Journal Articles: Present - 2016

Fernandez, R., G.D. Edgecombe, and G. Giribet. 2016. “Exploring Phylogenetic Relationships within Myriapoda and the Effects of Matrix Composition and Occupancy on Phylogenomic Reconstruction.” Systematic Biology 65 (5): 871–889. Publisher's VersionAbstract

Myriapods, including the diverse and familiar centipedes and millipedes, are one of the dominant terrestrial arthropod groups. Although molecular evidence has shown that Myriapoda is monophyletic, its internal phylogeny remains contentious and understudied, especially when compared to those of Chelicerata and Hexapoda. Until now, efforts have focused on taxon sampling (e.g., by including a handful of genes from many species) or on maximizing matrix size (e.g., by including hundreds or thousands of genes in just a few species), but a phylogeny maximizing sampling at both levels remains elusive. In this study, we analyzed 40 Illumina transcriptomes representing 3 of the 4 myriapod classes (Diplopoda, Chilopoda, and Symphyla); 25 transcriptomes were newly sequenced to maximize representation at the ordinal level in Diplopoda and at the family level in Chilopoda. Ten supermatrices were constructed to explore the effect of several potential phylogenetic biases (e.g., rate of evolution, heterotachy) at 3 levels of gene occupancy per taxon (50%, 75%, and 90%). Analyses based on maximum likelihood and Bayesian mixture models retrieved monophyly of each myriapod class, and resulted in 2 alternative phylogenetic positions for Symphyla, as sister group to Diplopoda + Chilopoda, or closer to Diplopoda, the latter hypothesis having been traditionally supported by morphology. Within centipedes, all orders were well supported, but 2 deep nodes remained in conflict in the different analyses despite dense taxon sampling at the family level. Relationships among centipede orders in all analyses conducted with the most complete matrix (90% occupancy) are at odds not only with the sparser but more gene-rich supermatrices (75% and 50% supermatrices) and with the matrices optimizing phylogenetic informativeness or most conserved genes, but also with previous hypotheses based on morphology, development, or other molecular data sets. Our results indicate that a high percentage of ribosomal proteins in the most complete matrices, in conjunction with distance from the root, can act in concert to compromise the estimated relationships within the ingroup. We discuss the implications of these findings in the context of the ever more prevalent quest for completeness in phylogenomic studies.

Giribet, G., and G. Y. Kawauchi. 2016. “How many species of Siphonaria pectinata (Gastropoda: Heterobranchia) are there?” Journal of Molluscan Studies 82 (1): 137–143. Publisher's VersionAbstract

Siphonaria pectinata (Linnaeus, 1758) has been considered a widespread species with Amphiatlantic distribution or a case of cryptic taxonomy where sibling species exist. We undertook molecular evaluation of 66 specimens from across its putative distribution range. We examined up to three molecular markers (mitochondrial cytochrome c oxidase subunit I and 16S rRNA, and nuclear internal transcribed spacer-2) of putative S. pectinata, including populations from the Mediterranean Sea, eastern Atlantic (Spain, Canary Islands, Cape Verde Islands, Cameroon and Gabon) and western Atlantic (Florida and Mexico), covering most of the natural range of the species. While little information could be derived from the shell morphology, molecular data clearly distinguished three lineages with no apparent connectivity. These lineages correspond to what we interpret as three species, two suspected from prior work: S. pectinata, restricted to the eastern Atlantic and Mediterranean and S. naufragum Stearns, 1872 in Florida and the Gulf of Mexico. A third species has been identified for the Cape Verde Archipelago, for which we use the available name S. placentula Menke, 1853.

Giribet, G. 2016. “New Animal Phylogeny: Future challenges for animal phylogeny in the age of phylogenomics.” Organisms Diversity & Evoution 16: 419–426. Publisher's VersionAbstract

The science of phylogenetics, and specially the subfield of molecular systematics, has grown exponentially not only in the amount of publications and general interest, but also especially in the amount of genetic data available. Modern phylogenomic analyses use large genomic and transcriptomic resources, yet a comprehensive molecular phylogeny of animals, including the newest types of data for all phyla, remains elusive. Future challenges need to address important issues with taxon sampling—especially for rare and small animals—orthology assignment, algorithmic developments, and data storage and to figure out better ways to integrate information from genomes and morphology in order to place fossils more precisely in the animal tree of life. Such precise placement will also aid in providing more accurate dates to major evolutionary events during the evolution of our closest kingdom.

Clouse, R.M., P. P. Sharma, J.C. Stuart, L.R. Davis, G. Giribet, S.L. Boyer, and W.C. Wheeler. 2016. “Phylogeography of the harvestman Metasiro (Arthropoda, Arachnida, Opiliones) reveals a potential solution to the Pangean paradox.” Organisms Diversity & Evoution 16: 167–184. Publisher's VersionAbstract

At both global and local scales, mite harvestmen (Opiliones, Cyphophthalmi) have been shown to have achieved their current global distribution strictly through vicariance. However, the implicit low dispersal capability of this group does not explain how they expand their ranges and come to occupy enormous landmasses prior to rifting. To investigate at the population level the limited vagility that characterizes the suborder generally, and how its dispersal capacity determines diversification dynamics, range expansion, and historical biogeography, we examined as a test case the phylogeography of the genus Metasiro. This genus consists of three widely separated, morphologically cryptic species that inhabit the Southeastern United States. Distances between sampling sites spanned a range of geographic scales, from 4 m to over 500 km. Population structure was inferred from fragments of six loci (three mitochondrial, three nuclear) amplified from 221 specimens. We tested for population structure and gene flow, constructed a dated phylogeny of the genus, and developed a program for estimating the effective population size with confidence intervals. Individuals of Metasiro americanus demonstrate remarkable population structure at scales of less than 25 m, but populations vary in their haplotypic diversity, and some exhibit evidence of historical gene flow. The estimated timing of cladogenesis within the genus accords closely with the geological history of the North American coastline, and the three species are at the endpoints of large watersheds. This suggests that mite harvestman lineages expand their ranges by hydrochory, providing for the first time a plausible mechanism whereby these animals dispersed across Pangea despite their low vagility in stable environments.