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Rise and Fall of the Beringian Steppe Bison

TLDR
A detailed genetic history of bison throughout the late Pleistocene and Holocene epochs is reconstructed using ancient DNA and Bayesian techniques to reconstruct a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically.
Abstract
The widespread extinctions of large mammals at the end of the Pleistocene epoch have often been attributed to the depredations of humans; here we present genetic evidence that questions this assumption. We used ancient DNA and Bayesian techniques to reconstruct a detailed genetic history of bison throughout the late Pleistocene and Holocene epochs. Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically. The timing of this decline correlates with environmental changes associated with the onset of the last glacial cycle, whereas archaeological evidence does not support the presence of large populations of humans in Eastern Beringia until more than 15,000 years later.

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Rise and Fall of the
Beringian Steppe Bison
Beth Shapiro,
1,2
Alexei J. Drummond,
2
Andrew Rambaut,
2
Michael C. Wilson,
3
Paul E. Matheus,
4
Andrei V. Sher,
5
Oliver G. Pybus,
2
M. Thomas P. Gilbert,
1,2
Ian Barnes,
6
Jonas Binladen,
7
Eske Willerslev,
1,7
Anders J. Hansen,
7
Gennady F. Baryshnikov,
8
James A. Burns,
9
Sergei Davydov,
10
Jonathan C. Driver,
11
Duane G. Froese,
12
C. Richard Harington,
13
Grant Keddie,
14
Pavel Kosintsev,
15
Michael L. Kunz,
16
Larry D. Martin,
17
Robert O. Stephenson,
18
John Storer,
19
Richard Tedford,
20
Sergei Zimov,
10
Alan Cooper
1,2
*
The widespread extinctions of large mammals at the end of the Pleistocene
epoch have often been attributed to the depredations of humans; here we
present genetic evidence that questions this assumption. We used ancient DNA
and Bayesian techniques to reconstruct a detailed genetic history of bison
throughout the late Pleistocene and Holocene epochs. Our analyses depict a
large diverse population living throughout Beringia until around 37,000 years
before the present, when the population’s genetic diversity began to decline
dramatically. The timing of this decline correlates with environmental changes
associated with the onset of the last glacial cycle, whereas archaeological
evidence does not support the presence of large populations of humans in
Eastern Beringia until more than 15,000 years later.
Climatic and environmental changes during
the Pleistocene epoch Efrom 2 million years
ago (Ma) to 10,000 years before the present
(ky B.P.)^ played an important role in the
distribution and diversity of modern plants
and animals (1, 2). In Beringia, local climate
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and geology created an ice-free refugium
stretching from eastern Siberia to Canada_s
Northwest Territories (3). Periodic exposure
of the Bering Land Bridge facilitated the
exchange of a diverse megafauna (such as
bison, mammoth, and musk ox) supported by
tundra-steppe grasses and shrubs (3, 4).
Humans are believed to have colonized
North America via this route, and the first
well-accepted evidence of human settlement
in Alaska dates to around 12 ky B.P. (5). The
latest Pleistocene saw the extinction of most
Beringian megafauna including mammoths,
short-faced bears, and North American lions.
The reasons for these extinctions remain
unclear but are attributed most often to
human impact (6, 7) and climate change
associated with the last glacial cycle (8).
Pleistocene bison fossils are abundant
across Beringia and they provide an ideal
marker of environmental change. Bison are
believed to have first entered eastern Beringia
from Asia during the middle Pleistocene
Emarine oxygen isotope stages (MISs) 8 to
6, circa (ca.) 300 to 130 ky B.P.^ and then
moved southward into central North America
during the MIS 5 interglacial period (130 to
75 ky B.P.), where they were distributed
across the continental United States (9). Dur-
ing this time, Beringian and central North
American bison populations may have been
periodically separated by glacial ice that
formed over most of Canada (10, 11). The
timing and extent of genetic exchange be-
tween these areas remain unclear (2).
The abundance and diversity of bison
fossils have prompted considerable paleon-
tological and archaeological research into
their use as stratigraphic markers. Extensive
morphological diversity, however, has com-
plicated discrimination between even the
most accepted forms of fossil bison, and the
lack of stratigraphy in Beringian sites has
prevented the development of a chronologi-
cal context. These complications create a
complex literature of conflicting hypotheses
about bison taxonomy and evolution (9, 12).
After a severe population bottleneck, which
ocurred only 200 years ago (13), two sub-
species survive in North America: Bison
bison bison, the plains bison, and B. b.
athabascae, the wood bison (9, 13).
To investigate the evolution and demo-
graphic history of Pleistocene bison, we col-
lected 442 bison fossils from Alaska, Canada,
Siberia, China, and the lower 48 United
States (14). We used ancient DNA tech-
niques to sequence a 685–base pair (bp)
fragment of the mitochondrial control region
(14). Accelerator mass spectrometry radio-
carbon dates were obtained for 220 samples,
which spanned a period of 960 ky (14).
The association of radiocarbon dates with
DNA sequences enables the calibration of
evolutionary rates within individual species
(15). Bayesian phylogenetic analyses pro-
duced an evolutionary rate estimate for the
bison mitochondrial control region of 32%
per million years (My) E95% highest poste-
rior density (HPD): 23 to 41% per My^ (14).
This estimate is independent of paleonto-
logical calibrations but agrees with fossil-
calibrated rates for cattle of 30.1% per My
(16) and 38% per My (17). This rate was
used to calculate the ages of key nodes in
the bison genealogy (14). The most recent
common ancestor (MRCA) of all bison in-
cluded in this analysis lived around 136 ky
B.P. (95% HPD: 164 to 111 ky B.P.). In the
majority (66%) of estimated trees, Eurasian
bison cluster into a single clade, with a
MRCA between 141 and 89 ky B.P. Although
1
Henry Wellcome Ancient Biomolecules Centre,
2
Department of Zoology, Oxford University, South
Parks Road, Oxford OX13PS, UK.
3
Department of
Geology and Department of Anthropology, Douglas
College, Post Office Box 2503, New Westminster,
British Columbia V3L 5B2, Canada.
4
Alaska Quater-
nary Center and Institute of Arctic Biology, University
of Alaska Fairbanks, 900 Yukon Drive, Fairbanks, AK
99775–5940, USA.
5
Severtsov Institute of Ecology
and Evolution, Russian Academy of Sciences, 33
Leninsky Prospect, 119071 Moscow, Russia.
6
The
Centre for Genetic Anthropology, Department of
Biology, Darwin Building, University College London,
Gower Street, London WC1E 6BT, UK.
7
Department
of Evolutionary Biology, Zoological Institute, Univer-
sity of Copenhagen, Universitetsparken 15–2100
Copenhagen, Denmark.
8
Zoological Institute, Russian
Academy of Sciences, 199034 St. Petersburg, Russia.
9
Quaternary Paleontology, Provincial Museum of
Alberta, Edmonton, Alberta T5N 0M6, Canada.
10
North-East Scientific Station of Russian Academy
of Science, Post Office Box 18, Cherskii, Republic
Sakha-Yakutia, Russia.
11
Department of Archaeology,
Simon Fraser University, Burnaby, British Columbia
V5A 1S6, Canada.
12
Department of Earth and
Atmospheric Sciences, University of Alberta, Edmon-
ton, Alberta T6G 2E3, Canada.
13
Canadian Museum of
Nature (Paleobiology), Ottawa, Ontario K1P 6P4,
Canada.
14
Department of Archaeology, Royal British
Columbia Museum, 675 Belleville Street, Victoria,
British Columbia V8V 1X4, Canada.
15
Institute of
Plant and Animal Ecology, Russian Academy of
Sciences, 202 8 Martas Street, Ekaterinburg 620144,
Russia.
16
Bureau of Land Management, 1150 Univer-
sity Avenue, Fairbanks, AK 99708 USA.
17
Department
of Ecology and Evolutionary Biology, University of
Kansas, Lawrence, KS 66045, USA.
18
Alaska Depart-
ment of Fish and Game, 1300 College Road, Fair-
banks, AK 99701, USA.
19
Yukon Paleontologist,
Heritage Resources, Yukon Department of Tourism
and Culture, Box 2703, Whitehorse, Yukon Territory
YTY1A 2C6, Canada.
20
Department of Paleontology,
American Museum of Natural History, Central Park
West at 79th Street, New York, NY 10024, USA.
*To whom correspondence should be addressed.
E-mail: alan.cooper@zoo.ox.ac.uk
Whitehorse
Vancouver
Edmonton
Ca l g ar y
Charlie Lake
Whitehorse
Vancouver
Edmonton
Ca l g ar y
Charlie Lake
2
5
2
1
3
9
5
8
4
150˚E
70˚N
65˚N
60˚N
55˚N
50˚N
45˚N
40˚N
70˚N
65˚N
60˚N
55˚N
50˚N
45˚N
40˚N
70˚N
65˚N
60˚N
55˚N
50˚N
45˚N
40˚N
ary
lie Lak
Edmonton
A
D
E
B
C
>25 ka BP
25-13 ka BP
13-9 ka BP
13-10 ka BP
10 ka BP - modern
(historical samples)
180˚
150˚W
120˚W
90˚W
eChar
Fig. 1. Distribution of bison in Beringia and central North America through time. (A to C) Double-
headed arrows show gene flow between regions. Black arrows indicate colonization events. Circles
in maps (D) and (E) designate either northern (red) or southern (blue) ancestry and the number of
samples from that location.
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these two estimates overlap, the age of the
MRCA of Eurasian bison was the same as
that of the root in 4.8% of 135,000 posterior
genealogies (with a Bayes factor of 20.83
that the Eurasian MRCA is not also the
MRCA of all clades), suggesting that the
Eurasian clade is not the oldest in the tree.
This suggests that late Pleistocene bison
from the Ural Mountains to northern China
are descendants of one or more dispersals
from North America. Several North Amer-
ican lineages fall within the Eurasian clade,
indicating subsequent asymmetric genetic
exchange, predominantly from Asia to North
America.
Figure 1A depicts inferred gene flow be-
tween bison populations in Beringia and
central North America during MIS 3 (È60
to 25 ky B.P.), which is the interstadial pe-
riod before the Last Glacial Maximum (LGM,
ca. 22 to 18 ky B.P.). Bison were continu-
ously distributed from eastern Beringia
southward into central North America during
this period, before the formation of the
Laurentide (eastern) and Cordilleran (west-
ern) ice sheets created a barrier to north-
south faunal exchange. Although any coales-
cence between these ice masses was brief
(11), the absence of faunal remains aged
22 to12 ky B.P. (Fig. 1B) (18) indicates that
the area was uninhabitable by large mam-
mals during this time. Bison fossils in central
North America during the LGM are sparsely
distributed across the continent (9). DNA
could be retrieved only from two specimens
from this period, both from Natural Trap
Cave, Wyoming (20,020 T 150 and 20,380 T
90 ky B.P.). These specimens are not closely
related (14), indicating that populations south
of the ice retained some genetic diversity
until the LGM.
The ice sheets began to retreat around
14 ky B.P., forming an ice-free corridor (IFC)
through which dispersal between Beringia
and North America could occur. The first
observed bison haplotypes in the IFC are
southern in origin (Fig. 1, C and D), with the
oldest specimen being in southern Alberta
by 11.3 ky B.P., and others near Athabas-
ca, northern Alberta, by 10.4 ky B.P. This
finding is consistent with evidence that the
first faunal assemblages and archaeological
presence in the IFC were southern in origin
(18–20). The opening of the northern end
of the IFC saw a limited southward disper-
sal of Beringian bison, with a subset of the
northern diversity found near the Peace Riv-
er (northwestern British Columbia) by 11.2
to 10.2 ky B.P. (Fig. 1C) (14). Southern bison
are also found in this area around 10.5 ky
B.P., making it the only location where post-
LGM northern and southern clades occurred
at the same time. Subsequent genetic ex-
change between Beringia and central North
America was limited by the rapid establish-
ment of spruce forest across Alberta around
10 ky B.P. (21) and by the widespread de-
velopment of peatland across western and
northwestern Canada (22). North of these
ecological barriers, grasslands were reduced
by invading trees and shrubs, yet despite the
decrease in quality and quantity of habitat
(3), bison persisted in eastern Beringia until
a few hundred years ago (14, 23).
It has been hypothesized that modern
bison descended from Beringian bison that
moved south through the IFC after the LGM
(9, 19) and have since undergone a decline in
diversity due to over-hunting and habitat loss
(13). In contrast, our data show that modern
bison are descended from populations that
were south of the ice before the LGM and
that diversity has been restricted to at least
12 ky B.P., around the time of the megafau-
nal extinctions. All modern bison belong to a
clade distinct from Beringian bison. This
clade has a MRCA between 22 and 15 ky
B.P., which is coincident with the separation
of northern and southern populations by the
western Canadian ice barrier. This clade
diverged from Beringian bison by 83 to
64 ky B.P. and was presumably part of an
early dispersal from Beringia, as indicated by
the long branch separating it from Beringian
bison (14). If other remnants of these early
dispersals survived the LGM, they contribut-
ed no mitochondrial haplotypes to modern
populations.
Coalescent theory is used to evaluate the
likelihood of a demographic history, given
plausible genealogies (24). Under a coales-
cent model, the timing of divergence dates
provides information about effective popula-
tion sizes through time. To visualize this for
bison, a technique called the skyline plot was
used (14, 25). The results showed two distinct
demographic trends since the MRCA, suggest-
ing that a simple demographic model, such as
constant population size or exponential
growth, was insufficient to explain the evolu-
tionary history of Beringian bison. We there-
fore extended the Bayesian coalescent method
(26) to a two-epoch demographic model with
exponential population growth at rate r
early
,
until a transition time, t
trans
,afterwhichanew
exponential rate, r
late
, applies until the present
effective population size, N
0
, is reached (Fig.
2A). In this model, both the early and late
epochs can have positive or negative growth
rates, with both the rates and the time of
transition estimated directly from the data.
The analysis strongly supported a boom-
bust demographic model (Table 1), in which
time (t)
0 ka BP
Effective population size, N(t)
transition time (t
trans
)
Early EpochLate Epoch
N
0
A
r
late
r
early
Population size x generation length
0 25000 50000 75000
100000 125000 150000
Radiocarbon years before present
95%
upper
95% lower
mean
10
5
Number of samples
5
10
15
0 25000 50000 75000 100000 125000 150000
Estimated transition time
Evidence of humans in E. Beringia
0
Estimated time of MRCA
10
6
10
7
10
4
10
3
10
2
10
1
B
Fig. 2. (A) The two-
epoch demographic
model with four demo-
graphic parameters: N
0
,
r
early
, r
late
, and t
trans
.
The effective popula-
tion size is a compound
variable considered lin-
early proportional to
census population size.
(B) Log-linear plot de-
scribing the results of
the full Bayesian analy-
ses. Smoothed curves provide mean and 95% HPD (blue-shaded region) values for
effective population size through time. Dashed vertical lines and gray-shaded
regions describe mean and 95% HPD for the estimated time of the MRCA (111 to
164 ky B.P.), transition time (32 to 43 ky B.P.), and the earliest unequivocal
reported human presence in eastern Beringia (È12 ky B.P.) (5). The stepped line
is the generalized skyline plot derived from the maximum a posteriori tree of the
exponential growth analysis. The bar graph shows the number of radiocarbon-
dated samples in bins of 1000 radiocarbon years. No relation is apparent
between the absolute number of samples and the estimated effective population
size or transition time.
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an exponential expansion of the bison popu-
lation was followed by a rapid decline, with a
transition around 37 ky B.P. (Fig. 2B).
At the height of the boom, the population
size was around 230 times (95% HPD: 71 to
454 times) that of the modern population.
When this model is applied to the modern
clade alone, a growth period peaks around
1000 years ago (95% HPD: 63 to 2300 yr
B.P.) and is followed by a rapid decline (14),
which is consistent with historical records
of a population bottleneck in the late 1800s
(13). These results illustrate the power of this
method to recover past demographic signals.
The effects of population subdivision
and patch extinction and recolonization on
coalescence patterns have not been fully
characterized, yet they can influence demo-
graphic estimates such as skyline plots (27).
To test for the effect of population subdivision
on our models, the two-epoch analysis was
repeated first without the Eurasian bison and
then without both Eurasian and central North
American bison. The results of these analyses
were consistent with those for the entire data
set (14), suggesting that the assumption of
panmixia does not affect the analysis. These
results suggest that the major signal for the
boom-bust scenario came from the well-
represented eastern Beringian population.
The timing of the decline in Beringian
bison populations (Fig. 2B) predates the
climatic events of the LGM and events at
the Pleistocene-Holocene boundary. The bi-
son population was growing rapidly through-
out MIS 4 and 3 (È75 to 25 ky B.P.),
approximately doubling every 10,200 (95%
HPD: 7500 to 15,500) years. The reversal of
this doubling trend at 42 to 32 ky B.P. and
the subsequent dramatic decrease in popula-
tion size are coincident with the warmest part
of MIS 3, which is marked by a reduction in
steppe-tundra due to treecover reaching its
late Pleistocene maximum (28). Modern bo-
real forests serve as a barrier to bison dis-
persal because they are difficult to traverse
and provide few food sources (3). After the
interstadial, cold and arid conditions in-
creasingly dominated, and some component
of these ecological changes may have been
sufficient to stress bison populations across
Beringia. Previous reports of local extinc-
tion of brown bears (29) and hemionid horses
(8) in Alaska around 32 to 35 ky B.P. sup-
port the possibility of a larger scale environ-
mental change affecting populations of large
mammals.
These results have considerable implica-
tions for understanding the end-Pleistocene
mass extinctions, because they offer the
first evidence of the initial decline of a pop-
ulation, rather than simply the resulting
extinction event. These events predate ar-
chaeological evidence of significant human
presence in eastern Beringia (5), arguing that
environmental changes leading up to the
LGM were the major cause of the observed
changes in genetic diversity. If other species
were similarly affected, differences in how
these species responded to environmental
stress may help to explain the staggered
nature of the megafaunal extinctions (7, 30).
However, it is possible that human popu-
lations were present in eastern Beringia by
30 ky B.P., with reports of human-modified
artifacts as old as 42 to 25 ky B.P. from the
Old Crow basin in Canada_s Yukon Terri-
tory (31). Although the archaeological sig-
nificance of these specimens is disputed
and the number of individuals would be
low, the specimens are consistent with the
timing of the population crash in bison. This
emphasizes that future studies of the end–
Pleistocene mass extinctions in North Amer-
ica should include events before the LGM.
Ancient DNA is a powerful tool for
studying evolutionary processes such as the
response of organisms to environmental
change. It should be possible to construct
a detailed paleoecological history for late
Pleistocene Beringia using similar methods
for other taxa. Almost none of the genetic
diversity present in Pleistocene bison survived
into Holocene populations, erasing signals of
the complex population dynamics that took
place as recently as 10,000 years ago.
References and Notes
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tion and Evolution (Univ. of California Press, Berkeley,
CA, 1981).
10. C. A. S. Mandryk, H. Josenhans, D. W. Fedje, R. W.
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89, 126 (1947).
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Table 1. Results of Bayesian analyses assuming constant population size,
exponential growth, and a two-epoch model for the full analysis of 191
bison associated with finite radiocarbon dates (14). Model parameters
are as defined in (26). The large difference between the mean goodness-of-
fit statistics [ln(posterior)] indicates that under either the Akaike
information criterion or Bayesian information criterion tests, the two-
epoch model is a significantly better fit to the data than the simpler
models.
Constant size Exponential growth Two epoch
Lower Mean Upper Lower Mean Upper Lower Mean Upper
Age estimates (yr B.P.)
Root height 117,000 152,000 189,000 113,000 146,000 181,000 111,000 136,000 164,000
Modern/southern
clade
20,200 28,000 36,600 18,600 26,400 35,000 15,400 23,200 32,200
Eurasian clade 85,000 116,000 151,000 83,000 112,000 144,000 89,000 114,000 141,000
Model parameters
Mean ln(posterior) 6530.795 6517.35 6394.568
Mutation rate
(substitutions/site/year)
2.79 10
–7
3.78 10
–7
4.85 10
–7
2.30 10
–7
3.20 10
–7
4.13 10
–7
2.30 10
–7
3.20 10
–7
4.13 10
–7
Kappa 19 27 37 19 27.4 37 19 27 37
Shape parameter 0.22 0.35 0.49 0.22 0.35 0.49 0.22 0.35 0.5
Proportion of
invariant sites
0.33 0.45 0.56 0.33 0.45 0.56 0.34 0.45 0.56
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25. K.Strimmer,O.G.Pybus,Mol. Biol. Evol. 18, 2298 (2001).
26. A. J. Drummond, G. K. Nicholls, A. G. Rodrigo, W.
Solomon, Genetics 161, 1307 (2002).
27. J. R. Pannell, Evolution 57, 949 (2003).
28. P. M. Anderson, A. V. Lozhkin, Quat. Sci. Rev. 20,93
(2001).
29. I. Barnes, P. E. Matheus, B. Shapiro, D. Jensen, A. Cooper,
Science 295, 2267 (2002).
30. D. K. Grayson, D. J. Meltzer, J. Archaeol. Sci. 30, 585
(2003).
31. R. E. Morlan, Quat. Res. 60, 123 (2003).
32. We thank the museums and collections that donated
material and T. Higham, A. Beaudoin, K. Shepherd, R. D.
Guthrie, B. Potter, C. Adkins, D. Gilichinsky, R. Gangloff,
S. C. Gerlach, C. Li, N. K. Vereshchagin, T. Kuznetsova,
G. Boeskorov, the Alaska Bureau of Land Manage-
ment, and the Yukon Heritage Branch for samples,
logistical support, and assistance with analyses. We
thank D. Rubenstein, R. Fortey, and P. Harvey for
comments on the manuscript; Balliol College; the
Royal Society; the Natural Environment Research
Council; the Biotechnology and Biological Sciences
Research Council; Rhodes Trust; Wellcome and
Leverhulme Trusts for financial support; and Oxford
Radiocarbon Dating Service and Lawrence Liver-
more National Laboratory for carbon dating.
Supporting Online Material
www.sciencemag.org/cgi/content/full/306/5701/1561/
DC1
Materials and Methods
SOM Text
Figs. S1 to S5
Tables S1 to S4
References
4 June 2004; accepted 4 October 2004
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1565

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Beyond Predictions: Biodiversity Conservation in a Changing Climate

TL;DR: This work introduces a framework that uses information from different sources to identify vulnerability and to support the design of conservation responses, and reviews the insights that different approaches bring to anticipating and managing the biodiversity consequences of climate change.
Journal ArticleDOI

Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)

TL;DR: The cross-platform software tool, TempEst (formerly known as Path-O-Gen), is introduced, for the visualization and analysis of temporally sampled sequence data and can be used to assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and identify sequences whose genetic divergence and sampling date are incongruent.
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Journal ArticleDOI

The genetic legacy of the Quaternary ice ages

TL;DR: The present genetic structure of populations, species and communities has been mainly formed by Quaternary ice ages, and genetic, fossil and physical data combined can greatly help understanding of how organisms were so affected.
Journal ArticleDOI

Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data

TL;DR: A Bayesian statistical inference approach to the joint estimation of mutation rate and population size that incorporates the uncertainty in the genealogy of such temporally spaced sequences by using Markov chain Monte Carlo (MCMC) integration.
Journal ArticleDOI

The Laurentide and Innuitian ice sheets during the Last Glacial Maximum

TL;DR: The Late Wisconsinan advance of the Laurentide Ice Sheet started from a Middle Wisconsinan interstadial minimum 27−30 14 C ka BP when the ice margin approximately followed the boundary of the Canadian Shield.

IL-13受体α2降低血吸虫病肉芽肿的炎症反应并延长宿主存活时间[英]/Mentink-Kane MM,Cheever AW,Thompson RW,et al//Proc Natl Acad Sci U S A

TL;DR: 曼氏血吸虫感染后,宿主活化CD4^+Th2细胞L分泌IL-4、IL-5和 IL-13。
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