Highly repeated DNA sequences and systematics of malagasy primates

The lemur revolution starts now: the genomic coming of age for a non-model organism

Morris Goodman was a revolutionary. Together with a mere handful of like-minded scientists, Morris established himself as a leader in the molecular phylogenetic revolution of the 1960s. The effects of this revolution are most evident in this journal, which he founded in 1992. Happily for lemur biologists, one of Morris Goodman's primary interests was in reconstructing the phylogeny of the primates, including the tooth-combed Lorisifomes of Africa and Asia, and the Lemuriformes of Madagascar (collectively referred to as the suborder Strepsirrhini). This paper traces the development of molecular phylogenetic and evolutionary genetic trends and methods over the 50-year expanse of Morris Goodman's career, particularly as they apply to our understanding of lemuriform phylogeny, biogeography, and biology. Notably, this perspective reveals that the lemuriform genome is sufficiently rich in phylogenetic signal such that the very earliest molecular phylogenetic studies - many of which were conducted by Goodman himself - have been validated by contemporary studies that have exploited advanced computational methods applied to phylogenomic scale data; studies that were beyond imagining in the earliest days of phylogeny reconstruction. Nonetheless, the frontier still beckons. New technologies for gathering and analyzing genomic data will allow investigators to build upon what can now be considered a nearly-known phylogeny of the Lemuriformes in order to ask innovative questions about the evolutionary mechanisms that generate and maintain the extraordinary breadth and depth of biological diversity within this remarkable clade of primates.

Concatenation and concordance in the reconstruction of mouse lemur phylogeny: an empirical demonstration of the effect of allele sampling in phylogenetics

The systematics and speciation literature is rich with discussion relating to the potential for gene tree/species tree discordance. Numerous mechanisms have been proposed to generate discordance, including differential selection, long-branch attraction, gene duplication, genetic introgression, and/or incomplete lineage sorting. For speciose clades in which divergence has occurred recently and rapidly, recovering the true species tree can be particularly problematic due to incomplete lineage sorting. Unfortunately, the availability of multilocus or "phylogenomic" data sets does not simply solve the problem, particularly when the data are analyzed with standard concatenation techniques. In our study, we conduct a phylogenetic study for a nearly complete species sample of the dwarf and mouse lemur clade, Cheirogaleidae. Mouse lemurs (genus, Microcebus) have been intensively studied over the past decade for reasons relating to their high level of cryptic species diversity, and although there has been emerging consensus regarding the evolutionary diversity contained within the genus, there is no agreement as to the inter-specific relationships within the group. We attempt to resolve cheirogaleid phylogeny, focusing especially on the mouse lemurs, by employing a large multilocus data set. We compare the results of Bayesian concordance methods with those of standard gene concatenation, finding that though concatenation yields the strongest results as measured by statistical support, these results are found to be highly misleading. By employing an approach where individual alleles are treated as operational taxonomic units, we show that phylogenetic results are substantially influenced by the selection of alleles in the concatenation process.

Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs

Lemurs and the other strepsirrhine primates are of great interest to the primate genomics community due to their phylogenetic placement as the sister lineage to all other primates. Previous attempts to resolve the phylogeny of lemurs employed limited mitochondrial or small nuclear data sets, with many relationships poorly supported or entirely unresolved. We used genomic resources to develop 11 novel markers from nine chromosomes, representing approximately 9 kb of nuclear sequence data. In combination with previously published nuclear and mitochondrial loci, this yields a data set of more than 16 kb and adds approximately 275 kb of DNA sequence to current databases. Our phylogenetic analyses confirm hypotheses of lemuriform monophyly and provide robust resolution of the phylogenetic relationships among the five lemuriform families. We verify that the genus Daubentonia is the sister lineage to all other lemurs. The Cheirogaleidae and Lepilemuridae are sister taxa and together form the sister lineage to the Indriidae; this clade is the sister lineage to the Lemuridae. Divergence time estimates indicate that lemurs are an ancient group, with their initial diversification occurring around the Cretaceous-Tertiary boundary. Given the power of this data set to resolve branches in a notoriously problematic area of primate phylogeny, we anticipate that our phylogenomic toolkit will be of value to other studies of primate phylogeny and diversification. Moreover, the methods applied will be broadly applicable to other taxonomic groups where phylogenetic relationships have been notoriously difficult to resolve.

Body size and scaling of the hands and feet of prosimian primates

The hands and feet of primates fulfill a variety of biological roles linked with food acquisition and positional behavior. Current explanations of shape differences in cheiridial morphology among prosimians are closely tied to body size differences. Although numerous studies have examined the relationships between body mass and limb morphology in prosimians, no scaling analysis has specifically considered hand and foot dimensions and intrinsic proportions. In this study, we present such an analysis for a sample of 270 skeletal specimens distributed over eight prosimian families. The degree of association between size and shape was assessed using nonparametric correlational techniques, while the relationship between each ray element length and body mass (from published data and a body mass surrogate) was tested for allometric scaling. Since tarsiers and strepsirrhines encompass many taxa of varying degrees of phylogenetic relatedness, effective degrees of freedom were calculated, and comparisons between families were performed to partially address the problem of statistical nonindependence and "phylogenetic inertia." Correlational analyses indicate negative allometry between relative phalangeal length (as reflected by phalangeal indices) and body mass, except for the pollex and hallux. Thus, as size increases, there is a significant decrease in the relative length of the digits when considering all prosimian taxa sampled. Regression analyses show that while the digital portion of the rays scales isometrically with body mass, the palmar/plantar portion of the rays often scales with positive allometry. Some but not all of these broadly interspecific allometric patterns remain statistically significant when effective degrees of freedom are taken into account. As is often the case in interspecific scaling, comparisons within families show different scaling trends in the cheiridia than those seen across families (i.e., lorisids, indriids, and lemurids exhibit rather different allometries). The interspecific pattern of positive allometry that appears to best characterize the metapodials of prosimians, especially those of the foot, parallels differences found in the morphology of the volar skin. Indeed, relatively longer metapodials appear to covary with flatter and more coalesced volar pads, which in turn slightly improve frictional force for animals that are at a comparative disadvantage while climbing because of their larger mass. Despite the essentially isometric relationship found between digit length and body mass across prosimians, examination of the residual variation reveals that tarsiers and Daubentonia possess, relative to their body sizes, remarkably long fingers. Such marked departures between body size and finger length observed in these particular primates are closely linked with specialized modes of prey acquisition and manipulation involving the hands.

Primate jumping genes elucidate strepsirrhine phylogeny

Transposable elements provide a highly informative marker system for analyzing evolutionary histories. To solve controversially discussed topics in strepsirrhine phylogeny, we characterized 61 loci containing short interspersed elements (SINEs) and determined the SINE presence-absence pattern at orthologous loci in a representative strepsirrhine panel. This SINE monolocus study was complemented by a Southern blot analysis tracing multiple loci of two different strepsirrhine specific SINEs. The results thereof were combined with phylogenetic trees reconstructed on the basis of complete mitochondrial cytochrome b sequences from all recognized strepsirrhine genera. Here we present evidence for (i) a sister group relationship of Malagasy Chiromyiformes and Lemuriformes, (ii) Lorisidae being a monophyletic sister clade to the Galagidae, and (iii) common ancestry of African and Asian lorisids. Based on these findings, we conclude that strepsirrhines originated in Africa and that Madagascar and Asia were colonized by respective single immigration events. In agreement with paleocontinental data, the molecular analyses suggest a crossing of the Mozambique channel by rafting between the late Cretaceous and the middle Eocene, whereas Asia was most likely colonized between the early Eocene and the middle Oligocene on a continental route. Furthermore, one SINE integration links the two Lemuriformes families, Lemuridae and Indriidae, indicating a common origin of diurnality or cathemerality and a later reversal to nocturnality by the indriid genus Avahi.

Molecular phylogeny of the lemur family cheirogaleidae (primates) based on mitochondrial DNA sequences

Cheirogaleidae currently comprises five genera whose relationships remain contentious. The taxonomic status and phylogenetic position of both Mirza coquereli and Allocebus trichotis are still unclear. The taxonomic status of the recently discovered Microcebus ravelobensis (a sympatric sibling species of Microcebus murinus) and its phylogenetic position also require further examination. A approximately 2.4-kb mitochondrial DNA sequence including part of the COIII gene, complete ND3, ND4L, and ND4 genes, and 5 tRNAs was used to clarify relationships among cheirogaleids. Mirza and Microcebus form a clade representing the sister group of Allocebus, with a clade containing Cheirogaleus major and Cheirogaleus medius diverging first. M. ravelobensis and Microcebus rufus form a subclade within Microcebus, with M. murinus as its sister group. The molecular data support the generic status of Mirza coquereli and species-level divergence of M. ravelobensis. Furthermore, "M. rufus" may well represent more than one species.

Molar morphology and variation in two malagasy lemur families (Lemuridae and Indriidae)

The lemurs of Madagascar represent a radiation of primates exhibiting considerable ecological and morphological diversity. Dentally, all lemurs possess the characteristic strepsirhine anterior tooth comb, but exhibit variation in their postcanine teeth that may be related to dietary differences. In this study, I examine two factors that could complicate a strictly functional interpretation of tooth form variation in two families of Malagasy primates, the Lemuridae and Indriidae. (1) Allometry may be responsible for observed variation. Body size, not specific tooth features, may be the object of selection; tooth features may vary among taxa as a consequence of differences in body size. (2) Taxonomic affiliation may "explain" variation without recourse to functional explanations. Tooth morphology among closely-related taxa may be constrained developmentally or as a result of stabilizing selection. Morphological variation between families, therefore, may not be the result of current functional differences related to physical dietary properties, but may result from past events that are lineage-specific. Morphological features from the upper and lower second molars of seven lemurid and four indriid taxa are compared. The results of this study indicate that the majority of second molar features scale isometrically. Initial separation by families is warranted by the homogeneous slopes but different elevations in analyses of covariance between families. Intrafamilial variation is considerable for lemurids, but more discrete among indriids. Functional explanations for tooth form variability should take into consideration the degree of variation within taxa. For this particular dataset, the two families should be analyzed separately, and, because of the considerable overlap of subspecies with full species among lemurids, the lowest taxonomic unit recognized should be used.