User:Manudouz/sandbox/Echimyidae phylogeny
< User:Manudouz | sandbox
Systematics
[edit]The current taxonomic content of the family Echimyidae has been reshaped over time, and its organization into coherent units stems from two realizations. The first is that cladistic approaches applied to morphological characters showed that many traits used to define taxa were plesiomorphic or homoplastic. The second realization came from the advent of phylogenetic analyses of DNA sequence and protein sequence data with probability methods — maximum likelihood and Bayesian inference —, leading to the identification of robust clades and the recognition of higher categorical ranks.[1][2]
Describe subfamilies and tribes:
| Genera | Vernacular names | Molecular-based subfamilies | Molecular-based tribes | Traditional systematics |
|---|---|---|---|---|
| Echimys | arboreal spiny rats | Echimyinae | Echimyini | Echimyinae |
| Phyllomys | Atlantic tree-rats | Echimyinae | Echimyini | Echimyinae |
| Makalata | — | Echimyinae | Echimyini | Echimyinae |
| Pattonomys | — | Echimyinae | Echimyini | Echimyinae |
| Toromys | giant tree-rat | Echimyinae | Echimyini | Echimyinae |
| Diplomys | — | Echimyinae | Echimyini | Echimyinae |
| Santamartamys | red-crested tree-rat | Echimyinae | Echimyini | Echimyinae |
| Isothrix | toros or brush-tailed rats | Echimyinae | Echimyini | Echimyinae |
| Dactylomys | bamboo rats | Echimyinae | Echimyini | Dactylomyinae |
| Olallamys | olalla rats | Echimyinae | Echimyini | Dactylomyinae |
| Kannabateomys | Atlantic bamboo rat | Echimyinae | Echimyini | Dactylomyinae |
| Lonchothrix | tuft-tailed spiny tree-rat | Echimyinae | Echimyini | Eumysopinae |
| Mesomys | spiny tree-rats | Echimyinae | Echimyini | Eumysopinae |
| Callistomys | painted tree-rat | Echimyinae | Myocastorini | Echimyinae |
| Myocastor | coypu | Echimyinae | Myocastorini | Myocastoridae |
| Thrichomys | punaré | Echimyinae | Myocastorini | Eumysopinae |
| Hoplomys | armored rat | Echimyinae | Myocastorini | Eumysopinae |
| Proechimys | spiny rats | Echimyinae | Myocastorini | Eumysopinae |
| Trinomys | Atlantic spiny rats | Euryzygomatomyinae | — | Eumysopinae |
| Euryzygomatomys | guiara | Euryzygomatomyinae | — | Eumysopinae |
| Clyomys | — | Euryzygomatomyinae | — | Eumysopinae |
| Carterodon | Owl's spiny rat | Incertae sedis | — | Eumysopinae |
| Plagiodontia | — | Capromyinae | Plagiodontini | Capromyidae |
| Geocapromys | — | Capromyinae | Capromyini | Capromyidae |
| Mesocapromys | — | Capromyinae | Capromyini | Capromyidae |
| Mysateles | — | Capromyinae | Capromyini | Capromyidae |
| Capromys | Desmarest's hutia | Capromyinae | Capromyini | Capromyidae |
Phylogeny
[edit]The phylogenetic tree of the Echimyidae shows a major split between the subfamily Echimyinae and an assemblage containing the Euryzygomatomyinae, Carterodon, and the Capromyidae. The first major clade contains a majority of arboreal genera (e.g., Phyllomys, Dactylomys, and Mesomys), a few terrestrial taxa (e.g., Proechimys), and a subaquatic one (Myocastor). The second major clade includes fossorial genera (e.g., Euryzygomatomys or Carterodon), a terrestrial one (Trinomys), and members inhabiting the Caribbean islands (Capromyidae).
Template
[edit]| Genus-level cladogram of the Echimyidae (including members of the family Capromyidae). | ||
|
| ||
| The cladogram has been reconstructed from mitochondrial and nuclear DNA characters.[5][6][7][8][9][10][11][12][2] The green bar shows the polyphyly of the arboreal taxa, due to closer affinities of Callistomys with Myocastorini rather than with Echimyini. The red bar shows the polyphyly of the fossorial taxa, due to closer affinities of Carterodon with Capromyidae rather than with Euryzygomatomyinae. |
With sub-templates
[edit]
| ||||||||||||
- ^ a b Fabre, Pierre-Henri; Patton, James L.; Leite, Yuri L. R. (2016). "Family Echimyidae (hutias, South American spiny-rats and coypu)". In Wilson, Don E.; Lacher, Thomas E. Jr; Mittermeier, Russell A. (eds.). Handbook of the Mammals of the World. Vol 6. Lagomorphs and Rodents I. Barcelona: Lynx Edicions. pp. 552–641. ISBN 978-84-941892-3-4.
- ^ a b c Fabre, Pierre-Henri; Upham, Nathan S.; Emmons, Louise H.; Justy, Fabienne; Leite, Yuri L. R.; Loss, Ana Carolina; Orlando, Ludovic; Tilak, Marie-Ka; Patterson, Bruce D.; Douzery, Emmanuel J. P. (2017-03-01). "Mitogenomic Phylogeny, Diversification, and Biogeography of South American Spiny Rats". Molecular Biology and Evolution. 34 (3): 613–633. doi:10.1093/molbev/msw261. ISSN 0737-4038. Cite error: The named reference "Fabre2017" was defined multiple times with different content (see the help page).
- ^ Woods, C.A.; Kilpatrick, C.W. (2005). "Family Echimyidae". In Wilson, D.E.; Reeder, D.M (eds.). Mammal Species of the World: A Taxonomic and Geographic Reference (3rd ed.). Johns Hopkins University Press. pp. 1575–1592. ISBN 978-0-8018-8221-0. OCLC 62265494.
- ^ Woods, C.A.; Kilpatrick, C.W. (2005). "Family Capromyidae". In Wilson, D.E.; Reeder, D.M (eds.). Mammal Species of the World: A Taxonomic and Geographic Reference (3rd ed.). Johns Hopkins University Press. ISBN 978-0-8018-8221-0. OCLC 62265494.
- ^ Lara, Márcia C.; Patton, James L.; da Silva, Maria Nazareth F. (1996). "The Simultaneous Diversification of South American Echimyid Rodents (Hystricognathi) Based on Complete Cytochrome b Sequences". Molecular Phylogenetics and Evolution. 5 (2): 403–413. doi:10.1006/mpev.1996.0035.
- ^ Leite, Yuri L. R.; Patton, James L. (2002). "Evolution of South American spiny rats (Rodentia, Echimyidae): the star-phylogeny hypothesis revisited". Molecular Phylogenetics and Evolution. 25 (3): 455–464. doi:10.1016/s1055-7903(02)00279-8.
- ^ Galewski, Thomas; Mauffrey, Jean-François; Leite, Yuri L. R.; Patton, James L.; Douzery, Emmanuel J. P. (2005). "Ecomorphological diversification among South American spiny rats (Rodentia; Echimyidae): a phylogenetic and chronological approach". Molecular Phylogenetics and Evolution. 34 (3): 601–615. doi:10.1016/j.ympev.2004.11.015.
- ^ Upham, Nathan S.; Patterson, Bruce D. (2012). "Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi)". Molecular Phylogenetics and Evolution. 63 (2): 417–429. doi:10.1016/j.ympev.2012.01.020.
- ^ Fabre, Pierre-Henri; Galewski, Thomas; Tilak, Marie-ka; Douzery, Emmanuel J. P. (2013-03-01). "Diversification of South American spiny rats (Echimyidae): a multigene phylogenetic approach". Zoologica Scripta. 42 (2): 117–134. doi:10.1111/j.1463-6409.2012.00572.x. ISSN 1463-6409.
- ^ Loss, Ana; Moura, Raquel T.; Leite, Yuri L. R. (2014). "Unexpected phylogenetic relationships of the painted tree rat Callistomys pictus (Rodentia: Echimyidae)" (PDF). Natureza on line. 12: 132–136.
- ^ Fabre, Pierre-Henri; Vilstrup, Julia T.; Raghavan, Maanasa; Der Sarkissian, Clio; Willerslev, Eske; Douzery, Emmanuel J. P.; Orlando, Ludovic (2014-07-01). "Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics". Biology Letters. 10 (7): 20140266. doi:10.1098/rsbl.2014.0266. ISSN 1744-9561.
- ^ Upham, Nathan S.; Patterson, Bruce D. (2015). "Evolution of Caviomorph rodents: a complete phylogeny and timetree for living genera". In Vassallo, Aldo Ivan; Antenucci, Daniel (eds.). Biology of caviomorph rodents: diversity and evolution. Buenos Aires: SAREM Series A, Mammalogical Research — Sociedad Argentina para el Estudio de los Mamíferos. pp. 63–120.