The most parsimonious tree generated from analysis of 138 <i>Alu</i> insertions in Lemuriformes.

<p>The amplification patterns of the <i>Alu</i> insertions were used to construct a Dollo parsimony tree of phylogenetic relationships with <i>G. senegalensis</i> and <i>H. sapiens</i> as outgroups using the MESQUITE and PAUP* programs. Numbers above branches are bootstrap values. The significance level of each node supported by insertions as determined by likelihood testing is indicated by either *(p<0.05) or **(p<0.01). Numbers below arrows indicate the number of unambiguous loci supporting that node. Numbers in brackets below arrows indicate the number of loci at a given informative node identified by McLain et al. (2012). Numbers in parentheses represent insertions that are only present in one species or group. These insertions are not parsimony-informative. Consistency index (CI): 1.000; Homoplasy index (HI): 0.000; Retention index (RI): 1.000.</p

PCR amplification of polymorphic <i>Alu</i> insertions in Lemuriformes.

<p>Gel photographs displaying the methodology for establishing evolutionary relationships using <i>Alu</i> elements. The presence and absence of elements, supplemented by sequencing to eliminate the possibility of confounding events, is used to determine which species are more closely related. A total of 5 gel electrophoresis results on a 24-species primate panel are shown with <i>H. sapiens</i> and <i>G. senegalensis</i> as outgroups. <b>A:</b> Amplification of locus Str71B, an <i>Alu</i> insertion shared by the infraorder Lemuriformes. <b>B:</b> Amplification of locus MmA39, an <i>Alu</i> insertion shared by the family Cheirogaleidae. <b>C:</b> Amplification of locus MmA27, an <i>Alu</i> insertion shared by the sister genera <i>Microcebus</i> and <i>Mirza</i>. <b>D:</b> Amplification of locus Str59, an <i>Alu</i> insertion specific to the genus <i>Microcebus</i>. <b>E:</b> Amplification of locus Em6, an <i>Alu</i> insertion affirming the monophyly of the family Lemuridae to the exclusion of other lemur species and outgroups.</p

DNA samples of all species examined in this study.

a<p>Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ 08103, USA.</p>b<p>Duke Lemur Center (DLC), Duke University, Durham, NC 27708, USA.</p>c<p>Integrated Primate Biomaterials and Information Resource (IPBIR), <a href="http://ccr.coriell.org/Sections/Collections/" target="_blank">http://ccr.coriell.org/Sections/Collections/</a>.</p>d<p>Frozen Zoo, San Diego Zoo (SDFZ), <a href="http://conservationandscience.org" target="_blank">http://conservationandscience.org</a>.</p>e<p>Gene Bank of Primates (GBP), German Primate Center, Göttingen, Germany.</p>f<p>Batzer: Adenovirus 12 SV40-transformed fibroblasts maintained in the lab of Dr. Mark Batzer.</p>g<p>From cell lines provided by American Type Culture Collection (ATCC), P.O. Box 1549, Manassas, VA 20108, USA.</p><p>DNA samples of all species examined in this study.</p

An <em>Alu</em>-Based Phylogeny of Lemurs (Infraorder: Lemuriformes)

<div><p>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 <em>Alu</em> elements, a family of primate-specific Short INterspersed Elements (SINEs), to construct a phylogeny of infraorder Lemuriformes. <em>Alu</em> 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 (<em>Microcebus murinus</em>) was computationally assayed for synapomorphic <em>Alu</em> 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 <em>Alu</em> 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 <em>Microcebus</em> and <em>Mirza</em> as sister genera, with <em>Cheirogaleus</em> the sister lineage to both. Our results also support the monophyly of the Lemuridae. Within Lemuridae we place <em>Lemur</em> and <em>Hapalemur</em> together to the exclusion of <em>Eulemur</em> and <em>Varecia</em>, with <em>Varecia</em> the sister lineage to the other three genera.</p> </div

lepitotalm23MrsBayes

The alignment and setting for Mrbayes bayesian analyse

lepitotalm23.phy

The phylip alignment file of complete mitochondrial genome sequences from 36 sportive lemur individuals with 15 outgroup taxa with total alignment of 1475

Lepitotalm23Mrbayes_consustree

The consensus tree by Mrbaye

Lepitotalm23BestSchemefromPartitionFinderV1.10

The best partition Scheme from PartitionFinderV1.1

lepitotalm23RAxML_bestTree

The best tree generated from Lepitotal23.phy by RAxML

lepitotalm23Beast

Mitogenome BEAST xml file from this publicatio