Reconstructing ancestral ranges in historical biogeography:properties and prospects

Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These 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 biogeography. Some 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 ranges. Methods 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 ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.

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

Rhododendron is famous for its high ornamental value.However,the genus is taxonomically difficult and the relationships within Rhododendron remain unresolved.In addition,the origin of key morphological characters with high horticulture value need to be explored.Both problems largely hinder utilization of germplasm resources.Most 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 signals.Here,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 state.Our results revealed high resolutions at subgenera and section levels of Rhododendron based on RAD-seq data.Both optimal phylogenetic tree and split tree recovered five lineages among Rhododendron.Subg.Therorhodion(cladeⅠ)formed the basal lineage.Subg.Tsutsusi and Azaleastrum formed cladeⅡand had sister relationships.CladeⅢincluded all scaly rhododendron species.Subg.Pentanthera(cladeⅣ)formed a sister group to Subg.Hymenanthes(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 color.This study shows significant distinguishability to resolve the evolutionary history of Rhododendron based on high clade support of phylogenetic tree constructed by RAD-seq data.It 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 relationships.Additionally,the reconstructed ancestral state of six important characters provides insights into the innovation of key characters in Rhododendron.

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

Two varieties of Bouteloua aristidoides have been recognized,the widespread var.aristidoides and the more narrowly distributed var.arizonica.The two varieties differ in inflorescence form even more than that seen between many other closely related species of Bouteloua.We 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 analyses.Except from the ITS tree,all results supported elevation of B.aristidoides var.arizonica to the rank of species,thus the new combination Bouteloua arizonica(M.E.Jones)L.F.Cuellar&Columbus comb.nov.et stat.nov.,is proposed.Chloroplast and combined chloroplast-nuclear molecular trees depicted var.arizonica as monophyletic(even in sympatric populations with var.aristidoides)and reveals phylogenetic structure within var.aristidoides for which the presence of new undescribed varieties of B.aristidoides(different from B.arizonica)is addressed.B.arizonica differs from B.aristidoides in having fewer branches per inflorescence,a bigger branch with more spikelets,and a shorter branch extension.Scanning electron microscopy revealed the presence of papillae on leaves of B.arizonica as a clear synapomorphy.Growing mature plants of B.arizonica from seeds in a greenhouse revealed a strong cleistogamous nature for this species for which gene flow in sympatric populations with B.aristidoides seems unlikely.A taxonomic treatment and distribution map for identification of B.arizonica is provided.

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

Our current understanding of how species have evolved is mainly based on comparative phylogenetic methods,which use phylogenies to infer the evolution of traits.The 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 paleontology.As there are different elements involved in those analyses,with different levels of uncertainty(i.e.relating 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 conclusions.To 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 character.Our results show that taxon sampling,character coding,tree shape,statistical framework and software all significantly affect ASR,both individually and in combination.Not 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 evolution.We 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.

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

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 lineages.Previously regarded as monophyletic, the two evolutionar?ily distant clades are now divided into five genera.Questions considered were whether chick plumage supports the dichotomy between spurfowls and francolins and what role habitat matching plays.Methods: The study was based mainly on photographs of chick skins from the American Museum of Natural History and the Natural History Museum at Tring.Eight plumage characters were selected for comparative scoring, summa?rised in a matrix.These characters were subsequently analysed phylogenetically and their evolution was traced on the existing molecular phylogeny using a parsimony approach.Results: 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 Phasianids.This possibly could have resulted in a high degree of polytomy particularly among the spurfowls and francolins.Furthermore, the ancestral state reconstructions revealed high prevalence of symplesiomorphic states and reversals which do not help in the classification of groups.Although the differences are described that separate some African francolins from spurfowls, other francolins(in Asia and Africa) share remarkably similar characteristics with spurfowls.Plain 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 colours and patterns, the traits rel?evant for habitat matching are combined in a manner which is determined(adaptation) by natural selection.

A re-evaluation of the Chaetothyriales using criteria of comparative biology

Chaetothyriales is an ascomycetous order within Eurotiomycetes.The order is particularly known through the black yeasts and filamentous relatives that cause opportunistic infections in humans.All species in the order are consistently melanized.Ecology and habitats of species are highly diverse,and often rather extreme in terms of exposition and toxicity.Families are defined on the basis of evolutionary history,which is reconstructed by time of divergence and concepts of comparative biology using stochastical character mapping and a multi-rate Brownian motion model to reconstruct ecological ancestral character states.Ancestry is hypothesized to be with a rock-inhabiting life style.Ecological disparity increased significantly in late Jurassic,probably due to expansion of cytochromes followed by colonization of vacant ecospaces.Dramatic diversification took place subsequently,but at a low level of innovation resulting in strong niche conservatism for extant taxa.Families are ecologically different in degrees of specialization.One of the clades has adapted ant domatia,which are rich in hydrocarbons.In derived families,similar processes have enabled survival in domesticated environments rich in creosote and toxic hydrocarbons,and this ability might also explain the pronounced infectious ability of vertebrate hosts observed in these families.Conventional systems of morphological classification poorly correspond with recent phylogenetic data.Species are hypothesized to have low competitive ability against neighboring microbes,which interferes with their laboratory isolation on routine media.The dataset is unbalanced in that a large part of the extant biodiversity has not been analyzed by molecular methods,novel taxonomic entities being introduced at a regular pace.Our study comprises all available species sequenced to date for LSU and ITS,and a nomenclatural overview is provided.A limited number of species could not be assigned to any extant family.

Phylogenetic and ecological reevaluation of the order Onygenales

The order Onygenales is classified in the class Eurotiomycetes of the subphylum Pezizomycotina.Families in this order have classically been isolated from soil and dung,and two lineages contain causative agents of superficial,cutaneous and systemic infections in mammals.The ecology and habitat choices of the species are driven mainly by the keratin and cellulose degradation abilities.The present study aimed to investigate whether the ecological trends of the members of Onygenales can be interpreted in an evolutionary sense,linking phylogenetic parameters with habitat preferences,to achieve polyphasic definitions of the main taxonomic groups.Evolutionary processes were estimated by multiple gene genealogies and divergence time analysis.Previously described families,namely,Arthrodermataceae,Ajellomycetaceae,Ascosphaeraceae,Eremascaceae,Gymnoascaceae,Onygenaceae and Spiromastigoidaceae,were accepted in Onygenales,and two new families,Malbrancheaceae and Neogymnomycetaceae,were introduced.A number of species could not be assigned to any of the defined families.Our study provides a revised overview of the main lines of taxonomy of Onygenales,supported by multilocus analyses of ITS,LSU,TUB,TEF1,TEF3,RPB1,RPB2,and ribosomal protein 60S L10(L1)(RP60S)sequences,combined with available data on ecology,physiology,morphology,and genomics.

Cultivated hawthorn(Crataegus pinnatifida var.major)genome sheds light on the evolution of Maleae(apple tribe)

Cultivated hawthorn(Crataegus pinnatifida var.major)is an important medicinal and edible plant with a long history of use for health protection in China.Herein,we provide a de novo chromosomelevel genome sequence of the hawthorn cultivar“Qiu Jinxing.”We assembled an 823.41 Mb genome encoding 40571 genes and further anchored the779.24 Mb sequence into 17 pseudo-chromosomes,which account for 94.64%of the assembled genome.Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae(apple tribe)at approximately 35.4 Mya.Notably,genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome.In addition,our results indicated that the Maleae share a unique ancient tetraploidization event;however,no recent independent whole-genome duplication event was specifically detected in hawthorn.The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome.Furthermore,we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms.We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleopolyploid origin patterns(autopolyploidization or allopolyploidization)of Maleae.Overall,our study provides an improved context for understanding the evolution of Maleae species,and this new highquality reference genome provides a useful resource for the horticultural improvement of hawthorn.

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

The subclass Peritrichia,containing two orders Sessilida and Mobilida,is a major group of ciliates with worldwide distribution and high species diversity.Several studies have investigated the phylogeny of peritrichs;however,the evolutionary relationships and classification of some families and genera within the Sessilida remain unclear.In 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 relationships.Ancestral character reconstruction was also carried out to infer evolutionary routes within the Sessilida.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 lorica.The close phylogenetic relationships of some morphologically distinct sessilids imply that the diagnoses of some genera and families should be improved.