While the analysis of genomic scale data would not solve all phylogenetic questions, it would help address the most important caveat of molecular systematics, namely the difference between gene and species trees resulting from sorting of ancestral polymorphism and introgression and magnified by difficulties of accurately reconstructing individual gene trees. Adaptive evolution of the insulin gene in caviomorph rodents. Analysis of genomic scale data reduces the uncertainty of phylogenetic inference and consequently increases the power of tree-based hypothesis testing.
In turn, Erethizontoidea and Cavioidea form a well-supported clade, whereas a clade formed by Chinchilloidea and Octodontoidea is less well-supported (Upham and Patterson, 2012; Voloch et al., 2013).
Inter-familial relationships within superfamilies, on the other hand, are much less strongly supported (Upham and Patterson, in press). Several major radiations, such as that of spiny rats and allies (Echimyidae, 88 species) and tuco-tucos (Ctenomyidae, 65 species) have been difficult to resolve in terms of phylogenetic relations or even number of species (e.g., Parada et al., 2011).
Three decades ago, the fossil record of caviomorphs traced back to only about 22 Mya (reviewed by Reig, 1981), their monophyly relative to other hystricognath rodents (phiomorphs: African mole rats, dassies, and cane rats, and hystricids: Old World porcupines) was questioned by myological and immunological analyses, and there was strong disagreement between proponents of an African connection to phiomorphs and champions of a North American origin. Classification and diversity (number of species and genera per family) of caviomorph rodents in South America (following Patton et al., in press), with a survey of the available taxonomic coverage for the most commonly used loci in caviomorph phylogenetic studies, and available and proposed genomic and transcriptomic coverage. Molecular data support the monophyly of caviomorph rodents and this clade is now widely thought to be sister to phiomorphs and to have originated from a single colonization from Africa (e.g., Cao et al., 1994; Frye and Hedges, 1995; Huchon and Douzery, 2001; Honeycutt et al., 2003; Rowe et al., 2010). A high-resolution map of human evolutionary constraint using 29 mammals. doi: 10.1038/nature10530 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Mac Manes, M.
DNA sequence analyses suggest that the divergence between caviomorphs and phiomorphs occurred 43–45 Ma, and that the early branching of caviomorphs took place 37–38 Ma (Poux et al., 2006; Voloch et al., 2013), effectively doubling the age of the group in South America.
Recent fossil findings document the presence of already diverse caviomorphs as early as 41 Ma in South America (Vucetich et al., 2010; Antoine et al., 2012; Bertrand et al., 2012). doi: 10.1006/mpev.2001.0961 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Lin, G.-H., Wang, K., Deng, X.-G., Nevo, E., Zhao, F., Su, J.-P., et al. Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia). doi: 10.1186/1471-2164-15-32 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Lindblad-Tohl, K., Garber, M., Zuk, O., Lin, M.
In spite of these significant advances, many unresolved issues remain that will require considerably greater genetic and taxonomic sampling.
Among them, we highlight the following: (a) Higher level relationships.
The organization of living caviomorph families into four superfamilies appears to be well-supported (Upham and Patterson, 2012). doi: 10.1016/S1055-7903(02)00368-8 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Huchon, D., and Douzery, E. From the Old World to the New World: a molecular chronicle of the phylogeny and biogeography of hystricognath rodents.
This exercise aims to stimulate the overall effort and may also serve as an example that can be extended to other taxonomic groups.