TARSII and CARSII: Two approaches for SNP-independent identification of germline differentially methylated regions in mammals.

Identifying germline differentially methylated regions (DMRs) in outbred mammals remains a challenge because of difficulty in obtaining single-nucleotide polymorphisms (SNPs). To overcome this difficulty, we developed two computational approaches, TARSII and CARSII, which allow accurate prediction of germline DMRs from DNA methylomes independent of SNPs. Furthermore, we introduce an easy and quick way to validate the predicted germline DMRs with allelic DNA methylation using CGmapTools. Collectively, our strategy can greatly facilitate de novo identification of germline DMRs in outbred mammals. For complete details on the use and execution of this protocol, please refer to Chu et al. (2021).

Evolution of the guanylate binding protein (GBP) genes: Emergence of GBP7 genes in primates and further acquisition of a unique GBP3 gene in simians.

Guanylate binding proteins (GBPs) are major players in the host immunity, providing defense against bacterial and viral invaders. Multigene families may suffer different processes of evolution. Gene families related to the immune system usually follow the birth-and-death evolution process, where duplicated genes can be deleted, gain new functions or become non-functional. We analyzed publicly available primate GBP sequences and their genomic organization and observed that GBP7 genes appear to have emerged from a duplication of GBP4 and seem to be only present in primates. Furthermore, GBP3 genes are only present in Simiiformes and probably originated from GBP1 genes. Finally, a duplication event occurred in the GBP6 in Tarsiiformes and became functional which might also explain the duplication of GBP6 in New World monkeys and Cercopithecidae. Taken together, this study provides new knowledge on the evolution of GBPs in primates and suggests that a revision of the GBPs nomenclature is necessary.

Internal nasal morphology of the Eocene primate Rooneyia viejaensis and extant Euarchonta: Using µCT scan data to understand and infer patterns of nasal fossa evolution in primates.

Primates have historically been viewed as having a diminished sense of smell compared to other mammals. In haplorhines, olfactory reduction has been inferred partly based on the complexity of the bony turbinals within the nasal cavity. Some turbinals are covered in olfactory epithelium, which contains olfactory receptor neurons that detect odorants. Accordingly, turbinal number and complexity has been used as a rough anatomical proxy for the relative importance of olfactory cues for an animal's behavioral ecology. Unfortunately, turbinals are delicate and rarely preserved in fossil specimens, limiting opportunities to make direct observations of the olfactory periphery in extinct primates. Here we describe the turbinal morphology of Rooneyia viejaensis, a late middle Eocene primate of uncertain phylogenetic affinities from the Tornillo Basin of West Texas. This species is currently the oldest fossil primate for which turbinals are preserved with minimal damage or distortion. Microcomputed tomography (µCT) reveals that Rooneyia possessed 1 nasoturbinal, 4 bullar ethmoturbinals, 1 frontoturbinal, 1 interturbinal, and an olfactory recess. This pattern is broadly similar to the condition seen in some extant strepsirrhine primates but differs substantially from the condition seen in extant haplorhines. Crown haplorhines possess only two ethmoturbinals and lack frontoturbinals, interturbinals, and an olfactory recess. Additionally, crown anthropoids have ethmoturbinals that are non-bullar. These observations reinforce the conclusion that Rooneyia is not a stem tarsiiform or stem anthropoid. However, estimated olfactory turbinal surface area in Rooneyia is greater than that of similar-sized haplorhines but smaller than that of similar-sized lemuriforms and lorisiforms. This finding suggests that although Rooneyia was broadly plesiomorphic in retaining a large complement of olfactory turbinals as in living strepsirrhines, Rooneyia may have evolved somewhat diminished olfactory abilities as in living haplorhines.

Estimating body size in early primates: The case of Archicebus and Teilhardina.

Obtaining accurate estimations of the body mass of fossil primates has always been a subject of interest in paleoanthropology because mass is an important determinant for so many other aspects of biology, ecology, and life history. This paper focuses on the issues involved in attempting to reconstruct the mass of two early Eocene haplorhine primates, Teilhardina and Archicebus, which pose particular problems due to their small size and temporal and phylogenetic distance from extant primates. In addition to a ranking of variables from more to less useful, the effect of using models of varying taxonomic and size compositions is examined. Phylogenetic correction is also applied to the primate database. Our results indicate that the choice of variable is more critical than the choice of model. The more reliable variables are the mediolateral breadth across the femoral condyles and the area of the calcaneocuboid facet of the calcaneus. These variables suggest a body mass of 39 g (range 33-46 g) for Archicebus and 48 g (range 44-56 g) for Teilhardina. The width of the distal femur is found to be the most consistent estimator across models of various composition and techniques. The effect of phylogenetic correction is small but the choice of branch length assumption affects point estimates for the fossils. The majority of variables and models predict the body mass of Archicebus and Teilhardina to be in the range of the smaller extant mouse lemurs, as expected.

Endocranial morphology of Microchoerus erinaceus (Euprimates, Tarsiiformes) and early evolution of the Euprimates brain.

OBJECTIVES: Innovations in brain structure and increase in brain size relative to body mass are key features of Primates evolutionary history. Surprisingly, the endocranial morphology of early Euprimates is still rather poorly known, and our understanding of early euprimate brain evolution (Eocene epoch) relies on a handful of specimens. MATERIALS AND METHODS: In this article, we describe the endocranial cast of the tarsiiform Microchoerus erinaceus from the late Early Eocene of Perrière (Quercy fissure filling, France) based on a virtual reconstruction extracted from CT scan data of the endocranial cavity of the complete, undeformed specimen UM-PRR1771. RESULTS: The endocast of M. erinaceus shows the derived features observed in other Euprimates (e.g. sylvian fissure and temporal lobe), with limited neocortical folding, and a telencephalic flexure comparable to that of extant primates. DISCUSSION: Comparison with the endocasts of other available late Eocene primates shows that they already exhibited a variety of brain morphologies, highlighting the complex history of the external features of the primate brain, as early as the Eocene. M. erinaceus was a fruit and gum eater considered as nocturnal based on its orbit size. However, its brain showed small olfactory bulbs--smaller than in the coeval diurnal taxa Adapis parisiensis--and a neocorticalization similar to folivorous taxa. These observations contrast with patterns observed in primates today where nocturnal taxa have larger olfactory bulbs than diurnal taxa, and call into question a direct correlation between frugivory and neocorticalization increase in primates.

Redescription and designation of a neotype for Pseudoloris reguanti Crusafont-Pairó, 1967, an Eocene primate from the Iberian Peninsula.

The species Pseudoloris reguanti (Microchoerinae, Omomyidae, Primates) was described by Miquel Crusafont-Pairó in 1967, based on a single lower molar from the Late Eocene Spanish site Sant Cugat de Gavadons. Sometime later, the holotype and unique material of P. reguanti was lost from the collections of the Institut Català de Paleontologia Miquel Crusafont. Recently, several isolated teeth of Pseudoloris from the type locality have been found in the collections of the Naturhistorisches Museum Basel, Switzerland, including two lower molars. According to the description of Crusafont-Pairó, one of the specimens may correspond to the holotype, but this statement cannot be proved due to the lack of illustrations accompanying the original definition of the species. In this work we designate this specimen as a neotype, also providing proper descriptions, measurements and illustrations of the new material and an emended diagnosis for the species.

New postcranial elements for the earliest Eocene fossil primate Teilhardina belgica.

Teilhardina belgica is one of the most primitive fossil primates known to date and the earliest haplorhine with associated postcranials, making it relevant to a reconstruction of the ancestral primate morphotype. Here we describe newly discovered postcranial elements of T. belgica. It is a small primate with an estimated body mass between 30 and 60 g, similar to the size of a mouse lemur. Its hindlimb anatomy suggests frequent and forceful leaping with excellent foot mobility and grasping capabilities. It can now be established that this taxon exhibits critical primate postcranial synapomorphies such as a grasping hallux, a tall knee, and nailed digits. This anatomical pattern and behavioral profile is similar to what has been inferred before for other omomyids and adapiforms. The most unusual feature of T. belgica is its elongated middle phalanges (most likely manual phalanges), suggesting that this early primate had very long fingers similar to those of living tarsiers.

A new species of Pseudoloris (Omomyidae, Primates) from the middle Eocene of Sant Jaume de Frontanyà (Eastern Pyrenees, Spain).

In this article we describe a new species of Pseudoloris (Omomyidae, Primates) from the Robiacian (middle Eocene) locality of Sant Jaume de Frontanyà (Eastern Pyrenees, Spain). Pseudoloris pyrenaicus is characterized by its medium size, thickened paracristid, absence of a distinct paraconid, and well-developed buccal cingulid in the lower molars, large hypoconulid in the M(3), paraconule and hypocone reduced in the M(1) and M(2) and absent in the M(3). The material from Sant Jaume de Frontanyà constitutes the most abundant sample of the genus Pseudoloris found until now in the Iberian Peninsula. Almost all the dental elements have been recovered, including those teeth hardly known for other species of the genus, such as lower and upper incisors. The new species shows intermediate features between Pseudoloris isabenae from Capella and Pseudoloris parvulus, present in different Spanish and French sites. Therefore, we consider that Pseudoloris pyrenaicus is an intermediate form between these two species.