The Complete Mitochondrial Genome of Dendrogale murina (Tupaiidae) and Phylogeny of Scandentia.

In this paper, we report the complete mitochondrial genome of the northern smooth-tailed treeshrew Dendrogale murina, which was sequenced for the first time using the Illumina next-generation sequencing (NGS) technology. The total length of the mitochondrial genome is 16,844-16,850 bp and encodes 37 genes, including two ribosomal RNAs (rRNAs) 12S and 16S, 22 transfer RNAs (tRNAs), 13 protein-coding genes (PCGs), and a D-loop in the characteristic arrangement of family Tupaiidae (Mammalia: Scandentia). The overall base composition of the complete mitochondrial DNA is A (33.5%), C (25.5%), G (13.9%), and T (27.1%). Phylogenetic analysis of Scandentia mitochondrial genomes showed a classic pattern, which was revealed previously while using individual phylogenetic markers. The result of the current study is consistent with one based on the latest morphological studies, with the basal position of Ptilocercus and Dendrogale sister to the rest of the Tupaiidae genera. The divergence time of the Dendrogale genus is estimated as Eocene-Oligocene, with the mean value of 35.8 MYA, and the Ptilocercus genus probably separated at about 46.3 MYA. We observe an increase in the age of all nodes within the Scandentia, except for a decrease in the age of separation of Ptilocercus. This result can be explained both by the addition of new mitochondrial genome data in the analysis and the usage of new calibration points from recently published data.

The northern treeshrew (Scandentia: Tupaiidae: Tupaia belangeri) in the context of primate locomotor evolution: A comprehensive analysis of gait, positional, and grasping behavior.

The locomotor behaviors of treeshrews are often reported as scurrying "squirrel-like" movements. As such, treeshrews have received little attention beyond passing remarks in regard to primate locomotor evolution. However, scandentians vary considerably in habitat and substrate use, thus categorizing all treeshrew locomotion based on data collected from a single species is inappropriate. This study presents data on gait characteristics, positional, and grasping behavior of the northern treeshrew (Tupaia belangeri) and compares these findings to the fat-tailed dwarf lemur (Cheirogaleus medius) to assess the role of treeshrews as a model for understanding the origins of primate locomotor and grasping evolution. We found that northern treeshrews were primarily arboreal and shared their activities between quadrupedalism, climbing and leaping in rates similar to fat-tailed dwarf lemurs. During quadrupedal locomotion, they exhibited a mixture of gait characteristics consistent with primates and other small-bodied non-primate mammals and demonstrated a hallucal grasping mode consistent with primates. These data reveal that northern treeshrews show a mosaic of primitive mammalian locomotor characteristics paired with derived primate features. Further, this study raises the possibility that many of the locomotor and grasping characteristics considered to be "uniquely" primate may ultimately be features consistent with Euarchonta.

First Record of the Tortoise Tick, Amblyomma geoemydae (Cantor, 1847) (Acari: Ixodidae) Parasitizing a Tree Shrew, Tupaia glis (Scandentia: Tupaiidae) in West Malaysia.

The tick genus Amblyomma Koch, 1844 (Acari: Ixodidae) has received little attention in Malaysia; therefore, its associated hosts and distribution records are poorly known. In this study, we collected six Amblyomma sp. individuals (two larvae and four adults) that infested a common treeshrew, Tupaia glis (Diard, 1820) (Scandentia: Tupaiidae) caught in a recreational area in Sungai Lembing, Pahang (West Malaysia). The adult female ticks were morphologically identified according to taxonomic keys prior to molecular identification using cytochrome oxidase subunit I (COI) and 16S rDNA genes. The ticks were genetically verified as Amblyomma geoemydae (Cantor, 1847) with 98%-99% similarity to the available GenBank sequences. Neighbor-joining (NJ) trees indicated that A. geoemydae was clearly distinguished from other Amblyomma ticks and this was supported with high bootstrap values. This paper is the first to report A. geoemydae ticks infesting T. glis and provides a new tick-host record from West Malaysia. This information is significant for further investigation, specifically on this tick species as potential vector of tick-borne disease (TBD) agents.

Survey anatomy and histological observation of the nasal cavity of Tupaia belangeri chinensis (Tupaiidae, Scandentia, Mammalia).

This study aimed to provide researchers with an atlas of the survey anatomy, histology, and imaging of the nasal cavity of Tupaia belangeri chinensis. Seven T. b. chinensis adult males were euthanized and scanned using micro-computed tomography (CT). The nose was separated, and tissue sections were made on the coronal and axial planes to observe the survey anatomy and histological and imaging characteristics of the nose. T. b. chinensis contains one maxilloturbinal and three ethmoturbinals, one nasoturbinal, one interturbinal, two frontoturbinals, and one lamina semicircularis in the unilateral nasal cavity. Other identified structures were the ostiomeatal complex, vomeronasal organ, superior nasal vault, maxillary sinus, and frontal recess. The drainage pathways of the sinuses and nasal airflow in T. b. chinensis were confirmed. The vault epithelium consisted of the squamous epithelium, respiratory epithelium, transitional epithelium, and olfactory epithelium. Micro-CT confirmed our findings of the coronal tissue sections. The nasal cavity anatomy of T. b. chinensis is similar to that of some strepsirrhine primates. However, the airflow and olfactory function are quite different from that of humans. Our gross and histological atlas of the nasal septum, turbinals, maxillary sinus, and frontal recess provides a reference for researchers to use T. b. chinensis for nasal cavity functional research.

Asymmetric Distribution of Gene Trees Can Arise under Purifying Selection If Differences in Population Size Exist.

Incomplete lineage sorting (ILS) is an important factor that causes gene tree discordance. For gene trees of three species, under neutrality, random mating, and the absence of interspecific gene flow, ILS creates a symmetric distribution of gene trees: the gene tree that accords with the species tree has the highest frequency, and the two discordant trees are equally frequent. If the neutral condition is violated, the impact of ILS may change, altering the gene tree distribution. Here, we show that under purifying selection, even assuming that the fitness effect of mutations is constant throughout the species tree, if differences in population size exist among species, asymmetric distributions of gene trees will arise, which is different from the expectation under neutrality. In extremes, one of the discordant trees rather than the concordant tree becomes the most frequent gene tree. In addition, we found that in a real case, the position of Scandentia relative to Primate and Glires, the symmetry in the gene tree distribution can be influenced by the strength of purifying selection. In current phylogenetic inference, the impact of purifying selection on the gene tree distribution is rarely considered by researchers. This study highlights the necessity of considering this impact.

White matter volume and white/gray matter ratio in mammalian species as a consequence of the universal scaling of cortical folding.

Because the white matter of the cerebral cortex contains axons that connect distant neurons in the cortical gray matter, the relationship between the volumes of the 2 cortical compartments is key for information transmission in the brain. It has been suggested that the volume of the white matter scales universally as a function of the volume of the gray matter across mammalian species, as would be expected if a global principle of wiring minimization applied. Using a systematic analysis across several mammalian clades, here we show that the volume of the white matter does not scale universally with the volume of the gray matter across mammals and is not optimized for wiring minimization. Instead, the ratio between volumes of gray and white matter is universally predicted by the same equation that predicts the degree of folding of the cerebral cortex, given the clade-specific scaling of cortical thickness, such that the volume of the gray matter (or the ratio of gray to total cortical volumes) divided by the square root of cortical thickness is a universal function of total cortical volume, regardless of the number of cortical neurons. Thus, the very mechanism that we propose to generate cortical folding also results in compactness of the white matter to a predictable degree across a wide variety of mammalian species.

Three-Dimensional Geometric Morphometric Analysis of Treeshrew (Scandentia) Lower Molars: Insight into Dental Variation and Systematics.

Scandentia (treeshrews) is an order of small-bodied Indomalayan mammals generally agreed to be a member of Euarchonta with Primates and Dermoptera (colugos). However, intraordinal relationships among treeshrews are less well understood. Although recent studies have begun to clarify treeshrew taxonomy using morphological and molecular datasets, previous analysis of treeshrew dentition has yielded little clarity in terms of species-level relationships within the order. However, these studies made use of character-based methods, scoring traits across the dental arcade, which depend on there being clear differences among taxa that can be encapsulated in coding schemes. Geometric morphometrics has the potential to capture subtler shape variation, so it may be better for examining similarities among closely related taxa whose teeth have a similar bauplan. We used three-dimensional geometric morphometrics on a sample of treeshrew lower second molars and compared the patterns of variation to the results of previous studies. We captured 19 landmarks on a sample of 43 specimens representing 15 species. Using specimen-based principal components analysis and between-group principal component analysis, the two treeshrew families (Tupaiidae and Ptilocercidae) were well separated in morphospace. Moreover, several treeshrew species plot in morphospace according to the clades established in previous molecular work, with closely related species plotting closer to one another than to more distantly related species, suggesting that dental morphology can be useful when studying relationships among treeshrews. As most extinct treeshrews are known only from teeth, understanding morphological patterns in treeshrew molars is important for future work on the evolutionary history of Scandentia. Anat Rec, 302:1154-1168, 2019. © 2019 Wiley Periodicals, Inc.

Scaling of bony canals for encephalic vessels in euarchontans: Implications for the role of the vertebral artery and brain metabolism.

Supplying the central nervous system with oxygen and glucose for metabolic activities is a critical function for all animals at physiologic, anatomical, and behavioral levels. A relatively proximate challenge to nourishing the brain is maintaining adequate blood flow. Euarchontans (primates, dermopterans and treeshrews) display a diversity of solutions to this challenge. Although the vertebral artery is a major encephalic vessel, previous research has questioned its importance for irrigating the cerebrum. This presents a puzzling scenario for certain strepsirrhine primates (non-cheirogaleid lemuriforms) that have reduced promontorial branches of the internal carotid artery and no apparent alternative encephalic vascular route except for the vertebral artery. Here, we present results of phylogenetic comparative analyses of data on the cross-sectional area of bony canals that transmit the vertebral artery (transverse foramina). These results show that, across primates (and within major primate subgroups), variation in the transverse foramina helps significantly to explain variation in forebrain mass even when variation in promontorial canal cross-sectional areas are also considered. Furthermore, non-cheirogaleid lemuriforms have larger transverse foramina for their endocranial volume than other euarchontans, suggesting that the vertebral arteries compensate for reduced promontorial artery size. We also find that, among internal carotid-reliant euarchontans, species that are more encephalized tend to have a promontorial canal that is larger relative to the transverse foramina. Tentatively, we consider the correlation between arterial canal diameters (as a proxy for blood flow) and brain metabolic demands. The results of this analysis imply that human investment in brain metabolism (∼27% of basal metabolic rate) may not be exceptional among euarchontans.

The gene tree delusion.

Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel deep-level phylogenetic problems that have stymied concatenation. Here, we reanalyze Song et al.'s (2012) data and leverage these re-analyses to explore key issues in systematics including the recombination ratchet, gene tree stoichiometry, the proportion of gene tree incongruence that results from deep coalescence versus other factors, and simulations that compare the performance of coalescence and concatenation methods in species tree estimation. Song et al. (2012) reported an average locus length of 3.1 kb for the 447 protein-coding genes in their phylogenomic dataset, but the true mean length of these loci (start codon to stop codon) is 139.6 kb. Empirical estimates of recombination breakpoints in primates, coupled with consideration of the recombination ratchet, suggest that individual coalescence genes (c-genes) approach ∼12 bp or less for Song et al.'s (2012) dataset, three to four orders of magnitude shorter than the c-genes reported by these authors. This result has general implications for the application of coalescence methods in species tree estimation. We contend that it is illogical to apply coalescence methods to complete protein-coding sequences. Such analyses amalgamate c-genes with different evolutionary histories (i.e., exons separated by >100,000 bp), distort true gene tree stoichiometry that is required for accurate species tree inference, and contradict the central rationale for applying coalescence methods to difficult phylogenetic problems. In addition, Song et al.'s (2012) dataset of 447 genes includes 21 loci with switched taxonomic names, eight duplicated loci, 26 loci with non-homologous sequences that are grossly misaligned, and numerous loci with >50% missing data for taxa that are misplaced in their gene trees. These problems were compounded by inadequate tree searches with nearest neighbor interchange branch swapping and inadvertent application of substitution models that did not account for among-site rate heterogeneity. Sixty-six gene trees imply unrealistic deep coalescences that exceed 100 million years (MY). Gene trees that were obtained with better justified models and search parameters show large increases in both likelihood scores and congruence. Coalescence analyses based on a curated set of 413 improved gene trees and a superior coalescence method (ASTRAL) support a Scandentia (treeshrews)+Glires (rabbits, rodents) clade, contradicting one of the three primary systematic conclusions of Song et al. (2012). Robust support for a Perissodactyla+Carnivora clade within Laurasiatheria is also lost, contradicting a second major conclusion of this study. Song et al.'s (2012) MP-EST species tree provided the basis for circular simulations that led these authors to conclude that the multispecies coalescent accounts for 77% of the gene tree conflicts in their dataset, but many internal branches of their MP-EST tree are stunted by an order of magnitude or more due to wholesale gene tree reconstruction errors. An independent assessment of branch lengths suggests the multispecies coalescent accounts for ⩽ 15% of the conflicts among Song et al.'s (2012) 447 gene trees. Unfortunately, Song et al.'s (2012) flawed phylogenomic dataset has been used as a model for additional simulation work that suggests the superiority of shortcut coalescence methods relative to concatenation. Investigator error was passed on to the subsequent simulation studies, which also incorporated further logical errors that should be avoided in future simulation studies. Illegitimate branch length switches in the simulation routines unfairly protected coalescence methods from their Achilles' heel, high gene tree reconstruction error at short internodes. These simulations therefore provide no evidence that shortcut coalescence methods out-compete concatenation at deep timescales. In summary, the long c-genes that are required for accurate reconstruction of species trees using shortcut coalescence methods do not exist and are a delusion. Coalescence approaches based on SNPs that are widely spaced in the genome avoid problems with the recombination ratchet and merit further pursuit in both empirical systematic research and simulations.

Mammalian Brains Are Made of These: A Dataset of the Numbers and Densities of Neuronal and Nonneuronal Cells in the Brain of Glires, Primates, Scandentia, Eulipotyphlans, Afrotherians and Artiodactyls, and Their Relationship with Body Mass.

Comparative studies amongst extant species are one of the pillars of evolutionary neurobiology. In the 20th century, most comparative studies remained restricted to analyses of brain structure volume and surface areas, besides estimates of neuronal density largely limited to the cerebral cortex. Over the last 10 years, we have amassed data on the numbers of neurons and other cells that compose the entirety of the brain (subdivided into cerebral cortex, cerebellum, and rest of brain) of 39 mammalian species spread over 6 clades, as well as their densities. Here we provide that entire dataset in a format that is readily useful to researchers of any area of interest in the hope that it will foster the advancement of evolutionary and comparative studies well beyond the scope of neuroscience itself. We also reexamine the relationship between numbers of neurons, neuronal densities and body mass, and find that in the rest of brain, but not in the cerebral cortex or cerebellum, there is a single scaling rule that applies to average neuronal cell size, which increases with the linear dimension of the body, even though there is no single scaling rule that relates the number of neurons in the rest of brain to body mass. Thus, larger bodies do not uniformly come with more neurons--but they do fairly uniformly come with larger neurons in the rest of brain, which contains a number of structures directly connected to sources or targets in the body.

Postsacral vertebral morphology in relation to tail length among primates and other mammals.

Tail reduction/loss independently evolved in a number of mammalian lineages, including hominoid primates. One prerequisite to appropriately contextualizing its occurrence and understanding its significance is the ability to track evolutionary changes in tail length throughout the fossil record. However, to date, the bony correlates of tail length variation among living taxa have not been comprehensively examined. This study quantifies postsacral vertebral morphology among living primates and other mammals known to differ in relative tail length (RTL). Linear and angular measurements with known biomechanical significance were collected on the first, mid-, and transition proximal postsacral vertebrae, and their relationship with RTL was assessed using phylogenetic generalized least-squares regression methods. Compared to shorter-tailed primates, longer-tailed primates possess a greater number of postsacral vertebral features associated with increased proximal tail flexibility (e.g., craniocaudally longer vertebral bodies), increased intervertebral body joint range of motion (e.g., more circularly shaped cranial articular surfaces), and increased leverage of tail musculature (e.g., longer spinous processes). These observations are corroborated by the comparative mammalian sample, which shows that distantly related short-tailed (e.g., Phascolarctos, Lynx) and long-tailed (e.g., Dendrolagus, Acinonyx) nonprimate mammals morphologically converge with short-tailed (e.g., Macaca tonkeana) and long-tailed (e.g., Macaca fascicularis) primates, respectively. Multivariate models demonstrate that the variables examined account for 70% (all mammals) to 94% (only primates) of the variance in RTL. Results of this study may be used to infer the tail lengths of extinct primates and other mammals, thereby improving our understanding about the evolution of tail reduction/loss.

Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.

Molecular cytogenetic studies in strepsirrhine primates, Dermoptera and Scandentia.

Since the first chromosome painting study between human and strepsirrhine primates was performed in 1996, nearly 30 species in Strepsirrhini, Dermoptera and Scandentia have been analyzed by cross-species chromosome painting. Here, the contribution of chromosome painting data to our understanding of primate genome organization, chromosome evolution and the karyotype phylogenetic relationships within strepsirrhine primates, Dermoptera and Scandentia is reviewed. Twenty-six to 43 homologous chromosome segments have been revealed in different species with human chromosome-specific paint probes. Various landmark rearrangements characteristic for each different lineage have been identified, as cytogenetic signatures that potentially unite certain lineages within strepsirrhine primates, Dermoptera and Scandentia.

Molecular phylogeny of treeshrews (Mammalia: Scandentia) and the timescale of diversification in Southeast Asia.

Resolving the phylogeny of treeshrews (Order Scandentia) has historically proven difficult, in large part because of access to specimens and samples from critical taxa. We used "antique" DNA methods with non-destructive sampling of museum specimens to complete taxon sampling for the 20 currently recognized treeshrew species and to estimate their phylogeny and divergence times. Most divergence among extant species is estimated to have taken place within the past 20 million years, with deeper divergences between the two families (Ptilocercidae and Tupaiidae) and between Dendrogale and all other genera within Tupaiidae. All but one of the divergences between currently recognized species had occurred by 4Mya, suggesting that Miocene tectonics, volcanism, and geographic instability drove treeshrew diversification. These geologic processes may be associated with an increase in net diversification rate in the early Miocene. Most evolutionary relationships appear consistent with island-hopping or landbridge colonization between contiguous geographic areas, although there are exceptions in which extinction may play an important part. The single recent divergence is between Tupaia palawanensis and Tupaia moellendorffi, both endemic to the Philippines, and may be due to Pleistocene sea level fluctuations and post-landbridge isolation in allopatry. We provide a time-calibrated phylogenetic framework for answering evolutionary questions about treeshrews and about evolutionary patterns and processes in Euarchonta. We also propose subsuming the monotypic genus Urogale, a Philippine endemic, into Tupaia, thereby reducing the number of extant treeshrew genera from five to four.

Cochlear labyrinth volume in euarchontoglirans: implications for the evolution of hearing in primates.

Using high resolution X-ray computed tomography data we examined the relationship between cochlear labyrinth volume and body mass in extant, non-primate euarchontoglirans, and in two fossils, to allow for comparison with the results of Kirk and Gosselin-Ildari (2009). Modern primates have significantly higher cochlear labyrinth volumes relative to body mass than other euarchontoglirans, which may be related to a downward shift in the highest and lowest audible frequencies over the course of primate evolution, and to the relative increase in brain size observed in Euprimates.

Ectoparasites of small mammals in four localities of wildlife reserves in Peninsular Malaysia.

Field surveys of ectoparasites on rodents and scandents were conducted in four localities of wildlife reserves in Peninsular Malaysia from October 2008 to November 2009. A total of 16 animals comprising 5 species of hosts were caught and examined for ectoparasites. The hosts examined were Maxomys rajah, Maxomys whiteheadi, Leopoldamys sabanus, Lariscus insignis and Tupaia glis. Of these hosts, 9 genera, consisting of 14 species of ectoparasites were extracted. Three species of ticks (Ixodidae), 7 species of mesostigmatid mites (Laelaptidae), 3 species of chiggers (Trombiculidae) and 1 species of listrophorid mites (Listrophoriidae) were identified. The infestation rate of ectoparasites observed ranged from 12.5% to 62.5%. Among the ectoparasites found, Ixodes granulatus and Leptotrombidium deliense are of known medical importance.

Forelimb proportions and kinematics: how are small primates different from other small mammals?

The crouched limb posture of small mammals enables them to react to unexpected irregularities in the support. Small arboreal primates would benefit from these kinematics in their arboreal habitat but it has been demonstrated that primates display certain differences in forelimb kinematics to other mammals. The objective of this paper is to find out whether these changes in forelimb kinematics are related to changes in body size and limb proportions. As primates descended from small ancestors, a comparison between living small primates and other small mammals makes it possible to determine the polarity of character transformations for kinematic and morphometric features proposed to be unique to primates. Walking kinematics of mouse lemurs, brown lemurs, cotton-top tamarins and squirrel monkeys was investigated using cineradiography. Morphometry was conducted on a sample of 110 mammals comprising of primates, marsupials, rodents and carnivores. It has been shown that forelimb kinematics change with increasing body size in such a way that limb protraction increases but retraction decreases. Total forelimb excursion, therefore, is almost independent of body size. Kinematic changes are linked to changes in forelimb proportions towards greater asymmetry between scapula and radius. Due to the spatial restriction inherent in the diagonal footfall sequence of primates, forelimb excursion is influenced by the excursion of the elongated hind limb. Hindlimb geometry, however, is highly conserved, as has been previously shown. The initial changes in forelimb kinematics might, therefore, be explained as solutions to a constraint rather than as adaptations to the particular demands of arboreal locomotion.

Molecular and genomic data identify the closest living relative of primates.

A full understanding of primate morphological and genomic evolution requires the identification of their closest living relative. In order to resolve the ancestral relationships among primates and their closest relatives, we searched multispecies genome alignments for phylogenetically informative rare genomic changes within the superordinal group Euarchonta, which includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews). We also constructed phylogenetic trees from 14 kilobases of nuclear genes for representatives from most major primate lineages, both extant colugos, and multiple treeshrews, including the pentail treeshrew, Ptilocercus lowii, the only living member of the family Ptilocercidae. A relaxed molecular clock analysis including Ptilocercus suggests that treeshrews arose approximately 63 million years ago. Our data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous.