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Preliminary attempt to distinguish the domesticated pigs from wild boars by the methods of carbon and nitrogen stable isotope analysis

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Science China Earth Sciences 2009年第1期52卷 85-92页

作者： Michael P.RICHARDS department of Human Evolution Max-Planck Institute for Evolutionary AnthropologyDeutscher Platz 6D-04103LeipzigGermany

Despite great achievements in the origins of domestic pigs made by the methods of zooarchaeology and molecular biology,how to scientifically distinguish the domesticated pigs from wild boars during the early stage of pig domestication is still poorly *** to wild boar's diets which come from the natural environment,the diets of domestic pigs are more easily influenced by human feeding ***,in principle,exploration of the dietary differences among pigs and understanding the impact on pig diets fed by humans can have great potential to differentiate between wild boars and domesticated *** reveal dietary differences among pigs and distinguish the domesticated pigs from wild boars based on comparison with the diets of humans and other animals,we analyzed the carbon and nitrogen stable isotopes of human bones from Xiaojingshan Site and animal bones from Yuezhuang Site,both of which belong to Houli Culture in Shandong Province and date to about 8500―7500 years *** mean δ 13C value((-17.8 ± 0.3)‰) and δ 15N value((9.0±0.6)‰) in human collagen indicate that although millet agriculture began it was not the main subsistence strategy as millets are typical of C4 plants and that humans made a living mainly by gathering,hunting or raising some domesticated *** δ 13C value(-16.1‰) and δ 15N value(6.9‰) in the bovine suggest that C3 plants were dominant in its diet with some C4 plants *** fish has lower δ 13C value(-24.9‰) and higher δ 15N value(8.8‰) than the bovine,which is the characteristic of the isotopic values from Eurasian freshwater *** on the differences in carbon and nitrogen isotope values,the pigs can be divided into three groups.A group,composed of two pigs,has low δ 13C values(-18.1‰,-20.0‰) and low δ 15N values(4.7‰,6.0‰).B group,only one pig,has the highest δ 13C value(-10.6‰) and mediate δ 15N value(6.4‰).As for the C group,also only one pig,low δ 13C value(-19.0‰) and the highest δ 15N value(9.1‰

关键词： origins of domestic pigs early stage of domestication differentiation of domesticated pigs from wild boars carbon and nitrogen stable isotope analysis millet agriculture

The duration of sociosexual behaviors in male meadow voles Microtus pennsylvanicus varies before, during, and after copulation

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Current Zoology 2011年第1期57卷 43-49页

作者： Ashlee A. VAUGHN Daniel A. FERKIN Javier delBARCO-TRILLO Michael H. FERKIN department of Biological Sciences The University of Memphis Memphis TN 38152 USA department of evolutionary anthropology Duke University Box 90383 Durham NC 27708 USA

The behaviors that surround copulation are characterized as sociosexual behaviors. These behaviors displayed by males that are directed at females may include allogrooming, wrestling, chasing, approach, and time spent together. The data supported the hypothesis that the duration of sociosexual behaviors differs during the pre-copulatory, peri-copulatory, and post-copulatory phases of the mating bout in meadow voles. Voles spent more time approaching conspecifics during the pre- and peri-copulatory phases than during the post-copulatory phase. Voles spent more time allogrooming, wrestling, and chasing during the pre-copulatory phase than during the peri- and post-copulatory phases. Voles spent similar amounts of time together during the pre-, peri-, and post-copulatory phases. The data suggest that sociosexual behaviors displayed by males may be involved in set- ring the pace and temporal components of the mating bout. During the pre-copulatory phase particular behaviors by male voles may attract females, during the peri-copulatory phase some of these behaviors may stimulate or motivate the female to mate, and during the post-copulatory phase certain behaviors may prepare the male to mate again

关键词： Copulatory behavior Meadow voles Odors Sociosexual behavior

Ethanol exposed maturing rat cerebellar granule cells show impaired energy metabolism and increased cell death after oxygen-glucose deprivation

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Neural Regeneration Research 2019年第3期14卷 485-490页

作者： Ana Spataru Diana Le Duc Leon Zagrean Ana-Maria Zagrean Division of Physiology and Neuroscience Carol Davila University of Medicine and Pharmacy King's College Hospital London UK Institute of Human Genetics University of Leipzig Hospitals and Clinics Leipzig GermanyDepartment of Evolutionary Genetics Max Planck Institute for Evolutionary Anthropology

Alcohol, a widely abused drug, has deleterious effects on the immature nervous system. This study investigates the effect of chronic in vitro ethanol exposure on the metabolism of immature rat cerebellar granular cells(CGCs) and on their response to oxygen-glucose deprivation(OGD). Primary CGC cultures were exposed to ethanol(100 mM in culture medium) or to control ethanol-free medium starting day one in vitro(DIV1). At DIV8, the expression of ATP synthase gene ATP5 g3 was quantified using real-time PCR, then cultures were exposed to 3 hours of OGD or normoxic conditions. Subsequently, cellular metabolism was assessed by a resazurin assay and by ATP level measurement. ATP5 g3 expression was reduced by 12-fold(P = 0.03) and resazurin metabolism and ATP level were decreased to 74.4 ± 4.6% and 55.5 ± 6.9%, respectively after chronic ethanol treatment compared to control values(P < 0.01). Additionally, after OGD exposure of ethanol-treated cultures, resazurin metabolism and ATP level were decreased to 12.7 ± 1.0% and 9.0 ± 2.0% from control values(P < 0.01). These results suggest that chronic ethanol exposure reduces the cellular ATP level, possibly through a gene expression down-regulation mechanism, and increases the vulnerability to oxygen-glucose deprivation. Thus, interventions which improve metabolic function and sustain ATP-levels could attenuate ethanol-induced neuronal dysfunction and should be addressed in future studies.

关键词： cell culture chronic ethanol exposure oxygen-glucose deprivation cerebellar granule cells toxicity gene expression cellular ATP cellular metabolism metabolic impairment cell death

Angiosperm phylogeny inferred from sequences of four mitochondrial genes

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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.

Foot strike patterns and hind limb joint angles during running in Hadza hunter-gatherers

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Journal of Sport and Health Science 2014年第2期3卷 95-101,153+156页

作者： Herman Pontzer Kelly Suchman David A.Raichlen Brian M.Wood Audax Z.P.Mabulla Frank W.Marlowe department of anthropology Hunter College City University of New York New York Consortium for evolutionary Primatology evolutionary anthropology Duke University School of anthropology University of Arizona department of anthropology Yale University department of Archeology University of Dar es Salaam department of Archaeology and anthropology University of Cambridge

Background:Investigations of running gait among barefoot and populations have revealed a diversity of foot strike behaviors,with some preferentially employing a rearfoot strike(RFS) as the foot touches down while others employ a midfoot strike(MFS) or forefoot strike(FFS).Here,we report foot strike behavior and joint angles among traditional Hadza hunter-gatherers living in Northern ***:Hadza adults(n = 26) and juveniles(n = 14) ran at a range of speeds(adults:mean 3.4 ± 0.7 m/s,juveniles:mean 3.2 ± 0.5 m/s) over an outdoor trackway while being recorded via high-speed digital *** strike type(*** FFS) and hind limb segment angles at foot strike were ***:Hadza men preferentially employed MFS(86.7%of men),while Hadza women and juveniles preferentially employed RFS(90.9%and85.7%of women and juveniles,respectively).No FFS was ***,the presence of footwear(sandals ***),and trial duration had no effect on foot strike ***:Unlike other habitually barefoot populations which prefer FFS while *** men preferred *** Hadza women and juveniles preferred *** and age differences in foot strike behavior among Hadza adults may reflect differences in running experience,with men learning to prefer MFS as they accumulate more running experience.

关键词： Barefoot Biomechanics Foot strike Foraging Running

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

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

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