and cost-effective method to assay genome-wide CNV in less traditional model organisms. Together these experiments provide a tantalizing glimpse of the genome-wide changes accompanying adaptation and radiation in an extreme environment.