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Angiosperm phylogeny inferred from sequences of four mitochondrial genes

Journal of Systematics and Evolution 2010年第6期48卷 391-425页

作者： Tory A.HENDRY Joseph W.BROWN Geordan T.HUDSON department of Ecology and evolutionary Biology University of Michigan

An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes,atp1,matR,nad5,and rps3,from 380 species that represent 376 genera and 296 families of seed *** is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB,matK,and rbcL,and nuclear 18S *** basalmost lineage consists of Amborella and Nymphaeales(including Hydatellaceae).Austrobaileyales follow this clade and are sister to the mesangiosperms,which include Chloranthaceae,Ceratophyllum,magnoliids,monocots,and *** the exception of Chloranthaceae being sister to Ceratophyllum,relationships among these five lineages are not well *** eudicots,Ranunculales,Sabiales,Proteales,Trochodendrales,Buxales,Gunnerales,Saxifragales,Vitales,Berberidopsidales,and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and *** rosids,the COM(Celastrales-Oxalidales-Malpighiales) clade is sister to malvids(or rosid II),instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of *** and Caryophyllales are members of an expanded asterid *** study shows that the mitochondrial genes are informative markers for resolving relationships among genera,families,or higher rank taxa across *** low substitution rates and low homoplasy levels of the mitochondrial genes relative to the chloroplast genes,as found in this study,make them particularly useful for reconstructing ancient phylogenetic relationships.A mitochondrial gene-based angiosperm phylogeny provides an independent and essential reference for comparison with hypotheses of angiosperm phylogeny based on chloroplast genes,nuclear genes,and non-molecular data to reconstruct the underlying organismal phylogeny.

关键词： angiosperm homoplasy mitochondrial gene molecular evolutionary rate phylogeny rosids.

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晚白垩世真兽类Zalamdalestes揭示哺乳动物独特的枢椎及其复杂的进化过程

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Science Bulletin 2024年第11期69卷 1767-1775页

作者： Patrick Arnold Katarzyna Janiszewska 李茜 Jingmai K.O'Connor Lucja Fostowicz-Frelik Institute of Biochemistry and Biology University of PotsdamPotsdam D-14476Germany Environmental paleobiology department Institute of PaleobiologyPolish Academy of SciencesWarsaw 00-818Poland Key Laboratory of evolutionary Systematics of Vertebrates Institute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijing 100044China The Field Museum of Natural History Chicago IL 60605USA department of Organismal Biology and Anatomy The University of ChicagoChicago IL 60637USA evolutionary paleobiology department Institute of PaleobiologyPolish Academy of SciencesWarsaw 00-818Poland

The typical mammalian neck consisting of seven cervical vertebrae(C1–C7)was established by the Late Permian in the cynodont forerunners of modern *** structure is precisely adapted to facilitate movements of the head during feeding,locomotion,predator evasion,and social ***,the clade including crown placentals,has a fossil record extending back more than 125 million years revealing significant morphological diversification in the *** very little is known concerning the early evolution of eutherian cervical morphology and its functional adaptations.A specimen of Zalambdalestes lechei from the Late Cretaceous of Mongolia boasts exceptional preservation of an almost complete series of cervical vertebrae(C2–C7)revealing a highly modified axis(C2).The significance of this cervical morphology is explored utilizing an integrated approach combining comparative anatomical examination across mammals,muscle reconstruction,geometric morphometrics and virtual range of motion *** compared the shape of the axis in Zalambdalestes to a dataset of 88 mammalian species(monotremes,marsupials,and placentals)using three-dimensional landmark *** results indicate that the unique axis morphology of Zalambdalestes has no close analog among living *** range of motion analysis of the neck strongly implies Zalambdalestes was capable of exerting very forceful head movements and had a high degree of ventral flexion for an animal its *** findings reveal unexpected complexity in the early evolution of the eutherian cervical morphology and suggest a feeding behavior similar to insectivores specialized in vermivory and defensive behaviors in Zalambdalestes akin to modern spiniferous mammals.

关键词： Atlas Axis Vertebral column Stem placental Morphology paleoecology

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Origination and evolution of orphan genes and de novo genes in the genome of Caenorhabditis elegans

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Science China(Life Sciences) 2019年第4期62卷 579-593页

作者： Wenyu Zhang Yuanxiao Gao Manyuan Long Bairong Shen Institutes for Systems Genetics West China Hospital Sichuan University department of Ecology and Evolution the University of Chicago department of evolutionary Genetics Max-Planck Institute for Evolutionary Biology department of evolutionary Theory Max-Planck Institute for Evolutionary Biology Committee on Genetics the University of Chicago

Orphan genes that lack detectable homologues in other lineages could contribute to a variety of biological functions. However,their origination and function mechanisms remain largely unknown. Herein, through a comprehensive and systematic computational pipeline, we identified 893 orphan genes in the lineage of C. elegans, of which only a low fraction(0.9%) were derived from transposon elements. Six new protein-coding genes that de novo originated from non-coding DNA sequences in the genome of C. elegans were also identified. The authenticity and functionality of these orphan genes and de novo genes are supported by three lines of evidences, consisting of transcriptional data, and in silico proteomic data, and the fixation status data in wild populations. Orphan genes and de novo genes exhibited simple gene structures, such as, short in protein length, of fewer exons,and are frequently X-linked. RNA-seq data analysis showed these orphan genes are enriched with expression in embryo development and gonad, and their potential function in early development was further supported by gene ontology enrichment analysis results. Meanwhile, de novo genes were found to be with significant expression in gonad, and functional enrichment analysis of the co-expression genes of these de novo genes suggested they may be functionally involved in signaling transduction pathway and metabolism process. Our results presented the first systematic evidence on the evolution of orphan genes and de novo origin of genes in nematodes and their impacts on the functional and phenotypic evolution, and thus could shed new light on our appreciation of the importance of these new genes.

关键词： Caenorhabditis elegans,orphan genes de novo genes

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Geographic variation in sexual selection and implications for speciation in the Barn Swallow

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Chinese Birds 2015年第1期5卷 30-42页

作者： Elizabeth SC Scordato Rebecca J Safran department of Ecology and evolutionary Biology The University of Colorado

Barn Swallows(Hirundo rustica), a group of passerine birds comprised of six closely related subspecies, are well known throughout their nearly worldwide distribution, in part because of their close association with human settlements.A tractable species for both individual-based and population-level studies, Barn Swallows are a prominent model system in evolutionary, ecological, and behavioral research. Here we review work on sexual selection and population divergence in this species complex, focusing on comparative studies among populations and *** summarize variation in the targets of mate choice and in the information conveyed by sexually selected traits, and conclude that the benefits advertised by different traits may vary geographically. Finally, we consider the role of sexual selection as a driver of population divergence in this widespread and phenotypically variable species complex.

关键词： Barn Swallow Geographic variation Natural selection Sexual selection Speciation Tail streamers Ventral color

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Alternative views of biological species: reproductively isolated units or genotypic clusters?

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National Science Review 2020年第8期7卷 1401-1407页

作者： James Mallet department of Organismic and evolutionary Biology Harvard University

Wang et al. in this journal argue that it may be time to abandon a classic idea about species, the biological species concept(BSC), given recent findings with genomic data on closely related taxa [1]. Furthermore, they propose a set of tests on genetic or genomic data that might lead to acceptance or rejection of the biological species concept.

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gFACs:Gene Filtering,Analysis,and Conversion to Unify Genome Annotations Across Alignment and Gene Prediction Frameworks

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Genomics, Proteomics & Bioinformatics 2019年第3期17卷 305-310页

作者： Madison Caballero Jill Wegrzyn department of Ecology and evolutionary Biology University of Connecticut

Published genomes frequently contain erroneous gene models that represent issues associated with identification of open reading frames,start sites,splice sites,and related structural *** source of these inconsistencies is often traced back to integration across text file formats designed to describe long read alignments and predicted gene *** addition,the majority of gene prediction frameworks do not provide robust downstream filtering to remove problematic gene annotations,nor do they represent these annotations in a format consistent with current file *** frameworks also lack consideration for functional attributes,such as the presence or absence of protein domains that can be used for gene model *** provide oversight to the increasing number of published genome annotations,we present a software package,the Gene Filtering,Analysis,and Conversion(gFACs),to filter,analyze,and convert predicted gene models and *** software operates across a wide range of alignment,analysis,and gene prediction files with a flexible framework for defining gene models with reliable structural and functional *** supports common downstream applications,including genome browsers,and generates extensive details on the filtering process,including distributions that can be visualized to further assess the proposed gene *** is freely available and implemented in Perl with support from BioPerl libraries at https://***/PlantGenomicsLab/gFACs.

关键词： Genome annotation Bioinformatics Protein annotation Gene prediction Alignment

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A New Fossil Scorpionfly(Insecta:Mecoptera:Holcorpidae) with Extremely Elongate Male Genitalia from Northeastern China

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Acta Geologica Sinica(English Edition) 2017年第3期91卷 797-805页

作者： LI Lei Chungkun SHIH WANG Chen REN Dong Key Lab of Insect Evolution and Environmental Changes Capital Normal University department of paleobiology National Museum of Natural HistorySmithsonian Institution

Since Holcorpa maculosa was first described in 1878, it has attracted lots of attention due to its extremely elongate abdominal segments from the sixth to the eighth. Fossil records of family Holcorpidae are very rare, comprising two species in one genus represented by three fossil specimens, resulting in limited knowledge on the structure and function of holcorpid＇s unique male organ, as well as its evolutionary relationship with other scorpionflies. Herein we describe a new genus with a new species, Conicholcorpa stigmosa gen. et sp. nov., of the Holcorpidae from the Middle Jurassic Jiulongshan Formation near Daohugou Village, Inner Mongolia, China. This is the first holcorpid documented from the Daohugou locality, albeit two previously reported species with extremely elongate male organs but deemed as Family Incertae sedis. C. stigmosa gen. et sp. nov. is the earliest holcorpid hitherto, extending its existence from the Early Eocene to the Middle Jurassic by 114 million years and providing one more early case of presenting exaggerated male body parts for sexual display and/or selection. Our analysis supports the sister relationship between Holcorpidae and Orthophlebiidae. Our results not only enhance our knowledge of the morphology of Holcorpidae but also elucidate the relationship of known species of this family.

关键词： Conicholcorpa Daohugou Holcorpidae Jiulongshan Formation Middle Jurassic

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A Century of Spinosaurs-A Review and Revision of the Spinosauridae with Comments on Their Ecology

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Acta Geologica Sinica(English Edition) 2017年第3期91卷 1120-1132页

作者： David William Elliott HONE Thomas Richard HOLTZ School of Biological and Chemical Sciences Queen Mary University of London department of Geology University of MarylandCollege Park department of paleobiology National Museum of Natural History

The spinosaurids represent an enigmatic and highly unusual form of large tetanuran theropods that were first identified in 1915. A recent flurry of discoveries and taxonomic revisions of this important and interesting clade has added greatly to our knowledge. Spinosaur body fossils are however generally rare and most species are known from only limited skeletal remains. Their unusual anatomical adaptations to the skull, limbs and axial column all differ from other large theropods and point to an unusual ecological niche and a lifestyle intimately linked to water.

关键词： Theropoda Megalosauroidea Baryonychinae Spinosaurinae palaeoecology

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Large males have a mating advantage in a species of darter with smaller,allopaternal males Etheostoma olmstedi

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Current Zoology 2010年第1期56卷 1-5页

作者： Kelly A.STIVER Suzanne H.ALONZO department of Ecology and evolutionary Biology Yale University

Theory suggests that males that are larger than their competitors may have increased mating success, due to both greater competitive ability and increased attractiveness to females. We examined how male mating suceess varies with male size in the tessellated darter Etheostoma olmstedi. Previous work has shown that large males tend to move around and breed in vacant breeding sites, and consequently provide less care for their eggs, while smaller individuals can be allopaternal, caring for the eggs of other males as well as for their own. We studied female egg deposition in a natural breeding population using artificial breeding sites and in the laboratory, where female choice of spawning site was restricted to two breeding sites tended by two males of different sizes. In both the field and the laboratory, nests tended by larger males were more likely to receive new eggs. Additionally, the mean size of males associated with a nest was positively correlated with both the maximum coverage of eggs at the nest and the number of times new eggs were deposited. We discuss how the increased mating success of larger males, despite their decreased parental care, may help explain aUopaternal care in this species [Current Zoology 56 （1）： 1-5, 2010].

关键词： Alloparental care Male competition Paternal care Sexual selection Mate choice Tessellated darter

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Anatomy of a eustatic event during the Turonian (Late Cretaceous) hot greenhouse climate

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Science China Earth Sciences 2017年第1期60卷 20-29页

作者： Bilal U. HAQ Brian T. HUBER department of paleobiology MRC-121Smithsonian InstitutionWashington D C 20013USA Sorbonne ISTEP Pierre&Marie Curie UniversityParis 75005France

Sequence stratigraphic studies consider relative change in sea level(as regulated by eustasy,local tectonics and sediment supply)as the main builder of the stratigraphic *** has generally been considered as a consequence of the growth and decay of continental ice sheets that would explain large,rapid changes in sea level,even during periods of relative global climatic ***,such a mechanism has become increasingly difficult to envision during times of extreme global warmth such as the Turonian,when the equator-to-pole temperature gradient was very low and the presence of polar ice seems *** paper investigates the timing and extent of sea level falls during the late Cenomanian through Turonian,especially the largest of those events,sequence boundary KTu4,which occurred during the middle to late Turonian peak of the Cretaceous hot greenhouse *** conclude that the amplitude of the widespread third-order sea level fall in the middle Turonian that is centered at^91.8 Ma varies at different locations depending on the influence of dynamic topography on local tectonics and regional climatic *** volume variations seem unlikely as a mechanism for controlling sea level at this ***,this causal factor cannot be ruled out completely since Antarctic highlands(if they existed in the Late Cretaceous)could sequester enough water as ice to cause eustatic *** ascertain this requires detailed tomographic imaging of Antarctica,followed by geodynamic modeling,to determine whether high plateaus could have existed to accumulate ephemeral ice *** mechanisms for sea level change,such as transference between ground water(a small amplitude shorter time scale effect)and the ocean and entrainment and release of water from the mantle to the oceanic reservoir(a potentially large amplitude and longer time scale process),are intriguing and need to be explored further to prove their efficacy at third-order time scales.

关键词： Eustatic event Turonian Hot greenhouse climate

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