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Challenges in estimating ancestral state reconstructions:the evolution of migration in Sylvia warblers as a study case

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Integrative Zoology 2020年第3期15卷 161-173页

作者： Raquel PONTI Angel ARCONES David R.VIEITES National Museum of Natural Sciences MadridSpain Department of Evolutionary Biology Ecology and Environmental SciencesFaculty of BiologyUniversity of BarcelonaBarcelonaSpain Biodiversity Research Institute(IRBIO) University of BarcelonaBarcelonaSpain

Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of *** development of ancestral state reconstruction(ASR)methods has provided the tools to reconstruct trait evolution,which are widely used in fields like evolutionary biology,macroecology and *** there are different elements involved in those analyses,with different levels of uncertainty(*** to branch length estimation,trait coding,statistical framework,taxon sampling or software),the various combinations of these elements likely have a strong impact on the reconstruction of the evolution of traits,potentially leading to opposite *** assess the impact of these different elements in ASR,we performed a set of analyses,including all possible combinations of such elements and using the evolution of migratory behavior in Sylvia warblers as a case study,which was coded as a continuous or as a discrete *** results show that taxon sampling,character coding,tree shape,statistical framework and software all significantly affect ASR,both individually and in *** all reconstructed tree nodes show discrepancies,but in the critical ones most pairwise comparisons between analyses lead to conflicting and unexpectedly antagonistic results(zero migration vs fully migratory),thus challenging interpretations of trait *** propose some possible solutions to partly inform decisions,involving the method selection and the incorporation of biological or fossil evidence regarding how traits evolve,but our results demand serious rethinking about how the research community currently uses ASR.

关键词： ancestral state reconstruction conflicting methods evolution of migration Sylvia warblers

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RAD-seq data reveals robust phylogeny and morphological evolutionary history of Rhododendron

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Horticultural Plant Journal 2024年第3期10卷 866-878页

作者： Yuanting Shen Gang Yao Yunfei Li Xiaoling Tian Shiming Li Nian Wang Chengjun Zhang Fei Wang Yongpeng Ma Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China University of Chinese Academy of Sciences Beijing 100049China Beijing Genomics of Institute ShenzhenGuangdong 518120China Guiyang Institute of Humanities and Technology GuiyangGuizhou 550025China state Forestry and Grassland Administration Key Laboratory of Silviculture in Downstream Areas of the Yellow River College of ForestryShandong Agricultural UniversityTai'anShandong 271018China The Southwest China of Germplasm Bank of Wild Species Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnan 650201China West China Subalpine Botanical Garden Institute of BotanyChinese Academy of SciencesChengduSichuan 611834China

Rhododendron is famous for its high ornamental ***,the genus is taxonomically difficult and the relationships within Rhododendron remain *** addition,the origin of key morphological characters with high horticulture value need to be *** problems largely hinder utilization of germplasm *** studies attempted to disentangle the phylogeny of Rhododendron,but only used a few genomic markers and lacked large-scale sampling,resulting in low clade support and contradictory phylogenetic ***,we used restriction-site associated DNA sequencing(RAD-seq)data and morphological traits for 144 species of Rhododendron,representing all subgenera and most sections and subsections of this species-rich genus,to decipher its intricate evolutionary history and reconstruct ancestral *** results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq *** optimal phylogenetic tree and split tree recovered five lineages among ***(cladeⅠ)formed the basal *** and Azaleastrum formed cladeⅡand had sister ***Ⅲincluded all scaly rhododendron ***(cladeⅣ)formed a sister group to ***(cladeⅤ).The results of ancestral state reconstruction showed that Rhododendron ancestor was a deciduous woody plant with terminal inflorescence,ten stamens,leaf blade without scales and broadly funnelform corolla with pink or purple *** study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq *** also provides an example to resolve discordant signals in phylogenetic trees and demonstrates the application feasibility of RAD-seq with large amounts of missing data in deciphering intricate evolutionary ***,the reconstructed ancestral state of six important characters provides insights into the inn

关键词： Rhododendron RAD-seq Missing data Quartet sampling(QS) ancestral state reconstruction

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Hidden in plain sight:Morphological and phylogenetic evidence for Bouteloua arizonica,a species distinct from Bouteloua aristidoides(Poaceae,Chloridoideae)

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Plant Diversity 2021年第2期43卷 125-133页

作者： Luis Fernando Cuellar-Garrido Maria Elena Siqueiros-Delgado Herbario Luz Maria Villarreal de Puga Del Instituto de Botanica(IBUG) Departamento de Botanica y ZoologíaCentro Universitario de Ciencias Biologicas y AgropecuariasUniversidad de GuadalajaraCamino Ing.Ramon Padilla Sanchez 2100CP 45200ZapopanJaliscoMexico Departamento de Biologia Centro de Ciencias BioasicasUniversidad Autonoma de AguascalientesAvenida Universidad 940CP 20131AguascalientesMexico

Two varieties of Bouteloua aristidoides have been recognized,the widespread *** and the more narrowly distributed *** two varieties differ in inflorescence form even more than that seen between many other closely related species of *** therefore asked whether these taxa might be better regarded as distinct species.A total of 93 vouchers were studied by using morphometry(principal components analysis and statistical tests),leaf micromorphology,ancestral state reconstruction,and/or molecular(ITS,trnC-rpoB and trnT-L-F)phylogenetic *** from the ITS tree,all results supported elevation of *** *** to the rank of species,thus the new combination Bouteloua arizonica(***)***&Columbus *** ***.,is *** and combined chloroplast-nuclear molecular trees depicted *** as monophyletic(even in sympatric populations with ***)and reveals phylogenetic structure within *** for which the presence of new undescribed varieties of ***(different from ***)is *** differs from *** in having fewer branches per inflorescence,a bigger branch with more spikelets,and a shorter branch *** electron microscopy revealed the presence of papillae on leaves of *** as a clear *** mature plants of *** from seeds in a greenhouse revealed a strong cleistogamous nature for this species for which gene flow in sympatric populations with *** seems unlikely.A taxonomic treatment and distribution map for identification of *** is provided.

关键词： ancestral state reconstruction Bouteloua arizonica Cleistogamy Morphology Phylogeny Sympatry

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The phylogeny of francolins(Francolinus, Dendroperdix, Peliperdix and Scleroptila) and spurfowls(Pternistis) based on chick plumage(Galliformes: Phasianidae)

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Avian Research 2018年第1期9卷 1-18页

作者： Johann H.van Niekerk Tshifhiwa G.Mandiwana-Neudani Department of Environmental Sciences College of Agriculture and Environmental ScienceUniversity of South Africa Department of Biodiversity University of Limpopo

Background: This paper describes the chick plumage of spurfowl(Pternistis) and francolin(Francolinus, Dendroperdix Peliperdix and Scleroptila) chicks, tests its significance for phylogenetic relationships and also explores the patterns of character evolution in the francolin and spurfowl *** regarded as monophyletic, the two evolutionar?ily distant clades are now divided into five *** considered were whether chick plumage supports the dichotomy between spurfowls and francolins and what role habitat matching ***: The study was based mainly on photographs of chick skins from the American Museum of Natural History and the Natural History Museum at *** plumage characters were selected for comparative scoring, summa?rised in a *** characters were subsequently analysed phylogenetically and their evolution was traced on the existing molecular phylogeny using a parsimony ***: Based on chick plumage the phylogeny of species groups among francolins and spurfowls, was largely unresolved possibly ascribed to a high degree of symplesiomorphy inherent among the *** possibly could have resulted in a high degree of polytomy particularly among the spurfowls and ***, the ancestral state reconstructions revealed high prevalence of symplesiomorphic states and reversals which do not help in the classification of *** the differences are described that separate some African francolins from spurfowls, other francolins(in Asia and Africa) share remarkably similar characteristics with *** dark dorsal plumage is probably advantageous for avoiding detection by predators in forests, while facial stripes optimise the breaking of body shapes in dense grass cover(as in Scleroptila spp.) and semi?striped faces are advantageous for stationary camouflage under tree and bush cover(as in Pternistis spp.).Conclusions: Although symplesiomorphy is a hereditary explanation for downy c

关键词： Spurfowl Francolin Phasianidae Chick plumage Phylogeny ancestral state reconstruction Habitat

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New considerations on the phylogeny of Sessilida(Protista:Ciliophora:Peritrichia)based on multiple-gene information,with emphasis on colonial taxa

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Marine Life Science & Technology 2022年第4期4卷 569-583页

作者： Zhe Wang Xiaoting Feng Lifang Li Khaled A.S.Al-Rasheid Alan Warren Chundi Wang Zemao Gu Marine College Shandong UniversityWeihai264209China College of Fisheries/Shuangshui ShuanglüInstitute Huazhong Agricultural UniversityWuhan430070China Hubei Engineering Technology Research Center for Aquatic Animal Diseases Control and Prevention Wuhan430070China Department of Zoology College of ScienceKing Saud UniversityRiyadh11451Saudi Arabia Department of Life Sciences Natural History MuseumLondonSW75BDUK

The subclass Peritrichia,containing two orders Sessilida and Mobilida,is a major group of ciliates with worldwide distribution and high species *** studies have investigated the phylogeny of peritrichs;however,the evolutionary relationships and classification of some families and genera within the Sessilida remain *** the present study,we isolated and identified 22 peritrich populations representing four families and six genera and obtained 64 rDNA sequences to perform phylogenetic analyses and assess their systematic *** character reconstruction was also carried out to infer evolutionary routes within the *** results indicate:(1)family Vaginicolidae is monophyletic and acquisition of the typical peritrich lorica represents a single evolutionary divergence;(2)core epistylidids evolved from a Zoothamnium-like ancestor and experienced spasmoneme loss during evolution;(3)Campanella clusters with species in the basal clade and shows stable morphological differences with other epistylidids,supporting its assignment to a separate family;(4)the structure of the peristomial lip may be a genus-level character rather than a diagnostic character for discriminating Epistylididae and Operculariidae,thus a redefinition of Operculariidae should be carried out when more species have been investigated;(5)some characters,such as lifestyle(solitary or colonial),spasmoneme and living habit(sessile or free-swimming),evolved repeatedly among sessilids indicating that species with non-contractile stalks or that are free-swimming have multiple evolutionary routes and might derive from any sessilid lineage without a *** close phylogenetic relationships of some morphologically distinct sessilids imply that the diagnoses of some genera and families should be improved.

关键词： ancestral state reconstruction Ciliates Morphology Peritrichs Phylogenetic analyses

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Reconstructing ancestral ranges in historical biogeography:properties and prospects

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Journal of Systematics and Evolution 2009年第5期47卷 369-382页

作者： Kristin S.LAMM Benjamin D.REDELINGS Bioinformatics Research Center North Carolina State University

Recent years have witnessed a proliferation of quantitative methods for biogeographic *** particular,novel parametric approaches represent exciting new opportunities for the study of range ***,we review a selection of current methods for biogeographic analysis and discuss their respective *** methods include generalized parsimony approaches,weighted ancestral area analysis,dispersal-vicariance analysis,the dispersal-extinction-cladogenesis model and other maximum likelihood approaches,and Bayesian stochastic mapping of ancestral ranges,including a novel approach to inferring range evolution in the context of island *** of these methods were developed specifically for problems of ancestral range reconstruction,whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral *** for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed,but also in the various historical events that may change the ancestral *** explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range ***,we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.

关键词： allopatry ancestral range ancestral state reconstruction biogeography dispersal historical biogeogra-phy review speciation statistics vicariance.

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