An Alu-Based Phylogeny of Lemurs (Infraorder: Lemuriformes)

Abstract

Lemurs (infraorder: Lemuriformes) are a radiation of strepsirrhine primates endemic to the island of Madagascar. As of 2012, 101 lemur species, divided among five families, have been described. Genetic and morphological evidence indicates all species are descended from a common ancestor that arrived in Madagascar ∼55–60 million years ago (mya). Phylogenetic relationships in this species-rich infraorder have been the subject of debate. Here we use Alu elements, a family of primate-specific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. Alu elements are particularly useful SINEs for the purpose of phylogeny reconstruction because they are identical by descent and confounding events between loci are easily resolved by sequencing. The genome of the grey mouse lemur (Microcebus murinus) was computationally assayed for synapomorphic Alu elements. Those that were identified as Lemuriformes-specific were analyzed against other available primate genomes for orthologous sequence in which to design primers for PCR (polymerase chain reaction) verification. A primate phylogenetic panel of 24 species, including 22 lemur species from all five families, was examined for the presence/absence of 138 Alu elements via PCR to establish relationships among species. Of these, 111 were phylogenetically informative. A phylogenetic tree was generated based on the results of this analysis. We demonstrate strong support for the monophyly of Lemuriformes to the exclusion of other primates, with Daubentoniidae, the aye-aye, as the basal lineage within the infraorder. Our results also suggest Lepilemuridae as a sister lineage to Cheirogaleidae, and Indriidae as sister to Lemuridae. Among the Cheirogaleidae, we show strong support for Microcebus and Mirza as sister genera, with Cheirogaleus the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place Lemur and Hapalemur together to the exclusion of Eulemur and Varecia, with Varecia the sister lineage to the other three genera.

Flexible patterns in energy savings: heterothermy in primates

“…2a). If insulation capacities are less pronounced, in the case of eastern and western Cheirogaleus occupying less Pastorini et al, 2001, Horvath et al, 2008McLain et al, 2012).…”

“…Since the Cheirogaleidae are the most primitive of the extant lemur families, and heterothermy is so widespread within this family, it was suggested that the first primate inhabitants of Madagascar also exhibited this trait (Nowack, Mzilikazi & Dausmann, 2010). Genetic and morphological evidence indicate that all lemur species originate from one single colonization event, when a common ancestor arrived in Madagascar 55-60 million years ago (McLain et al, 2012). Possibly, the capacity of lemurs to use heterothermy even facilitated the successful colonization of Madagascar by lemurs from mainland Africa via rafting (Kappeler, 2000, but see Masters, Lovegrove & De Wit, 2007).…”

“… Phylogenetic relationships among the extant Strepsirrhini families and C heirogaleidae genera (after Pastorini et al ., , Horvath et al ., ; McLain et al ., ). …”

Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis

“…Retrotransposons are being used with increasing frequency as genetic markers for identification of taxa ranging from individuals to orders ( Ryan and Dugaiczyk 1989 ; Murata et al 1993 ; Schmitz et al 2001 ) (for additional examples, see Ray et al 2005 ; Xing et al 2005 , 2007 ; Herke et al 2007 ; Suh et al 2011 , 2014 ; Haddrath and Baker 2012 ; McLain et al 2012 ; Meyer et al 2012 ). In the past, identifying polymorphic SINE loci required expensive and time-consuming laboratory techniques such as modified bubble-PCR ( Roy et al 1999 ; Ray and Batzer 2005 ; Xing et al 2005 ) or inverse PCR from circularized DNA fragments ( Suh et al 2012 ).…”

A computational reconstruction of Papio phylogeny using Alu insertion polymorphisms

“…Alu elements are well-established DNA markers for the study of systematic and population genetic relationships [ 37 – 47 ]. In part, they are effective evolutionary characters because of their high copy number in primate genomes and sustained mobilization throughout the course of primate evolution (~ 65 MY) [ 48 – 50 ].…”