Digging for the spiny rat and hutia phylogeny using a gene capture approach, with the description of a new mammal subfamily

Abstract

Next generation sequencing (NGS) and genomic database mining allow biologists to gather and select large molecular datasets well suited to address phylogenomics and molecular evolution questions. Here we applied this approach to a mammal family, the Echimyidae, for which generic relationships have been difficult to recover and often referred to as a star phylogeny. These South-American spiny rats represent a family of caviomorph rodents exhibiting a striking diversity of species and life history traits. Using a NGS exon capture protocol, we isolated and sequenced ca. 500 nuclear DNA exons for 35 species belonging to all major echimyid and capromyid clades. Exons were carefully selected to encompass as much diversity as possible in terms of rate of evolution, heterogeneity in the distribution of site-variation and nucleotide composition. Supermatrix inferences and coalescence-based approaches were subsequently applied to infer this family's phylogeny. The inferred topologies were the same for both approaches, and support was maximal for each node, entirely resolving the ambiguous relationships of previous analyses. Fastevolving nuclear exons tended to yield more reliable phylogenies, as slower-evolving sequences were not informative enough to disentangle the short branches of the Echimyidae radiation. Based on this resolved phylogeny and on molecular and morphological evidence, we confirm the rank of the Caribbean hutias-formerly placed in the Capromyidae family-as Capromyinae, a clade nested within Echimyidae. We also name and define Carterodontinae, a new subfamily of Echimyidae, comprising the extant monotypic genus Carterodon from Brazil, which is the closest living relative of West Indies Capromyinae.

Early Oligocene chinchilloid caviomorphs from Puerto Rico and the initial rodent colonization of the West Indies

“…Indeed, recent gene-based phylogenies of extant Neotropical echimyids (including Caribbean capromyines and mainland echimyines and euryzygomatomyines) support an Early-Middle Miocene divergence of hutias from their sister taxon Carterodon, thereby suggesting a Neogene West Indian colonization by octodontoids [12,14]. The presence of capromyine echimyids in the Greater Antilles is besides attested in lower Miocene deposits of Cuba with Zazamys [5,11].…”

Ancient DNA and high-resolution chronometry reveal a long-term human role in the historical diversity and biogeography of the Bahamian hutia

“…We placed this fossil on the node of the clade containing Capromyinae and the sister subfamily Carterodontinae with the following settings: Mean = 0, SD 0.7, Offset = 16.56. With Z. veronicae at this node we constrained the topology following the results of Fabre et al 52 and Courcelle et al 16 that recovered Carterodon sulcidens sister to the Capromyinae. Mitochondrial data alone does not recover this sister relationship between Capromyinae and Carterodontinae (RAxML phylogeny herein; see 52 ).…”

A phylogenomic tree inferred with an inexpensive PCR‐generated probe kit resolves higher‐level relationships among Neptis butterflies (Nymphalidae: Limenitidinae)

“…One of these reduced representation methods for isolating homologous loci is sequence capture, also known as targeted capture or hybrid enrichment. This method can isolate many orthologous loci, even from low quality or degraded DNA samples (Hawkins et al, 2016;Knyshov et al, 2019), and has been increasingly used in phylogenetic research of many different groups (Haddad et al, 2018;Courcelle et al, 2019;Liu et al, 2019;Van Dam et al, 2019;Zhang et al, 2019). This technique is particularly useful when working with rare or geographically isolated species represented only by dried specimens in museum collections that would be difficult to collect as fresh specimens.…”