Giribet, G, E. McIntyre, E. Christian, L. Espinasa, RL. Ferreira, OF. Francke, MS. Harvey, et al. 2014. “The first phylogenetic analysis of Palpigradi (Arachnida)-the most enigmatic arthropod order.” Invertebrate Systematics 28: 350-360.
Giribet, G, R. Fernandez, and SL. Boyer. 2014. “On four poorly known harvestmen from New Zealand (Arachnida, Opiliones: Cyphophthalmi, Eupnoi, Dyspnoi, Laniatores).” New Zealand Journal of Zoology 41: 223-233.
Lopez, JV, H. Bracken-Grissom, AG. Collins, T. Collins, K. Crandall, D. Distel, C. Dunn, et al. 2014. “The Global Invertebrate Genomics Alliance (GIGA): Developing community resources to study diverse invertebrate genomes.” Journal of Heredity 105: 1-18.
Laumer, CE, and G. Giribet. 2014. “Inclusive taxon sampling suggests a single, stepwise origin of ectolecithality in Platyhelminthes.” Biological Journal of the Linnean Society 111: 570-588.
Riesgo, A, M. Novo, PP. Sharma, M. Peterson, M. Maldonado, and G. Giribet. 2014. “Inferring the ancestral sexuality and reproductive condition in sponges.” Zoologica Scripta 43: 101-117.
Bieler, R., PM. Mikkelsen, TM. Collins, EA. Glover, VL. Gonzalez, DL. Graf, EM. Harper, et al. 2014. “Investigating the Bivalve Tree of Life - an exemplar-based approach combining molecular and novel morphological characters.” Invertebrate Systematics 28: 32-115.
Velez, S, R. Fernandez, and G. Giribet. 2014. “A molecular phylogenetic approach to the New Zealand species of Enantiobuninae (Opiliones : Eupnoi : Neopilionidae).” Invertebrate Systematics 28: 565-589.
Gonzalez, V. L., and G. Giribet. 2014. “A multilocus phylogeny of archiheterodont bivalves (Mollusca, Bivalvia, Archiheterodonta).” Zoologica Scripta 44: 41-58.
Kvist, S, CE. Laumer, J. Junoy, and G. Giribet. 2014. “New insights into the phylogeny, systematics and DNA barcoding of Nemertea.” Invertebrate Systematics 28: 287-308.
Gainett, G, PP. Sharma, R. Pinto-da-Rocha, G. Giribet, and RH. Willemart. 2014. “Walk it off: Predictive power of appendicular characters toward inference of higher-level relationships in Laniatores (Arachnida: Opiliones).” Cladistics 30: 120-138.
Riesgo, A., N. Farrar, P. J. Windsor, G. Giribet, and S. P. Leys. 2014. “The analysis of eight transcriptomes from all poriferan classes reveals surprising genetic complexity in sponges.” Mol Biol Evol 31: 1102-20. Abstract

Sponges (Porifera) are among the earliest evolving metazoans. Their filter-feeding body plan based on choanocyte chambers organized into a complex aquiferous system is so unique among metazoans that it either reflects an early divergence from other animals prior to the evolution of features such as muscles and nerves, or that sponges lost these characters. Analyses of the Amphimedon and Oscarella genomes support this view of uniqueness-many key metazoan genes are absent in these sponges-but whether this is generally true of other sponges remains unknown. We studied the transcriptomes of eight sponge species in four classes (Hexactinellida, Demospongiae, Homoscleromorpha, and Calcarea) specifically seeking genes and pathways considered to be involved in animal complexity. For reference, we also sought these genes in transcriptomes and genomes of three unicellular opisthokonts, two sponges (A. queenslandica and O. carmela), and two bilaterian taxa. Our analyses showed that all sponge classes share an unexpectedly large complement of genes with other metazoans. Interestingly, hexactinellid, calcareous, and homoscleromorph sponges share more genes with bilaterians than with nonbilaterian metazoans. We were surprised to find representatives of most molecules involved in cell-cell communication, signaling, complex epithelia, immune recognition, and germ-lineage/sex, with only a few, but potentially key, absences. A noteworthy finding was that some important genes were absent from all demosponges (transcriptomes and the Amphimedon genome), which might reflect divergence from main-stem lineages including hexactinellids, calcareous sponges, and homoscleromorphs. Our results suggest that genetic complexity arose early in evolution as shown by the presence of these genes in most of the animal lineages, which suggests sponges either possess cryptic physiological and morphological complexity and/or have lost ancestral cell types or physiological processes.

Lenihan, J., S. Kvist, R. Fernandez, G. Giribet, and A. Ziegler. 2014. “A dataset comprising four micro-computed tomography scans of freshly fixed and museum earthworm specimens.” Gigascience 3: 6. Abstract

BACKGROUND: ALTHOUGH MOLECULAR TOOLS ARE INCREASINGLY EMPLOYED TO DECIPHER INVERTEBRATE SYSTEMATICS, EARTHWORM (ANNELIDA: Clitellata: 'Oligochaeta') taxonomy is still largely based on conventional dissection, resulting in data that are mostly unsuitable for dissemination through online databases. In order to evaluate if micro-computed tomography (muCT) in combination with soft tissue staining techniques could be used to expand the existing set of tools available for studying internal and external structures of earthworms, muCT scans of freshly fixed and museum specimens were gathered. FINDINGS: Scout images revealed full penetration of tissues by the staining agent. The attained isotropic voxel resolutions permit identification of internal and external structures conventionally used in earthworm taxonomy. The muCT projection and reconstruction images have been deposited in the online data repository GigaDB and are publicly available for download. CONCLUSIONS: The dataset presented here shows that earthworms constitute suitable candidates for muCT scanning in combination with soft tissue staining. Not only are the data comparable to results derived from traditional dissection techniques, but due to their digital nature the data also permit computer-based interactive exploration of earthworm morphology and anatomy. The approach pursued here can be applied to freshly fixed as well as museum specimens, which is of particular importance when considering the use of rare or valuable material. Finally, a number of aspects related to the deposition of digital morphological data are briefly discussed.

Fernandez, R., C. E. Laumer, V. Vahtera, S. Libro, S. Kaluziak, P. P. Sharma, A. R. Perez-Porro, G.D. Edgecombe, and G. Giribet. 2014. “Evaluating topological conflict in centipede phylogeny using transcriptomic data sets.” Mol Biol Evol 31: 1500-13. Abstract

Relationships between the five extant orders of centipedes have been considered solved based on morphology. Phylogenies based on samples of up to a few dozen genes have largely been congruent with the morphological tree apart from an alternative placement of one order, the relictual Craterostigmomorpha, consisting of two species in Tasmania and New Zealand. To address this incongruence, novel transcriptomic data were generated to sample all five orders of centipedes and also used as a test case for studying gene-tree incongruence. Maximum likelihood and Bayesian mixture model analyses of a data set composed of 1,934 orthologs with 45% missing data, as well as the 389 orthologs in the least saturated, stationary quartile, retrieve strong support for a sister-group relationship between Craterostigmomorpha and all other pleurostigmophoran centipedes, of which the latter group is newly named Amalpighiata. The Amalpighiata hypothesis, which shows little gene-tree incongruence and is robust to the influence of among-taxon compositional heterogeneity, implies convergent evolution in several morphological and behavioral characters traditionally used in centipede phylogenetics, such as maternal brood care, but accords with patterns of first appearances in the fossil record.