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Evidence for a clade composed of molluscs with serially repeated structures: Monoplacophorans are related to chitons

May 16, 2006
103 (20) 7723-7728

Abstract

Monoplacophorans are among the rarest members of the phylum Mollusca. Previously only known from fossils since the Cambrian, the first living monoplacophoran was discovered during the famous second Galathea deep-sea expedition. The anatomy of these molluscs shocked the zoological community for presenting serially repeated gills, nephridia, and eight sets of dorsoventral pedal retractor muscles. Seriality of organs in supposedly independent molluscan lineages, i.e., in chitons and the deep-sea living fossil monoplacophorans, was assumed to be a relict of ancestral molluscan segmentation and was commonly accepted to support a direct relationship with annelids. We were able to obtain one specimen of a monoplacophoran Antarctic deep-sea species for molecular study. The first molecular data on monoplacophorans, analyzed together with the largest data set of molluscs ever assembled, clearly illustrate that monoplacophorans and chitons form a clade. This “Serialia” concept may revolutionize molluscan systematics and may have important implications for metazoan evolution as it allows for new interpretations for primitive segmentation in molluscs.
Molluscs (snails, slugs, clams, mussels, squids, octopuses, chitons, etc.) exhibit the largest disparity of all animal phyla and rank second behind arthropods in species diversity. Although the majority of species still remain in the oceans, where they inhabit all types of ecosystems from the upper littoral to the abyss, they are also major components of freshwater and terrestrial habitats. Molluscan diversity can be extraordinary in tropical and temperate regions (1) but can be found at all latitudes.
The phylogenetic position of molluscs within Spiralia is supported by the presence of spiral cleavage and a trochophore larva (2, 3), although their immediate sister group remains uncertain. Although some have proposed a relationship to sipunculans (peanut worms) (4) or entoprocts (5), most researchers still consider molluscs closely related to annelids, in part because of the assumption that they retain traces of segmentation (3). The removal of arthropods and their relatives from the clade Spiralia (6) and the evolutionary importance given to segmentation in annelids have contributed to reengaging the debate about ancestral segmentation in other spiralian clades such as molluscs. This supposed segmentation in molluscs is often justified by the presence of eight sets of pedal retractor muscles and serially repeated gills in both chitons (Polyplacophora) (7) and members of the living fossil class Monoplacophora (810), based on the assumption that both groups are basal within their distinct lineages. Certain bivalves also exhibit multiple pedal retractor muscles (11), and caudofoveate larvae show seven transverse rows of calcareous spicules on the dorsal side (3).
Monoplacophorans are perhaps the least known members of the phylum Mollusca. They have been thought to be “primitive” forms based on their rich fossil record, which dates back to Cambrian–Devonian periods (8). After the recent discovery of the first living monoplacophoran, Neopilina galatheae, during the second Danish Galathea expedition (8), it was suggested that its dorsal uncoiled cap-like shell (Fig. 1) fit the prevalent HAM (hypothetical ancestor mollusc) theories (12). This idea positioned monoplacophorans at the base of “Conchifera,” a clade that includes all molluscs with a true dorsal shell (the classes Monoplacophora, Gastropoda, Cephalopoda, Bivalvia, and Scaphopoda). Neopilina’s newly discovered anatomy [with serially repeated gills and eight sets of dorsoventral pedal retractor muscles, as those found in chitons, and serially repeated nephridia (8, 10)] suggested that serial homology was present at least in two extant molluscan lineages, Aculifera (molluscs with spicules) and Conchifera (molluscs with a true shell).
Fig. 1.
Details of L. antarctica Warén & Hain, 1992. (A) Shell, dorsal view. Note the limpet-like shape with anterior apex and light reflection caused by prismatic and inner nacreous layers. (B) Scanning electron micrograph of the shell (dorsolateral view from left side). (C) Soft body (shell removed) (dorsal view). Note the characteristic spiral intestine (left) filled with mineral particles, brown-dotted esophageal pouches (right), and serial shell muscles (arrows). (D) Soft body, ventral view. Note the round sucker-like foot (central), serial gills (arrows), and mouth area with tentacles (right).
Although a generalized mollusc is portrayed as a limpet-like form with a creeping foot and a dorsal shell made of calcium carbonate (as in the class Monoplacophora), other body plans such as those of the worm-like, shell-less fossorial chaetodermomorphs (class Caudofoveata) and neomeniomorphs (class Solenogastres), or the bentho-pelagic cephalopods (class Cephalopoda) differ radically from this prototype. Mussels, clams and their kind (class Bivalvia) are also quite divergent from this model. Furthermore, modern chitons (class Polyplacophora) have a distinct dorsal “shell” formed by eight interlocking plates. In fact, the disparity of mollusc body plans is so great that it is quite difficult to find a single trait shared by all seven classes of molluscs (13).
Our understanding of relationships among the major molluscan lineages is still in its infancy. Recent attempts to resolve their relationships by using morphological data found limitations in character homology definitions and polarization because of uncertainty regarding the molluscan sister group (4, 5, 14). Molecular attempts have not been conclusive, but they have aided to refute the “Diasoma” hypothesis (a clade uniting bivalves and scaphopods). Most recent molecular analyses suggest a relationship of scaphopods to cephalopods and gastropods (1517), further corroborated through morphological and developmental studies (5, 18). To date, the phylogenetic position of monoplacophorans remained untested using molecular data because of difficulties in collecting live samples of these enigmatic animals.

Results and Discussion

An Antarctic Benthic Deep-Sea Biodiversity oceanographic campaign (ANDEEP III) with the RV Polarstern to the Weddell Sea (Antarctica), 3 km southwest of Wegener Canyon at ≈3,100-m depth, yielded one small specimen (1.7-mm shell length) of the monoplacophoran Laevipilina antarctica Warén & Hain, 1992 (19), one of the 26 known species of this group of molluscs (9, 20). The single specimen was obtained from an epibenthic sledge sample that had been fixed with precooled 96% EtOH for molecular studies and stored at −20°C for 48 h. The shell (ZSM Moll 20050866; Fig. 1 A and B) was removed for gross anatomy and SEM examination, the soft body was photographed (Fig. 1 C and D), and half of the specimen was used for molecular work.
Although monoplacophoran DNA was highly degraded, perhaps because of bulk fixation of the sediment performed in the vessel, we were able to amplify and sequence a 1.2-kb fragment of the large nuclear ribosomal subunit (28S rRNA). This gene has proven to be highly informative in recent studies on metazoan and molluscan evolution (17, 21).
Analysis of the data using a single-step phylogenetic approach with direct optimization (Fig. 2) and a two-step approach using Bayesian phylogenetics (Fig. 4, which is published as supporting information on the PNAS web site) exhibited congruent results suggesting monophyly of molluscs as well as that of the molluscan classes Caudofoveata, Solenogastres, Scaphopoda, and Cephalopoda. Resolution with high jackknife support is found mostly within the main clades of Scaphopoda (Dentaliida and Gadilida), Cephalopoda (Nautiloidea, Coleoidea, and the sister group relationship of the vampire squid to decabrachians, which include the giant squid Architeuthis dux and the pygmy squid Idiosepius pygmaeus), as well as within Bivalvia (Palaeoheterodonta and Euheterodonta) and Gastropoda (Patellogastropoda, Neritopsina, Caenogastropoda, and Heterobranchia). However, the available sequence data do not recover monophyly of Gastropoda or Bivalvia, which are both diphyletic, with patellogastropods separated from the other gastropods and heteroconchs separated from the remainder of the bivalves (protobranchs and pteriomorphians).
Fig. 2.
Phylogenetic tree depicting the relationships of Monoplacophora to other molluscs based on the combined analysis of all molecular loci. Shown is strict consensus of two most parsimonious trees at 64,679 weighted steps (gap opening cost of 3, gap extension cost of 1, all base transformations cost 2) for the analysis of all data under direct optimization with tree fusing. Numbers on branches indicate jackknife support values. Gastropods (in red) and bivalves (in blue) appear diphyletic. Polyplacophora and Monoplacophora form a well supported clade (95% jackknife support). The monoplacophoran species (purple) appears nested within chitons (dark green), but nodal support for its exact position is low. The tree shows monophyly of molluscs, as well as that of Scaphopoda, Cephalopoda, Caudofoveata, and Solenogastres.
Nodal support for interclass relationships or for the relationships of the two clades of bivalves and gastropods is low in general, but a clade containing Monoplacophora and Polyplacophora received strong nodal support (90–100% jackknife support value depending on the analysis, as well as 1.0 posterior probability). Interestingly, this clade, which we name “Serialia,” contains the two classes whose members present a variable number of serially repeated gills and eight sets of dorsoventral pedal retractor muscles. This result clearly contrasts with previous cladistic hypotheses suggesting that Monoplacophora constitute the sister group to the remainder of the conchiferans (4, 5, 14), those molluscs with a true shell unlike that of chitons or the vermiform aplacophorans, although it finds no clear support for the exact position of Serialia. To our knowledge, this is also the first published analysis that demonstrates monophyly of the phylum Mollusca using a range of appropriate outgroups, but we caution the reader to consider that jackknife support for molluscan monophyly is low. The results further support a previous study (22) that indicates that Xenoturbella is not a bivalve mollusc.
All analyses (including different optimality criteria and alternative models of indel and base substitutions) support a Polyplacophora plus Monoplacophora clade. However, L. antarctica appears nested within the chiton tree in some analyses, a result that may look suspicious at first. Evidence for including Monoplacophora within Polyplacophora is restricted to one node, which groups nonlepidopleurid chitons with the monoplacophoran species (70% jackknife support; Fig. 1), but this is not the case when considering only the 1.2-kb region of 28S rRNA amplified for Laevipilina (tree not shown). Furthermore, detailed examination of the DNA sequences clearly illustrates that chitons share unambiguous positions in the alignment not found in L. antarctica (Fig. 3). This fact eliminates the possibility of contaminant DNA in our analysis.
Fig. 3.
Alignment of one of the regions of 28S rRNA illustrating that L. antarctica does not share unique chiton synapomorphies (asterisks).
Evidence for a clade of serialian molluscs is important for our current understanding of molluscan relationships and may have implications for deeper metazoan evolution. This new evidence may imply that serially repeated structures (e.g., gills and pedal retractor muscles in both monoplacophorans and chitons) are not primitive for molluscs, as was previously thought (9). However, it is fair to mention that additional types of serial repetition of dorsoventral musculature have been reported in other molluscan groups (23), including the eight sets of pedal retractors of the Ordovician lucinoid bivalve Babinka (11), the serially repeated rows of spicules in caudofoveate larvae (3), or the two pairs of gills and nephridia in cephalopods (3). Whether these represent true seriality or not may have profound implications in reconstructing the molluscan common ancestor, but it does not contradict the evidence of our Serialia clade.
The classical hypothesis for the position of monoplacophorans as basal conchiferans relies heavily on the presence of a true dorsal shell with similar mineralogical composition to that of many basal members of each conchiferan class. However, the mode of shell deposition by the mantle edge and the microstructure and composition of the chitinous organic layer in monoplacophorans differ from those of higher conchiferans or polyplacophorans (9, 24, 25), which makes monoplacophorans apomorphic (derived) in the form of shell deposition. The rejection of conchiferan monophyly based on shell deposition would be consistent with our findings, which suggest that serial repetition of anatomical structures such as gills and muscles may have evolved once in the common ancestor of chitons and monoplacophorans. Therefore, serial repetition of these structures could constitute a derived feature that would not support the hypothesis of a segmented ancestral mollusc. Again, other interpretations may exist if the pedal scars of Bibankia were the result of muscles homologous to the serialian dorsoventral pedal muscles.
Molluscs are undoubtedly one of the animal phyla with the largest disparity. Numerous Cambrian forms such as Wiwaxia and Halkieria or the Silurian Acaenoplax have been more or less ambiguously assigned to this animal phylum (2628). Kimberella is another putative mollusc extending the age of the group back to the Neoproterozoic (29). Although chitons were once thought to have changed little since their first appearance in the Late Cambrian period (30), recent discoveries of articulated polyplacophorans and multiplacophorans from the Ordovician to the Carboniferous (31, 32) suggest that a much larger disparity evolved during the Paleozoic. Perhaps such an episode of diversification is responsible for the two modern anatomies of molluscs with conspicuous serial repetition of organs, but no explanation for their divergent evolution of shell morphologies can be provided at this point. Recognition of a serialian clade comprised of chitons and monoplacophorans broadens our perspective toward new interpretations of molluscan anatomy and once more questions preconceived ideas on molluscan relationships that rely almost entirely on shell morphology.
Here we provide the first molecular test for the phylogenetic position of Monoplacophora by using sequence data from a deep-sea monoplacophoran species from Antarctica. Contrary to all previously published accounts, which placed monoplacophorans as a sister group to higher, i.e., shelled, molluscs, our data strongly support a clade including Monoplacophora and Polyplacophora. This rather surprising result from a conchological perspective is congruent with soft anatomy data. It furthermore reopens the debate about the putative ancestral segmentation of molluscs (3), because serial repetition of gills and pedal retractor muscles may be derived and not primitive features within molluscs. If this were the case, little evidence would remain for the case of homology of segmentation in annelids and serial repetition in molluscs (33), as confirmed in part by recent reevaluation of their early development (34, 35).

Materials and Methods

Species Sampling.

Taxon sampling was carefully designed following original and published work on the internal phylogeny of chitons, bivalves, cephalopods, gastropods, and scaphopods (15, 16, 3638). Outgroups were selected among other spiralian protostomes (lophotrochozoans) (39). The enigmatic Xenoturbella was also included because it was once postulated to be a derived mollusc, although more recent data consider it to be an ancestral deuterostome (22). In total, we analyzed 101 molluscs including 2 Caudofoveata, 2 Solenogastres, 13 Polyplacophora, 1 Monoplacophora, 9 Scaphopoda, 32 Gastropoda, 24 Bivalvia, and 18 Cephalopoda (see Table 1).
Table 1.
Taxon sampling and GenBank accession numbers employed in this study
Phylum/class Species GenBank accession nos.
18S rRNA 28S rRNA H3 COI 16S rRNA
Nemertea Lineus bilineatus DQ279932 DQ279947 DQ279996 DQ280014 DQ280022
Annelida Paranerilla limicola DQ279933 DQ279948     DQ280023
Brachiopoda Neocrania anomala DQ279934 DQ279949 DQ279997   DQ280024
Entoprocta Loxosomella murmanica AY218100 DQ279950 AY218150    
Xenoturbellida Xenoturbella bocki AY291292 DQ279951      
Sipuncula Phascolion strombi DQ299984 AY210468 DQ279998    
Cycliophora Symbion americanus AY218107 AY210472 AY218153 AY218085 DQ280025
Mollusca            
    Caudofoveata Chaetoderma nitidulum AY377658 AY145397 AY377763 AY377726 AY377612
  Scutopus ventrolineatus X91977        
    Solenogastres Helicoradomenia sp. AY21210   AY377764 AY377725 AY377613
  Epimenia cinerea AY377657 AY377691 AY377765 AY377723 AY377615
    Polyplacophora Lepidopleurus cajetanus AF120502 AF120565 AY377735 AF120626 AY377585
  Leptochiton asellus AY377631 AY145414 AY377734   AY377586
  Callochiton septemvalvis AY377632 DQ279952 AY377736 AY377700  
  Chaetopleura apiculata AY377636 AY145398 AY377741 AY377704 AY377590
  Ischnochiton comptus AY377639 AY145412 AY377744 AY377709 AY377593
  Callistochiton antiquus AY377645 DQ279953 AY377749 AY377712 AY377599
  Lorica volvox AY377647 DQ279954 AY377751   AY377601
  Chiton olivaceus AY377651 DQ279955 AY377755 AY377716 AY377605
  Mopalia muscosa AY377648 DQ279956 AY377752 AY377713 AY377602
  Tonicella lineata AY377635 AY377665 AY377739 AY377702 AY377588
  Acanthochitona crinita AF120503 DQ279957 AY377759 AF120627 AY377609
  Cryptochiton stelleri AY377655 AY377686 AY377760 AY377720 AY377610
  Cryptoplax japonica AY377656 AY145402 AY377761   AY377611
Monoplacophora Laevipilina antarctica   DQ279958      
Scaphopoda Dentalium inaequicostatum DQ279935 DQ279959 DQ279999 DQ280015 DQ280026
  Rhabdus rectius AF120523 AF120580 AY377772 AF120640 AY377619
  Antalis pilsbryi AF120522 AF120579   AF120639  
  Antalis entalis DQ279936 AY145388 DQ280000 DQ280016 DQ280027
  Fustiaria rubescens AF490597        
  Entalina tetragona AF490598        
  Pulsellum affine AF490600        
  Siphonodentalium lobatum AF490601        
  Cadulus subfusiformis AF490603        
Bivalvia Solemya velum AF120524 AY145421 AY070146 U56852 DQ280028
  Nucula sulcata DQ279937 DQ279960 DQ280001 DQ280017 DQ280029
  Nuculana minuta DQ279938 DQ279961 DQ280002 DQ280018 DQ280030
  Yoldia limatula AF120528 AY145424 AY070149 AF120642  
  Mytilus galloprovincialis L33452 AB103129 AY267748 AY497292 AY497292
  Arca imbricata/A. ventricosa AY654986 AB101612 AY654989 AY654988  
  Pteria hirundo/P. loveni AF120532 AB102767   AF120647 DQ280031
  Ostrea edulis L49052 AF137047/AF120596 AY070151 AF120651 DQ280032
  Limaria hians/L. fragilis AF120534 AB102742 AY070152 AF120650  
  Anomia ephippium/A. sinensis AF120535 AB102739      
  Chlamys varia DQ279939 DQ279962 DQ280003   DQ280033
  Neotrigonia margaritacea AF411690 DQ279963 AY070155 U56850 DQ280034
  Margaritifera auricularia AY579097 AY579113 AY579137 AY579125 DQ280035
  Anodonta sp. AY579090 DQ279964 AY579132 AY579122  
  Cardita calyculata AF120549 AF120610 AY070156 AF120660  
  Astarte castanea AF120551 AF131001 DQ280004 AF120662  
  Abra nitida DQ279940 DQ279965 DQ280005    
  Phaxas pellucidus DQ279941 AY145420 DQ280006 DQ280019 DQ280036
  Parvicardium minimum DQ279942 DQ279966 DQ280007   DQ280037
  Dreissena polymorpha AF120552 AF131006 AY070165 AF120663 DQ280038
  Corbicula fluminea/C. japonica AF120557 AB126330 AY070161 AF120666 DQ280039
  Mercenaria mercenaria AF120559 AF131019 DQ280008 AF120668 DQ280040
  Chamelea striatula DQ279943 DQ279967 DQ280009   DQ280041
  Mya arenaria AF120560 AB126332 AY377770 AY070140 AY377618
Cephalopoda Nautilus pompilius AY557452 AY145417   AY557514 AY377628
  Nautilus scrobiculatus AF120504 AF120567 AF033704   U11606
  Stauroteuthis syrtensis AY557457 DQ279968 AY557406 AF000067 DQ280042
  Vampyroteuthis infernalis AY557459 AH012197 AY557408 AF000071 DQ280043
  Bathypolypus arcticus AY557465 AY557554   AF000029 DQ280044
  Sepia officinalis AY557471 AY557560 AY557415 AF000062 DQ093491
  Sepiola affinis AY557474 AY557562 AY557418 AY557523 AY293667
  Heteroteuthis hawaiiensis AY557472 DQ279969 AY557416 AF000044 AY293680
  Rossia palpebrosa AY557473 AY557561 AY557417 AF000061 DQ280045
  Spirula spirula AY557476 AY557563 AY557420 AY293709 AY293659
  Idiosepius pygmaeus AY557477 AY293684 AY557421 AY293708 AY293658
  Loligo pealei AT557479 AH012196 AY557423 AF120629 AF110079
  Architeuthis dux AY557482 DQ279970 AY557426 AF000027 AY377629
  Cranchia scabra AY557487 AY557571 AY557430 AF000035 DQ280046
  Histioteuthis hoylei AY557500 AY557584 AY557442 AF000045 DQ280047
  Lepidoteuthis grimaldii AY577503 AY557587 AY557445 AF000049 DQ280048
  Ommastrephes bartrami AY557510 AY557594 AY557451 AF000057 DQ280049
  Moroteuthis knipovitchi AY557512 AY557596 AY557453 AY557543 DQ280050
    Gastropoda Cellana sp. DQ093425 DQ279971 DQ093493 DQ093515 DQ093467
  Eulepetopsis vitrea DQ093427 DQ279972 DQ093495 DQ093516 DQ093468
  Cocculina messingi/Cocculina sp. AF120508 DQ279973 AY377777 AY377731 AY377624
  Alcadia dysonia DQ093428 DQ279974 DQ093496   DQ093469
  Theodoxus fluviatilis AF120515 DQ279975   AF120633 DQ093470
  Nerita funiculata DQ093429 DQ279976 DQ093497 DQ093517 DQ093471
  Cyathermia naticoides DQ093430 DQ279977 DQ093498 DQ093518 DQ093472
  Depressigyra globulus DQ093431 DQ279978 DQ093499 DQ093519 DQ093473
  Perotrochus midas AF120510 DQ093453 DQ093500 AY296820 DQ093474
  Entemnotrochus adansonianus AF120509 DQ279979 AY377774   AY377621
  Lepetodrilus elevatus DQ093432 AY145413 DQ093501 DQ093520 DQ093475
  Diodora graeca AF120513 DQ279980 DQ093502 AF120632 DQ093476
  Haliotis tuberculata/H. discus AF120511 AY145418 AY070145 AY377729 AY377622
  Sinezona confusa AF120512 DQ279981 AY377773 AF120631  
  Bathymargarites symplector DQ093433 DQ279982 DQ093503 DQ093521 DQ093477
  Aperostoma palmeri DQ093435 DQ279983 DQ093505 DQ093523 DQ093479
  Pomacea bridgesi DQ093436 DQ279984 DQ093506 DQ093524 DQ093480
  Viviparus georginaus AF120516 AF120574 AY377779 AF120634 AY377626
  Balcis eburnea AF120519 AF120576   AF120636 DQ280051
  Crepidula fornicata AY377660 AY145406 AY377778 AF353154 AY377625
  Littorina littorea DQ093437 DQ279985 DQ093507 DQ093525 DQ093481
  Truncatella guerini AF120518 AF120575   AF120635  
  Bolinus brandaris DQ279944 DQ279986 DQ280010 DQ280020 DQ280052
  Raphitoma linearis DQ279945 DQ279987 DQ280011   DQ280053
  Philine aperta DQ093438 DQ279988 DQ093508   DQ093482
  Creseis sp. DQ279946 DQ279989 DQ280012 DQ280021  
  Peltodoris atromaculata AF120521 DQ279990 DQ280013 AF120637 DQ280054
  Salinator solida DQ093440 DQ279991 DQ093510 DQ093528 DQ093484
  Onchidella sp. DQ093441 DQ279992 DQ093511 DQ093529 DQ093485
  Siphonaria pectinata X91973 DQ279993 AY377780 AF120638 AY377627
  Ophicardelus ornatus DQ093442 DQ279994 DQ093512 DQ093530 DQ093486
  Micromelo undatus DQ093443 DQ279995 DQ093513   DQ093487

Molecular Data.

Molecular data were obtained from ethanol-preserved specimens following standard protocols for molluscan samples (15, 37, 38, 40). Monoplacophoran DNA samples were extracted from the half specimen preserved in 96% EtOH. DNA from preserved tissues was extracted by using the Qiagen DNeasy tissue kit. Data include complete sequences of 18S rRNA, a 3-kb fragment of 28S rRNA, the protein-coding nuclear gene histone H3, and two mitochondrial gene fragments for cytochrome c oxidase subunit I and 16S rRNA, totaling ≈6.5 kb per complete taxon (see Table 1). The amplified samples were purified by using the QIAquick PCR purification kit (Qiagen), labeled by using BigDye Terminator 3.0 (Applied Biosystems), and sequenced with an ABI 3730 genetic analyzer (Applied Biosystems) following the manufacturer’s protocols. Chromatograms obtained from the automatic sequencer were read, and “contig sequences” were assembled by using the editing software sequencher 4.0 and further manipulated in gde 2.2 (41).
From the five different molecular loci chosen for this study, only one yielded positive amplification for the monoplacophoran specimen. This fragment corresponds to a 1.2-kb segment of 28S rRNA obtained by amplifying two overlapping fragments using primer pairs 28Sa and 28S rd5b (5′-GACCCGTCTTGAAGCACG-3′ and 5′-CCACAGCGCCAGTTCTGCTTAC-3′) and 28S rd4.8a and 28S rd7b1 (5′-ACCTATTCTCAAACTTTAAATGG-3′ and 5′-GACTTCCCTTACCTACAT-3′).

Data Analyses.

DNA sequence data were analyzed following two approaches. First, a dynamic homology approach (“single-step phylogenetics”) using parsimony as an optimality criterion for direct optimization (42) was undertaken in the computer package poy 3.0.11 (43). Second, a static homology approach (“two-step phylogenetics”) using a model-based approach was executed under Bayesian phylogenetics in mrbayes 3.1.1 (44).
For the direct optimization analysis, tree searches were conducted by a combination of random addition sequences with multiple rounds of tree fusing (45) on a small 50-processor cluster assembled at Harvard University. Support measures were estimated by using jackknifing with a character probability of deletion of e−1 (46). The data were analyzed for all genes in combination as well as restricted to the 28S rRNA fragment sequenced for L. antarctica under different analytical parameter sets (47, 48).
Bayesian posterior probabilities were calculated by using a general time-reversible model with corrections for the proportion of invariant sites and a discrete gamma distribution, as selected in modeltest 3.7 (49) under the Akaike Information Criterion (50). Two runs of 106 generations were performed, storing 1/100th visited trees. Results from mrbayes 3.1.1 were visualized in the program tracer 1.3 (51), which served to determine the burnin, which differed considerably in the two runs. Aligned data were obtained from the implied alignment (52) generated in poy 3.0.11 for the analyses presented in Fig. 2.

Data Availability

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. DQ279932–DQ280054).

Acknowledgments

We are indebted to the numerous colleagues who supplied tissue samples, without whom this work would not have been possible. Rebecca Budinoff assisted with laboratory work. Angelika Brandt organized the ANDEEP III expedition. Katrin Linse, Enrico Schwabe, and the onboard sorting team provided the monoplacophoran specimen. Greg Edgecombe, Andy Knoll, Sigurd von Boletzky, Claus Nielsen, Jim Valentine, and an anonymous reviewer provided comments that helped to improve this article. Enrico Schwabe provided pictures for Fig. 1 A and B. This material is based on work supported by the National Science Foundation Assembling the Tree of Life Program (Grant 0334932 to G.G.) and Population Biology Program (Grant 0316516 to M.K.N.). Field activities of M.S. and his team were supported by the GeoBioCenterLMU. This article is ANDEEP contribution no. 58.

Supporting Information

Adobe PDF - 02578Fig4.pdf
Adobe PDF - 02578Fig4.pdf

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Information & Authors

Information

Published in

Go to Proceedings of the National Academy of Sciences
Go to Proceedings of the National Academy of Sciences
Proceedings of the National Academy of Sciences
Vol. 103 | No. 20
May 16, 2006
PubMed: 16675549

Classifications

Data Availability

Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. DQ279932–DQ280054).

Submission history

Received: December 5, 2005
Published online: May 16, 2006
Published in issue: May 16, 2006

Keywords

  1. Antarctica
  2. deep sea
  3. Mollusca
  4. Monoplacophora
  5. phylogeny

Acknowledgments

We are indebted to the numerous colleagues who supplied tissue samples, without whom this work would not have been possible. Rebecca Budinoff assisted with laboratory work. Angelika Brandt organized the ANDEEP III expedition. Katrin Linse, Enrico Schwabe, and the onboard sorting team provided the monoplacophoran specimen. Greg Edgecombe, Andy Knoll, Sigurd von Boletzky, Claus Nielsen, Jim Valentine, and an anonymous reviewer provided comments that helped to improve this article. Enrico Schwabe provided pictures for Fig. 1 A and B. This material is based on work supported by the National Science Foundation Assembling the Tree of Life Program (Grant 0334932 to G.G.) and Population Biology Program (Grant 0316516 to M.K.N.). Field activities of M.S. and his team were supported by the GeoBioCenterLMU. This article is ANDEEP contribution no. 58.

Authors

Affiliations

Gonzalo Giribet [email protected]
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 16 Divinity Avenue, BioLabs 1119, Cambridge, MA 02138;
Akiko Okusu
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 16 Divinity Avenue, BioLabs 1119, Cambridge, MA 02138;
Annie R. Lindgren
Department of Biology, New Mexico State University, P.O. Box 30001, Las Cruces, NM 88003; and
Present address: Department of Evolution, Ecology, and Organismal Biology, Ohio State University, 1315 Kinnear Road, Columbus, OH 43215.
Stephanie W. Huff
Department of Organismic and Evolutionary Biology and Museum of Comparative Zoology, Harvard University, 16 Divinity Avenue, BioLabs 1119, Cambridge, MA 02138;
Michael Schrödl
Zoologische Staatssammlung München, Münchhausenstrasse 21, 81247 München, Germany
Michele K. Nishiguchi
Department of Biology, New Mexico State University, P.O. Box 30001, Las Cruces, NM 88003; and

Notes

To whom correspondence should be addressed. E-mail: [email protected]
Communicated by James W. Valentine, University of California, Berkeley, CA, April 3, 2006
Author contributions: G.G., A.O., A.R.L., M.S., and M.K.N. designed research; G.G., A.O., A.R.L., S.W.H., M.S., and M.K.N. performed research; G.G. analyzed data; and G.G., A.O., A.R.L., S.W.H., M.S., and M.K.N. wrote the paper.

Competing Interests

Conflict of interest statement: No conflicts declared.

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    Evidence for a clade composed of molluscs with serially repeated structures: Monoplacophorans are related to chitons
    Proceedings of the National Academy of Sciences
    • Vol. 103
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