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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

Nutritional needs and mortality risk combine to shape foraging decisions in ants

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Current Zoology 2023年第6期69卷 747-755页

作者： Bryce Barbee Noa Pinter-Wollman Department of ecology and evolutionary biology University of CaliforniaLos AngelesCAUSA

When foraging,internal needs for particular nutrients might affect food choice,and external constraints,such as predation risk,might impact trade-offs between foraging and risk *** both internal and external constraints simultaneously can provide important insights into how animals make *** examined how internal nutritional needs and external cues of mortality risk jointly impact the foraging behavior of *** colonies require carbohydrates to support workers energetically and proteins to raise ***,colonies adjust their foraging activity in response to the environment,such as food availability and the presence of predators or *** we exam-ine the foraging decisions of groups of Argentine ants Linepithema humile,which differ in their nutritional needs in high-risk *** starved groups of ants for either proteins or carbohydrates and determined the foraging choices that ants made when cues of heterospecifics were *** found that ants preferentially forage for carbohydrates in high-risk ***,starvation for carbohydrates increased the ants'preference for carbohydrates,even when cues of heterospecifics were present at both carbohydrates and protein *** for protein also resulted in preferential foraging for carbohydrates,but it increased visitation to a protein food source in high-risk envi-ronments compared to when ants were starved for carbohydrates or for both *** the effect of both nutrition and mortality risk on foraging simultaneously provides insights about state-dependent risk-taking behavior that may have important implications for predicting theinvasionofspecies intonovelhabitats.

关键词： decision-making foraging nutrition risk trade-offs

Studying the genetic basis of speciation in high gene flow marine invertebrates

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Current Zoology 2016年第6期62卷 643-653页

作者： Grant H. POGSON Department of ecology and evolutionary biology University of California Santa Cruz CA 95064 USA

A growing number of genes responsible for reproductive incompatibilities between species （barrier loci） exhibit the signals of positive selection. However, the possibility that genes experiencing positive selection diverge early in speciation and commonly cause reproductive incompatibilities has not been systematically investigated on a genome-wide scale. Here, I outline a research program for studying the genetic basis of speciation in broadcast spawning marine invertebrates that uses a priori genome-wide information on a large, unbiased sample of genes tested for positive selection. A targeted sequence capture approach is proposed that scores single-nucleotide polymorphisms （SNPs） in widely separated species populations at an early stage of allopatric divergence. The targeted capture of both coding and non-coding sequences enables SNPs to be characterized at known locations across the genome and at genes with known selective or neutral histories. The neutral coding and non-coding SNPs provide robust background distributions for identifying Fsm-outliers within genes that can, in principle, identify specific mutations experiencing diversifying selection. If natural hybridization occurs between species, the neutral coding and noncoding SNPs can provide a neutral admixture model for genomic clines analyses aimed at finding genes exhibiting strong blocks to introgression. Strongylocentrotid sea urchins are used as a model system to outline the approach but it can be used for any group that has a complete reference genome available.

关键词： barrier loci Bobzhansky-Muller incompatibilities FsToutliers genome scan introgression positive selection sequence capture speciation.

What Has Genomics Taught An evolutionary Biologist?

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Genomics, Proteomics & Bioinformatics 2023年第1期21卷 1-12页

作者： Jianzhi Zhang Department of ecology and evolutionary biology University of MichiganAnn ArborMI 48109USA

Genomics,an interdisciplinary field of biology on the structure,function,and evolution of genomes,has revolutionized many subdisciplines of life sciences,including my field of evolutionary biology,by supplying huge data,bringing high-throughput technologies,and offering a new approach to *** this review,I describe what I have learned from genomics and highlight the fundamental knowledge and mechanistic insights gained.I focus on three broad topics that are central to evolutionary biology and beyond—variation,interaction,and selection—and use primarily my own research and study subjects as *** the next decade or two,I expect that the most important contributions of genomics to evolutionary biology will be to provide genome sequences of nearly all known species on Earth,facilitate high-throughput phenotyping of natural variants and systematically constructed mutants for mapping genotype–phenotype–fitness landscapes,and assist the determination of causality in evolutionary processes using experimental evolution.

关键词： Variation Interaction Selection Evolution Genetics Mutation

Natural selection contributes to the myopia epidemic

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National Science Review 2021年第6期8卷 128-135页

作者： Erping Long Jianzhi Zhang Department of ecology and evolutionary biology University of Michigan State Key Laboratory of Ophthalmology Zhongshan Ophthalmic CenterSun Yat-sen University

The prevalence of myopia, or nearsightedness, has skyrocketed in the past few decades, creating a public health crisis that is commonly attributed to lifestyle changes. Here we report an overall increase in the frequencies of myopia-associated mutant alleles over 25 years among participants of the UK *** myopia itself appears to be selected against, many of the mutant alleles are associated with reproductive benefits, suggesting that reproduction-related selection inadvertently contributes to the myopia epidemic. We estimate that, in the UK alone, natural selection adds more than 100 000 myopia cases per generation, and argue that antagonistic pleiotropy be broadly considered in explaining the spreads of apparently disadvantageous phenotypes in humans and beyond.

关键词： allele frequency natural selection antagonistic pleiotropy evolution myopia reproduction

Factors influencing mercury accumulation in three species of forage fish from Caddo Lake, Texas, USA

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Journal of Environmental Sciences 2010年第8期22卷 1158-1163页

作者： Matthew M Chumchal Ray W Drenner David R Cross K David Hambright Department of biology Texas Christian University 2800 S. University Dr Department of Psychology Texas Christian University 2800 S. University Dr program in ecology and evolutionary biology Biological Station and Department of Zoology 730 Van Vleet Oval University of Oklahoma

Most studies that have examined mercury （Hg） contamination of fish have focused on game species feeding near the top of the food web, while studies that examine forage fish that feed near the base of the food web are rare. We conducted a survey of Hg contamination in three species of forage fish, brook silverside （Labidesthes sicculus）, threadfin shad （Dorosoma petenense） and gizzard shad （Dorosoma cepedianum）, from Caddo Lake, Texas, USA and found species-specific differences in Hg concentrations. We examined total length, age, trophic position （determined using δ15N）, and growth rate of forage fish as factors that could have influenced within-and between-species differences in Hg concentration. Total length and age were the best predictors of within-species differences in Hg concentration. Between-species differences in Hg concentrations were most strongly influenced by trophic position.

关键词： mercury trophic position forage fish

Biotic Homogenization Caused by the Invasion of Solidago canadensis in China

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Journal of Integrative Agriculture 2013年第5期12卷 835-845页

作者： CHEN Guo-qi ZHANG Chao-bin MA Ling QIANG Sheng John ASilander Li Li Qi Weed Research Laboratory Nanjing Agricultural University Department of ecology and evolutionary biology University of Connecticut Northern Crop Science Laboratory USDA-ARS

Although studies argue that invasive species can cause biotic differentiation, some cases show that biological invasions actually decrease biodiversity through biotic homogenization. The concept of biotic homogenization through the invasion of a certain serious invasive plant species merit more studies. Hence, we used field surveys to quantitatively compare invasive populations of Solidago canadensis （SC） in China with the control sites （adjacent sites to SC present sites yet without the species） and SC native populations in the USA. We found that plant communities in SC invaded habitats shared similarities with those in SC native ranges. Bray-Curtis similarity clearly showed that the composition of plant communities in SC invaded habitats were similar to those in SC native ranges. Both in the native and introduced range, plant communities with SC present were characterized by SC being dominant, significantly lower species richness, or-diversity and p-diversity, as well as a decrease in the correlation coefficient between geographic distance and floristic similarities. SC favors fertile and moist loam habitat, while it dominated in various habitats in China, where more than 20 different dominants should have occurred. In conclusion, serious invasive species can quickly remodel and homogenize diverse communities by dominating them.

关键词： biodiversity control site field survey geographic distance invasive population native population similarity

Soil Respiration and Litter Decomposition Increased Following Perennial Forb Invasion into an Annual Grassland

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Pedosphere 2016年第4期26卷 567-576页

作者： ZHANG Ling MA Xiaochi WANG Hong LIU Shuwei Evan SIEMANN ZOU Jianwen College of Forestry Jiangxi Agricultural University College of Resources and Environmental Sciences Nanjing Agricultural University Department of ecology and evolutionary biology Rice University

Exotic plant invasions may alter ecosystem carbon processes, especially when native plants are displaced by plants of a different functional group. Forb invasions into grasslands are common, yet little is known about how they impact carbon cycling. We conducted a field study over 2 years from April 2010 to March 2012 in China to examine changes in soil respiration （Rsoil） following invasion of exotic perennial forb species （Alternanthera philoxeroides or Solidago canadensis） into an annual grassland dominated by a native annual graminoid （Eragrostis pilosa）. Measurements of Rsoil were taken once a week in stands of the native annual graminoid or one of the forb species using static chamber-gas chromatograph method. Aboveground litterfall of each of the three focal species was collected biweekly and litter decomposition rates were measured in a 6-month litterbag experiment. The monthly average and annual cumulative Rsoil increased following invasion by either forb species. The increases in cumulative Rsoil were smaller with invasion of Solidago （36%） than Alternanthera （65%）. Both invasive forbs were associated with higher litter quantity and quality （e.g., C：N ratio） than the native annum graminoid. Compared to the native annual graminoid, the invasive forbs Altevnanthera （155%） and Solidago （361%） produced larger amounts of more rapidly decomposing litter, with the litter decay constant k being 3.8, 2.0 and 1.0 for Alternanthera, Solidago and Eragrostis, respectively. Functional groups of the invasive plants and the native plants they replaced appear to be useful predictors of directions of changes in Rsoil, but the magnitude of changes in Rsoil seems to be sensitive to variations in invader functional traits.

关键词： carbon cycling exotic plant functional group functional traits invasive plants litterfall native plants

Large-scale spatial synchrony and the stability of forest biodiversity revisited

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Journal of Plant ecology 2012年第1期5卷 52-63页

作者： Annette M.Ostling Department of ecology and evolutionary biology University of Michigan830 North University AvenueAnn ArborMI 48109-1048USA

Aims Mechanisms contributing to species coexistence have at least one of two modes of action:(i)stabilization of populations through restoring forces and(ii)equalization of fitness across individuals of different ***,ecologists have begun gleaning the relative roles of these by testing the predictions of neutral theory,which predicts the properties of communities under pure fitness *** null hypothesis was rejected for forests of southern Ontario based on large-scale(;100 km)spatial synchrony evident in the fossil pollen record over the entire Holocene,and the argument that a species’relative abundance would instead vary independently at such distances in the absence of stabilizing *** test of neutral theory was criticized based on the idea that the synchrony might be produced by dispersal ***,I revisit this test of neutral theory by explicitly calculating the synchrony expected in these forests using a novel simulation method enabling examination of the distribution of a species over large spatial and temporal *** A novel neutral simulation algorithm tracking only the focal species was used to calculate the neutral expectation for spatial synchrony properties examined empirically by Clark and MacLachlan[(2003)Stability of forest *** 423:635–8]using fossil pollen data from eight lake *** coefficient of variation(CV)in a species’relative abundance across the eight sites(initiated at about 10%with a small CV)was calculated for 10 runs over a 10000 year time *** CV reflects the level of spatial synchrony in that less synchronous dynamics should lead to more variation across space(a higher equilibrium CV),and in particular,a greater increase in the CV over time from a small initial value.A‘two dimensional t’fat-tailed dispersal kernel was assumed with parameters set to the median derived from seed trap data for deciduous wind-dispersed *** of results to assumed dispersal

关键词： neutral theory community dynamics turnover

Sinobaatar gen. nov.: First multituberculate from the Jehol Biota of Liaoning,Northeast China

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Chinese Science Bulletin 2002年第11期47卷 933-938,970页

作者： HU Yaoming & WANG YuanqingInstitute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 10044, China American Museum of Natural History, New York, NY 10024, USA biology program (ecology, evolutionary biology, and Behavio Institute of Vertebrate Paleontology and Paleoanthropology Chinese Academy of Sciences Beijing China American Museum of Natural History New York USA biology program (ecology Evolutionary Biology and Behavior) Graduate School and City College City University of New York USA

A multituberculate skeleton from the Lower Cretaceous Yixian Formation at Dawangzhangzi, Lingyuan City, Liaoning Province, Northeast China, provides new morphological information for early multituberculates. The specimen is the holotype of Sinobaatar lingyuanensis gen. et sp. nov. It has a narrow skull that lacks the superorbital crest or postorbital process. The dental formula is 3·?·5·2/1·0·3·2. The dental morphology, especially that of cheek teeth, of S. lingyuanensis is similar to that of Eobaatar, which places it in the family Eobaataridae. The postcranial skeleton of Sinobaatar is similar to that of other multituberculates. As in Holotheria, Metatarsal V of Sinobaatar articulates only with the cuboid and has no contact with the calcaneus, which probably represents the primitive condition of multituberculates. Nine carpals of Sinobaatar resemble those of Zhang-heotherium, except the centrale being larger than the trape-zoid. The dental features of Sinobaatar show again that eo-baatarids are

关键词： Lingyuan western Liaoning Yixian Formation Early Cretaceous Jehol Biota multituberculates Sinobaatar.