Papers by Gonzalo Giribet
Cladistics, 2004
Micrognathozoa is the most recently discovered higher metazoan lineage. The sole known species of... more Micrognathozoa is the most recently discovered higher metazoan lineage. The sole known species of the group, Limnognathia maerski, was originally reported from running freshwater in Disko Island (Greenland), and has recently been recorded from the subantarctic region. Because of the presence of a particular type of jaws formed of special cuticularized rods, similar to those of gnathostomulids and rotifers, the three metazoan lineages were considered closely related, and assigned to the clade Gnathifera. A phylogenetic comparison of four molecular loci for Limnognathia maerski and other newly generated sequences of mainly acoelomate animals showed that Micrognathozoa may constitute an independent lineage from those of Gnathostomulida and Rotifera. However, the exact position of Micrognathozoa could not be determined due to the lack of support for any given relationships and due to the lack of stability in the position of Limnognathia maerski under analysis of different loci and of different parameter sets for sequence comparison. Nuclear loci tend to place Micrognathozoa with the syndermatan ⁄ cycliophoran taxa, but the addition of the mitochondrial gene cytochrome c oxidase subunit I favors a relationship of Micrognathozoa to Entoprocta.
Molecular Phylogenetics and Evolution, 1999
... such as random addition sequences, branch swapping (ie, SPR and TBR in PAUP or NONA), and bra... more ... such as random addition sequences, branch swapping (ie, SPR and TBR in PAUP or NONA), and branch swapping in suboptimal trees (such as the ''jump'' command in NONA). ... Aguinaldo, AMA, Turbeville, JM, Lindford, LS, Rivera, MC, Garey, JR, Raff, RA, and Lake, JA (1997). ...
Molecular Phylogenetics and Evolution, 2002
The study of metazoan evolution has fascinated biologists for centuries, and it will certainly ke... more The study of metazoan evolution has fascinated biologists for centuries, and it will certainly keep doing so. Recent interest on the origin of metazoan body plans, early metazoan evolution, genetic mechanisms generating disparity and diversity, molecular clock information, paleontology, and biogeochemistry is contributing to a better understanding of the current phyletic diversity. Unfortunately, the pattern of the metazoan tree of life still shows some important gaps in knowledge. It is the aim of this article to review some of the most important issues related to the inference of the metazoan tree, and point towards possible ways of solving certain obscure aspects in the history of animal evolution. A new hypothesis of the metazoan diversification during the Cambrian explosion is proposed by synthesizing ideas from phylogenetics, molecular evolution, paleontology, and developmental biology. Ó
Molecular Phylogenetics and Evolution, 2006
The phylogeny of selected members of the phylum Rotifera is examined based on analyses under pars... more The phylogeny of selected members of the phylum Rotifera is examined based on analyses under parsimony direct optimization and Bayesian inference of phylogeny. Species of the higher metazoan lineages Acanthocephala, Micrognathozoa, Cycliophora, and potential outgroups are included to test rotiferan monophyly. The data include 74 morphological characters combined with DNA sequence data from four molecular loci, including the nuclear 18S rRNA, 28S rRNA, histone H3, and the mitochondrial cytochrome c oxidase subunit I. The combined molecular and total evidence analyses support the inclusion of Acanthocephala as a rotiferan ingroup, but do not support the inclusion of Micrognathozoa and Cycliophora. Within Rotifera, the monophyletic Monogononta is sister group to a clade consisting of Acanthocephala, Seisonidea, and Bdelloidea-for which we propose the name Hemirotifera. We also formally propose the inclusion of Acanthocephala within Rotifera, but maintaining the name Rotifera for the new expanded phylum. Within Monogononta, Gnesiotrocha and Ploima are also supported by the data. The relationships within Ploima remain unstable to parameter variation or to the method of phylogeny reconstruction and poorly supported, and the analyses showed that monophyly was questionable for the families Dicranophoridae, Notommatidae, and Brachionidae, and for the genus Proales. Otherwise, monophyly was generally supported for the represented ploimid families and genera.
Cladistics, 2004
Cephalopoda represents a highly diverse group of molluscs, ranging in habitat from coastal region... more Cephalopoda represents a highly diverse group of molluscs, ranging in habitat from coastal regions to deep benthic waters. While cephalopods remain at the forefront of modern biology, in providing insight into fields such as neurobiology and population genetics, little is known about the relationships within the group. This study provides a comprehensive phylogenetic analysis of Cephalopoda (Mollusca) using a combination of molecular and morphological data. Four loci (three nuclear 18S rRNA, fragments of 28S rRNA and histone H3 and one mitochondrial cytochrome c oxidase subunit I) were combined with 101 morphological characters to test the relationships of 60 species of cephalopods, with emphasis within Decabrachia (squids and cuttlefishes). Individual and combined data sets were analyzed using the direct optimization method, with parsimony as the optimality criterion. Analyses were repeated for 12 different parameter sets accounting for a range of indel ⁄ change and transversion ⁄ transition cost ratios. Most analyses support the monophyly of Cephalopoda, Nautiloidea, Coleoidea and Decabrachia, however, the monophyly of Octobrachia was refuted due to the lack of support for a Cirroctopoda + Octopoda group. When analyzing all molecular evidence in combination and for total evidence analyses, Vampyromorpha formed the sister group to Decabrachia under the majority of parameters, while morphological data and some individual data sets supported a sister relationship between Vampyromorpha and Octobrachia. Within Decabrachia, a relationship between the sepioids Idiosepiida, Sepiida, Sepiolida and the teuthid Loliginidae was supported. Spirulida fell within the teuthid group in most analyses, further rendering Teuthida paraphyletic. Relationships within Decabrachia and specifically Oegopsida were found to be highly parameter-dependent.
Cladistics, 2000
Ribosomal gene sequence data are used to explore phylogenetic relationships among higher arthropo... more Ribosomal gene sequence data are used to explore phylogenetic relationships among higher arthropod groups.
Molecular Phylogenetics and Evolution, 1999
Gaps result from the alignment of sequences of unequal length during primary homology assessment.... more Gaps result from the alignment of sequences of unequal length during primary homology assessment. Viewed as character states originating from particular biological events (mutation), gaps contain historical information suitable for phylogenetic analysis. The effect of gaps as a source of phylogenetic data is explored via sensitivity analysis and character congruence among different data partitions. Example data sets are provided to show that gaps contain important phylogenetic information not recovered by those methods that omit gaps in their calculations. However, gap cost schemes are arbitrary (although they must be explicit) and thus data exploration is a necessity of molecular analyses, while character congruence is necessary as an external criterion for hypothesis decision.
Systematic Entomology, 2002
Relationships in Henicopidae, the dominant southern temperate clade of Lithobiomorpha, are apprai... more Relationships in Henicopidae, the dominant southern temperate clade of Lithobiomorpha, are appraised based on parsimony analysis of forty-nine morphological characters and sequence data from ®ve loci (nuclear ribosomal RNAs 18S and 28S, mitochondrial ribosomal RNAs 12S and 16S, protein-coding mitochondrial cytochrome c oxidase I). A combined analysis of these data used direct character optimization, and tested stability of hypotheses through parametersensitivity analysis. The morphology dataset highlighted the mandibles as a source of new characters. Morphology, as well as the most congruent parameters for the sequence data and combined analysis, resolved Zygethobiini within Henicopini. Groups retrieved by combined analysis of the sequences and combination with morphology for all parameters include Anopsobiinae/Henicopinae, Lamyctes + Lamyctinus + Henicops, Paralamyctes (Paralamyctes)
Molecular Phylogenetics and Evolution, 1998
Morphological evidence for the phylogeny of the animal kingdom has been discussed by numerous aut... more Morphological evidence for the phylogeny of the animal kingdom has been discussed by numerous authors. DNA sequencing and phylogenetic methods for analyzing these data are alternative approaches to animal phylogeny, but the phenomenon of long branch attraction and poor taxonomic sampling have caused misinterpretations of metazoan relationships. Here we report a cladistic approach to metazoan evolution including 133 18S rDNA sequences of 31 animal phyla. Despite the difficulties associated with analyzing large data sets, our data suggest that the Bilateria and Protostomia are monophyletic. The internal phylogeny of the protostomes is divided into two main clades. One clade includes the classical protostome worms (annelids, sipunculans, echiurans, pogonophorans, and vestimentiferans), mollusks, nemerteans, "lophophorates," platyhelminths, rotiferans, and acanthocephalans, although the internal resolution of the clade is very low. The second clade includes arthropods and other molting animals: tardigrades, onychophorans, nematodes, nematomorphans, kinorhynchs, and priapulans. The arthropods and related phyla lack a ciliated larvae, lack a multiciliate (locomotory) epithelium, and share many features, notably, a reduced coelomic cavity and the presence of a cuticle which molts. The use of these outgroups within the molting clade to root arthropod phylogenies is recommended instead of using annelids or other spiralians. The data are quite conclusive in those phyla with a good taxonomic sampling (i.e., platyhelminths and arthropods).
Invertebrate Biology, 2005
Abstract. Bivalve classification has suffered in the past from the crossed-purpose discussions am... more Abstract. Bivalve classification has suffered in the past from the crossed-purpose discussions among paleontologists and neontologists, and many have based their proposals on single character systems. More recently, molecular biologists have investigated bivalve relationships by using only gene sequence data, ignoring paleontological and neontological data. In the present study we have compiled morphological and anatomical data with mostly new molecular evidence to provide a more stable and robust phylogenetic estimate for bivalve molluscs. The data here compiled consist of a morphological data set of 183 characters, and a molecular data set from 3 loci: 2 nuclear ribosomal genes (18S rRNA and 28S rRNA), and 1 mitochondrial coding gene (cytochrome c oxidase subunit I), totaling ∼3 Kb of sequence data for 76 molluscs (62 bivalves and 14 outgroup taxa). The data have been analyzed separately and in combination by using the direct optimization method of Wheeler (1996), and they have been evaluated under 12 analytical schemes. The combined analysis supports the monophyly of bivalves, paraphyly of protobranchiate bivalves, and monophyly of Autolamellibranchiata, Pteriomorphia, Heteroconchia, Palaeoheterodonta, and Heterodonta s.l., which includes the monophyletic taxon Anomalodesmata. These analyses strongly support the conclusion that Anomalodesmata should not receive a class status, and that the heterodont orders Myoida and Veneroida are not monophyletic. Among the most stable results of the analysis are the monophyly of Palaeoheterodonta, grouping the extant trigoniids with the freshwater unionids, and the sister-group relationship of the heterodont families Astartidae and Carditidae, which together constitute the sister taxon to the remaining heterodont bivalves. Internal relationships of the main bivalve groups are discussed on the basis of node support and clade stability.
Cladistics, 2002
The ordinal level phylogeny of the Arachnida and the sets. However, the internal phylogeny of the... more The ordinal level phylogeny of the Arachnida and the sets. However, the internal phylogeny of the Opiliones is robust to parameter choice and allows the discarding suprafamilial level phylogeny of the Opiliones were studied on the basis of a combined analysis of 253 morpholog-of previous hypotheses of opilionid phylogeny such as the "Cyphopalpatores" or "Palpatores." The topology ical characters, the complete sequence of the 18S rRNA gene, and the D3 region of the 28S rRNA gene. Molecular obtained is congruent with the previous hypothesis of "Palpatores" paraphyly as follows: (Cyphophthalmi data were collected for 63 terminal taxa. Morphological data were collected for 35 exemplar taxa of Opiliones, (Eupnoi (Dyspnoi ؉ Laniatores))). Resolution within the Eupnoi, Dyspnoi, and Laniatores (the latter two united as but groundplans were applied to some of the remaining chelicerate groups. Six extinct terminals, including Dyspnolaniatores nov.) is also stable to the superfamily level, permitting a new classification system for the Opili-Paleozoic scorpions, are scored for morphological characters. The data were analyzed using strict parsimony for ones. ᭧ the morphological data matrix and via direct optimization for the molecular and combined data matrices. A noi; Dyspnoi; fossils; cladistics; morphology; molecular; phylogeny; 18S rRNA; 28S rRNA. sensitivity analysis of 15 parameter sets was undertaken, and character congruence was used as the optimality criterion to choose among competing hypotheses. The results obtained are unstable for the high-level chelic-1 Communicated by
Journal of Zoological Systematics and Evolutionary Research, 2004
Proceedings of The National Academy of Sciences, 2006
Monoplacophorans are among the rarest members of the phylum Mollusca. Previously only known from ... more 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.
Molecular Phylogenetics and Evolution, 1999
The phylogenetic relationships among the main evolutionary lines of the arachnid order Opiliones ... more The phylogenetic relationships among the main evolutionary lines of the arachnid order Opiliones were investigated by means of molecular (complete 18S rDNA and the D3 region of the 28S rDNA genes) and morphological data sets. Equally and differentially weighted parsimony analyses of independent and combined data sets provide evidence for the monophyly of the Opiliones. In all the analyses, the internal relationships of the group coincide in the monophyly of the following main groups: Cyphophthalmi, Eupnoi Palpatores, Dyspnoi Palpatores, and Laniatores. The Cyphophthalmi are monophyletic and sister to a clade that includes all the remaining opilionid taxa (؍Phalangida). Within the Phalangida the most supported hypothesis suggests that Palpatores are paraphyletic, as follows: (Eupnoi (Dyspnoi ؉ Laniatores)), but the alternative hypothesis (Laniatores (Eupnoi ؉ Dyspnoi)) is more parsimonious in some molecular data analyses. Relationships within the four main clades are also addressed. Evolution of some morphological characters is discussed, and plesiomorphic states of these characters are evaluated using molecular data outgroup polarization. Finally, Martens' hypothesis of opilionid evolution is assessed in relation to our results.
American Museum Novitates, 2001
The SSU rRNA gene is one of the most widely utilized loci for phylogenetic inference among eukary... more The SSU rRNA gene is one of the most widely utilized loci for phylogenetic inference among eukaryotic organisms. Although they have an average length of 1800 to 1900 bp, several unusually large 18S rDNA sequences have been reported. After examining GenBank sequences and 180 new 18S rRNA sequences from several metazoan groups, we report many other extraordinary sequences ranging between ca. 1350 bp (in symphylan myriapods) to ca. 3300 bp (in some strepsipteran insects). Myriapods are particularly interesting, having independently evolved extraordinary sequences in the four classes (Chilopoda, Diplopoda, Symphyla, and Pauropoda). An insertion event of ca. 300 bp has been detected in all but the most basal family of geophilomorphan centipedes. Other major insertions are also found in other arthropod groups, in onychophorans, molluscs, chaetognaths, echinoderms, and parasitic platyhelminths. The use of information derived from secondary structure predictions combined with a new method to analyze DNA sequence data without multiple sequence alignments is proposed as a solution for analyzing sequence data that possess alternatively conservative and variable regions, such as ribosomal genes.
Organisms Diversity & Evolution, 2003
This study represents the first phylogenetic analysis of the molluscan class Polyplacophora using... more This study represents the first phylogenetic analysis of the molluscan class Polyplacophora using DNA sequence data. We employed DNA from a nuclear protein-coding gene (histone H3), two nuclear ribosomal genes (18S rRNA and the D3 expansion fragment of 28S rRNA), one mitochondrial protein-coding gene (cytochrome c oxidase subunit I), and one mitochondrial ribosomal gene (16S rRNA). A series of analyses were performed on independent and combined data sets. All these analyses were executed using direct optimization with parsimony as the optimality criterion, and analyses were repeated for nine combinations of parameters affecting indel and transversion/transition cost ratios. Maximum likelihood was also explored for the combined molecular data set, also using the direct optimization method, with a model equivalent to GTR + I + Γ that accommodates gaps. The results of all nine parameter sets for the combined parsimony analysis of all molecular data (as well as ribosomal data) and the maximum-likelihood analysis of all molecular data support monophyly of Polyplacophora. The resulting topologies mostly agree with a division of Polyplacophora into two major lineages: Lepidopleuridae and Chitonida (sensu Sirenko 1993). In our analyses the genus Callochiton is positioned as the sister group to Lepidopleuridae, and not as sister group to the remaining Chitonida (sensu Buckland-Nicks & Hodgson 2000), nor as the sister group to the remaining Chitonina (sensu Buckland-Nicks 1995). Chitonida (excluding Callochiton) is monophyletic, but conventional subgroupings of Chitonida are not supported. Acanthochitonina (sensu Sirenko 1993) is paraphyletic, or alternatively monophyletic, and is split into two clades, both with abanal gills only and cupules in the egg hull, but one has simple cupules whereas the other has more strongly hexagonal cupules. Sister to the Acanthochitonina clades is Chitonina, including taxa with adanal gills and a spiny egg hull. Schizochiton, the only genus with adanal gills that has an egg hull with cupules, is the sister-taxon to one of the Acanthochitonina clades plus Chitonina, or alternatively basal to Chitonina. Support values for either position are low, leaving this relationship unsettled. Our results refute several aspects of conventional classifications of chitons that are based primarily on shell characters, reinforcing the idea that chiton classification should be revised using additional characters.
Nature, 2008
Long-held ideas regarding the evolutionary relationships among animals have recently been upended... more Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data 1,2 . These new hypotheses include a clade of moulting animals (Ecdysozoa) 3 and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa) 4 . Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods 5 ), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.
Proceedings of The Royal Society B: Biological Sciences, 2009
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Papers by Gonzalo Giribet