When Did Decapods Invade Hydrothermal Vents? Clues from
the Western Pacific and Indian Oceans
Jin-Shu Yang,1 Bo Lu,1 Dian-Fu Chen,1 Yan-Qin Yu,1 Fan Yang,1 Hiromichi Nagasawa,2 Shinji Tsuchida,3
Yoshihiro Fujiwara,3 and Wei-Jun Yang*,1
1
Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and College of Life Sciences, Zhejiang
University, Hangzhou, Zhejiang, People’s Republic of China
2
Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo,
Tokyo, Japan
3
Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka,
Kanagawa, Japan
*Corresponding author: E-mail: [email protected].
Associate editor: Andrew Roger
Abstract
Key words: hydrothermal vent, decapod, mitogenome, molecular estimation, West Pacific–Indian Ocean.
Hydrothermal vents, well known for their unusual chemistry,
are home to unique life forms. Despite the presence of extremely high temperatures, low oxygen levels, and high levels
of toxins, invertebrates thrive in these extreme environments
(Van Dover 2000). Concerning the origin and distribution of
vent fauna, the argument between the antiquity and extinction/repopulation hypotheses has been going on almost since
the discovery of the hydrothermal vent (Little and Vrijenhoek
2003). Molecular divergence estimates of vent taxa may provide powerful evidence to help uncover the real story.
Decapods represent approximately 10% of all taxa identified from hydrothermal vents (Desbruyères et al. 2006) and
are dominant in many of these sites (Martin and Haney 2005).
Current opinions on decapod evolutionary histories are based
mainly on morphology and fossils. Although many research
groups have devoted considerable effort to this area since the
last century (reviewed by Bracken et al. 2009), results from
molecular dating of Decapoda remain sparse in comparison
with that of vertebrates such as mammals and amphibians.
The growing number of sequenced mitochondrial genomes
may provide sufficient sequence data from organisms with
relatively comparable evolutionary rates. In addition, in spite
of the relative richness of decapod fossils (Schweitzer et al.
2010), validity of using these fossils as molecular constraints
needs strict tests. In this study, we performed mitochondrial
phylogenomics and divergence time estimation using multiple fossils to reconstruct the systematic relationships,
evolutionary origins, and possible history of the distribution
of decapods from hydrothermal vents in the Western Pacific
and Indian Oceans.
In addition to the mitogenome sequences of Shinkaia
crosnieri and Gandalfus yunohana (Yang et al. 2008, 2010),
we sequenced the mitogenomes of five other vent decapods
(supplementary tables S1 and S3, Supplementary Material
online). We applied a multilocus phylogeny that proved
more apt to recover true relationships (Thorne and Kishino
2002). First, we separated mitogenomic sequences according
to the codon positions of protein-coding genes (PCGs) and
the stem/loop structures of RNA genes. Saturation analysis
discarded every third codon. Five representative partitioning
ß The Author 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please
e-mail: [email protected]
Mol. Biol. Evol. 30(2):305–309 doi:10.1093/molbev/mss224 Advance Access publication September 21, 2012
305
Letter
Hydrothermal vents are typically located in midocean ridges and back-arc basins and are usually generated by the movement of
tectonic plates. Life thrives in these environments despite the extreme conditions. In addition to chemoautotrophic bacteria,
decapod crustaceans are dominant in many of the hydrothermal vents discovered to date. Contrary to the hypothesis that these
species are remnants of relic fauna, increasing evidence supports the notion that hydrothermal vent decapods have diversified in
more recent times with previous research attributing the origin of alvinocarid shrimps to the Miocene. This study investigated
seven representative decapod species from four hydrothermal vents throughout the Western Pacific and Indian Oceans.
A partitioned mix-model phylogenomic analysis of mitochondrial DNA produced a consistent phylogenetic topology of these
vent-endemic species. Additionally, molecular dating analysis calibrated using multiple fossils suggested that both bythograeid
crabs and alvinocarid shrimps originated in the late Mesozoic and early Cenozoic. Although of limited sampling, our estimates
support the extinction/repopulation hypothesis, which postulates recent diversification times for most hydrothermal vent
species due to their mass extinction by global deep-water anoxic/dysoxic events during the Late Cretaceous and Early
Tertiary. The continental-derived property of the West Pacific province is compatible with the possibility that vent decapods
diversified from ancestors from shallow-water regions such as cold seeps. Our results move us a step closer toward understanding
the evolutionary origin of hydrothermal vent species and their distribution in the Western Pacific–Indian Ocean Region.
MBE
Yang et al. . doi:10.1093/molbev/mss224
strategies were compared using both harmonic mean (HM)
and generalized stepping-stone (SS) algorithms in Phycas (Fan
et al. 2011), where all 32 nucleotide partitions (p32; all partitions treated separately; supplementary table S4,
Supplementary Material online) were always assigned the
highest scores (supplementary table S6, Supplementary
Material online) and were therefore sustained throughout
our phylogenetic and molecular dating analyses.
Phylogeny was reconstructed under both the likelihood
and Bayesian frameworks. Three data sets were used: p32,
PCG nucleotides (26 partitions), and PCG amino acids
(13 partitions). Partitioned mix-model phylogenies were conducted by RAxML and MrBayes and by PhyloBayes, which
introduced the CAT mixture model. Six topologies were
observed (supplementary fig. S1, Supplementary Material
online), where conflicting points may have resulted from
short branches of shallow relationships (Wiens et al. 2008)
or phylogenetic bias by amino acids (Yang et al. 2008). A
Shimodaira-Hasegawa test assigned the highest score to
tree3; the other topologies showed no significant differences
(P > 0.05). Thus, we used tree3 for divergence time estimates.
Although sample sizes were limited, the relationships
within the endemic vent crabs and shrimps provided some
clues to their origin and distribution. Compared with
Austinograea alayseae (1,600–2,500 m) and A. rodriguezensis
(2,447–3,300 m), G. yunohana was associated with relatively
shallow waters (400–1,600 m) (Fujikura et al. 2008).
Interestingly, this shallow-to-deep pattern was also observed
for Bathymodilinae mussels (Jones et al. 2006), which may
indicate a universal mechanism for vent taxa distribution.
Also, Alvinocaris longirostris lies at the basal location of
Bresilioidea (Alvinocarididae). Considering A. longirostris is
the only decapod that occurs in both hydrothermal vents
and cold seeps (Kikuchi and Ohta 1995; Fujikura et al.
1999) and this species (and younger vent shrimp species)
may have emerged in regions other than hydrothermal
vents (e.g., cold seeps).
Multiple-fossil calibration can effectively reduce the
inaccuracy introduced by a single calibration. We selected
eight decapod fossil calibrations (table 1), some previously
validated (nodes 51, 59, 76, and 78; Porter et al. 2005) and
the rest unclear. However, we did not include the fossil record
of a hydrocarbon-seep decapod (S. katapsyxis; Schweitzer and
Feldmann 2008) as its date of 40 Ma was obviously too
young to calibrate the divergence between S. crosnieri and
Pagurus longicarpus. In the fossil-based cross-validation test
(Near et al. 2005), sequential fossil removals from greater to
smaller SS values did not effectively improve the estimation
(F < F0.05; supplementary fig. S2, Supplementary Material
online). No fossils showed a significant discrepancy and
could safely be used for the minimum constraints. In addition,
using Marshall’s method (2008), node 78 (“Reptantia”)
proved the calibration lineage with 529.3 and 396.9 Ma
being assessed with 95% and 50% confidence intervals
(CIs), respectively (supplementary calculation, Supplementary
Material online). Both constraints were used for molecular
dating, but no essential difference was identified (supplementary table S7, Supplementary Material online). Therefore, a
narrower calibration interval (354.0–396.9 Ma) was assigned
to node 78 for the final estimations. The Kolmogorov–
Smirnov test showed that these fossils were uniformly distributed, and none could be excluded as outliers.
Both the relative rate test of all taxon pairs (supplementary
table S8, Supplementary Material online) and the molecular
clock test of the whole data set rejected the null hypothesis of
global equal rates. This favored the relaxed molecular clock
model. To compare the impact of hard versus soft bounds on
the partitioned data set, we chose both multidivtime and
mcmctree for estimation. Multidivtime only supports hard
bounds, whereas mcmctree also implements soft bounds,
which can correct poor calibrations to help provide more
accurate estimates (Yang and Rannala 2005). Final results
were obtained from multidivtime analysis with eight minimum and two maximum hard constraints and from
mcmctree analysis with eight hard minimum and two soft
maximum constraints. Thirty-five out of 40 node intervals
overlapped on the two chronograms (fig. 1 and table 2).
The intersections of two 95% CI estimates on the Bythograeoidea and Bresilioidea nodes are located at 48.4–55.9
and 51.5–69.7 Ma, respectively, which refers to the Early Tertiary origin of bythograeid crabs and the Late Cretaceous/
Early Tertiary divergence of alvinocarid shrimps. Similar results
were obtained from molecular dating of five other topologies
with the exception of an underestimation from tree2
Table 1. Calibrations Used to Constraint the Divergence Time Estimates.
Nodea
63
71
51
53
74
76
59
78b
58
a
Taxonomy
Species
Eriocheir japonica
Eriocheir japonica
Scylla (genus)
Scylla costata
Palaemonoidea (superfamily)
Palaemon antonellae
Atyoidea (superfamily)
Delclosia roselli
Xanthoidea (superfamily)
Icriocarcinus xestos
Brachyura (infraorder)
Eocarcinus praecursor
Astacidea (infraorder)
Chimaerastacus pacifluvialis
“Reptantia”
Palaeopalaemon newberryi
Split of the Astacoidea and Parastacoidea
Geological Age (Ma)
Early Pliocene (Zanclean) (3.6–5.3)
Late Oligocene (Chattian) (23.0–28.4)
Early Cretaceous (Albian) (99.6–112)
Late Jurassic (145.5–161)
Late Cretaceous (Campanian-Maastrichtian) (65.5–83.5)
Early Jurassic (Pliensbachian) (190–195)
Middle Triassic (Upper Ladinian) (227–234)
Late Devonian (Famennian) (354–364)
Splitting of Pangea (–185)
Node numbers correspond to those in figure 1 and table 2.
A maximum constraint of 396.9 Ma was calculated and used for the divergence time estimates (supplementary methods, Supplementary Material online).
b
306
When Did Hydrothermal-Vent Decapods Appear? . doi:10.1093/molbev/mss224
MBE
FIG. 1. Chronogram of all decapod mitogenomes identified to date. Estimates are based on tree3 (supplementary fig. S1, Supplementary Material
online). Nodes are numbered for use throughout the article. Calibrated nodes are marked with solid circles (red for minimum, green for maximum, and
a mix for both constraints), and calibration dates are indicated by arrows. Multidivtime and mcmctree 95% CIs are shown as error bars in gray and light
blue, respectively. Time estimates and geological ages are depicted beneath the tree in different colors. Tectonic maps (adapted from Parker and Gealey
1985) describe several representative periods, indicated by double arrows on the time axis, and the current map with the locations of sampling shown
on the lower right.
(supplementary fig. S3, Supplementary Material online),
which may have resulted from a nucleotide calculation
based on the amino acid tree.
Although only three species were involved, our result on
vent shrimp origin contrasts with a previous Miocene estimate (Shank et al. 1999), where the evolutionary rate of the
mitochondrial cox1 gene was inferred from the geological age
of the closure of the Isthmus of Panama. However, this rate
may have been underestimated if the gene flow between the
Pacific and Atlantic vents did not occur directly through the
Isthmus of Panama but rather indirectly through the Indian
Ocean (Tunnicliffe et al. 1996). The present preliminary
hypothesis on the intermediate role of the Indian Ocean
should be supported with more extensive sampling, especially
from Atlantic species.
The Late Cretaceous/Early Tertiary, an active period in
both biological and geological terms, was marked by the
continuing separation of continents (fig. 1; Parker and
Gealey 1985). During this period, the back-arc systems of
Southeast Asia and northeast Australia were opened and
subsequently formed the main back-arc basins of the
Western Pacific. A new spreading center, the present
Rodriguez Triple Junction, also emerged in the southern
Indian Ocean. This period was also marked by global
deep-water anoxic/dysoxic events, which are thought to
underlie the extinction of nearly all contemporary vent
307
MBE
Yang et al. . doi:10.1093/molbev/mss224
Table 2. Divergence Time Estimates Obtained Using Multidivtime
and Mcmctree.
Nodea
41
42
43
44
45
46
47
48
49
50
51 ( > 99.6)
52
53 ( > 145.5)
54
55
56
57
58 (<185.0)
59 (>227.0)
60
61
62
63 (>3.6)
64
65
66
67
68
69
70
71 (>23.0)
72
73
74 (>65.5)
75
76 (>190.0)
77
78 (>354.0<396.9)
79
80 (root)
Multidivtimeb
82.3 ± 9.6
39.9 ± 5.5
66.6 ± 7.6
108.3 ± 10.5
132.6 ± 12.5
16.9 ± 3.8
62.5 ± 7.7
46.0 ± 6.4
66.0 ± 8.0
177.1 ± 15.9
250.3 ± 17.5
271.5 ± 17.2
312.8 ± 18.1
24.6 ± 3.8
35.0 ± 4.7
110.2 ± 10.8
103.6 ± 9.9
182.7 ± 2.1
258.3 ± 10.4
334.2 ± 9.4
264.6 ± 15.4
9.4 ± 2.1
12.1 ± 2.4
163.2 ± 12.3
215.7 ± 12.6
25.1 ± 3.4
27.8 ± 3.7
44.6 ± 5.1
64.2 ± 6.9
87.1 ± 7.8
100.0 ± 8.3
36.1 ± 4.8
64.2 ± 6.9
151.6 ± 10.6
192.1 ± 11.3
232.4 ± 11.9
339.5 ± 8.8
357.5 ± 3.3
404.3 ± 15.3
411.4 ± 16.8
Mcmctreeb
58.1 ± 7.0
29.8 ± 3.9
40.4 ± 4.4
77.6 ± 6.8
84.2 ± 7.4
10.2 ± 2.8
42.9 ± 6.1
50.2 ± 6.0
63.9 ± 6.7
200.8 ± 15.3
280.8 ± 17.1
306.5 ± 16.8
313.7 ± 17.0
25.7 ± 3.4
33.1 ± 3.4
110.1 ± 12.1
134.1 ± 14.2
257.5 ± 15.8
334.1 ± 10.7
346.8 ± 9.1
286.6 ± 13.6
3.7 ± 1.5
5.1 ± 1.0
183.1 ± 12.2
224.4 ± 11.6
25.7 ± 2.8
26.9 ± 2.8
37.6 ± 4.1
69.7 ± 6.6
92.8 ± 7.2
100.0 ± 7.3
41.0 ± 4.6
58.4 ± 5.5
170.2 ± 10.7
201.6 ± 10.2
238.0 ± 10.4
344.8 ± 9.2
359.9 ± 5.5
431.0 ± 13.5
433.2 ± 13.6
NOTE.—Lines of calibrated nodes and Bythograeoidea/Bresilioidea nodes appear in
italicized and underlined text, respectively.
a
Node numbers correspond to those in figure 1. Minimum and maximum calibrations are shown as “>” and “<” respectively.
b
Estimated ages are expressed as the mean ± standard error of the mean.
species (Jacobs and Lindberg 1998). The vent areas of these
continental-derived back-arc basins may have been recolonized by surrounding shallow-water species after this mass
extinction, for example, via stepping stones from cold seeps
(as in the case of A. longirostris). Evidence for the recent diversification of many vent invertebrate species (<100 Ma)
also supports the extinction/repopulation hypothesis (Van
Dover et al. 2002; Little and Vrijenhoek 2003).
308
Future investigations of deep-sea hydrothermal fields
should help clarify the evolutionary history and historical distribution events associated with vent taxa. Our findings shed
some light on these processes.
Materials and Methods
See supplementary methods, Supplementary Material online.
Supplementary Material
Supplementary tables S1–S8, figures S1–S3, methods, and
calculation are available at Molecular Biology and Evolution
online (http://www.mbe.oxfordjournals.org/).
Acknowledgments
The authors thank Andrew Roger and four anonymous
reviewers for their helpful comments. They also thank Chris
Wood of Zhejiang University for critical reading of this
manuscript. This work was supported by the National Basic
Research Program of China (973 Program, 2010CB833803),
the National Natural Sciences Foundation of China
(41006085), and the 863 Program of China (2012AA092103).
References
Bracken HD, Toon A, Felder DL, Martin JW, Finley M, Rasmussen J,
Palero F, Crandall KA. 2009. The decapod tree of life: compiling
the data and moving toward a consensus of decapod evolution.
Arthropod Syst Phylogeny. 67:99–116.
Desbruyères D, Segonzac M, Bright M. 2006. Handbook of deep-sea
hydrothermal vent fauna. Linz (Austria): Landesmuseen.
Fan Y, Wu R, Chen MH, Kuo L, Lewis PO. 2011. Choosing among
partition models in Bayesian phylogenetics. Mol Biol Evol. 28:
523–532.
Fujikura K, Hashimoto J, Okutani T. 1999. Estimated population densities of megafauna in two chemosynthetic-based communities: a
cold seep in Sagami Bay and a hydrothermal vent in the Okinawa
Trough. Benthos Res. 57:21–30.
Fujikura K, Okutani T, Maruyama T. 2008. Deep-sea life: biological observations using research submersibles. Hadano (Japan): Tokai
University Press.
Jacobs DK, Lindberg DR. 1998. Oxygen and evolutionary patterns in the
sea: onshore/offshore trends and recent recruitment of deep-sea
faunas. Proc Natl Acad Sci U S A. 95:9396–9401.
Jones WJ, Won Y-J, Maas PAY, Smith PJ, Lutz RA, Vrijenhoek RC. 2006.
Evolution of habitat use by deep-sea mussels. Mar Biol. 148:841–851.
Kikuchi T, Ohta S. 1995. Two caridean shrimps of the families
Bresiliidae and Hippolytidae from a hydrothermal field on
the Iheya Ridge, off the Ryukyu Islands, Japan. J Crust Biol. 15:
771–785.
Little CTS, Vrijenhoek RC. 2003. Are hydrothermal vent animals living
fossils? Trends Ecol Evol. 18:582–588.
Marshall CR. 2008. A simple method for bracketing absolute divergence
times on molecular phylogenies using multiple fossil calibration
points. Am Nat. 171:726–742.
Martin JW, Haney TA. 2005. Decapod crustaceans from hydrothermal
vents and cold seeps: a review through 2005. Zool J Linn Soc. 145:
445–522.
Near TJ, Meylan PA, Shaffer HB. 2005. Assessing concordance of fossil
calibration points in molecular clock studies: an example using turtles. Am Nat. 165:137–146.
When Did Hydrothermal-Vent Decapods Appear? . doi:10.1093/molbev/mss224
Parker ES, Gealey WK. 1985. Plate tectonic evolution of the Western
Pacific-Indian Ocean region. Energy 10:249–261.
Porter ML, Pérez-Losada M, Crandall KA. 2005. Model-based multi-locus
estimation of decapod phylogeny and divergence times. Mol Phyl
Evol. 37:355–369.
Schweitzer CE, Feldmann RM. 2008. New Eocene hydrocarbon seep
decapod crustacean (Anomura: Galatheidae: Shinkaiinae) and its
paleobiology. J Paleontol. 82:1021–1029.
Schweitzer CE, Feldmann RM, Garassino A, Karasawa H, Schweigert G.
2010. Systematic list of fossil decapod crustacean species. Leiden
(the Netherlands): BRILL.
Shank TM, Black MB, Halanych KM, Lutz RA, Vrijenhoek RC. 1999.
Miocene radiation of deep-sea hydrothermal vent shrimp
(Caridea: Bresiliidae): evidence from mitochondrial cytochrome oxidase subunit I. Mol Phyl Evol. 13:244–254.
Thorne JL, Kishino H. 2002. Divergence time and evolutionary
rate estimation with multilocus data. Syst Biol. 51:689–702.
Tunnicliffe V, Fowler CMR, McArthur AG. 1996. Plate tectonics history
and hot vent biogeography. In: MacLeod CJ, Tyler CJ, Tyler PA,
Walker CL, editors. Tectonics, magmatic, hydrothermal and biological segmentation of mid-ocean ridges. London (UK): The
Geological Society. p. 225–238.
MBE
Van Dover CL. 2000. The ecology of deep-sea hydrothermal vents.
Princeton (NJ): Princeton University Press.
Van Dover CL, German CR, Speer KG, Parson LM, Vrijenhoek RC. 2002.
Evolution and biogeography of deep-sea vent and seep invertebrates. Science 295:1253–1257.
Wiens JJ, Kuczynski CA, Smith SA, Mulcahy DG, Sites JW Jr, Townsend
TM, Reeder TW. 2008. Branch lengths, support, and congruence:
testing the phylogenomic approach with 20 nuclear loci in snakes.
Syst Biol. 57:420–431.
Yang J-S, Nagasawa H, Fujiwara Y, Tsuchida S, Yang W-J. 2008. The
complete mitochondrial genome sequence of the hydrothermal
vent galatheid crab Shinkaia crosnieri (Crustacea: Decapod:
Anomura): a novel arrangement and incomplete tRNA suite. BMC
Genomics 9:504.
Yang J-S, Nagasawa H, Fujiwara Y, Tsuchida S, Yang W-J. 2010.
The complete mitogenome of the hydrothermal vent crab
Gandalfus yunohana (Crustacea: Decapoda: Brachyura): a link
between the Bythograeoidea and Xanthoidea. Zool Scr. 39:
621–630.
Yang Z, Rannala B. 2005. Bayesian estimation of species divergence times
under a molecular clock using multiple fossil calibrations with soft
bounds. Mol Biol Evol. 23:212–226.
309