Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate

Lin, Jiannan; Chen, Guangfeng; Gu, Liang; Shen, Yuefeng; Zheng, Min; Zheng, Weisheng; Hu, Xinjie; Zhang, Xiaobai; Qiu, Yue; Liu, Xiaoqing; Jiang, Cizhong

doi:10.1016/j.ympev.2013.12.001

Cited by 27 publications

(20 citation statements)

References 40 publications

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“…2), Tupaia chinensis is depicted as a sister taxon to Oryctolagus cuniculus (European rabbit) and Erinaceus europaeus (European hedgehog) with high nodal support. This placement of the tree shrew most closely mimics the phylogenetic placement proposed by Murphy et al (2001), as well as the maximum-likelihood trees of third codon positions and all codons proposed by Lin et al (2014). Although either tree could be correct, we propose that because the phylogeny recovered from the stop codons in Fig.…”

Section: Discussionsupporting

confidence: 79%

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Missing something? Codon aversion as a new character system in phylogenetics

et al. 2017

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Although many studies have documented codon usage bias in different species, the importance of codon usage in a phylogenetic framework remains largely unknown. We demonstrate that a phylogenetic signal is present in the codon usage and non‐usage biases of 17 717 orthologues evaluated across 72 tetrapod species using a simple parsimony analysis of a binary matrix of codon characters. Phylogenies estimated using stop codons were more congruent with previous hypotheses than phylogenies based on any other single codon or a combination of codons. Although each codon is present in every species, specific genes have different codon preferences and may or may not use every possible codon. This observation allowed us to map the pattern of codon usage and non‐usage across the topology. These results suggest that codon usage is phylogenetically conserved across shallow and deep levels within tetrapods.

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Section: Discussionsupporting

confidence: 79%

“…(), as well as the maximum‐likelihood trees of third codon positions and all codons proposed by Lin et al. (). Although either tree could be correct, we propose that because the phylogeny recovered from the stop codons in Fig.…”

Section: Discussionmentioning

confidence: 99%

Missing something? Codon aversion as a new character system in phylogenetics

et al. 2017

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“…For the first time, we hybridized PNA probes on T. minor , a representative of the order Scandentia, a taxon very close to Primates and used as an outgroup in the phylogenetic perspective [Lin et al, 2014;Zhou et al, 2015]. Moreover, we compared the ITS distribution pattern with the C-banding pattern in order to verify a possible correspondence of C-positive bands with ITS signals.…”

Section: Its Distribution In Tupaia and Comparison With Primatesmentioning

confidence: 99%

Distribution of Interstitial Telomeric Sequences in Primates and the Pygmy Tree Shrew (Scandentia)

Mazzoleni

Schillaci²,

Sineo³

et al. 2017

Cytogenet Genome Res

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It has been hypothesized that interstitial telomeric sequences (ITSs), i.e., repeated telomeric DNA sequences found at intrachromosomal sites in many vertebrates, could be correlated to chromosomal rearrangements and plasticity. To test this hypothesis, we hybridized a telomeric PNA probe through FISH on representative species of 2 primate infraorders, Strepsirrhini (Lemur catta, Otolemur garnettii, Nycticebus coucang) and Catarrhini (Erythrocebus patas, Cercopithecus petaurista, Chlorocebus aethiops, Colobus guereza), as well as on 1 species of the order Scandentia, Tupaia minor, used as an outgroup for primates in phylogenetic reconstructions. In almost all primate species analyzed, we found a telomeric pattern only. In Tupaia, the hybridization revealed many bright ITSs on at least 11 chromosome pairs, both biarmed and acrocentric. These ITS signals in Tupaia correspond to fusion points of ancestral human syntenic associations, but are also present in other chromosomes showing synteny to only a single human chromosome. This distribution pattern was compared to that of the heterochromatin regions detected through sequential C-banding performed after FISH. Our results in the analyzed species, compared with literature data on ITSs in primates, allowed us to discuss different mechanisms responsible for the origin and distribution of ITSs, supporting the correlation between rearrangements and ITSs.

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“…Previous studies have reported different clustering patterns regarding the phylogenetic affinity of the tree shrew to primates, lagomorphs and rodents on the basis of various kinds of genetic data (Fan et al, 2013; Lin et al, 2014; O'Leary et al, 2013; Song et al, 2012; Xu et al, 2012, 2013a; Zhou et al, 2015). The recent comparative genome analysis of the Chinese tree shrew ( Tupaia belangeri chinensis ) and related vertebrate species (including primates) has provided sufficient evidence to resolve this question and has showed that the tree shrew has a much closer affinity to primates than that of rodents (Fan et al, 2013; Lin et al, 2014; Xu et al, 2013a). Note that a recent phylogenomic analysis of 1 912 exons from 22 representative mammals claimed that the position of tree shrews within the Euarchonta is unstable (Zhou et al, 2015).…”

Section: The Close Genetic Relationship Of the Tree Shrew To Primatesmentioning

confidence: 99%

创制动物模型,为何不用树鼩呢?

姚永刚¹,

Yao²

2017

Zool. Res.

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The Chinese tree shrew (Tupaia belangeri chinensis), a squirrel-like and rat-sized mammal, has a wide distribution in Southeast Asia, South and Southwest China and has many unique characteristics that make it suitable for use as an experimental animal. There have been many studies using the tree shrew (Tupaia belangeri) aimed at increasing our understanding of fundamental biological mechanisms and for the modeling of human diseases and therapeutic responses. The recent release of a publicly available annotated genome sequence of the Chinese tree shrew and its genome database () has offered a solid base from which it is possible to elucidate the basic biological properties and create animal models using this species. The extensive characterization of key factors and signaling pathways in the immune and nervous systems has shown that tree shrews possess both conserved and unique features relative to primates. Hitherto, the tree shrew has been successfully used to create animal models for myopia, depression, breast cancer, alcohol-induced or non-alcoholic fatty liver diseases, herpes simplex virus type 1 (HSV-1) and hepatitis C virus (HCV) infections, to name a few. The recent successful genetic manipulation of the tree shrew has opened a new avenue for the wider usage of this animal in biomedical research. In this opinion paper, I attempt to summarize the recent research advances that have used the Chinese tree shrew, with a focus on the new knowledge obtained by using the biological properties identified using the tree shrew genome, a proposal for the genome-based approach for creating animal models, and the genetic manipulation of the tree shrew. With more studies using this species and the application of cutting-edge gene editing techniques, the tree shrew will continue to be under the spot light as a viable animal model for investigating the basis of many different human diseases.

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Phylogenetic affinity of tree shrews to Glires is attributed to fast evolution rate

Cited by 27 publications

References 40 publications

Missing something? Codon aversion as a new character system in phylogenetics

Missing something? Codon aversion as a new character system in phylogenetics

Distribution of Interstitial Telomeric Sequences in Primates and the Pygmy Tree Shrew (Scandentia)

创制动物模型,为何不用树鼩呢?

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