Review
Southern Ocean diversity: new
paradigms from molecular ecology
A. Louise Allcock1 and Jan M. Strugnell2
1
Department of Zoology and Ryan Institute, National University of Ireland Galway, University Road, Galway, Ireland
2
Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, VIC 3086, Australia
Southern Ocean biodiversity reflects past climate,
oceanographic, and tectonic changes. Molecular data
from contemporary populations carry signatures of these
processes. Here, we review new molecular studies on
Southern Ocean benthic fauna. Many of these studies
focus on species with extensive geographic or bathymet-
ric distributions, and resolve taxonomic questions.
Reviewing all available data, we show that, in addition
to reflecting life-history characteristics, the molecular
signals found in these studies provide an insight into
how species survived the last glacial maximum (LGM).
We identify molecular signatures that are characteristic of
surviving glacial cycles in small refugia on the continental
shelf and distinguish them from molecular signatures
that are indicative of surviving glacial cycles in the deep
sea.
Environmental pressures and their potential effects on
Southern Ocean biodiversity
One of the remarkable characteristics of the extant South-
ern Ocean fauna is that much of it appears to have survived
the massive disturbance caused by Pliocene–Pleistocene
glacial cycles in situ [1]. Benthic marine fauna (see Glos-
sary) would have been particularly vulnerable to the
impacts of glacial cycles because, at glacial maxima,
grounded ice sheets extended over much of the Antarctic
continental shelf, destroying the available habitat [2]. Ice
shelves extended even further and summer sea ice extend-
ed north of 608S [3] (Box 1, Figure I) and would have
restricted light penetration to the ocean below, thereby
limiting primary production. Nonetheless, fauna did sur-
vive, and new molecular data are now helping to elucidate
where and how.
Earlier authors proposed that the continental-shelf fau-
na was completely eradicated by glacial cycles [4] and
recolonized from the slope (e.g., [5]) or deep sea [6]. The
ability of organisms to prosper at a wide range of oceano-
graphic depths, known as eurybathy, has been championed
in support of recolonization of the shelf from deeper waters
following glacial maxima [7]. Eurybathy is one of the long-
held paradigms of Southern Ocean fauna. Indeed, the
deeper shelf of the Antarctic continent and the periodic
destruction of benthic habitat on the shelf might be natural
evolutionary drivers towards eurybathy. Other proposals
have been put forward that suggest that some fauna
survived on the continental shelf itself [2,7,8]. Ice-free
regions are known to have existed on a range of temporal
Corresponding author: Allcock, A.L. (louise.allcock@gmail.com)
520 0169-5347/$ – see front matter ß 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.tree.2012.05.009 Trends in Ecology and Evolution, September 2012, Vol. 27, No. 9
and spatial scales. Glacial models suggest that parts of
East Antarctica were permanently free of grounded ice
during the LGM [9]. There is also increasing evidence for
variation in the timing (diachrony) of ice-sheet formation
around the continent during the last glacial period; there-
fore, all areas might not have been glaciated at the same
time [9]. Ice-free polynyas, which can act as hotspots of
productivity, were probably widespread at the LGM [10]
and there is specific evidence for these on the continental
Glossary
Antarctic Circumpolar Current (ACC): bounded by the Subtropical Front to the
north and the Southern Boundary Front to the south, and enclosing the Polar
Front, this current flows in a clockwise direction around Antarctica and is one
of the largest currents in the world.
Benthic: on the sea floor.
Bottleneck: a massive reduction in population size that results in an associated
reduction of genetic diversity.
Brooder: an organism that protects its embryos on or near its body.
Cenozoic: the geological period extending from 65.5 million years ago to the
present.
Cryptic species: species that are genetically distinct but that have not
previously been distinguished morphologically.
Direct developer: an organism that has no larval dispersal stage and whose
hatchlings are miniature adults.
Eurybathy: distribution encompassing a wide range of water depths.
Founder event: the founding of a new population with a very small number of
individuals. The resulting population has a limited amount of genetic
variability.
Genetic drift: random changes in the frequency of alleles due to random
mating. Changes are more marked in very small populations.
Glacial refugia: small isolated regions where populations survived during
glacial maxima.
Haplotype network: method of visualizing the relations between DNA
sequences, usually using a simple measure of genetic difference, such as the
number of mutations between the sequences.
Katabatic wind: a wind driven by the descent of cold dense air from an
elevated area. In Antarctica, these winds descend from elevated ice-sheets and
glaciers.
Last glacial maximum (LGM): 26 500–18 000 years ago when ice sheets were at
the maximal extent seen during the last glacial cycle.
Orbital forcing: the effect on climate of slow variations in the orbital plain, axial
tilt and precession of the Earth, which affect the amount of insolation received.
Although it is not fully understood how the periodicities of these orbital
variations interact, they are thought to be responsible for the 100 000-year
glacial cycles that occurred during the late Cenozoic.
Planktotrophic: having a developmental mode with a larva that feeds in the
plankton and that can be dispersed on ocean currents.
Pleistocene: the geological epoch extending from 2 588 000 to 11 700 years
ago.
Pliocene: the geological epoch extending from 5 332 000 to 2 588 000 years
ago.
Polar front: marks the boundary between cold surface Antarctic waters and
warmer northerly waters and is one of several fronts found in the ACC.
Polynya: an area of ice-free sea surrounded by sea ice.
Rarefaction curves: an ecological concept that, when applied to genetic data,
usually provides information on the rate of discovery of new haplotypes or
statistical parsimony networks with increased sampling.
Review
shelf edge in the Weddell and Ross Seas at that time (Box 1)
[8]. It has been proposed that shelf refugia must have existed
in the Weddell Sea [11], off George V Land and off Adélie
Land [12], because the shallow-water faunas in these loca-
tions are substantially different from those found in deeper
waters [11,12]. Hence, these faunas are unlikely to have
resulted from recolonization of the continental shelf by
eurybathic species.
Studies in terrestrial ecosystems [13,14] and in freshwa-
ter [15] and marine environments [16] in the Northern
Hemisphere show that isolation into refugia during glacial
cycles often results in characteristic genetic signatures.
Dramatic population reduction results in a loss of diversity
and recovery from these ‘bottlenecks’ can leave molecular
evidence of rapid demographic expansion. Hence, studies of
phylogeography and molecular ecology could be helpful in
elucidating the role of refugia in shaping the biota of the
Southern Ocean. The early focus of population genetic stud-
ies was on charismatic megafauna, such as seals (e.g., [17])
and penguins (e.g., [18]), and commercial species of fish [19]
and krill [20]. Because these species are pelagic, the destruc-
tion of benthic habitat by glacial cycles is less likely to be
reflected in their DNA. Indeed, Convey et al. [1] reviewed the
effects of glacial history on Antarctic biota and found just
two studies [21,22] that helped elucidate the impact of
glacial cycles and the role of refugia in the marine realm.
However, the International Polar Year (IPY 2007–2008) and
a renewed focus on biodiversity through the Antarctic pro-
gram of the Census of Marine Life, CAML (Census of
Antarctic Marine Life), have led to coordinated sampling
and international cooperation. Consequently, a wealth of
molecular data has recently been published on Southern
Ocean marine invertebrates and it is these data that are
revealing the role of different refugia and providing new
understanding of Southern Ocean diversity patterns.
Molecular signatures indicative of refugia
Patterns of genetic diversity in the marine environment
have been investigated more widely in the Northern
Hemisphere, where molecular sequence data have also
been analyzed to investigate patterns of haplotype diver-
sity in marine areas affected by Pliocene–Pleistocene
glacial cycles [16]. During the LGM, ice sheets expanded
over the continental shelves in northern areas, causing
Box 1. The glacial history of the Southern Ocean
Glacial conditions first developed in Antarctica approximately
34 million years ago (Mya) [52]. Shortly afterwards (probably
approximately 30 Mya [53]), the deepening seaway through the
Drake Passage (Figure I), resulting from continental drift of South
America away from the Antarctic, facilitated development of the
ACC.
Orbital forcing has had a major role in Antarctic climate. Orbitally
forced fluctuations in ice-sheet volume have been detected between
34 Mya and 15 Mya [54] and a marked decline in temperature in the
mid-Miocene (c. 14 Mya), associated with a significant increase in ice-
sheet volume, also appears to have been at least partially driven by
orbital forcing [55]. Ice-core data [56] provide detailed temperature
records for the past 800 000 years, showing the 100 000-year
periodicity of glaciation cycles during this time. Sediment core data
suggest at least 38 cycles, of varying periodicity, over the past
5 million years [57].
Trends in Ecology and Evolution September 2012, Vol. 27, No. 9
major extinction events. Further south, continental
shelves were not covered by ice sheets and acted as refugia
for many northern species. Continental shelf habitat was
reduced in southern areas because water was incorporated
into expanding ice sheets, such that sea levels were as
much as 130 m below their interglacial levels [23]; how-
ever, although population sizes were reduced here, large
populations were maintained. Low haplotype diversity is
predicted in northern areas that suffered extinction
events and were recolonized from southern areas after
the LGM because colonizers bring a limited number of
alleles. However, Maggs et al. [16] also considered small
northern ice-free refugia in which populations could sur-
vive but in which they would suffer bottleneck events (i.e.,
the loss of genetic diversity associated with population
crashes). The authors were able to distinguish the genetic
signatures of recolonized northern areas from those of
northern refugia. The latter had more private alleles
(i.e., alleles unique to particular populations) as a result
of their isolation. Not surprisingly, southern refugial
areas that had maintained large populations throughout
the LGM, had higher levels of diversity compared with
northern refugial, or recolonized areas.
In the Southern Hemisphere, the patterns are likely to
be different as Antarctica comprises a single continental
landmass surrounded by deep sea. In the Southern Ocean,
organisms surviving the LGM in shelf refugia are likely to
show evidence of bottlenecks with one haplotype being
dominant. There should also be evidence of recent (after
the LGM) demographic expansion in the molecular data.
By contrast, eurybathic species, with the ability to survive
in deeper refugia off the shelf, are likely to show greater
diversity, because their population size will not have
been drastically reduced. Species that have recolonized
from sub-Antarctic islands are likely to exhibit very low
diversity because of the limited number of colonists (i.e., a
founder effect).
Evidence for continental-shelf refugia
The genetic signatures predicted above for continental-
shelf refugia are seen in several Southern Ocean species
[24,25]. When the relation between different haplotypes
is visualized with a haplotype network, many reveal a
‘star-like’ pattern (Figure 1a). Although there is high
Most evidence for the effects of glacial cycles comes from the last
glacial period. Glacialogical models suggest a massive advance of
Antarctic ice sheets during the LGM, a fall in global sea levels and a
grounding of ice sheets out across much of the continental shelf of
the Southern Ocean (e.g., [58]). However, it appears that the East and
West Antarctic ice sheets have not advanced and retreated in concert
[9] and ice-free areas of the continental shelves might have existed
even at glacial maxima. More recent data [8] derived from foramini-
feran assemblages in sediments from the northwest Weddell Sea
suggest the presence of areas of open water (polynyas) along the
continental margin during the LGM. Polynyas might have been
widespread on the continental shelf edges during the LGM and could
have been caused by katabatic winds. During interglacial periods, the
West Antarctic Ice Sheet might have collapsed on multiple occasions,
opening up a seaway between the Weddell and Ross Seas [59,60],
providing a potential route of recolonization.
521
Review Trends in Ecology and Evolution September 2012, Vol. 27, No. 9

0°

South
Georgia Glacial cycle variation in SSI limit.
Shag Rocks Cycle periodicity 41k and 100k years.
At least 38 cycles in the past
5 millions of years.
Scotia
Sea
South Orkney
Islands
Drake Passage

Kerguelen
Plateau
South
America
Weddell
Sea

Prydz
South
Bay
Shetland Potential seaway
Islands during West Antarctic
90°W Ice Sheet collapse East 90°E
Antarctic
West Antarctic Ice Sheet
Ice Sheet

Ross
Sea
George V
Key: Land
Sea Ice limits Adélie Land
M-SSI
LGM-SSI
Fronts
STF
SAF
PF
SACCB
180°
TRENDS in Ecology & Evolution

Figure I. The Antarctic, indicating key locations mentioned in the text and the important fronts of the Antarctic Circumpolar Current (ACC). The ACC flows clockwise around
Antarctica. It is bounded by the subtropical front (STF) to the north and the Southern Boundary Current (SACCB) to the south, with most of the transport between the sub-
Antarctic front (SAF) and the Polar Front (PF). The modern summer sea ice limit (M-SSI) and the summer sea-ice limit at the last glacial maximum (LGM-SSI) [3] are marked.
Bathymetry is indicated with increased color depth with increasing sea-floor depth, with the 600-m contour (the approximate edge of the Antarctic continental shelf)
artificially emphasized by a jump in color intensity. The Weddell Sea [11,48,49], the Mertz Bank, off George V land [12], the seas off Adélie Land [12,48,49], the Ross Sea
[48,49], South Georgia [49], Shag Rocks [49], the South Shetland Islands [48], the South Orkney Islands [48], and the Kerguelen Plateau [48] have been proposed as sites of
glacial refugia. The thick red broken line indicates the potential seaway between the Weddell and Ross Seas [59,60] that might have acted as a route of recolonization from
refugia for some taxa [40,49].

haplotype diversity, most haplotypes occur at a very low
frequency and are little differentiated from a dominant
(probably ancestral) haplotype. This pattern is indicative
of a bottleneck event followed by population expansion
[26]. One could expect such a bottleneck provided the
refugial population was small and that extinction else-
where was catastrophic: the massive reduction in popula-
tion size would result in a severe decline in haplotype
diversity. Recent molecular studies in the Southern
Ocean have found this haplotype network pattern in the
sea urchin Sterechinus neumayeri [27], the nemertean
522
Parbolasia corrugatus [28], and the shrimp Chorismus
antarcticus [29]. All these species are able to disperse
widely and this allows the dominant haplotype to become
rapidly distributed around Antarctica once the glacial
maximum has passed and the ice sheets retreat.
Once the ice sheets are in retreat, one could also expect
rapid population expansion as large swathes of benthic
habitat become available again. Various molecular analyt-
ical techniques can provide evidence of demographic
expansions. Their details are outside the scope of this
review, but essentially these methods compare addition
 Review Trends in Ecology and Evolution September 2012, Vol. 27, No. 9

Glacial refugium Deep-sea refugium

30
31
(a) Star-like (c) Diffuse 49
5 *
51 33 50
32
29
dispersal stage
36 34
*
Species with

35
28

27 3 * 39
25 54
19 13 14
11 53
* 52
15
4 41 38
17
18 40 37
1 10
12
26 * 2
9 48
16 22
42
6 23
8 47 44
43
24 45
21
46 20
7

(b) Cryptic speciation (d) Parochial

Species lacking
dispersal stage

TRENDS in Ecology & Evolution

Figure 1. Haplotype network patterns predicted by the type of refugium and life-history strategy. Geographic locations of samples (which are not specified) are indicated by
colors. Each unique sequence (haplotype) is represented by a circle, and the most closely related sequences (haplotypes) are neighbors in the network. The frequency of
occurrence of haplotypes is indicated by the size of the circle representing that haplotype, and unsampled haplotypes are represented by a dot. (a) ‘Star-like’ network with
one or two dominant haplotypes and multiple rare haplotypes differing by a single mutation. Illustrated is the median joining haplotype network of cytochrome C oxidase I
(COI) from Sterechinus neumayeri [27]. Similar networks are seen in Parbolasia corrugatus [28] and Chorismus antarcticus [29]. (b) Cryptic speciation. Illustrated is the
statistical parsimony network of mitochondrial COI haplotypes from Eusirus spp [32]. Other occurrences of cryptic speciation have been found in Southern Ocean
arthropods [22,33,36–39], mollusks [34,35,40], echinoderms [21,41,42], annelids [43], and nemerteans [28]. (c) ‘Diffuse’ network with geographic locations dispersed
throughout. Illustrated is the statistical parsimony network of mitochondrial COI haplotypes from Nematocarcinus lanceopes [29]. Similar networks are seen in Astrotoma
agassizi [31], Odontaster validus [45], Nacella concinnus [30], and Gobionotothen gibberifrons [46]. (d) ‘Parochial’ network with differentiation between geographical
locations. Illustrated is the statistical parsimony network of mitochondrial COI haplotypes of Eusirus spp. [32]. Similar networks are seen in Nymphon australe [44],
Pareledone cornuta, Pareledone aequipapillae [35], and Promachocrinus sp. [21]. Reproduced, with permission, from [27] (a), [32] (b,d) and [29] (c).

of variation by mutation and the removal of variation by
genetic drift, and test for departure from a model of
mutation–drift equilibrium. There are difficulties in esti-
mating the dates of these expansions accurately (Box 2),
and date estimates often have wide confidence intervals.
Nonetheless, molecular data from the Southern Ocean are
broadly supportive of Late Pleistocene demographic ex-
pansion in some species [24]. DNA sequence data from the
shrimp C. antarcticus indicate the onset of a demographic
expansion approximately 85 000 years ago [29], although
with wide confidence intervals from 0 to 270 000 years.
Data from the Antarctic limpet Nacella concinna [30] also
indicate a population expansion, but whether that demo-
graphic change was before or subsequent to the LGM
depends on whether a correction is applied for short-term
mutation rates (Box 2). A population expansion, possibly
occurring after the LGM, has also been reported for two
species of Southern Ocean benthic fish, Trematomus ber-
nacchii and Trematomus pennelli [31], whose distribution
is restricted to benthic habitat on the continental shelf. By
contrast, a different demographic signal was found in two
pelagic fish species, Trematomus newnesi and Pagothenia
borchgrevinki [31]. Evidence for demographic growth was
not clear in these pelagic species but, if demographic expan-
sion occurred, then the onset of this process significantly
predated that of the benthic fish and the LGM. This high-
lights the differential effect of glacial cycles on benthic and
pelagic species. The three-dimensional pelagic habitat is not
limited spatially to the same extent as the benthic habitat,
and the impact of extending ice sheets is lessened. This
explains why early studies focusing on pelagic taxa [17–20]
did not help elucidate the role of refugia.
A ‘disjunct’ statistical parsimony haplotype network
that is fragmented into multiple networks with very low
haplotype diversity (Figure 1b) appears to result when
species without a dispersive stage take refuge on the
continental shelf. The pattern is indicative of small popu-
lations isolated in glacial refugia that undergo bottlenecks.
Reduced genetic diversity is a consequence of the severe
reduction in population size. Genetic drift then has a much
more pronounced effect on this reduced gene pool than it
would have on larger, more genetically diverse popula-
tions. Because these species are poor dispersers, recoloni-
zation of the vast Antarctic continental shelf is slow,
allowing time for further genetic drift and possible
speciation before secondary contact of isolated populations.
523
Review
Box 2. Difficulties in dating demographic expansions
To calculate the date of demographic expansion events, it is
necessary to use a rate of molecular evolution. However, several
difficulties are associated with obtaining and applying evolutionary
rates, as they are understood to vary markedly among loci, lineages,
taxa, and also timescale of measurement.
In many cases, molecular rates for mitochondrial genes have been
obtained by estimating divergence times on phylogenetic trees
through the use of palaeontological or geological events (usually on
the order of several million years) to calibrate the tree.
Unfortunately, useful palaeontological (and geological events)
for Southern Ocean taxa are not common. Many Antarctic fossil
beds are covered in ice or have been damaged by the erosion of
sediments after glacial maxima. Although some fossil-rich areas
exist (e.g., the La Meseta formation, Seymour Island, Antarctic
Peninsula), few fossils of Southern Ocean taxa appear suitable for
divergence time estimation. For example, the single fossil elegi-
nopid fish on which all notothenioid fish divergence times are
based is controversial [31,61,62] and might not even be a
notothenioid.
Furthermore, it has been demonstrated that rates are significantly
slower on evolutionary timescales (i.e., mutation rate) than within
genealogical timescales (i.e., substitution rate) [63]. Therefore, if
molecular rates estimated on evolutionary timescales are applied to
very recent timescales, they will lead to an overestimation of
divergence times and also possibly to overestimates of effective
population sizes [64]. In response to these rate issues, some authors
have applied correction factors, altering their date estimates by as
much as a factor of ten (e.g., [30]).
Although the application of ancient DNA methodologies to
historical museum specimens (collected by early Antarctic ex-
plorers) or specimens frozen in situ permit the calculation of
relevant evolutionary rates for genealogical studies and/or demo-
graphic expansions (as was done for Adélie penguins [65]), such
samples are rare. Crandall et al. [66] recently developed a
coalescent-based method for calibrating molecular clock rates that
utilizes a population expansion event rather than divergence, to
estimate rates. This might prove useful in dating demographic
events in future studies.
Furthermore, in small populations, selection leads to rapid
fixation, so it is possible that sympatric speciation might
also result from an ecological cline in a refugium. Tradi-
tionally, when this pattern has been found, each network
has been considered a potential separate species (e.g.,
[32,33]), although there are some caveats associated with
this (Box 3). Species with this pattern of haplotype network
include the amphipods Eusirus spp. [32], the sea spider
Colossendeis megalonyx [33], the nudibranch Doris kergue-
lensis [34] and various octopus species [35].
Numerous recent molecular studies have suggested the
presence of cryptic species at shelf and slope depths around
the Antarctic continent. These studies have encompassed a
wide variety of taxa, including amphipods [32,36,37], iso-
pods [38], ostracods [39], sea spiders [22,33], bivalves [40],
sea slugs [34], octopods [35], brittlestars [41], sea-cucum-
bers [42], crinoids [21], polychaetes [43], and nemerteans
[28]. Were this effect confined to just a few taxa, it could be
argued that the effects were lineage specific and not caused
by a broad phenomenon, such as isolation in shelf refugia;
however, the effect is widely seen. Interestingly, rarefac-
tion curves (where the rate of discovery of haplotypes is
plotted against sampling effort) have indicated an under-
sampling of genetic diversity in several studies [32,34].
Routine inclusion of such analyses will probably suggest
that the true number of cryptic species is higher than
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Trends in Ecology and Evolution September 2012, Vol. 27, No. 9
Box 3. Using molecular sequence data to delimit species
A common method to identify individual species from molecular
sequence data is to use methods that search for discontinuities in
sequence variation. An example is the statistical parsimony method
[67], which is used to build haplotype networks. This method splits a
network when the probability of homoplasy in a branch connecting
two parts increases above a certain threshold level. Although
analyses across multiple taxa show that there is often congruence
between networks and Linnean species [68], it is not always the
case, especially where groups have radiated rapidly [68,69].
Incongruence is found in Southern Ocean octopod species: multiple
closely related species that can be distinguished morphologically
form a single haplotype network using standard thresholds [35].
Discontinuities in sequence variation are also often used in DNA
barcoding studies to delimit species. Here, evidence for a ‘barcoding
gap’ is sought. This gap is the difference between the highest
genetic distance found within species and the lowest genetic
distance between species. If these values vary by a certain factor,
then the gap between them is considered to be indicative of a true
species boundary. Opinions vary as to the appropriate size of the
factor, with estimates ranging from at least four [70] to at least ten
[71].
Most studies using DNA to delimit Southern Ocean taxa have
utilized at least one of these methods. A more rigorous statistical
technique is now available that uses a maximum likelihood frame-
work to locate a predicted shift in branch lengths at species
boundaries [72]. A discontinuity is expected as the processes
controlling branch lengths change from speciation and extinction
rates between species, to coalescence processes within species. At
least one study [39] has used this approach for the Southern Ocean
and it is likely that it will be more widely applied in future.
Most molecular studies of Southern Ocean taxa suggesting the
discovery of new species have been based on mitochondrial
sequence data (although see [73]). Some Southern Ocean studies
have found congruence between mitochondrial and nuclear markers
[32,38,74,75], whereas others have not [39,40]. Incomplete lineage
sorting in recombining (nuclear) loci might account for the
differences [39,68]. However, issues with using mitochondrial data
alone for species delineation have been documented in arthropods
(e.g., [76]) and future Southern Ocean studies must try to establish
whether the mitochondrial genome is representative of the evolu-
tionary history of any given species.
currently detected and provide additional evidence for
the role of continental-shelf glacial refugia.
Evidence for deep-sea refugia
The discovery of so many suites of potential cryptic species
has led to a decrease in the reported prevalence of euryb-
athy, the paradigm that itself has been invoked in support
of deep-sea rather than continental-shelf refugia. In the
polychaete Glycera kerguelensis, extreme eurybathy (from
above 150 m to below 4000 m) has been refuted by the
recognition of numerous cryptic species [43], each occupy-
ing a restricted depth stratum. However, genetic data have
also provided evidence that supports this paradigm in
some taxa. Extreme eurybathy (310–4409 m) has been
confirmed in an undescribed amphipod of the genus Abys-
sorchomene [37] and in the sea spider Nymphon australe
sampled from the shelf and slope [44]. The reported depth
range of this sea spider extends to below 4000 m. Hence,
although eurybathy is less prevalent than once thought,
there are Southern Ocean species that display extreme
eurybathy and that could have found refuge from glacial
cycles in deep-sea environments.
There are two distinctive patterns that appear to be
associated with taking refuge in the deep sea during glacial
Review
maxima. A ‘diffuse’ haplotype network (Figure 1c) was
found for the deep-sea shrimp Nematocarcinus lanceopes
[29]. Because of its depth distribution (extending to below
4000 m), it is likely that this species found refuge in the
deep sea during glacial periods. Extinction from shelf and
slope waters would provide a less dramatic reduction in
haplotype diversity and high dispersal capability would
ensure that surviving haplotypes would soon occur in a
wide range of locations following glacial retreat. The high
haplotype diversity seen (Figure 1c) is consistent with this
scenario.
A ‘parochial’ haplotype network (Figure 1d) has a large
number of haplotypes, but most are restricted to a single
geographic location. Furthermore, haplotypes from any
given location are positioned close together in the network.
This reflects local diversification and poor dispersal and,
therefore, is indicative of species without a dispersal stage.
However, this pattern also indicates that there has been no
major bottleneck because high haplotype diversity is main-
tained. This is again consistent with a large refugial area,
such as that provided by the deep sea. Such a network is
found, as might be expected, in N. australe [44], the eury-
bathic sea-spider discussed above that, similar to other
pycnogonids, has no planktonic stage.
Deep-sea refugia versus multiple shelf refugia
Fairly ‘diffuse’ haplotype networks have also been found
for species whose present-day distribution is not known to
extend beyond the shelf and/or slope and, therefore, are
less likely to have taken refuge in the deep sea. Examples
include haplotype networks from the brittle star Astrotoma
agassizi [41], the sea star Odontaster validus [45], the
limpet N. concinna [30], and the benthic fish Gobionotothen
gibberifrons [46]. These networks have fewer haplotypes
than illustrated in Figure 1c and fewer shared haplotypes.
This might reflect less extensive sampling but might also
represent secondary contact of lineages from multiple
shallow-water refugia. As shelf refugia were probably
small, each refugial population would have undergone a
considerable bottleneck, reducing the overall number of
haplotypes. The recent demographic expansion seen in N.
concinna [30] suggests that secondary contact of lineages
from multiple shallow-water refugia is a more probable
scenario, at least in this species, because population
reduction would be less likely in a deep-sea refuge, given
the extent of deep-sea habitat available.
The fairly diffuse haplotype network found in A. agassizi
[41] was originally difficult to explain as this species was
thought to lack a dispersive stage. However, a larval
barcoding (i.e., sequencing of the mitochondrial gene
cytochrome C oxidase, COI) program has identified a
planktonic dispersive stage for this species [47]. The
importance of larval barcoding in elucidating life-history
strategies is clear and it is important not to overinterpret
molecular data when life-history processes are uncertain.
If diffuse haplotype networks with fewer haplotypes
could result from multiple shelf refugia then parochial
networks with fewer haplotypes might similarly result
from species surviving glaciations in multiple continental
shelf refugia. Post-glacial expansions from each refugium
and secondary contact of populations (before they had
Trends in Ecology and Evolution September 2012, Vol. 27, No. 9
become reproductively isolated) would mean that the spe-
cies still had a wide geographic extent. Nonetheless, the
geographic spread of haplotypes (assuming different hap-
lotypes persisted in different refugia) would be limited
because of poor dispersal ability. This might explain the
patterns seen in some cryptic species of the giant amphipod
Eusirus spp. [32] and the feather star Promachocrinus spp.
[21]. In the latter study the authors also estimated the
timing of lineage divergence and found it to be consistent
with a scenario of isolation in glacial refugia during the
past 5 million years. A subsequent study on Promachocri-
nus with a larger data set (>1400 individuals sequenced)
suggested that secondary contact from several refugia was
the best explanation of the haplotype patterns [48], pro-
posing the Ross Sea, the Weddell Sea, off Adélie Land, the
South Shetland Islands, the South Orkney Islands, and the
Kerguelen Plateau as probable refugial locations (Box 1,
Figure I). Studies on the Antarctic octopus genus Parele-
done [35,49] have also revealed similar patterns. In a study
on Pareledone turqueti [49], molecular data suggested
refugia in the Ross Sea, Weddell Sea, and Adélie Land,
with a separate lineage of the species finding refuge in
South Georgia and Shag Rocks, islands at the Northern
boundary of the Scotia Sea. Furthermore, this study indi-
cated a close relation between fauna of the Weddell and
Ross Seas, suggesting this as a potential route of recoloni-
zation during West Antarctic Ice Sheet collapse (Box 1,
Figure I).
Hence, there is strong genetic evidence for survival of
populations in both continental-shelf refugia and deep-sea
refugia. In some cases, the available molecular evidence
points clearly to one or other scenario, but there are cases
that cannot yet be confidently distinguished. Nonetheless,
where haplotype network patterns can be analyzed in
concert with indicators of demographic expansion, and
where the geographic extent and depth distribution of a
species are also known, conclusions can be more easily
drawn.
Are there alternative explanations for the molecular
signatures?
Raupach et al. [29] favored survival in sub-Antarctic refugia
(rather than deep-sea or continental-shelf refugia) as an
explanatory hypothesis for the star-like haplotype network
(Figure 1a) seen in the shallow-water shrimp C. antarcticus.
They proposed that a similar pattern of a dominant haplo-
type might occur following a founder event, such as recolo-
nization of the Antarctic shelf from the sub-Antarctic, and
concluded that this scenario was most probable, given the
planktotrophic larval stage of this species. Molecular
evidence for a founder effect is not normally accompanied
by evidence for rapid demographic expansion, but this
merely reflects the fact that founders are not usually
colonizing a newly available habitat and must compete with
an already established community. However, although
refuge in sub-Antarctic islands might provide a satisfactory
explanation for C. antarcticus, the sub-Antarctic is unlikely
to have provided refuge for species that are now restricted to
the high Antarctic. S. neumayeri, which exhibits this
star-like pattern [27], has such a restricted range. Although
it is possible that the range of S. neumayeri extended further
525
Review
north during glacial maxima, it is probable that this species
persisted in a continental shelf refugium.
We have shown that some direct developers appear to
have speciated as a result of isolation in continental shelf
glacial refugia. This could account for at least some of the
prevalence of this life-history strategy in the Southern
Ocean. Pearse et al. [50] evaluated two different scenarios
under which brooding species might preferentially under-
go speciation. Under a scenario of continental shelf refugia,
they predicted the ‘presence of many closely related cryptic
species around the Antarctic continent, mainly at shelf and
slope depths’, which is what recent molecular studies have
revealed. Under the second scenario, they propose that,
when the Drake Passage (Box 1, Figure I) was narrower,
the Antarctic Circumpolar Current (ACC) flow was partic-
ularly intense in this region and infrequently dislodged
and carried individuals of species with non-pelagic devel-
opment to new habitats in the Scotia Sea, where they could
(through genetic drift and selection) establish new species.
This scenario predicts highest diversity in the Scotia Sea,
downstream of the Drake Passage (Box 1, Figure I). A
study on the brooding bivalve Lissarca notorcadensis [40]
also suggested the Scotia Sea as a centre of speciation and
found four distinct lineages of this species in the surround-
ing island arc. Clearly, there is support for both scenarios
and it is likely that both mechanisms have contributed to
the abundance of brooders in the Southern Ocean.
Although we have focused on species that have survived
glacial maxima, it is likely that these glacial maxima have
also been the cause of periodic extinctions. A study of
extinction rather than speciation, based on a molecular
phylogeny of bivalves, revealed that Antarctic extinctions
appeared to favor derived families, resulting in a prolifer-
ation of basal lineages [51], possibly due in part to the effect
of glaciation on shelf habitats. Families of the derived
Veneroidea appear to have flourished in the Arctic, but
several are not present in the Southern Ocean. Many
members of these families prefer shallow-water habitats
(i.e., those particularly obliterated by glacial advance), so it
appears that continental-shelf glacial refugia have not
provided a solution to all shallow-water fauna.
Concluding remarks
Much research on Southern Ocean biodiversity has been
directed towards investigation of traits such as eurybathy,
circumpolarity, and the prevalence of brooders. Having
reviewed all available Southern Ocean molecular studies
on these topics, we suggest that a greater understanding is
provided when these characteristics are considered in
concert with the pressures exerted on biota by Pliocene–
Pleistocene glacial cycles. Eurybathy has probably been
selected for because it allows shallow-water species to
survive glacial maxima in the deep sea. Circumpolarity
probably results when species with a dispersive stage
rebound after a glacial maximum and quickly colonize
newly available habitat without having to compete with
established, locally adapted communities. The high preva-
lence of brooders can be partially explained by glacial
cycles causing isolation in refugia followed by vicariant
speciation.
526
Trends in Ecology and Evolution September 2012, Vol. 27, No. 9
Hence, we suggest that a paradigm shift is required in
Southern Ocean molecular research. A wider focus in
future molecular ecology studies will enable greater un-
derstanding of how species survived previous glacial max-
ima. A broadening of the geographic range of studies will
help pinpoint specific locations of refugia and elucidate
hotspots of diversity. Expanding the range of molecular
tools applied will enable a better understanding of the
differential processes acting on mitochondrial and nuclear
DNA and the direct investigation of the role of selection.
We believe that such a paradigm shift will enable research-
ers to better understand the effects of past and future
glacial cycles on Antarctic organisms.
Acknowledgments
Pete Convey, Huw Griffiths, Chris Maggs, Alex Rogers, Mark Johnson,
two anonymous referees, and Ceridwen Fraser provided valuable
feedback on the manuscript. We thank Martin Genner for fruitful
discussions on speciation. This manuscript contributes to the SCAR
EBA programme.
References
1 Convey, P. et al. (2009) Exploring biological constraints on the glacial
history of Antarctica. Quat. Sci. Rev. 28, 3035–3048
2 Thatje, S. et al. (2005) On the origin of Antarctic marine benthic
community structure. Trends Ecol. Evol. 20, 534–540
3 Gersonde, R. et al. (2005) Sea-surface temperature and sea ice
distribution of the Southern Ocean at the EPILOG Last Glacial
Maximum – a circum-Antarctic view based on siliceous microfossil
records. Quat. Sci. Rev. 24, 869–896
4 Dell, R.K. (1972) Antarctic benthos. Adv. Mar. Biol. 10, 1–216
5 Brey, T. et al. (1996) Do Antarctic benthic invertebrates show an
extended level of eurybathy? Antarct. Sci. 8, 3–6
6 Kussakin, O.G. (1973) Peculiarities of the geographical and vertical
distribution of marine isopods and the problem of deep-sea fauna
origin. Mar. Biol. 23, 19–34
7 Clarke, A. and Crame, J.A. (1989) The origin of the Southern Ocean
marine fauna. In Origins and Evolution of the Antarctic Biota (Crame,
J., ed.), pp. 254–268, Geological Society Special Publications
8 Smith, J.A. et al. (2010) The presence of polynyas in the Weddell Sea
during the last glacial period with implications for the reconstruction of
sea-ice limits and ice sheet history. Earth Planet. Sci. Lett. 296,
287–298
9 Anderson, J.B. et al. (2002) The Antarctic ice sheet during the last
glacial maximum and its subsequent retreat history: a review. Quat.
Sci. Rev. 21, 49–70
10 Thatje, S. et al. (2008) Life hung by a thread: endurance of Antarctic
fauna in glacial periods. Ecology 89, 682–692
11 Barnes, D.K.A. and Kuklinski, P. (2010) Bryozoans of the Weddell Sea
continental shelf, slope and abyss: did marine life colonize the
Antarctic shelf from deep water, outlying islands or in situ refugia
following glaciations. J. Biogeogr. 37, 1648–1656
12 Post, A.L. et al. (2010) Community structure and benthic habitats
across the George V Shelf, East Antarctica: trends through space
and time. Deep-Sea Res. II 58, 105–118
13 Hewitt, G.M. (1996) Some genetic consequences of ice ages, and their
role in divergence and speciation. Biol. J. Linn. Soc. 58, 247–276
14 Hewitt, G.M. (1999) Post-glacial re-colonization of European biota.
Biol. J. Linn. Soc. 68, 87–112
15 Bernatchez, L. and Wilson, C.C. (1998) Comparative phylogeography of
Nearctic and Palearctic fishes. Mol. Ecol. 7, 431–452
16 Maggs, C.A. et al. (2008) Evaluating signatures of glacial refugia for
North Atlantic benthic marine taxa. Ecology 89, S108–S122
17 Davis, C.S. et al. (2002) Dinucleotide microsatellite markers from the
Antarctic seals and their use in other pinnipeds. Mol. Ecol. Notes 2,
203–308
18 Roeder, A.D. et al. (2001) Gene flow on the ice: genetic differentiation
among Adelie penguin colonies around Antarctica. Mol. Ecol. 10,
1645–1656
Review
19 Gaffney, P.M. (2000) Molecular tools for understanding population
structure in Antarctic species. Antarct. Sci. 12, 288–296
20 Zane, L. et al. (1998) Molecular evidence for genetic subdivision of
Antarctic krill (Euphausia superba Dana) populations. Proc. R. Soc.
Lond. B: Biol. Sci. 265, 2387–2391
21 Wilson, N.G. et al. (2007) Multiple lineages and absence of panmixia in
the ‘circumpolar’ crinoid Promachocrinus kerguelensis from the
Atlantic sector of Antarctica. Mar. Biol. 152, 895–904
22 Mahon, A.R. et al. (2010) DNA uncovers Antarctic nemertean
biodiversity and exposes a decades-old cold case of asymmetric
inventory. Polar Biol. 33, 193–202
23 Lambeck, K. et al. (2002) Links between climate and sea levels for the
past three million years. Nature 419, 199–206
24 Rogers, A.D. (2012) Evolution and biodiversity of Antarctic organisms:
a molecular perspective. In Antarctic Ecosystems: An Extreme
Environment in a Changing World (Rogers, A.D. et al., eds), pp.
417–467, Blackwell Publishing
25 Fraser, C.I. et al. (2012) Poleward bound: biological impacts of
Southern Hemisphere glaciation. Trends Ecol. Evol. 27, 462–471
26 Slatkin, M. and Hudson, R.R. (1991) Pairwise comparisons of
mitochondrial DNA sequences in stable and exponentially growing
populations. Genetics 129, 555–562
27 Diaz, A. et al. (2011) Evolutionary pathways among shallow and deep-
sea echinoids of the genus Sterechinus in the Southern Ocean. Deep-
Sea Res. II 58, 205–211
28 Thornhill, D.J. et al. (2008) Open-ocean barriers to dispersal: a test case
with the Antarctic Polar Front and the ribbon worm Parbolasia
corrugatus (Nemertea: Lineidae). Mol. Ecol. 17, 5104–5117
29 Raupach, M.J. et al. (2010) Genetic homogeneity and circum-Antarctic
distribution of two benthic shrimp species of the Southern Ocean,
Chorismus antarcticus and Nematocarcinus lanceopes. Mar. Biol.
157, 1783–1797
30 González-Wevar, C.A. et al. (2011) Phylogeography and demographic
inference in Nacella (Patinigera) concinna (Strebel, 1908) in the
western Antarctic Peninsula. Deep-Sea Res. II 58, 220–229
31 Janko, K. et al. (2007) Did glacial advances during the Pleistocene
influence differently the demographic histories of benthic and
pelagic Antarctic shelf fishes? Inferences from intraspecific
mitochondrial and nuclear DNA sequence diversity. BMC Evol.
Biol. 7, 220
32 Baird, H.P. et al. (2011) Evidence of hidden biodiversity, ongoing
speciation and diverse patterns of genetic structure in giant
Antarctic amphipods. Mol. Ecol. 20, 3439–3454
33 Krabbe, K. et al. (2010) Cryptic mitochondrial lineages in the
widespread pycnogonid Colossendeis megalonyx Hoek, 1881 from
Antarctic and Subantarctic waters. Polar Biol. 33, 281–292
34 Wilson, N.G. et al. (2009) Ocean barriers and glaciation: evidence for
explosive radiation of mitochondrial lineages in the Antarctic sea
slug Doris kerguelensis (Mollusca, Nudibranchia). Mol. Ecol. 18,
965–984
35 Allcock, A.L. et al. (2011) Cryptic speciation and the circumpolarity
debate: a case study on endemic Southern Ocean octopuses using the
COI barcode of life. Deep-Sea Res. II 58, 242–249
36 Lörz, A.N. et al. (2009) Do circum-Antarctic species exist in peracarid
Amphipoda?. A case study in the genus Epimeria Costa, 1851
(Crustacea, Peracarida, Epimeriidae). ZooKeys 18, 91–128
37 Havermans, C. (2011) DNA barcoding reveals new insights into
the diversity of Antarctic species of Orchomene sensu lato
(Crustacea: Amphipoda: Lysianassoidea). Deep-Sea Res. II 58, 230–
241
38 Leese, F. and Held, C. (2008) Identification and characterization
of microsatellites from the Antarctic isopod Ceratoserolis
trilobitoides: nuclear evidence for cryptic species. Conserv. Genet.
9, 1369–1372
39 Brandão, S.N. et al. (2010) Circumantarctic distribution in Southern
Ocean benthos? A genetic test using the genus Macroscapha
(Crustacea, Ostracoda) as a model. Mol. Phylogenet. Evol. 55,
1055–1069
40 Linse, K. et al. (2007) Is the Scotia Sea a centre of Antarctic marine
diversification? Some evidence of cryptic speciation in the circum-
Antarctic bivalve Lissarca notorcadensis (Arcoidea: Philobryidae).
Polar Biol. 30, 1059–1068
Trends in Ecology and Evolution September 2012, Vol. 27, No. 9
41 Hunter, R.L. and Halanych, K.M. (2008) Evaluating connectivity in the
brooding brittle star Astrotoma agassizii across the Drake Passage in
the Southern Ocean. J. Hered. 99, 137–148
42 O’Loughlin, P.M. et al. (2011) The Antarctic region as a marine
biodiversity hotspot for echinoderms: diversity and diversification of
sea cucumbers. Deep-Sea Res. II 58, 264–275
43 Schueller, M. (2011) Evidence for a role of bathymetry and emergence
in speciation in the genus Glycera (Glyceridae, Polychaeta) from the
deep Eastern Weddell Sea. Polar Biol. 34, 549–564
44 Arango, C.P. et al. (2011) Genetic differentiation in the circum-Antarctic
sea spider Nymphon australe (Pycnogonida; Nymphonidae). Deep-Sea
Res. II 58, 212–219
45 Janosik, A.M. et al. (2011) Evolutionary history of Southern Ocean
Odontaster sea star species (Odontasteridae; Asteroidea). Polar Biol.
34, 575–586
46 Matschiner, M. et al. (2009) Gene flow by larval dispersal in the
Antarctic notothenioid fish Gobionotothen gibberifrons. Mol. Ecol.
18, 2574–2587
47 Heiemeyer, D. et al. (2010) Molecular species identification of
Astrotoma agassizii from planktonic embryos: further evidence for a
cryptic species complex. J. Hered. 101, 775–779
48 Hemery, L.G. et al. (2012) Comprehensive sampling reveals
circumpolarity and sympatry in seven mitochondrial lineages of the
Southern Ocean crinoid species Promachocrinus kerguelensis
(Echinodermata). Mol. Ecol. 21, 2502–2518
49 Strugnell, J.M. et al. (2012) Persistent genetic signatures of historic
climatic events in an Antarctic octopus. Mol. Ecol. 21, 2775–2787
50 Pearse, J.S. et al. (2009) Brooding and species diversity in the Southern
Ocean: selection for brooders or speciation within brooding clades? In
Smithsonian at the Poles: Contributions to International Polar Year
Science (Krupnik, I. et al., eds), pp. 181–196, Smithsonian Institution
Press
51 Krug, A.Z. et al. (2011) Differential extinction and the contrasting
structure of polar marine faunas. PLoS ONE 5, e15362
52 Zachos, J.C. et al. (2001) Trends, rhythms, and aberrations in global
climate 65 Ma to present. Science 292, 686–693
53 Lawver, L.A. and Gahagan, L.M. (2003) Evolution of Cenozoic seaways
in the circum-Antarctic region. Palaeogeog. Palaeoclim. Palaeoecol.
198, 11–37
54 Naish, T.R. et al. (2001) Orbitally induced oscillations in the East
Antarctic ice sheet at the Oligocene/Miocene boundary. Nature 413,
719–723
55 Holbourn, A. et al. (2005) Impacts of orbital forcing and atmospheric
carbon dioxide on Miocene ice-sheet expansion. Nature 438,
483–487
56 EPICA (2004) Eight glacial cycles from an Antarctic ice core. Nature
429, 623–628
57 Naish, T. et al. (2009) Obliquity-paced Pliocene West Antarctic ice
sheet oscillations. Nature 458, 322–328
58 Huybrechts, P. (2002) Sea-level changes at the LGM from ice-dynamic
reconstructions of the Greenland and Antarctic ice sheets during the
glacial cycles. Quat. Sci. Rev. 22, 203–231
59 Pollard, D. and DeConto, R.M. (2009) Modelling West Antarctic ice
sheet growth and collapse through the past five million years. Nature
458, 329–333
60 Vaughan, D.G. et al. (2011) Potential seaways across West Antarctica.
Geochem. Geophys. Geosyst. 12, Q10004
61 Near, T.J. (2004) Estimating divergence times of notothenioid fishes
using a fossil-calibrated molecular clock. Antarct. Sci. 16, 37–44
62 Janko, K. et al. (2011) Multilocus analyses of an Antarctic fish species
flock (Teleostei, Notothenioidei, Trematominae): phylogenetic
approach and test of the early-radiation event. Mol. Phylogenet.
Evol. 60, 305–316
63 Ho, S.Y.W. and Larson, G. (2006) Molecular clocks: when times are a-
changing. Trends Genet. 22, 79–83
64 Ho, S.Y.W. et al. (2007) Time dependency of molecular rate estimates.
Syst. Biol. 56, 515–522
65 Lambert, D.M. et al. (2002) Rates of evolution in ancient DNA from
Adelie penguins. Science 295, 2270–2273
66 Crandall, E.D. et al. (2012) Expansion dating: calibrating molecular
clocks in marine species from expansions onto the Sunda Shelf
following the Last Glacial Maximum. Mol. Biol. Evol. 29, 707–719
527
Review
67 Templeton, A.R. et al. (1992) A cladistic analysis of phenotypic
associations with haplotypes inferred from restriction endonuclease
mapping and DNA sequence data. III. Cladogram estimation. Genetics
132, 619–633
68 Hart, M.W. and Sunday, J. (2007) Things fall apart: biological species
form unconnected parsimony networks. Biol. Lett. 3, 509–512
69 Monaghan, M.T. et al. (2006) Beyond barcodes: complex DNA
taxonomy of a south pacific island radiation. Proc. R. Soc. Lond. B:
Biol. Sci. 273, 887–893
70 Birky, C.W. et al. (2005) Speciation and selection without sex.
Hydrobiologia 546, 29–45
71 Hebert, P.D.N. et al. (2004) Identification of birds through DNA
barcodes. PLoS Biol. 2, 1657–1663
72 Pons, J. et al. (2006) Sequence-based species delimitation for the DNA
taxonomy of undescribed insects. Syst. Biol. 55, 595–609
528
Trends in Ecology and Evolution September 2012, Vol. 27, No. 9
73 Hoffman, J.I. et al. (2011) Effects of brooding and broadcasting
reproductive modes on the population genetic structure of two
Antarctic gastropod molluscs. Mar. Biol. 158, 287–296
74 Leese, F. et al. (2010) Long-distance island hopping without
dispersal stages: transportation across major zoogeographic
barriers in a Southern Ocean isopod. Naturwissensch 97,
583–594
75 Raupach, M.J. et al. (2007) Molecular data reveal a highly diverse
species flock within the munnopsoid deep-sea isopod Betamorpha
fusiformis (Barnard, 1920) (Crustacea: Isopoda: Asellota) in the
Southern Ocean. Deep-Sea Res. II 54, 1820–1830
76 Hurst, G.D.D. and Jiggins, F.M. (2005) Problems with mitochondrial
DNA as a marker in population, phylogeographic and phylogenetic
studies: the effects of inherited symbionts. Proc. R. Soc. B 272,
1525–1534