Phylogenetic relationships among the Lorisoidea as indicated by craniodental morphology and mitochondrial sequence data

Comparative morphology and physiology of the vocal production apparatus and the brain in the extant primates

Objective data mainly from the comparative anatomy of various organs related to human speech and language is considered to unearth clues about the mechanisms behind language development. The two organs of the larynx and hyoid bone are considered to have evolved towards suitable positions and forms in preparation for the occurrence of the large repertoire of vocalization necessary for human speech. However, some researchers have asserted that there is no significant difference of these organs between humans and non-human primates. Speech production is dependent on the voluntary control of the respiratory, laryngeal, and vocal tract musculature. Such control is fully present in humans but only partially so in non-human primates, which appear to be able to voluntarily control only supralaryngeal articulators. Both humans and non-human primates have direct cortical innervation of motor neurons controlling the supralaryngeal vocal tract but only human appear to have direct cortical innervation of motor neurons controlling the larynx. In this review, we investigate the comparative morphology and function of the wide range of components involved in vocal production, including the larynx, the hyoid bone, the tongue, and the vocal brain. We would like to emphasize the importance of the tongue in the primary development of human speech and language. It is now time to reconsider the possibility of the tongue playing a definitive role in the emergence of human speech.

Vocalization Analyses of Nocturnal Arboreal Mammals of the Taita Hills, Kenya

Three poorly known nocturnal mammal species from the montane forests of the Taita Hills in Kenya, were studied via vocalization analysis. Here, their acoustic behaviour is described. The studied animals were the tree hyrax (Dendrohyrax sp.), the small-eared greater galago (Otolemur garnettii), and the dwarf galago (Paragalago sp.). High-quality loud calls were analysed using RAVEN PRO, and compared to calls of presumed closest relatives. Our findings include the first detailed descriptions of tree hyrax songs. Moreover, our results suggest that the tree hyrax of Taita Hills may be a taxon new to science, as it produces a characteristic call, the ‘strangled thwack’, not previously known from other Dendrohyrax populations. Our data confirms that the small-eared greater galago subspecies living in the Taita Hills is Otolemur garnettii lasiotis. The loud calls of the elusive Taita Hills dwarf galago closely resemble those of the Kenya coast dwarf galago (Paragalago cocos). Thus, the population in the Taita Hills probably belongs to this species. The Taita Hills dwarf galagos are geographically isolated from other dwarf galago populations, and live in montane cloud forest, which is an unusual habitat for P. cocos. Intriguingly, two dwarf galago subpopulations living in separate forest patches in the Taita Hills, Ngangao and Mbololo, have clearly different contact calls. The Paragalagos in Mbololo Forest may represent a population of P. cocos with a derived call repertoire, or, alternatively, they may actually be mountain dwarf galagos (P. orinus). Hence, differences in habitat, behaviour, and contact call structure suggest that there may be two different Paragalago species in the montane forests of the Taita Hills.

Population genetic structure of the thick-tailed bushbaby (Otolemur crassicaudatus) from the Soutpansberg Mountain range, Northern South Africa, based on four mitochondrial DNA regions

Greater bushbabies, strepsirrhine primates, that are distributed across central, eastern and southern Africa, with northern and eastern South Africa representing the species' most southerly distribution. Greater bushbabies are habitat specialists whose naturally fragmented habitats are getting even more fragmented due to anthropogenic activities. Currently, there is no population genetic data or study published on the species. The aim of our study was to investigate the genetic variation in a thick-tailed bushbaby, Otolemur crassicaudatus, population in the Soutpansberg mountain range, Limpopo Province, South Africa. Four mitochondrial regions, ranging from highly conserved to highly variable, were sequenced from 47 individuals. The sequences were aligned and genetic diversity, structure, as well as demographic analyses were performed. Low genetic diversity (π = 0.0007-0.0038 in coding regions and π = 0.0127 in non-coding region; Hd = 0.166-0.569 in coding regions and Hd = 0.584 in non-coding region) and sub-structuring (H = 2-3 in coding regions and H = 4 in non-coding region) was observed with two divergent haplogroups (haplotype pairwise distance = 3-5 in coding region and 6-10 in non-coding region) being identified. This suggests the population may have experienced fixation of mitochondrial haplotypes due to limited female immigration, which is consistent with philopatric species, that alternative haplotypes are not native to this population, and that there may be male mobility from adjacent populations. This study provides the first detailed insights into the mitochondrial genetic diversity of a continental African strepsirrhine primate and demonstrates the utility of mitochondrial DNA in intraspecific genetic population analyses of these primates.

Using a multi-gene approach to infer the complicated phylogeny and evolutionary history of lorises (Order Primates: Family Lorisidae)

Extensive phylogenetic studies have found robust phylogenies are modeled by using a multi-gene approach and sampling from the majority of the taxa of interest. Yet, molecular studies focused on the lorises, a cryptic primate family, have often relied on one gene, or just mitochondrial DNA, and many were unable to include all four genera in the analyses, resulting in inconclusive phylogenies. Past phylogenetic loris studies resulted in lorises being monophyletic, paraphyletic, or an unresolvable trichotomy with the closely related galagos. The purpose of our study is to improve our understanding of loris phylogeny and evolutionary history by using a multi-gene approach. We used the mitochondrial genes cytochrome b, and cytochrome c oxidase subunit 1, along with a nuclear intron (recombination activating gene 2) and nuclear exon (the melanocortin 1 receptor). Maximum Likelihood and Bayesian phylogenetic analyses were conducted based on data from each locus, as well as on the concatenated sequences. The robust, concatenated results found lorises to be a monophyletic family (Lorisidae) (PP ≥ 0.99) with two distinct subfamilies: the African Perodictinae (PP ≥ 0.99) and the Asian Lorisinae (PP ≥ 0.99). Additionally, from these analyses all four genera were all recovered as monophyletic (PP ≥ 0.99). Some of our single-gene analyses recovered monophyly, but many had discordances, with some showing paraphyly or a deep-trichotomy. Bayesian partitioned analyses inferred the most recent common ancestors of lorises emerged ∼42 ± 6 million years ago (mya), the Asian Lorisinae separated ∼30 ± 9 mya, and Perodictinae arose ∼26 ± 10 mya. These times fit well with known historical tectonic shifts of the area, as well as with the sparse loris fossil record. Additionally, our results agree with previous multi-gene studies on Lorisidae which found lorises to be monophyletic and arising ∼40 mya (Perelman et al., 2011; Pozzi et al., 2014). By taking a multi-gene approach, we were able to recover a well-supported, monophyletic loris phylogeny and inferred the evolutionary history of this cryptic family.

Remarkable ancient divergences amongst neglected lorisiform primates

Lorisiform primates (Primates: Strepsirrhini: Lorisiformes) represent almost 10% of the living primate species and are widely distributed in sub-Saharan Africa and South/South-East Asia; however, their taxonomy, evolutionary history, and biogeography are still poorly understood. In this study we report the largest molecular phylogeny in terms of the number of represented taxa. We sequenced the complete mitochondrial cytochrome b gene for 86 lorisiform specimens, including ∼80% of all the species currently recognized. Our results support the monophyly of the Galagidae, but a common ancestry of the Lorisinae and Perodicticinae (family Lorisidae) was not recovered. These three lineages have early origins, with the Galagidae and the Lorisinae diverging in the Oligocene at about 30 Mya and the Perodicticinae emerging in the early Miocene. Our mitochondrial phylogeny agrees with recent studies based on nuclear data, and supports Euoticus as the oldest galagid lineage and the polyphyletic status of Galagoides. Moreover, we have elucidated phylogenetic relationships for several species never included before in a molecular phylogeny. The results obtained in this study suggest that lorisiform diversity remains substantially underestimated and that previously unnoticed cryptic diversity might be present within many lineages, thus urgently requiring a comprehensive taxonomic revision of this primate group. 

Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes

The origins and the divergence times of the most basal lineages within primates have been difficult to resolve mainly due to the incomplete sampling of early fossil taxa. The main source of contention is related to the discordance between molecular and fossil estimates: while there are no crown primate fossils older than 56Ma, most molecule-based estimates extend the origins of crown primates into the Cretaceous. Here we present a comprehensive mitogenomic study of primates. We assembled 87 mammalian mitochondrial genomes, including 62 primate species representing all the families of the order. We newly sequenced eleven mitochondrial genomes, including eight Old World monkeys and three strepsirrhines. Phylogenetic analyses support a strong topology, confirming the monophyly for all the major primate clades. In contrast to previous mitogenomic studies, the positions of tarsiers and colugos relative to strepsirrhines and anthropoids are well resolved. In order to improve our understanding of how fossil calibrations affect age estimates within primates, we explore the effect of seventeen fossil calibrations across primates and other mammalian groups and we select a subset of calibrations to date our mitogenomic tree. The divergence date estimates of the Strepsirrhine/Haplorhine split support an origin of crown primates in the Late Cretaceous, at around 74Ma. This result supports a short-fuse model of primate origins, whereby relatively little time passed between the origin of the order and the diversification of its major clades. It also suggests that the early primate fossil record is likely poorly sampled.

A multilocus phylogeny reveals deep lineages within African galagids (Primates: Galagidae)

BACKGROUND

Bushbabies (Galagidae) are among the most morphologically cryptic of all primates and their diversity and relationships are some of the most longstanding problems in primatology. Our knowledge of galagid evolutionary history has been limited by a lack of appropriate molecular data and a paucity of fossils. Most phylogenetic studies have produced conflicting results for many clades, and even the relationships among genera remain uncertain. To clarify galagid evolutionary history, we assembled the largest molecular dataset for galagos to date by sequencing 27 independent loci. We inferred phylogenetic relationships using concatenated maximum-likelihood and Bayesian analyses, and also coalescent-based species tree methods to account for gene tree heterogeneity due to incomplete lineage sorting.

RESULTS

The genus Euoticus was identified as sister taxon to the rest of the galagids and the genus Galagoides was not recovered as monophyletic, suggesting that a new generic name for the Zanzibar complex is required. Despite the amount of genetic data collected in this study, the monophyly of the family Lorisidae remained poorly supported, probably due to the short internode between the Lorisidae/Galagidae split and the origin of the African and Asian lorisid clades. One major result was the relatively old origin for the most recent common ancestor of all living galagids soon after the Eocene-Oligocene boundary.

CONCLUSIONS

Using a multilocus approach, our results suggest an early origin for the crown Galagidae, soon after the Eocene-Oligocene boundary, making Euoticus one of the oldest lineages within extant Primates. This result also implies that one - or possibly more - stem radiations diverged in the Late Eocene and persisted for several million years alongside members of the crown group.

Lumbar vertebral body bone microstructural scaling in small to medium-sized strepsirhines

Bone mass, architecture, and tissue mineral density contribute to bone strength. As body mass (BM) increases any one or combination of these properties could change to maintain structural integrity. To better understand the structural origins of vertebral fragility and gain insight into the mechanisms that govern bone adaptation, we conducted an integrative analysis of bone mass and microarchitecture in the last lumbar vertebral body from nine strepsirhine species, ranging in size from 42 g (Microcebus rufus) to 2,440 g (Eulemur macaco). Bone mass and architecture were assessed via µCT for the whole body and spherical volumes of interest (VOI). Allometric equations were estimated and compared with predictions for geometric scaling, assuming axial compression as the dominant loading regime. Bone mass, microarchitectural, and vertebral body geometric variables predominantly scaled isometrically. Among structural variables, the degree of anisotropy (Tb.DA) was the only parameter independent of BM and other trabecular architectural variables. Tb.DA was related to positional behavior. Orthograde primates had higher average Tb.DA (1.60) and more craniocaudally oriented trabeculae while lorisines had the lowest Tb.DA (1.25), as well as variably oriented trabeculae. Finally, lorisines had the highest ratio of trabecular bone volume to cortical shell volume (∼3x) and while there appears to be flexibility in this ratio, the total bone volume (trabecular + cortical) scales isometrically (BM(1.23) , r(2) = 0.93) and appears tightly constrained. The common pattern of isometry in our measurements leaves open the question of how vertebral bodies in strepsirhine species compensate for increased BM.

Evolution and allometry of calcaneal elongation in living and extinct primates

Specialized acrobatic leaping has been recognized as a key adaptive trait tied to the origin and subsequent radiation of euprimates based on its observed frequency in extant primates and inferred frequency in extinct early euprimates. Hypothesized skeletal correlates include elongated tarsal elements, which would be expected to aid leaping by allowing for increased rates and durations of propulsive acceleration at takeoff. Alternatively, authors of a recent study argued that pronounced distal calcaneal elongation of euprimates (compared to other mammalian taxa) was related primarily to specialized pedal grasping. Testing for correlations between calcaneal elongation and leaping versus grasping is complicated by body size differences and associated allometric affects. We re-assess allometric constraints on, and the functional significance of, calcaneal elongation using phylogenetic comparative methods, and present an evolutionary hypothesis for the evolution of calcaneal elongation in primates using a Bayesian approach to ancestral state reconstruction (ASR). Results show that among all primates, logged ratios of distal calcaneal length to total calcaneal length are inversely correlated with logged body mass proxies derived from the area of the calcaneal facet for the cuboid. Results from phylogenetic ANOVA on residuals from this allometric line suggest that deviations are explained by degree of leaping specialization in prosimians, but not anthropoids. Results from ASR suggest that non-allometric increases in calcaneal elongation began in the primate stem lineage and continued independently in haplorhines and strepsirrhines. Anthropoid and lorisid lineages show stasis and decreasing elongation, respectively. Initial increases in calcaneal elongation in primate evolution may be related to either development of hallucal-grasping or a combination of grasping and more specialized leaping behaviors. As has been previously suggested, subsequent increases in calcaneal elongation are likely adaptations for more effective acrobatic leaping, highlighting the importance of this behavior in early euprimate evolution.

Age at first reproduction explains rate variation in the strepsirrhine molecular clock

Although the molecular clock hypothesis posits that the rate of molecular change is constant over time, there is evidence that rates vary among lineages. Some of the strongest evidence for variable molecular rates comes from the primates; e.g., the "hominoid slowdown." These rate differences are hypothesized to correlate with certain species attributes, such as generation time and body size. Here, we examine rates of molecular change in the strepsirrhine suborder of primates and test whether body size or age at first reproduction (a proxy for generation time) explains patterns of rate variation better than a null model where the molecular clock is independent of these factors. To examine these models, we analyzed DNA sequences from four pairs of recently diverged strepsirrhine sister taxa to estimate molecular rates by using sign tests, likelihood ratio tests, and regression analyses. Our analysis does not support a model where body weight or age at first reproduction strongly influences rates of molecular evolution across mitochondrial and nuclear sites. Instead, our analysis supports a model where age at first reproduction influences neutral evolution in the nuclear genome. This study supports the generation time hypothesis for rate variation in the nuclear molecular clock. Molecular clock variation due to generation time may help to resolve the discordance between molecular and paleontological estimates for divergence date estimates in primate evolution.

Patterns of macroevolution among Primates inferred from a supermatrix of mitochondrial and nuclear DNA

Here, we present a new primate phylogeny inferred from molecular supermatrix analyses of size 42 kb containing 70% of missing data, and representing 75% of primate species diversity. The supermatrix was analysed using a gene-partitioned maximum likelihood approach to obtain an exhaustive molecular phylogenetic framework. All clades recovered from recent molecular works were upheld in our analyses demonstrating that the presence of missing data did not bias our supermatrix inference. The resulting phylogenetic tree was subsequently dated with a molecular dating method to provide a timescale for speciation events. Results obtained from our relaxed molecular clock analyses concurred with previous works based on the same fossil constraints. The resulting dated tree allowed to infer of macroevolutionary processes among the primates. Shifts in diversification rate and speciation rates were determined using the SymmeTREE method and a birthdeath process. No significant asymmetry was detected for the primate clade, but significant shifts in diversification rate were identified for seven clades: Anthropoidea, Lemuriformes, Lemuridae, Galagidae, Callithrix genus, the Cercopithecinae and Asian Macaca. Comparisons with previous primate supertree results reveal that (i) there was a diversification event at the root of the Lemuriformes, (ii) a higher diversification rate is detected for Cercopithecidae and Anthropoidea and (iii) a shift in diversification is always recovered for Macaca genus. Macroevolutionary inferences and primate divergence dates show that major primate diversification events occurred after the Paleogene, suggesting the extinction of ancient primate lineages.

Phylogeny and molecular evolution in primates

Statistical methods for estimating the branching order and the branching dates from DNA sequence data, taking into account of the rate variation among lineages, are reviewed. An application of the methods to data from primates suggests that chimpanzee is the closest relative of man, and further suggests that these two species diverged about 4-5 million years ago.