Poster presented during the 79th Annual Meeting of the American Society of Mammalogists, 
University of Washington, Seattle, WA, 20-24 June 1999. Abstract # 89

Phylogenetic relationships among echimyid rodents combining morphological and molecular data

Yuri L. R. Leite 
Museum of Vertebrate Zoology, 3101 Valley Life Sciences Building, University of California, 
Berkeley CA 94720-3160. E-mail:


Neotropical spiny rats, family Echimyidae (sensu McKenna & Bell 1997), are the most taxonomically, ecologically, and morphologically diverse of all living hystricognath rodents. The earliest fossils date from the Late Oligocene (25 MYBP), but modern taxa only appeared in the fossil record in the Late Miocene (6.8-9 MYBP). Today, there are at least 70 species distributed from Central to South America, occupying a wide variety of habitats and presenting a broad range of dietary and locomotory habits. Despite this diversity, systematic studies of the group are still in their infancy, and the evolutionary relationships among the genera are still unclear.
Lara, Patton, & da Silva (1996) concluded that a nearly simultaneous diversification of the most recent echimyids is likely the explanation for the pattern of divergence found in a phylogenetic analyses of the complete sequence of the mitochondrial gene cytochrome b (Figure 1). Their opinion was supported by the lack of resolution for relationships among genera (polytomy); contrasted with strong support both above and bellow this polytomy. Nevertheless, as pointed out by these authors, this star-phylogeny hypothesis is potentially falsifiable by examining more taxa and other markers. 
My main goal is to test the star-phylogeny hypothesis for the echimyid diversification. This can be achieved by adding molecular data from different genes and by using morphological data, which allow the inclusion of more taxa.

(fig. 1)


Molecular data:

A total of 31 specimens were sequenced, including 27 echimyids belonging to12 different genera, plus 3 outgroup genera. The same DNA extracts used by Lara, Patton, & da Silva (1996) were used as templates for PCR amplification. The complete 12S gene (851 bp) was amplified using three pairs of primers, and the last 581 bp of the 16 S gene was amplified using two primers. Automated sequencing in both directions was performed in an ABI Prism 377 DNA Sequencer, using the same sets of PCR primers. Sequences were aligned by eye, based on the secondary structures of the corresponding large and small subunits of the ribosomal RNA in the mitochondria. Additional sequences from the genera Mus, Rattus, Cavia, Myocastor, Capromys, and Proechimys were downloaded from Genbank.

Morphological data:

Fourteen out of nineteen living echimyid genera were included in the morphological analysis. The caviomorphs Coendou, Myoprocta, and Ctenomys were used as outgroups. The data matrix was assembled using diagnostic traits previously described in the literature, characters used in cladistic analysis of other rodent groups, and new features assessed from direct examination of the specimens. The final data matrix consisted of 41 characters, most of them related to tooth and skull morphology.

Phylogenetic analyses

Parsimony analyses were performed using the computer program PAUP* 4.0b2a (Swofford, 1997). Heuristic searches were conducted using the tree-bisection-reconnection algorithm, via random stepwise addition with 10 replicates. Character states were optimized using the accelerated transformation option. The robustness of clades within trees was assessed using bootstrap analysis (at least 100 replicates and 10 random sequence additions per replicate). Pairwise sequence divergences were calculated using the Kimura 2-parameter model.


Both 12S and 16S produced a polytomy for intra-generic relationships among echimyids:

(fig. 2)
Figure 2.: Phylogenetic relationships among echimyid genera based on sequences of the 12S (left) and 16S (right) genes. Both are bootstrap consensus trees based on 1,000 replicates. Numbers are bootstrap values above 50%. Outgroups taxa used were Mus, Rattus, Cavia, Myoprocta, and Coendou. Clades in red denote strongly supported sister-group relationships between genera. The shaded area indicates the region of the tree with no resolution (polytomy). Note that in the 12S tree the polytomy includes the coypu Myocastor (considered an echimyid, especially by paleontologists) as well as the hutia (Capromys) and the tuco-tuco (Ctenomys), both non-echimyid octodontoids.

The star-phylogeny persists when sequence data from 12S, 16S and cyt b are combined: 

(fig. 3)
Figure 3: Phylogenetic relationships among 12 echimyid genera based on the combined sequences of the cyt b, 12S, and 16S genes(2,457 bp). This is a bootstrap consensus tree based on 1,000 replicates. Numbers are bootstrap values above 50%. The three clades in red denote strongly supported sister-group relationships between genera. In addition, there is very weak support for a Trinomys-Euryzygomatomys clade and an Isothrix-(Lonchothrix-Mesomys) clade. The shaded area indicates the region of the tree with no resolution (polytomy). 

Morphological data offer some resolution, but most relationships are still unresolved:

(fig. 4)
Figure 4: Phylogenetic relationships among 14 echimyid genera based on 41 morphological characters. This is a bootstrap consensus tree based on 1,000 replicates. Numbers are bootstrap values above 50%. The current taxonomic classification, indicated at the right, suggests the paraphyly of the subfamily "Echimyinae". The results support the distinction between the recently described painted tree rat Callistomys (Emmons & Vucetich 1998) and the brush tailed rat Isothrix, although its relationship to other "echimyines" is still equivocal. 


  • The results presented here corroborate the star-phylogeny hypothesis. A protein-coding gene (cyt b), two ribosomal RNA genes (12S and 16S), and morphological data were unable to resolve the polytomy, suggesting that it reflects the true cladogenetic history of the group. 
  • The molecular results unequivocally support three clades within echimyids: (Lonchothrix-Mesomys), (Proechimys-Hoplomys), and (Makalata(Nelomys-Echimys)). These results indicate that the split between these lineages occurred after the basal split of most living echimyid genera.
  • If we translate the Proechimys-Hoplomys clade into a classification, then Trinomys must be recognized as a full genus and not as a sub-genus of Proechimys, as suggested by Lara, Patton & da Silva (1996).
  • The subfamily "Echimyinae" is paraphyletic according to the morphological data. The tree rats are more closely related to the bamboo rats (Dactylomyinae) than to the brushed tailed rat Isothrix.


The results show substantial support for the star-phylogeny hypothesis, especially if we assume that mtDNA evolves in a roughly clock-like manner within echimyids. However, if nucleotide substitutions occurred at relatively low rates during the time when the clades containing the extant genera diverged, then cladogenesis was not necessarily simultaneous. To further address this question, additional sequences from independent sources like the nuclear genome would be very important. Further, a cladistic analysis based on morphological traits that includes fossil material may potentially unveil these relationships, especially considering that the family is relatively old and 30 out of 49 echimyid genera are extinct.


Financial support for this research was provided by the Brazilian Research Council (CNPq), the Museum of Vertebrate Zoology, and NSF grants to J. L. Patton. Thanks to Jim Patton, Eileen Lacey, Peg Smith, Diogo Meyer and Leonora Pires Costa for helpful discussions and continuous support.


Emmons, L. H., & M. G. Vucetich. 1998. The identity of Winge's Lasiuromys villosus and the description of a new genus of echimyid rodent (Rodentia: Echimyidae). American Museum Novitates, 3223:1-12.

Lara, M. C., J. L. Patton, & M. N. F. Da Silva. 1996. The simultaneous diversification of South American echimyid rodents (Hystricognathi) based on complete cytochrome b sequences. Molecular Phylogenetics and Evolution, 5:403-413.

McKenna, M. C. & S. K. Bell. 1997. Classification of mammals above the species level. Columbia University Press, New York.

Swofford, D. L. 1999. PAUP*. Phylogenetic Analysis Using Parsimony (*and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.