Networks, trees, and treeshrews: assessing support and identifying conflict with multiple loci and a problematic root

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.

Complete mitogenome of the endangered and endemic Nicobar treeshrew (Tupaia nicobarica) and comparison with other Scandentians

The Nicobar treeshrew (Tupaia nicobarica) is an endangered small mammal endemic to the Nicobar Island of the Andaman Sea, India regarded as an alternative experimental animal model in biomedical research. The present study aimed to assemble the first mitochondrial genome of T. nicobarica to elucidate its phylogenetic position with respect to other Scandentians. The structure and variation of the novel mitochondrial genome were analyzed and compared with other Scandentians. The complete mitogenome (17,164 bp) encodes 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs), and one control region (CR). Most of the genes were encoded on majority strand, except nad6 and eight tRNAs. The nonsynonymous/synonymous ratio in all PCGs indicates strong negative selection among all Tupaiidae species. The comparative study of CRs revealed the occurrence of tandem repeats (CGTACA) found in T. nicobarica. The phylogenetic analyses (Maximum Likelihood and Bayesian Inference) showed distinct clustering of T. nicobarica with high branch supports and depict a substantial divergence time (12–19 MYA) from the ancestor lineage of Tupaiidae. The 16S rRNA dataset corroborates the taxonomic rank of two subspecies of T. nicobarica from the Great and Little Nicobar Islands. In the future, whole nuclear genome sequencing is necessary to further improve our understanding of evolutionary relationships among treeshrews, and will have implications for biomedical research.

Zoogeographical barriers causing discontinuous osteometrical variations in the northern treeshrew skulls

Morphological variation of the skull was examined in the northern treeshrew (Tupaia belangeri) from various localities across Southeast Asia. Through a multivariate analysis, the treeshrews from South Vietnam exhibited distinct morphological characteristics compared to other populations from Thailand and Laos, and Malaysia. The plots of the specimens of North Vietnam are not randomly mixed with Thailand plots segregation in the scatteregrams of canonical discriminant analysis. Since the skulls of the population from North Vietnam were morphologically similar to those form central Laos and northern and northeastern Thailand, the zoogeographical barrier effect of Mekong River was not clearly confirmed. The population of the Kanchanaburi in western Thailand is clearly smaller in size compared to the other populations. The southern border of the distribution of this species is determined by the Isthmus of Kra or Kangar-Pattani Line. In the northern treeshrew, which is distributed from southern China to Bangladesh and southern Thailand, we have detected osteometrical geographical variation driven by geography. These results indicate that the skull morphology in the Tupaia glis-belangeri complex distinctively differs in South Vietnam, western Thailand, and southern Thailand. The zoogeographical barrier and factor separating these districts are expected to clarify in the future.

Opsin genes of select treeshrews resolve ancestral character states within Scandentia

Treeshrews are small, squirrel-like mammals in the order Scandentia, which is nested together with Primates and Dermoptera in the superordinal group Euarchonta. They are often described as living fossils, and researchers have long turned to treeshrews as a model or ecological analogue for ancestral primates. A comparative study of colour vision-encoding genes within Scandentia found a derived amino acid substitution in the long-wavelength sensitive opsin gene (OPN1LW) of the Bornean smooth-tailed treeshrew (Dendrogale melanura). The opsin, by inference, is red-shifted by ca 6 nm with an inferred peak sensitivity of 561 nm. It is tempting to view this trait as a novel visual adaptation; however, the genetic and functional diversity of visual pigments in treeshrews is unresolved outside of Borneo. Here, we report gene sequences from the northern smooth-tailed treeshrew (Dendrogale murina) and the Mindanao treeshrew (Tupaia everetti, the senior synonym of Urogale everetti). We found that the opsin genes are under purifying selection and that D. murina shares the same substitution as its congener, a result that distinguishes Dendrogale from other treeshrews, including T. everetti. We discuss the implications of opsin functional variation in light of limited knowledge about the visual ecology of smooth-tailed treeshrews.

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.

Assembled Plastid and Mitochondrial Genomes, as well as Nuclear Genes, Place the Parasite Family Cynomoriaceae in the Saxifragales

Cynomoriaceae, one of the last unplaced families of flowering plants, comprise one or two species or subspecies of root parasites that occur from the Mediterranean to the Gobi Desert. Using Illumina sequencing, we assembled the mitochondrial and plastid genomes as well as some nuclear genes of a Cynomorium specimen from Italy. Selected genes were also obtained by Sanger sequencing from individuals collected in China and Iran, resulting in matrices of 33 mitochondrial, 6 nuclear, and 14 plastid genes and rDNAs enlarged to include a representative angiosperm taxon sampling based on data available in GenBank. We also compiled a new geographic map to discern possible discontinuities in the parasites’ occurrence. Cynomorium has large genomes of 13.70–13.61 (Italy) to 13.95–13.76 pg (China). Its mitochondrial genome consists of up to 49 circular subgenomes and has an overall gene content similar to that of photosynthetic angiosperms, while its plastome retains only 27 of the normally 116 genes. Nuclear, plastid and mitochondrial phylogenies place Cynomoriaceae in Saxifragales, and we found evidence for several horizontal gene transfers from different hosts, as well as intracellular gene transfers.

An early Oligocene fossil demonstrates treeshrews are slowly evolving "living fossils"

Treeshrews are widely considered a “living model” of an ancestral primate, and have long been called “living fossils”. Actual fossils of treeshrews, however, are extremely rare. We report a new fossil species of Ptilocercus treeshrew recovered from the early Oligocene (~34 Ma) of China that represents the oldest definitive fossil record of the crown group of treeshrews and nearly doubles the temporal length of their fossil record. The fossil species is strikingly similar to the living Ptilocercus lowii, a species generally recognized as the most plesiomorphic extant treeshrew. It demonstrates that Ptilocercus treeshrews have undergone little evolutionary change in their morphology since the early Oligocene. Morphological comparisons and phylogenetic analysis support the long-standing idea that Ptilocercus treeshrews are morphologically conservative and have probably retained many characters present in the common stock that gave rise to archontans, which include primates, flying lemurs, plesiadapiforms and treeshrews. This discovery provides an exceptional example of slow morphological evolution in a mammalian group over a period of 34 million years. The persistent and stable tropical environment in Southeast Asia through the Cenozoic likely played a critical role in the survival of such a morphologically conservative lineage.

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.

Recent trends in molecular phylogenetic analysis: where to next?

The acquisition of large multilocus sequence data is providing researchers with an unprecedented amount of information to resolve difficult phylogenetic problems. With these large quantities of data comes the increasing challenge regarding the best methods of analysis. We review the current trends in molecular phylogenetic analysis, focusing specifically on the topics of multiple sequence alignment and methods of tree reconstruction. We suggest that traditional methods are inadequate for these highly heterogeneous data sets and that researchers employ newer more sophisticated search algorithms in their analyses. If we are to best extract the information present in these data sets, a sound understanding of basic phylogenetic principles combined with modern methodological techniques are necessary.