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Giribet, Gonzalo

Understanding animal terrestrialization, the process through which animals colonized the land, is crucial to clarify extant biodiversity and biological adaptation. Arthropoda (insects, spiders, centipedes and their allies) represent the largest majority of terrestrial biodiversity. Here we implemented a molecular palaeobiological approach, merging molecular and fossil evidence, to elucidate the deepest history of the terrestrial arthropods. We focused on the three independent, Palaeozoic arthropod terrestrialization events (those of Myriapoda, Hexapoda and Arachnida) and showed that a marine route to the colonization of land is the most likely scenario. Molecular clock analyses confirmed an origin for the three terrestrial lineages bracketed between the Cambrian and the Silurian. While molecular divergence times for Arachnida are consistent with the fossil record, Myriapoda are inferred to have colonized land earlier, substantially predating trace or body fossil evidence. An estimated origin of myriapods by the Early Cambrian precedes the appearance of embryophytes and perhaps even terrestrial fungi, raising the possibility that terrestrialization had independent origins in crown-group myriapod lineages, consistent with morphological arguments for convergence in tracheal systems. This article is part of the themed issue ‘Dating species divergences using rocks and clocks’.

Mussels (Mytilida) are a group of bivalves with ancient origins and some of the most important commercial shellfish worldwide. Mytilida consists of approximately 400 species found in various littoral and deep-sea environments, and are part of the higher clade Pteriomorphia, but their exact position within the group has been unstable. The multiple adaptive radiations that occurred within Pteriomorphia have rendered phylogenetic classifications difficult and uncertainty remains regarding the relationships among most families. To address this phylogenetic uncertainty, novel transcriptomic data were generated to include all five orders of Pteriomorphia. Our results, derived from complex analyses of large datasets from 41 transcriptomes and evaluating possible pitfalls affecting phylogenetic reconstruction (matrix occupancy, heterogeneity, evolutionary rates, evolutionary models), consistently recover a well-supported phylogeny of Pteriomorphia, with the only exception of the most complete but smallest data matrix (Matrix 3: 51 genes, 90% gene occupancy). Maximum-likelihood and Bayesian mixture model analyses retrieve strong support for: (i) the monophyly of Pteriomorphia, (ii) Mytilida as a sister group to Ostreida, and (iii) Arcida as sister group to all other pteriomorphians. The basal position of Arcida is congruent with its shell microstructure (solely composed of aragonitic crystals), whereas Mytilida and Ostreida display a combination of a calcitic outer layer with an aragonitic inner layer composed of nacre tablets, the latter being secondarily lost in Ostreoidea.

Abstract The genus Newportia Gervais, 1847, includes some 60 nominal species distributed in the Caribbean islands and from Mexico to central South America. Modern keys to species and subspecies are available, greatly facilitating identification, but some species are based on few specimens and have incomplete documentation of taxonomically-informative characters. In order to explore genetic variability and evolutionary relationships within geographically-widespread morphospecies, specimens of Newportia (Newportia) stolli (Pocock, 1896) and Newportia (Newportia) divergens Chamberlin, 1922, two nominal species distinguished principally by differences in suture patterns on T1, were sequenced for mitochondrial 16S rRNA and cytochrome c oxidase subunit I (COI) genes from populations in southern Mexico, Guatemala, Honduras and Brazil. Newportia (Newportia) stolli is paraphyletic with respect to Newportia (Newportia) divergens within a clade from Guatemala, Honduras, and Chiapas (Mexico), most trees being consistent with a single loss of a connection between the anterior transverse suture on T1, whereas specimens of “Newportia (Newportia) stolli” from Brazil are not closely allied to those from the Mesomerican type area. The widespread morphospecies Newportia (Newportia) monticola Pocock, 1890, was sequenced for the same loci from populations in Costa Rica, Colombia and Brazil, finding that specimens from these areas do not unite as a monophyletic group. Samples of Newportia (Newportia) oreina Chamberlin, 1915, from different regions of Mexico form geographic clusters that resolve as each other’s closest relatives. These results suggest that some widespread species of Newportia may be taxa of convenience more so than natural groupings. In several cases geographic proximity fits the phylogeny better than taxonomy, suggesting that non-monophyletic species do not result from use of inappropriate molecular markers. Molecular identification is possible for specimens missing taxonomically informative morphological characters, notably damaged specimens that lack the ultimate leg pair, a protocol that may also apply to other taxonomically difficult genera that are prone to damage (such as Cryptops).

Members of the New Zealand Enantiobuninae constitute some of the most charismatic soil arthropods of the archipelago, and a striking example of sexual dimorphism, with nondescript females but colourful males boasting exaggerated chelicerae many times longer than their bodies. The genera Forsteropsalis and Pantopsalis recently underwent revision, but many questions remained about the validity of species designations owing to historical issues of characters of dubious taxonomic value, female specimens designated as holotypes despite the males holding all the diagnostic characters, and the suspected presence of more than one male form within some species. We present the first phylogeny based on molecular data for the New Zealand species in the genera Forsteropsalis, Pantopsalis and Mangatangi, and comment on the taxonomic implications of our results, including the diagnostic viability of important morphological characters. Our analyses reject the monophyly of Neopilionidae and Forsteropsalis, but support the monophyly of Pantopsalis. Finally, we comment on the taxonomic implications of the results, including the diagnostic validity of morphological characters traditionally used on the groups.

Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked ‘microturbellarian’ groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates. DOI: http://dx.doi.org/10.7554/eLife.05503.001

The advent of numerical methods for analyzing phylogenetic relationships, along with the study of morphology and molecular data, have driven our understanding of animal relationships for the past three decades. Within the protostome branch of the animal tree of life, these data have sufficed to establish two major clades; Ecdysozoa, a clade of animals that all moult, and Spiralia (often called Lophotrochozoa), a clade whose most recent common ancestor had spiral cleavage. In this chapter, we outline the current knowledge of protostome relationships and discuss future perspectives and strategies to increase our understanding of relationships within the main spiralian clades. Novel approaches to coding morphological characters are a pressing concern, best dealt with by scoring real observations on species selected as terminals. Methodological issues, such as the treatment of inapplicable characters and the coding of absences, may require novel algorithmic developments. Taxon sampling is another pressing issue, as terminals within phyla should include enough species to represent their span of anatomical disparity. Furthermore, key fossil taxa that can contribute novel character state combinations, such as the so-called 'stem-group lophotrochozoans', should not be neglected. In the molecular forum, EST-based phylogenomics is playing an increasingly important role in elucidating animal relationships. Large-scale sequencing has recently exploded for Spiralia, and phylogenomic data are lacking from only a few phyla, including the three most recently discovered animal phyla (Cycliophora, Loricifera, and Micrognathozoa). While the relationships between many groups now find strong support, others require additional information to be positioned with confidence. Novel morphological observations and phylogenomic data will be critical to resolving these remaining questions. Recent EST-based analyses underpin a new taxonomic proposal, Kryptrochozoa (the least inclusive clade containing the Brachiopoda and Nemertea).

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.

Multiple sequence alignment (MSA) is a potentially useful technique in phylogenetic analysis. This chapter examines the relative effectiveness of MSA and constructs and evaluates phylogenetic hypotheses without the use of this technique, first defining phylogenetic hypothesis, the problem, and the criteria used to assay the relative merits of hypotheses. It also defines the meaning of the utility of a technique, compares the results of alternate techniques, and criticizes the traditional approach to alignment and phylogenetic analysis, with a specific implementation of simultaneous phylogeny and alignment construction. The final section compares the results of a “one-step” optimization heuristic embodied in POY4 with the MSA + Search approach embodied by Clustal, using a large number of small data set simulations run under a variety of conditions and a few larger real data sets.

Peter Weygoldt pioneered studies of arachnid phylogeny by providing the first synapomorphy scheme to underpin inter-ordinal relationships. Since this seminal work, arachnid relationships have been evaluated using morphological characters of extant and fossil taxa as well as multiple generations of molecular sequence data. While nearly all datasets agree on the monophyly of Tetrapulmonata, and modern analyses of molecules and novel morphological and genomic data support Arachnopulmonata (a sister group relationship of Scorpiones to Tetrapulmonata), the relationships of the apulmonate arachnid orders remain largely unresolved. Three threads may allow us to resolve the recalcitrant phylogeny of arachnids: the careful evaluation of large amounts of molecular data; novel techniques grounded in comparative morphology and evolutionary developmental biology, which add improved homology statements and explain the transition between character states; and new fossil discoveries, which continue to incorporate relevant novel data to the discussion of the relationships among the arachnid orders.