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.
As sequence technology progresses, associated costs reduce, computational capacity increases, and analytical protocols improve (e.g., Chan and Ragan, 2013; Dunn et al., 2013), the transition from traditional molecular systematics based on few loci to matrices of hundreds or thousands of genomic regions becomes feasible for most organisms. doi: 10.1093/molbev/msi117 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Parada, A., D' Elía, G., Bidau, C.
Holistic voucher specimens with rich data and materials that are made widely available would then facilitate expansion in multiple directions in the future, including ecology, physiology, developmental biology, and public health arenas. A molecular timescale for caviomorph rodents (Mammalia, Hystricognathi).
To outline such a research program and examine its feasibility, we focus on rodents.
On a related line, analyses of complete mitochondrial genomes and selected mitochondrial genes (Tomasco and Lessa, 2011, 2014) of subterranean and non-subterranean octodontoid species have suggested adaptive processes in relation to hypoxic environments. Monophyly of the order Rodentia inferred from mitochondrial DNA sequences of the genes for 12S r RNA, 16S r RNA, and t RNA-valine.
A full understanding of these processes requires analysis of whole genomes to develop a complete picture of the changes involved in the origin of the subterranean lifestyle. Guinea pigs provide a fascinating example of the evolution of domestication (in traditional Andean cultures and into modern biomedical sciences).
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. The role of proinsulin as a growth factor (De Meyts, 2012), coupled with the unusual developmental biology of caviomorph, suggest that insulins may be involved in some of their unusual adaptations. Characterization of the kidney transcriptome of the South American olive mouse Abrothrix olivacea. Because insulin is known to affect the expression of at least 150 genes, a systems approach, rather than a gene-by-gene approach, is required (see Mac Manes et al., in press). doi: 10.1093/oxfordjournals.molbev.a040186 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Giorello, F., Feijoo, M., D' Elía, G., Valdez, L., Opazo, J. BMC Genomics 6 doi: 10.1186/1471-2164-15-446 Pubmed Abstract | Pubmed Full Text | Cross Ref Full Text Honeycutt, R. 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. Caviomorph rodents possess changes in several other physiological axes that are otherwise well conserved across mammals (Wriston, 1981), but these changes are not fully understood.