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Asymmetric biotic interchange across the Bering land bridge between Eurasia and North America

National Science Review 2019年第4期6卷 739-745页

作者： Dechun Jiang Sebastian Klaus Ya-Ping Zhang david m.hillis Jia-Tang Li CAS Key Laboratory of mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province Chengdu Institute of Biology Chinese Academy of Sciences Department of Ecology and Evolution J.W.Goethe University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Department of Integrative Biology and Biodiversity Center University of Texas at Austin

The exchange of biotas between Eurasia and North America across the Bering land bridge had a major impact on ecosystems of both continents throughout the Cenozoic. This exchange has received particular attention regarding placental mammals dispersing into the Americas, including humans after the last glacial period, and also as an explanation for the disjunct distribution of related seed plants in eastern Asia and eastern North America. Here, we investigate bi-directional dispersal across the Bering land bridge from estimates of dispersal events based on time-calibrated phylogenies of a broad range of plant, fungus and animal taxa. We reveal a long-lasting phase of asymmetrical biotic interchange, with a peak of dispersal from Asia into North America during the late Oligocene warming(26–24 ma), when dispersal in the opposite direction was greatly decreased. Influx from North America into Asia was lower than in the opposite direction throughout the Cenozoic, but with peak rates of dispersal at the end of the Eocene(40–34 ma)and again in the early to middle miocene(16–14 ma). The strong association between dispersal patterns and environmental changes suggests that plants, fungi and animals have likely dispersed from stable to perturbed environments of North America and Eurasia throughout the Cenozoic.

关键词： multiple taxa biogeography Bering land bridge Cenozoic

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molecular evolution of Na^(+) channels in teleost fishes

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Integrative Zoology 2009年第1期4卷 64-74页

作者： Harold H.ZAKON manda C.JOST Derrick J.ZWICKL Ying LU david m.hillis Section of Neurobiology Section of Integrative Biology The University of TexasAustinTXUSA

Voltage-dependent sodium channels are critical for electrical *** possess a single sodium channel gene;two rounds of genome duplication early in vertebrates increased the number to *** the teleost-tetrapod split,independent gene duplications in each lineage have further increased the number of sodium channel genes to 10 in tetrapods and 8 in *** we review how the occurrence of multiple sodium channel paralogs has influenced the evolutionary history of three groups of fishes:pufferfish,gymnotiform and mor-myriform electric ***(tetraodontidae)produce a neurotoxin,tetrodotoxin,that binds to and blocks the pore of sodium *** evolved resistance to their own toxins by amino acid substitutions in the pore of their sodium *** substitutions had to occur in parallel across multiple paralogs for organismal re-sistance to *** and mormyriform fishes independently evolved electric organs to generate elec-tricity for communication and object *** sodium channel genes are expressed in muscle in most *** both groups of weakly electric fishes,one gene lost its expression in muscle and became compartmen-talized in the evolutionary novel electric organ,which is a muscle *** gene then evolved at elevated rates,whereas the gene that is still expressed in muscle does not show elevated rates of *** the electric organ-expressing gene,amino acid substitutions occur in parts of the channel involved in determining how long the channel will be open or *** enhanced rate of sequence evolution of this gene likely underlies the spe-cies-level variations in the electric signal.

关键词： electric fish molecular evolution pufferfish sodium channels tetrodotoxin.

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Herpetological phylogeographic analyses support a miocene focal point of Himalayan uplift and biological diversification

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National Science Review 2021年第9期8卷 137-144页

作者： Wei Xu Wen-Jie Dong Ting-Ting Fu Wei Gao Chen-Qi Lu Fang Yan Yun-He Wu Ke Jiang Jie-Qiong Jin Hong-man Chen Ya-Ping Zhang david m.hillis Jing Che State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Department of Integrative Biology and Biodiversity Center University of Texas at Austin

The Himalaya are among the youngest and highest mountains in the world, but the exact timing of their uplift and origins of their biodiversity are still in debate. The Himalayan region is a relatively small area but with exceptional diversity and endemism. One common hypothesis to explain the rich montane diversity is uplift-driven diversification—that orogeny creates conditions favoring rapid in situ speciation of resident lineages. We test this hypothesis in the Himalayan region using amphibians and reptiles, two environmentally sensitive vertebrate groups. In addition, analysis of diversification of the herpetofauna provides an independent source of information to test competing geological hypotheses of Himalayan orogenesis. We conclude that the origins of the Himalayan herpetofauna date to the early Paleocene, but that diversification of most groups was concentrated in the miocene. There was an increase in both rates and modes of diversification during the early to middle miocene, together with regional interchange(dispersal) between the Himalaya and adjacent regions. Our analyses support a recently proposed stepwise geological model of Himalayan uplift beginning in the Paleocene, with a subsequent rapid increase of uplifting during the miocene, finally giving rise to the intensification of the modern South Asian monsoon.

关键词： orogenesis monsoon system biotic assembly in situ diversification amphibians and reptiles

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Taxon sampling and the accuracy of phylogenetic analyses

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植物分类学报 2008年第3期46卷 239-257页

作者： Tracy A. HEATH Shannon m. HEDTKE david m. hillis Section of lntegrative Biology and Center for Computational Biology and Bioinformatics One University Station C0930 The University of Texas Austin TX 78712 USA

Appropriate and extensive taxon sampling is one of the most important determinants of accurate phylogenetic estimation. In addition, accuracy of inferences about evolutionary processes obtained from phyloge-netic analyses is improved significantly by thorough taxon sampling efforts. many recent efforts to improve phylogenetic estimates have focused instead on increasing sequence length or the number of overall characters in the analysis, and this often does have a beneficial effect on the accuracy of phylogenetic analyses. However, phylogenetic analyses of few taxa (but each represented by many characters) can be subject to strong systematic biases, which in turn produce high measures of repeatability (such as bootstrap proportions) in support of incor-rect or misleading phylogenetic results. Thus, it is important for phylogeneticists to consider both the sampling of taxa, as well as the sampling of characters, in designing phylogenetic studies. Taxon sampling also improves estimates of evolutionary parameters derived from phylogenetic trees, and is thus important for improved applica-tions of phylogenetic analyses. Analysis of sensitivity to taxon inclusion, the possible effects of long-branch attraction, and sensitivity of parameter estimation for model-based methods should be a part of any careful and thorough phylogenetic analysis. Furthermore, recent improvements in phylogenetic algorithms and in computa-tional power have removed many constraints on analyzing large, thoroughly sampled data sets. Thorough taxon sampling is thus one of the most practical ways to improve the accuracy of phylogenetic estimates, as well as the accuracy of biological inferences that are based on these phylogenetic trees.

关键词：动物物种分类方法取样方法

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Complement-dependent neuroinflammation in spinal cord injury:from pathology to therapeutic implications

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Neural Regeneration Research 2025年第5期20卷 1324-1335页

作者： Hassan Saad Bachar El Baba Ali Tfaily Firas Kobeissy Juanmarco Gutierrez Gonzalez Daniel Refai Gerald R.Rodts Christian mustroph david Gimbel Jonathan Grossberg Daniel L.Barrow matthew F.Gary Ali m.Alawieh Department of Neurosurgery Emory University School of MedicineAtlantaGAUSA Department of Neurology Yale UniversityNew HavenCTUSA Center for Neurotrauma Multiomics&Biomarkers(CNMB)Morehouse School of MedicineAtlantaGAUSA

Spinal cord injury remains a major cause of disability in young adults,and beyond acute decompression and rehabilitation,there are no pharmacological treatments to limit the progression of injury and optimize recovery in this *** the thorough investigation of the complement system in triggering and propagating cerebral neuroinflammation,a similar role for complement in spinal neuroinflammation is a focus of ongoing *** this work,we survey the current literature investigating the role of complement in spinal cord injury including the sources of complement proteins,triggers of complement activation,and role of effector functions in the *** study relevant data demonstrating the different triggers of complement activation after spinal cord injury including direct binding to cellular debris,and or activation via antibody binding to damage-associated molecular *** effector functions of complement have been implicated in spinal cord injury,and we critically evaluate recent studies on the dual role of complement anaphylatoxins in spinal cord injury while emphasizing the lack of pathophysiological understanding of the role of opsonins in spinal cord *** this pathophysiological review,we systematically review the different translational approaches used in preclinical models of spinal cord injury and discuss the challenges for future translation into human *** review emphasizes the need for future studies to dissect the roles of different complement pathways in the pathology of spinal cord injury,to evaluate the phases of involvement of opsonins and anaphylatoxins,and to study the role of complement in white matter degeneration and regeneration using translational strategies to supplement genetic models.

关键词： complement neuroinflammation neuroplasticity regeneration spinal cord injury targeted therapy

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Roles of secreted frizzled-related proteins in cancer

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Acta Pharmacologica Sinica 2007年第9期28卷 1499-1504页

作者： david m JABLONS Thoracic Oncology Laboratory Department of SurgeryComprehensive Cancer CenterUniversity of CaliforniaSan FranciscoCA 94115USASRI International333 Ravenswood AvenueMenlo ParkCA 94025 USA

The Wnt signaling pathway is implicated in a variety of biological processesranging from developmental cell fate to human *** components involvedin Wnt signaling have been under intense investigation over the last 2 *** canonical Wnt activation has been linked to tumor formation andinvolves activation of effector molecules or loss of tumor suppressor *** frizzled-related proteins (sFRPs) are Wnt *** recent years,accumulating evidence has suggested that sFRPs act as tumor suppressorsbecause their expression is frequently silenced in cancer by promoter ***,sFRPs may also promote cell growth in some ***,wefocus on the known knowledge of sFRPs in tumorigenesis.

关键词： Wnt signaling pathway secreted frizzledrelated proteins cancer

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The embryology of persistent cloaca and urogenital sinus malformations

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Asian Journal of Andrology 2020年第2期22卷 124-128页

作者： david F m Thomas University of Leeds LeedsWest Yorkshire LS29JTUK

Cloacal malformations are characterized by the confluence of the lower urinary tract,the female reproductive tract,and the rectum to create a common channel with a single opening on the *** presence of a cloaca is a normal phase of early human embryological *** the 4^th and 7^th weeks of gestation,the cloaca undergoes subdivision to form the hindgut and urogenital *** of this process results in the congenital anomaly termed persistent cloaca(PC).The term urorectal septum malformation sequence(URSmS)is also used to describe this *** classic description of this process which is still cited in many standard textbooks dates from the 19th ***,this has been increasingly called into question by the findings of studies using modern scientific *** sinus anomalies are defined by the confluence of the urethra and vagina to form a common channel of varying length with a single perineal *** this condition,the anorectal canal opens separately on the *** presence of a urogenital sinus represents a transient phase of the normal development of the lower genital tract in the female ***,the form of urogenital sinus most commonly encountered in the developed world is a feature of disordered sexual differentiation and does not arise simply from the persistence of the anatomical structure which is a feature of normal fetal development.

关键词： cloaca embryology urogenital sinus

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Duplication and diversification of insulin genes in ray-finned fish

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Zoological Research 2019年第3期40卷 185-197页

作者： david m.Irwin Department of Laboratory medicine and Pathobiology University of Toronto Banting and Best Diabetes Centre University of Toronto

Insulin is a key hormone for the regulation of metabolism in *** is produced by pancreatic islet cells in response to elevated glucose levels and leads to the uptake of glucose by tissues such as liver and adipose tissue to store *** also has additional functions in regulating *** work has shown that the proglucagon gene,which encodes hormones counter regulating insulin,is duplicated in teleost fish,and that the peptide hormones encoded by these genes have diversified in function.I sought to determine whether similar processes have occurred to insulin genes in these *** of fish genomes revealed an unexpected diversity of insulin genes.A triplication of the insulin gene occurred at the origin of teleost fish,however one of these three genes,insc,has been lost in most teleost fish *** two other insulin genes,insa and insb,have been retained but show differing levels of selective constraint suggesting that they might have diversified in ***,a duplicate copy of the insa gene,which I named insab,is found in many *** coding sequenee encoded by insab genes is under weak selective constraint,with its predicted protein sequences losing their potential to be processed into a two-peptide ***,these sequences have retained perfectly conserved cystine residues,suggesting that they maintain insulin's three-dimensional structure and therefore might modulate the processing and secretion of insulin produced by the other genes.

关键词： Insulin Teleost fish Gene duplicati on Adaptive evolution Gene loss

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The role of N-glycosylation in cancer

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Acta Pharmaceutica Sinica B 2024年第3期14卷 1098-1110页

作者： Yu Lin david m.Lubman Department of Surgery University of Michigan Medical CenterAnn ArborMI 48109USA

Despite advances in understanding the development and progression of cancer in recent years,there remains a lack of comprehensive characterization of the cancer *** play an important role in medicine and are involved in various human disease conditions including ***-moieties participate in fundamental cancer processes like cell signaling,invasion,angiogenesis,and *** N-glycosylation significantly impacts cancer processes and targeted therapies in ***,understanding N-glycosylation in a tumor is essential for comprehending disease progression and discovering anti-cancer targets and biomarkers for therapy monitoring and *** review presents the fundamental process of protein N-glycosylation and summarizes glycosylation changes in tumor cells,including increased terminal sialylation,N-glycan branching,and ***,the role of N-glycosylation in tumor signaling pathways,migration,and metabolism are *** and glycopeptides as potential biomarkers for early detection of cancer based on site specificity have been ***,understanding and exploring the cancer glycoproteome,along with its role in medicine,implication in cancer and other human diseases,highlights the significance of N-glycosylation in tumor processes,necessitating further research for potential anticancer targets and biomarkers.

关键词： N-Glycosylated proteins Cancer signaling Cancer angiogenesis Cancer metabolism Cancer biomarkers

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motilin and ghrelin gene experienced episodic evolution during primitive placental mammal evolution

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Science China(Life Sciences) 2010年第6期53卷 677-682页

作者： IRWIN m. david Departments of Laboratory medicine and Pathobiology and the Banting and Best Diabetes Centre University of Toronto

motilin and ghrelin,members of a structure-function-related hormone family,play important roles in gastrointestinal function,regulation of energy homeostasis and growth hormone *** observed episodic evolution in both of their prehormone gene sequences during primitive placental mammal evolution,during which most of the nonsynonymous changes result in radical *** note,a functional obestatin hormone might have only originated after this episodic evolution *** in placental mammal evolution,a series of biology complexities *** the same time the motilin and ghrelin prehormone genes,which play important roles in several of these processes,experienced episodic evolution with dramatic changes in their coding *** observations suggest that some of the lineage-specific physiological adaptations are due to episodic evolution of the motilin and ghrelin genes.

关键词： motilin ghrelin episodic evolution

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