Molecular and morphological supertrees for eutherian (placental) mammals

A Guide to Phylogenomic Inference

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.

The orbitotemporal region and the mandibular joint in the skull of shrews (Soricidae, Mammalia)

Modern phylogenetics place the Soricidae (shrews) into the order Lipotyphla, which belongs to the relatively new superorder clade Laurasiatheria. Their most derived skull feature is the unusual position and shape of the jaw articulation: Whereas in all other mammals the glenoid region of the squamosum is more or less tightly attached to the otic capsule or petrosal, respectively, in the soricids it is attached to the nasal capsule. This new position of the jaw articulation becomes possible by the posterior extension of the nasal capsule and the rostral shift of the glenoid fossa. By the study of dated postnatal ontogenetic stages of Crocidura russula and Sorex araneus, we show that the glenoid part of the squamosal becomes fixed to the nasal capsule by the ossified alae orbitalis and temporalis. The ala orbitalis is displaced laterally by the expanded cupula nasi posterior; this posterior expansion is well documented by the lamina terminalis, which incorporates parts of the palatinum and alisphenoid. Both alae consist largely of ‘Zuwachsknochen’ (‘appositional bone’) and are then named orbitosphenoid and alisphenoid. By the forward move of the pars glenoidea and of the alisphenoid, the foramen lacerum medium (‘fenestra piriformis’) also expands rostrally. Functionally, the forward shift of the jaw joint helps to keep the incisal biting force high. Biomechanically the jaws can be considered as a tweezer, and the rostral position of the jaw joints makes the interorbital pillar and the shell-like walls of the facial skull a lever for the highly specialized incisal dentition.

Washed Microbiota Transplantation Accelerates the Recovery of Abnormal Changes by Light-Induced Stress in Tree Shrews

The gut and brain interact constantly in a complex fashion. Its intricacy and intrigue is progressively being revealed in the study of the "gut-brain axis". Among many factors, abnormal light exposure is a potential powerful stressor, which is becoming ever more pervasive in our modern society. However, little is known about how stress, induced by staying up late by light, affects the gut-brain axis. We addressed this question by extending the normal circadian light for four hours at night in fifteen male tree shrews to simulate the pattern of staying up late in humans. The behavior, biochemical tests, microbiota dynamics, and brain structure of tree shrews were evaluated. The simple prolongation of light in the environment resulted in substantial changes of body weight loss, behavioral differences, total sleep time reduction, and an increased level of urine cortisol. These alterations were rescued by the treatment of either ketamine or washed microbiota transplantation (WMT). Importantly, the sustainability of WMT effect was better than that of ketamine. Magnetic Resonance Imaging analysis indicated that ketamine acted on the hippocampus and thalamus, and WMT mainly affected the piriform cortex and lateral geniculate nucleus. In conclusion, long-term light stimulation could change the behaviors, composition of gut microbiota and brain structure in tree shrews. Targeting microbiota thus certainly holds promise as a treatment for neuropsychiatric disorders, including but not limited to stress-related diseases.

Effects of body size on estimation of mammalian area requirements

Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum.

Conserved sequences identify the closest living relatives of primates

Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. However, the phylogenetic placement of these primate relatives remains controversial, with three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, we used two algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. We assessed different genomic histories and compared with other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny showed Cercopithecinae to have low levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.

Donepezil improves the cognitive impairment in a tree shrew model of Alzheimer's disease induced by amyloid-β1-40 via activating the BDNF/TrkB signal pathway

Alzheimer's disease (AD) is a chronic neurodegenerative disorder which can contribute to memory loss and cognitive damage in the elderly; moreover, evidence from clinical and animal studies demonstrated that AD always exhibit severe cognitive deficits. However, the effects of donepezil medications on cognition are controversial. Additionally, it is unclear whether donepezil can protect neurons to improve cognitive function through the brain-derived neurotropic factor (BDNF)/tyrosine receptor kinase B (TrkB) signalling pathway in the tree shrew (TS), which has a closer evolutionary relationship to primates than rodents. Here, we designed a study on an amyloid-β_1-40 (Aβ_1-40)-induced TS model of AD and investigated the molecular mechanism by which donepezil protects neurons and improves cognitive function through activating the BDNF/TrkB signalling pathway. The results showed that donepezil could rescue Aβ_1-40-induced spatial cognition deficits, and reverse Aβ_1-40-induced temporal horn along with ADC enlargement in the TS brain. Meanwhile, it suppressed Aβ_1-40-induced neuronal damage and loss of body weight. Intriguingly, donepezil could increase the choline acetyl transferase (ChAT) expression level and reduce the fibrillary acid protein (GFAP) expression level in the hippocampus and cortex of TS. Additionally, donepezil significantly upregulated the expression level of BDNF, as well as the phosphorylated level of TrkB. These results suggested that donepezil could protect neurocytes from senility and ameliorate learning and memory impairment in the TS model of AD, which appeared to be through regulating the cholinergic system and inhibiting the BDNF/TrkB-dependent signalling pathway. Moreover, the study underlines the potency of TS to be a novel animal model for research on AD, and it deserves intensive attention.

Phylogenomics

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. The abundance of genomic data for an enormous variety of organisms has enabled phylogenomic inference of many groups, and this has motivated the development of many computer programs implementing the associated methods. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.

Super-Resolution Track-Density Imaging Reveals Fine Anatomical Features in Tree Shrew Primary Visual Cortex and Hippocampus

Diffusion-weighted magnetic resonance imaging (dMRI) is widely used to study white and gray matter (GM) micro-organization and structural connectivity in the brain. Super-resolution track-density imaging (TDI) is an image reconstruction method for dMRI data, which is capable of providing spatial resolution beyond the acquired data, as well as novel and meaningful anatomical contrast that cannot be obtained with conventional reconstruction methods. TDI has been used to reveal anatomical features in human and animal brains. In this study, we used short track TDI (stTDI), a variation of TDI with enhanced contrast for GM structures, to reconstruct direction-encoded color maps of fixed tree shrew brain. The results were compared with those obtained with the traditional diffusion tensor imaging (DTI) method. We demonstrated that fine microstructures in the tree shrew brain, such as Baillarger bands in the primary visual cortex and the longitudinal component of the mossy fibers within the hippocampal CA3 subfield, were observable with stTDI, but not with DTI reconstructions from the same dMRI data. The possible mechanisms underlying the enhanced GM contrast are discussed.

A diffusion tensor imaging atlas of white matter in tree shrew

Tree shrews are small mammals now commonly classified in the order of Scandentia, but have relatively closer affinity to primates than rodents. The species has a high brain-to-body mass ratio and relatively well-differentiated neocortex, and thus has been frequently used in neuroscience research, especially for studies on vision and neurological/psychiatric diseases. The available atlases on tree shrew brain provided only limited information on white matter (WM) anatomy. In this study, diffusion tensor imaging (DTI) was used to study the WM anatomy of tree shrew, with the goal to establish an image-based WM atlas. DTI and T₂-weighted anatomical images were acquired in vivo and from fixed brain samples. Deterministic tractography was used for three-dimensional reconstruction and rendering of major WM tracts. Myelin and neurofilaments staining were used to study the microstructural properties of certain WM tracts. Taking into account prior knowledge on tree shrew neuroanatomy, tractography results, and comparisons to the homologous structures in rodents and primates, an image-based WM atlas of tree shrew brain was constructed, which is available to research community upon request.

Why should we investigate the morphological disparity of plant clades?

BACKGROUND

Disparity refers to the morphological variation in a sample of taxa, and is distinct from diversity or taxonomic richness. Diversity and disparity are fundamentally decoupled; many groups attain high levels of disparity early in their evolution, while diversity is still comparatively low. Diversity may subsequently increase even in the face of static or declining disparity by increasingly fine sub-division of morphological 'design' space (morphospace). Many animal clades reached high levels of disparity early in their evolution, but there have been few comparable studies of plant clades, despite their profound ecological and evolutionary importance. This study offers a prospective and some preliminary macroevolutionary analyses.

METHODS

Classical morphometric methods are most suitable when there is reasonable conservation of form, but lose traction where morphological differences become greater (e.g. in comparisons across higher taxa). Discrete character matrices offer one means to compare a greater diversity of forms. This study explores morphospaces derived from eight discrete data sets for major plant clades, and discusses their macroevolutionary implications.

KEY RESULTS

Most of the plant clades in this study show initial, high levels of disparity that approach or attain the maximum levels reached subsequently. These plant clades are characterized by an initial phase of evolution during which most regions of their empirical morphospaces are colonized. Angiosperms, palms, pines and ferns show remarkably little variation in disparity through time. Conifers furnish the most marked exception, appearing at relatively low disparity in the latest Carboniferous, before expanding incrementally with the radiation of successive, tightly clustered constituent sub-clades.

CONCLUSIONS

Many cladistic data sets can be repurposed for investigating the morphological disparity of plant clades through time, and offer insights that are complementary to more focused morphometric studies. The unique structural and ecological features of plants make them ideally suited to investigating intrinsic and extrinsic constraints on disparity.

The position of tree shrews in the mammalian tree: Comparing multi-gene analyses with phylogenomic results leaves monophyly of Euarchonta doubtful

The well-accepted Euarchonta grandorder is a pruned version of Archonta nested within the Euarchontoglires (or Supraprimates) clade. At present, it includes tree shrews (Scandentia), flying lemurs (Dermoptera) and primates (Primates). Here, a phylogenomic dataset containing 1912 exons from 22 representative mammals was compiled to investigate the phylogenetic relationships within this group. Phylogenetic analyses and hypothesis testing suggested that tree shrews can be classified as a sister group to Primates or to Glires or even as a basal clade within Euarchontoglires. Further analyses of both modified and original previously published datasets found that the phylogenetic position of tree shrews is unstable. We also found that two of three exonic indels reported as synapomorphies of Euarchonta in a previous study do not unambiguously support the monophyly of such a clade. Therefore, the monophyly of both Euarchonta and Sundatheria (Dermoptera + Scandentia) are suspect. Molecular dating and divergence rate analyses suggested that the ancestor of Euarchontoglires experienced a rapid divergence, which may cause the unresolved position of tree shrews even using the whole genomic data.

Elaboration and Innervation of the Vibrissal System in the Rock Hyrax (Procavia capensis)

Mammalian tactile hairs are commonly found on specific, restricted regions of the body, but Florida manatees represent a unique exception, exhibiting follicle-sinus complexes (FSCs, also known as vibrissae or tactile hairs) on their entire body. The orders Sirenia (including manatees and dugongs) and Hyracoidea (hyraxes) are thought to have diverged approximately 60 million years ago, yet hyraxes are among the closest relatives to sirenians. We investigated the possibility that hyraxes, like manatees, are tactile specialists with vibrissae that cover the entire postfacial body. Previous studies suggested that rock hyraxes possess postfacial vibrissae in addition to pelage hair, but this observation was not verified through histological examination. Using a detailed immunohistochemical analysis, we characterized the gross morphology, innervation and mechanoreceptors present in FSCs sampled from facial and postfacial vibrissae body regions to determine that the long postfacial hairs on the hyrax body are in fact true vibrissae. The types and relative densities of mechanoreceptors associated with each FSC also appeared to be relatively consistent between facial and postfacial FSCs. The presence of vibrissae covering the hyrax body presumably facilitates navigation in the dark caves and rocky crevices of the hyrax's environment where visual cues are limited, and may alert the animal to predatory or conspecific threats approaching the body. Furthermore, the presence of vibrissae on the postfacial body in both manatees and hyraxes indicates that this distribution may represent the ancestral condition for the supraorder Paenungulata.

Hominids adapted to metabolize ethanol long before human-directed fermentation

Paleogenetics is an emerging field that resurrects ancestral proteins from now-extinct organisms to test, in the laboratory, models of protein function based on natural history and Darwinian evolution. Here, we resurrect digestive alcohol dehydrogenases (ADH4) from our primate ancestors to explore the history of primate-ethanol interactions. The evolving catalytic properties of these resurrected enzymes show that our ape ancestors gained a digestive dehydrogenase enzyme capable of metabolizing ethanol near the time that they began using the forest floor, about 10 million y ago. The ADH4 enzyme in our more ancient and arboreal ancestors did not efficiently oxidize ethanol. This change suggests that exposure to dietary sources of ethanol increased in hominids during the early stages of our adaptation to a terrestrial lifestyle. Because fruit collected from the forest floor is expected to contain higher concentrations of fermenting yeast and ethanol than similar fruits hanging on trees, this transition may also be the first time our ancestors were exposed to (and adapted to) substantial amounts of dietary ethanol.

Ultrastructural localization of tyrosine hydroxylase in tree shrew nucleus accumbens core and shell

Many behavioral, physiological, and anatomical studies utilize animal models to investigate human striatal pathologies. Although commonly used, rodent striatum may not present the optimal animal model for certain studies due to a lesser morphological complexity than that of non-human primates, which are increasingly restricted in research. As an alternative, the tree shrew could provide a beneficial animal model for studies of the striatum. The gross morphology of the tree shrew striatum resembles that of primates, with separation of the caudate and putamen by the internal capsule. The neurochemical anatomy of the ventral striatum, specifically the nucleus accumbens, has never been examined. This major region of the limbic system plays a role in normal physiological functioning and is also an area of interest for human striatal disorders. The current study uses immunohistochemistry of calbindin and tyrosine hydroxylase (TH) to determine the ultrastructural organization of the nucleus accumbens core and shell of the tree shrew (Tupaia glis belangeri). Stereology was used to quantify the ultrastructural localization of TH, which displays weaker immunoreactivity in the core and denser immunoreactivity in the shell. In both regions, synapses with TH-immunoreactive axon terminals were primarily symmetric and showed no preference for targeting dendrites versus dendritic spines. The results were compared to previous ultrastructural studies of TH and dopamine in rat and monkey nucleus accumbens. Tree shrews and monkeys show no preference for the postsynaptic target in the shell, in contrast to rats which show a preference for synapsing with dendrites. Tree shrews have a ratio of asymmetric to symmetric synapses formed by TH-immunoreactive terminals that is intermediate between rats and monkeys. The findings from this study support the tree shrew as an alternative model for studies of human striatal pathologies.

K-mer natural vector and its application to the phylogenetic analysis of genetic sequences

Based on the well-known k-mer model, we propose a k-mer natural vector model for representing a genetic sequence based on the numbers and distributions of k-mers in the sequence. We show that there exists a one-to-one correspondence between a genetic sequence and its associated k-mer natural vector. The k-mer natural vector method can be easily and quickly used to perform phylogenetic analysis of genetic sequences without requiring evolutionary models or human intervention. Whole or partial genomes can be handled more effective with our proposed method. It is applied to the phylogenetic analysis of genetic sequences, and the obtaining results fully demonstrate that the k-mer natural vector method is a very powerful tool for analysing and annotating genetic sequences and determining evolutionary relationships both in terms of accuracy and efficiency.

Evolutionary history and metabolic insights of ancient mammalian uricases

Uricase is an enzyme involved in purine catabolism and is found in all three domains of life. Curiously, uricase is not functional in some organisms despite its role in converting highly insoluble uric acid into 5-hydroxyisourate. Of particular interest is the observation that apes, including humans, cannot oxidize uric acid, and it appears that multiple, independent evolutionary events led to the silencing or pseudogenization of the uricase gene in ancestral apes. Various arguments have been made to suggest why natural selection would allow the accumulation of uric acid despite the physiological consequences of crystallized monosodium urate acutely causing liver/kidney damage or chronically causing gout. We have applied evolutionary models to understand the history of primate uricases by resurrecting ancestral mammalian intermediates before the pseudogenization events of this gene family. Resurrected proteins reveal that ancestral uricases have steadily decreased in activity since the last common ancestor of mammals gave rise to descendent primate lineages. We were also able to determine the 3D distribution of amino acid replacements as they accumulated during evolutionary history by crystallizing a mammalian uricase protein. Further, ancient and modern uricases were stably transfected into HepG2 liver cells to test one hypothesis that uricase pseudogenization allowed ancient frugivorous apes to rapidly convert fructose into fat. Finally, pharmacokinetics of an ancient uricase injected in rodents suggest that our integrated approach provides the foundation for an evolutionarily-engineered enzyme capable of treating gout and preventing tumor lysis syndrome in human patients.

Anatomical MRI templates of tree shrew brain for volumetric analysis and voxel-based morphometry

BACKGROUND

Tree shrews are close relatives of primates, and are increasingly used as models in the research of vision, social stress and neurological/psychiatric diseases. However, neuroimaging techniques, for example magnetic resonance (MR) imaging, are only rarely applied to this species to study the structure and function of the brain. A template MR image set, which is essential for morphometry/volumetric analysis, of tree shrew brain has been lacking in the literature.

NEW METHOD

High-resolution anatomical MR images and diffusion tensor images of the brain were acquired from male Chinese tree shrews (Tupaia belangeri chinensis), and resampled to an isotropic resolution of 200 μm × 200 μm × 200 μm. Population-based image templates of tree shrew brain, including gray matter/white matter/cerebrospinal fluid probability maps and a fractional anisotropy template, were constructed at this spatial resolution, all in a reference space. Digital masks of representative anatomical structures, including hippocampus, amygdala and cingulum bundle, were created.

RESULT

With the templates constructed, the volumes of bilateral hippocampus and amygdala were measured using a template-facilitated semi-automated approach to be 59.8 ± 8.3 and 64.3 ± 3.4 mm(3), respectively.

COMPARISON WITH EXISTING METHOD(S)

For the first time, high-resolution MR image templates of tree shrew brain were reported. The average volume of bilateral hippocampus measured with the template-facilitated semi-automated approach was found to be similar to the result obtained by the much more labor-intensive manual approach.

CONCLUSIONS

The MR image templates obtained in this study are useful for analyzing neuroimage data of tree shrew brain. The templates are freely available to the scientific community upon request.

Comparative Anatomy of the Bony Labyrinth (Inner Ear) of Placental Mammals

BACKGROUND

Variation is a naturally occurring phenomenon that is observable at all levels of morphology, from anatomical variations of DNA molecules to gross variations between whole organisms. The structure of the otic region is no exception. The present paper documents the broad morphological diversity exhibited by the inner ear region of placental mammals using digital endocasts constructed from high-resolution X-ray computed tomography (CT). Descriptions cover the major placental clades, and linear, angular, and volumetric dimensions are reported.

PRINCIPAL FINDINGS

The size of the labyrinth is correlated to the overall body mass of individuals, such that large bodied mammals have absolutely larger labyrinths. The ratio between the average arc radius of curvature of the three semicircular canals and body mass of aquatic species is substantially lower than the ratios of related terrestrial taxa, and the volume percentage of the vestibular apparatus of aquatic mammals tends to be less than that calculated for terrestrial species. Aspects of the bony labyrinth are phylogenetically informative, including vestibular reduction in Cetacea, a tall cochlear spiral in caviomorph rodents, a low position of the plane of the lateral semicircular canal compared to the posterior canal in Cetacea and Carnivora, and a low cochlear aspect ratio in Primatomorpha.

SIGNIFICANCE

The morphological descriptions that are presented add a broad baseline of anatomy of the inner ear across many placental mammal clades, for many of which the structure of the bony labyrinth is largely unknown. The data included here complement the growing body of literature on the physiological and phylogenetic significance of bony labyrinth structures in mammals, and they serve as a source of data for future studies on the evolution and function of the vertebrate ear.

A glimpse on the pattern of rodent diversification: a phylogenetic approach

Background

Development of phylogenetic methods that do not rely on fossils for the study of evolutionary processes through time have revolutionized the field of evolutionary biology and resulted in an unprecedented expansion of our knowledge about the tree of life. These methods have helped to shed light on the macroevolution of many taxonomic groups such as the placentals (Mammalia). However, despite the increase of studies addressing the diversification patterns of organisms, no synthesis has addressed the case of the most diversified mammalian clade: the Rodentia.

Results

Here we present a rodent maximum likelihood phylogeny inferred from a molecular supermatrix. It is based on 11 mitochondrial and nuclear genes that covers 1,265 species, i.e., respectively 56% and 81% of the known specific and generic rodent diversity. The inferred topology recovered all Rodentia clades proposed by recent molecular works. A relaxed molecular clock dating approach provided a time framework for speciation events. We found that the Myomorpha clade shows a greater degree of variation in diversification rates than Sciuroidea, Caviomorpha, Castorimorpha and Anomaluromorpha. We identified a number of shifts in diversification rates within the major clades: two in Castorimorpha, three in Ctenohystrica, 6 within the squirrel-related clade and 24 in the Myomorpha clade. The majority of these shifts occurred within the most recent familial rodent radiations: the Cricetidae and Muridae clades. Using the topological imbalances and the time line we discuss the potential role of different diversification factors that might have shaped the rodents radiation.

Conclusions

The present glimpse on the diversification pattern of rodents can be used for further comparative meta-analyses. Muroid lineages have a greater degree of variation in their diversification rates than any other rodent group. Different topological signatures suggest distinct diversification processes among rodent lineages. In particular, Muroidea and Sciuroidea display widespread distribution and have undergone evolutionary and adaptive radiation on most of the continents. Our results show that rodents experienced shifts in diversification rate regularly through the Tertiary, but at different periods for each clade. A comparison between the rodent fossil record and our results suggest that extinction led to the loss of diversification signal for most of the Paleogene nodes.

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.

[Morphological characteristics and cryodamage of Chinese tree shrew (Tupaia belangeri chinensis) sperm]

The tree shrew (Tupaia belangeri chinensis) is a small non-rodent mammal, which is a relatively new experimental animal in medicine due to its close evolutionary relationship to primates and its rapid propagation. Sperm characteristics and cryopreservation in the tree shrew were the main contents of our spermatological research. Epididymal sperm were surgically harvested from male tree shrews captured from the Kunming area. The rate of testis weight to body weight was (1.05±0.07)%, volume of both testis was (1.12 ± 0.10) mL, total sperm from epididymis and vas deferens were 2.2-8.8×10(7), and sperm motility and acrosome integrity were (68.8 ± 3.9)% and (90.0 ± 2.1)%, respectively. Sperm ultrastructure of the tree shrew was examined by scanning electron microscopy and transmission electron microscopy. Tree shrew sperm had a round or oval shaped head of approximately 6.65×5.82 μm, and midpiece, principal piece, tail, and total sperm lengths were 13.39, 52.35, 65.74, and 73.05 μm, respectively. The mitochondria in the midpiece consisted of approximately 48 gyres and had a 9+9+2 axonemal pattern. After freezing and thawing, sperm showed partly intact acrosomes and plasma membrane defects, and sperm breakages, twists, and swellings were found. The tree shrew had similar ultrastructure with other mammalians except for the mitochondria number and the sperm size. Ultrastructural alteration is still the main cause resulting in poor sperm after cryopreservation.

Sequencing of 21 varicella-zoster virus genomes reveals two novel genotypes and evidence of recombination

Genotyping of 21 varicella-zoster virus (VZV) strains using a scattered single nucleotide polymorphism (SNP) method revealed ambiguous SNPs and two nontypeable isolates. For a further genetic characterization, the genomes of all strains were sequenced using the 454 technology. Almost-complete genome sequences were assembled, and most remaining gaps were closed with Sanger sequencing. Phylogenetic analysis of 42 genomes revealed five established and two novel VZV genotypes, provisionally termed VIII and IX. Genotypes VIII and IX are distinct from the previously reported provisional genotypes VI and VII as judged from the SNP pattern. The alignments showed evidence of ancient recombination events in the phylogeny of clade 4 and recent recombinations within single strains: 3/2005 (clade 1), 11 and 405/2007 (clade 3), 8 and DR (clade 4), CA123 and 413/2000 (clade 5), and strains of the novel genotypes VIII and IX. Bayesian tree inference of the thymidine kinase and the polymerase genes of the VZV clades and other varicelloviruses revealed that VZV radiation began some 110,000 years ago, which correlates with the out-of-Africa dispersal of modern humans. The split of ancestral clades 2/4 and 1/3/5/VIII/IX shows the greatest node height.

Neurochemical characterization of the tree shrew dorsal striatum

The striatum is a major component of the basal ganglia and is associated with motor and cognitive functions. Striatal pathologies have been linked to several disorders, including Huntington’s, Tourette’s syndrome, obsessive–compulsive disorders, and schizophrenia. For the study of these striatal pathologies different animal models have been used, including rodents and non-human primates. Rodents lack on morphological complexity (for example, the lack of well defined caudate and putamen nuclei), which makes it difficult to translate data to the human paradigm. Primates, and especially higher primates, are the closest model to humans, but there are ever-increasing restrictions to the use of these animals for research. In our search for a non-primate animal model with a striatum that anatomically (and perhaps functionally) can resemble that of humans, we turned our attention to the tree shrew. Evolutionary genetic studies have provided strong data supporting that the tree shrews (Scadentia) are one of the closest groups to primates, although their brain anatomy has only been studied in detail for specific brain areas. Morphologically, the tree shrew striatum resembles the primate striatum with the presence of an internal capsule separating the caudate and putamen, but little is known about its neurochemical composition. Here we analyzed the expression of calcium-binding proteins, the presence and distribution of the striosome and matrix compartments (by the use of calbindin, tyrosine hydroxylase, and acetylcholinesterase immunohistochemistry), and the GABAergic system by immunohistochemistry against glutamic acid decarboxylase and Golgi impregnation. In summary, our results show that when compared to primates, the tree shrew dorsal striatum presents striking similarities in the distribution of most of the markers studied, while presenting some marked divergences when compared to the rodent striatum.

Neural response dynamics of spiking and local field potential activity depend on CRT monitor refresh rate in the tree shrew primary visual cortex

Entrainment of neural activity to luminance impulses during the refresh of cathode ray tube monitor displays has been observed in the primary visual cortex (V1) of humans and macaque monkeys. This entrainment is of interest because it tends to temporally align and thus synchronize neural responses at the millisecond timescale. Here we show that, in tree shrew V1, both spiking and local field potential activity are also entrained at cathode ray tube refresh rates of 120, 90, and 60 Hz, with weakest but still significant entrainment even at 120 Hz, and strongest entrainment occurring in cortical input layer IV. For both luminance increments ("white" stimuli) and decrements ("black" stimuli), refresh rate had a strong impact on the temporal dynamics of the neural response for subsequent luminance impulses. Whereas there was rapid, strong attenuation of spikes and local field potential to prolonged visual stimuli composed of luminance impulses presented at 120 Hz, attenuation was nearly absent at 60-Hz refresh rate. In addition, neural onset latencies were shortest at 120 Hz and substantially increased, by ∼15 ms, at 60 Hz. In terms of neural response amplitude, black responses dominated white responses at all three refresh rates. However, black/white differences were much larger at 60 Hz than at higher refresh rates, suggesting a mechanism that is sensitive to stimulus timing. Taken together, our findings reveal many similarities between V1 of macaque and tree shrew, while underscoring a greater temporal sensitivity of the tree shrew visual system.

A novel method of characterizing genetic sequences: genome space with biological distance and applications

BACKGROUND

Most existing methods for phylogenetic analysis involve developing an evolutionary model and then using some type of computational algorithm to perform multiple sequence alignment. There are two problems with this approach: (1) different evolutionary models can lead to different results, and (2) the computation time required for multiple alignments makes it impossible to analyse the phylogeny of a whole genome. This motivates us to create a new approach to characterize genetic sequences.

METHODOLOGY

To each DNA sequence, we associate a natural vector based on the distributions of nucleotides. This produces a one-to-one correspondence between the DNA sequence and its natural vector. We define the distance between two DNA sequences to be the distance between their associated natural vectors. This creates a genome space with a biological distance which makes global comparison of genomes with same topology possible. We use our proposed method to analyze the genomes of the new influenza A (H1N1) virus, human rhinoviruses (HRV) and mammalian mitochondrial. The result shows that a triple-reassortant swine virus circulating in North America and the Eurasian swine virus belong to the lineage of the influenza A (H1N1) virus. For the HRV and mammalian mitochondrial genomes, the results coincide with biologists' analyses.

CONCLUSIONS

Our approach provides a powerful new tool for analyzing and annotating genomes and their phylogenetic relationships. Whole or partial genomes can be handled more easily and more quickly than using multiple alignment methods. Once a genome space has been constructed, it can be stored in a database. There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences. Furthermore, one can make a global comparison of all genomes simultaneously, which no other existing method can achieve.

Phylogenomic analyses and improved resolution of Cetartiodactyla

The remarkable antiquity, diversity, and significance in the ecology and evolution of Cetartiodactyla have inspired numerous attempts to resolve their phylogenetic relationships. However, previous analyses based on limited samples of nuclear genes or mitochondrial DNA sequences have generated results that were either inconsistent with one another, weakly supported, or highly sensitive to analytical conditions. Here, we present strongly supported results based upon over 1.4 Mb of an aligned DNA sequence matrix from 110 single-copy nuclear protein-coding genes of 21 Cetartiodactyla species, which represent major Cetartiodactyla lineages, and three species of Perissodactyla and Carnivora as outgroups. Phylogenetic analysis of this newly developed genomic sequence data using a codon-based model and recently developed models of the rate autocorrelation resolved the phylogenetic relationships of the major cetartiodactylan lineages and of those lineages with a high degree of confidence. Cetacea was found to nest within Artiodactyla as the sister group of Hippopotamidae, and Tylopoda was corroborated as the sole base clade of Cetartiodactyla. Within Cetacea, the monophyletic status of Odontoceti relative to Mysticeti, the basal position of Physeteroidea in Odontoceti, the non-monophyly of the river dolphins, and the sister relationship between Delphinidae and Monodontidae+Phocoenidae were strongly supported. In particular, the groups of Tursiops (bottlenose dolphins) and Stenella (spotted dolphins) were validated as unnatural groups. Additionally, a very narrow time frame of ∼3 My (million years) was found for the rapid diversification of delphinids in the late Miocene, which made it difficult to resolve the phylogenetic relationships within the Delphinidae, especially for previous studies with limited data sets. The present study provides a statistically well-supported phylogenetic framework of Cetartiodactyla, which represents an important step toward ending some of the often-heated, century-long debate on their evolution.

Sperm competition and the evolution of sperm design in mammals

Background

The influence of sperm competition upon sperm size has been a controversial issue during the last 20 years which remains unresolved for mammals. The hypothesis that, when ejaculates compete with rival males, an increase in sperm size would make sperm more competitive because it would increase sperm swimming speed, has generated contradictory results from both theoretical and empirical studies. In addition, the debate has extended to which sperm components should increase in size: the midpiece to accommodate more mitochondria and produce more energy to fuel motility, or the principal piece to generate greater propulsion forces.

Results

In this study we examined the influence of sperm competition upon sperm design in mammals using a much larger data set (226 species) than in previous analyses, and we corrected for phylogenetic effects by using a more complete and resolved phylogeny, and more robust phylogenetic control methods. Our results show that, as sperm competition increases, all sperm components increase in an integrated manner and sperm heads become more elongated. The increase in sperm length was found to be associated with enhanced swimming velocity, an adaptive trait under sperm competition.

Conclusions

We conclude that sperm competition has played an important role in the evolution of sperm design in mammals, and discuss why previous studies have failed to detect it.

Reconstructing mammalian phylogenies: a detailed comparison of the cytochrome B and cytochrome oxidase subunit I mitochondrial genes

The phylogeny and taxonomy of mammalian species were originally based upon shared or derived morphological characteristics. However, genetic analyses have more recently played an increasingly important role in confirming existing or establishing often radically different mammalian groupings and phylogenies. The two most commonly used genetic loci in species identification are the cytochrome oxidase I gene (COI) and the cytochrome b gene (cyt b). For the first time this study provides a detailed comparison of the effectiveness of these two loci in reconstructing the phylogeny of mammals at different levels of the taxonomic hierarchy in order to provide a basis for standardizing methodologies in the future. Interspecific and intraspecific variation is assessed and for the first time, to our knowledge, statistical confidence is applied to sequence comparisons. Comparison of the DNA sequences of 217 mammalian species reveals that cyt b more accurately reconstructs their phylogeny and known relationships between species based on other molecular and morphological analyses at Super Order, Order, Family and generic levels. Cyt b correctly assigned 95.85% of mammal species to Super Order, 94.31% to Order and 98.16% to Family compared to 78.34%, 93.36% and 96.93% respectively for COI. Cyt b also gives better resolution when separating species based on sequence data. Using a Kimura 2-parameter p-distance (x100) threshold of 1.5-2.5, cyt b gives a better resolution for separating species with a lower false positive rate and higher positive predictive value than those of COI.

Cellular scaling rules for primate spinal cords

The spinal cord can be considered a major sensorimotor interface between the body and the brain. How does the spinal cord scale with body and brain mass, and how are its numbers of neurons related to the number of neurons in the brain across species of different body and brain sizes? Here we determine the cellular composition of the spinal cord in eight primate species and find that its number of neurons varies as a linear function of cord length, and accompanies body mass raised to an exponent close to 1/3. This relationship suggests that the extension, mass and number of neurons that compose the spinal cord are related to body length, rather than to body mass or surface. Moreover, we show that although brain mass increases linearly with cord mass, the number of neurons in the brain increases with the number of neurons in the spinal cord raised to the power of 1.7. This faster addition of neurons to the brain than to the spinal cord is consistent with current views on how larger brains add complexity to the processing of environmental and somatic information.

Analyzing the relationship between sequence divergence and nodal support using Bayesian phylogenetic analyses

Determining the appropriate gene for phylogeny reconstruction can be a difficult process. Rapidly evolving genes tend to resolve recent relationships, but suffer from alignment issues and increased homoplasy among distantly related species. Conversely, slowly evolving genes generally perform best for deeper relationships, but lack sufficient variation to resolve recent relationships. We determine the relationship between sequence divergence and Bayesian phylogenetic reconstruction ability using both natural and simulated datasets. The natural data are based on 28 well-supported relationships within the subphylum Vertebrata. Sequences of 12 genes were acquired and Bayesian analyses were used to determine phylogenetic support for correct relationships. Simulated datasets were designed to determine whether an optimal range of sequence divergence exists across extreme phylogenetic conditions. Across all genes we found that an optimal range of divergence for resolving the correct relationships does exist, although this level of divergence expectedly depends on the distance metric. Simulated datasets show that an optimal range of sequence divergence exists across diverse topologies and models of evolution. We determine that a simple to measure property of genetic sequences (genetic distance) is related to phylogenic reconstruction ability in Bayesian analyses. This information should be useful for selecting the most informative gene to resolve any relationships, especially those that are difficult to resolve, as well as minimizing both cost and confounding information during project design.

A simulation study comparing supertree and combined analysis methods using SMIDGen

Background

Supertree methods comprise one approach to reconstructing large molecular phylogenies given multi-marker datasets: trees are estimated on each marker and then combined into a tree (the "supertree") on the entire set of taxa. Supertrees can be constructed using various algorithmic techniques, with the most common being matrix representation with parsimony (MRP). When the data allow, the competing approach is a combined analysis (also known as a "supermatrix" or "total evidence" approach) whereby the different sequence data matrices for each of the different subsets of taxa are concatenated into a single supermatrix, and a tree is estimated on that supermatrix.

Results

In this paper, we describe an extensive simulation study we performed comparing two supertree methods, MRP and weighted MRP, to combined analysis methods on large model trees. A key contribution of this study is our novel simulation methodology (Super-Method Input Data Generator, or SMIDGen) that better reflects biological processes and the practices of systematists than earlier simulations. We show that combined analysis based upon maximum likelihood outperforms MRP and weighted MRP, giving especially big improvements when the largest subtree does not contain most of the taxa.

Conclusions

This study demonstrates that MRP and weighted MRP produce distinctly less accurate trees than combined analyses for a given base method (maximum parsimony or maximum likelihood). Since there are situations in which combined analyses are not feasible, there is a clear need for better supertree methods. The source tree and combined datasets used in this study can be used to test other supertree and combined analysis methods.

Phylogenetic evidence for early hemochorial placentation in eutheria

The eutherian placenta is remarkable for its structural and functional variability. In order to construct and test comparative hypotheses relating ecological, behavioral and physiological traits to placental characteristics it is first necessary to reconstruct the historical course of placental evolution. Previous attempts to do so have yielded inconsistent results, particularly with respect to the early evolution of structural relationships between fetal and maternal circulatory systems. Here, we bring a battery of phylogenetic methods - including parsimony, likelihood and Bayesian approaches - to bear on the question of placental evolution. All of these approaches are consistent in indicating that highly invasive hemochorial placentation, as found in human beings and numerous other taxa, was an early evolutionary innovation present in the most ancient ancestors of the living placental mammals.

Architectonic subdivisions of neocortex in the tree shrew (Tupaia belangeri)

Tree shrews are small mammals that bear some semblance to squirrels, but are actually close relatives of primates. Thus, they have been extensively studied as a model for the early stages of primate evolution. In this study, subdivisions of cortex were reconstructed from brain sections cut in the coronal, sagittal, or horizontal planes, and processed for parvalbumin, SMI-32-immunopositive neurofilament protein epitopes, vesicle glutamate transporter 2 (VGluT2), free ionic zinc, myelin, cytochrome oxidase, and Nissl substance. These different procedures revealed similar boundaries between areas, suggesting the detection of functionally relevant borders and allowed a more precise demarcation of cortical areal boundaries. Primary cortical areas were most clearly revealed by the zinc stain, because of the poor staining of layer 4, as thalamocortical terminations lack free ionic zinc. Area 17 (V1) was especially prominent, as the broad layer 4 was nearly free of zinc stain. However, this feature was less pronounced in primary auditory and somatosensory cortex. In primary sensory areas, thalamocortical terminations in layer 4 densely express VGluT2. Auditory cortex consists of two architectonically distinct subdivisions, a primary core region (Ac), surrounded by a belt region (Ab) that had a slightly less developed koniocellular appearance. Primary motor cortex (M1) was identified by the absence of VGluT2 staining in the poorly developed granular layer 4 and the presence of SMI-32-labeled pyramidal cells in layers 3 and 5. The presence of well-differentiated cortical areas in tree shrews indicates their usefulness in studies of cortical organization and function.

Trees from trees: construction of phylogenetic supertrees using clann

Supertree methods combine multiple phylogenetic trees to produce the overall best "supertree." They can be used to combine phylogenetic information from datasets only partially overlapping and from disparate sources (like molecular and morphological data), or to break down problems thought to be computationally intractable. Some of the longest standing phylogenetic conundrums are now being brought to light using supertree approaches. We describe the most widely used supertree methods implemented in the software program "clann" and provide a step by step tutorial for investigating phylogenetic information and reconstructing the best supertree. Clann is freely available for Windows, Mac and Unix/Linux operating systems under the GNU public licence at (http://bioinf.nuim.ie/software/clann).

Colugos: obscure mammals glide into the evolutionary limelight

Substantial molecular evidence indicates that tree-shrews, colugos and primates cluster together on the mammalian phylogenetic tree. Previously, a sister-group relationship between colugos and primates seemed likely. A new study of colugo chromosomes indicates instead an affinity between colugos and tree-shrews.

Flying lemurs--the 'flying tree shrews'? Molecular cytogenetic evidence for a Scandentia-Dermoptera sister clade

Background

Flying lemurs or Colugos (order Dermoptera) represent an ancient mammalian lineage that contains only two extant species. Although molecular evidence strongly supports that the orders Dermoptera, Scandentia, Lagomorpha, Rodentia and Primates form a superordinal clade called Supraprimates (or Euarchontoglires), the phylogenetic placement of Dermoptera within Supraprimates remains ambiguous.

Results

To search for cytogenetic signatures that could help to clarify the evolutionary affinities within this superordinal group, we have established a genome-wide comparative map between human and the Malayan flying lemur (Galeopterus variegatus) by reciprocal chromosome painting using both human and G. variegatus chromosome-specific probes. The 22 human autosomal paints and the X chromosome paint defined 44 homologous segments in the G. variegatus genome. A putative inversion on GVA 11 was revealed by the hybridization patterns of human chromosome probes 16 and 19. Fifteen associations of human chromosome segments (HSA) were detected in the G. variegatus genome: HSA1/3, 1/10, 2/21, 3/21, 4/8, 4/18, 7/15, 7/16, 7/19, 10/16, 12/22 (twice), 14/15, 16/19 (twice). Reverse painting of G. variegatus chromosome-specific paints onto human chromosomes confirmed the above results, and defined the origin of the homologous human chromosomal segments in these associations. In total, G. variegatus paints revealed 49 homologous chromosomal segments in the HSA genome.

Conclusion

Comparative analysis of our map with published maps from representative species of other placental orders, including Scandentia, Primates, Lagomorpha and Rodentia, suggests a signature rearrangement (HSA2q/21 association) that links Scandentia and Dermoptera to one sister clade. Our results thus provide new evidence for the hypothesis that Scandentia and Dermoptera have a closer phylogenetic relationship to each other than either of them has to Primates.

A quantitative analysis of the Eutherian orbit: correlations with masticatory apparatus

The mammalian orbit, or eye-socket, is a highly plastic region of the skull. It comprises between seven and nine bones, all of which vary widely in their contribution to this region among the different mammalian orders and families. It is hypothesised that the structure of the mammalian orbit is principally influenced by the forces generated by the jaw-closing musculature. In order to quantify the orbit, fourteen linear, angular and area measurements were taken from 84 species of placental mammals using a Microscribe-3D digitiser. The results were then analysed using principal components analysis. The results of the multivariate analysis on untransformed data showed a clear division of the mammalian taxa into temporalis-dominant forms and masseter-dominant forms. This correlation between orbital structure and masticatory musculature was reinforced by results from the size-corrected data, which showed a separation of the taxa into the three specialised feeding types proposed by Turnbull (1970): i.e. 'carnivore-shear', 'ungulate-grinding' and 'rodent-gnawing'. Moreover, within the rodents there was a clear distinction between species in which the masseter is highly developed and those in which the temporalis has more prominence. These results were reinforced by analysis of variance which showed significant differences in the relative orbital areas of certain bones between temporalis-dominant and masseter-dominant taxa. Subsequent cluster analysis suggested that most of the variables could be grouped into three assemblages: those associated with the length of the rostrum; those associated with the width of the skull; and those associated with the relative size of the orbit and the shape of the face. However, the relative area of the palatine bone showed weak correlations with the other variables and did not fit into any group. Overall the relative area of the palatine was most closely correlated with feeding type, and this measure that appeared to be most strongly associated with the arrangement of the masticatory musculature. These results give a strong indication that, although orbital structure is in part determined by the relative size and orientation of the orbits, the forces generated by the muscles of mastication also have a large effect.

Mitochondrially encoded cysteine predicts animal lifespan

The role of genetic factors in the determination of lifespan is undisputed. However, numerous successful efforts to identify individual genetic modulators of longevity have not yielded yet a quantitative measure to estimate the lifespan of a species from scratch, merely based on its genomic constitution. Here, we report on a meta-examination of genome sequences from 248 animal species with known maximum lifespan, including mammals, birds, fish, insects, and helminths. Our analysis reveals that the frequency with which cysteine is encoded by mitochondrial DNA is a specific and phylogenetically ubiquitous molecular indicator of aerobic longevity: long-lived species synthesize respiratory chain complexes which are depleted of cysteine. Cysteine depletion was also found on a proteome-wide scale in aerobic versus anaerobic bacteria, archaea, and unicellular eukaryotes; in mitochondrial versus hydrogenosomal sequences; and in the mitochondria of free-living, aerobic versus anaerobic-parasitic worms. The association of longevity with mitochondrial cysteine depletion persisted after correction for body mass and phylogenetic interdependence, but it was uncoupled in helminthic species with predominantly anaerobic lifestyle. We conclude that protein-coding genes on mitochondrial DNA constitute a quantitative trait locus for aerobic longevity, wherein the oxidation of mitochondrially translated cysteine mediates the coupling of trait and locus. These results provide distinct support for the free radical theory of aging.