Article

The infrageneric taxonomy of Chaerophyllum (Apiaceae) revisited: New evidence from nuclear ribosomal DNA ITS sequences and fruit anatomy

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Abstract

Evolutionary relationships among 65 Chaerophyllum spp. were inferred from nuclear ribosomal DNA internal transcribed spacer (ITS) sequence variation. Thirty-one species, represented by 158 mericarp samples, were analysed for fruit anatomical character variation, employing phylogenetic and phenetic methods to explore their congruence with infrageneric divisions based on molecular data. Phylogenetic trees inferred from molecular data using maximum likelihood (ML) and Bayesian inference (BI) methods corroborated the division of the genus into four sections: Chaerophyllum, Dasypetalon, Physocaulis and Chrysocarpum. From among the newly sequenced species, the Greek endemic C. heldreichii was grouped with section Chaerophyllum, whereas the highly variable Asian C. reflexum–C. villosum complex formed an early-branching paraphyletic assemblage in section Chrysocarpum. The recently described C. karsianum has an identical ITS sequence to C. bulbosum, whereas C. aksekiense was clearly separated from the morphologically similar C. macrospermum. Our study confirmed the postulated synonymy of several species on the basis of morphology, but also demonstrated distant relationships between some morphologically similar species. With the exception of the monotypic section Physocaulis, we were unable to find carpological traits matching sectional divisions. We hypothesize that fruit characters evolved rapidly as a result of diversification of members of the genus in different habitats.

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... Phylogenetic analyses using ITS region, although popular due to its high substitution rate and high number of copies facilitating its amplification even from old samples, have not resolved the relationships within many rapidly radiating genera (e.g. Banasiak et al., 2016;Kurzyna-Młynik et al., 2008;Piwczyński et al., 2015). The problem is not ameliorated by combining ITS and pDNA sequences. ...
... The tribe is characterized by an unprecedented array of fruit morphologies likely related to various dispersal syndromes including anemochory (dispersal by wind), barochory (by gravity), and zoochory (by animals). Recent analyses of fruit evolution within particular groups of Scandiceae have been hindered, however, by an arbitrary choice of topologies characterized by many poorly supported nodes (Banasiak et al., 2016;Piwczyński et al., 2015;Wojewódzka et al., 2019). For example, secondary ribs (protuberance of fruit wall usually without vascular bundles) are unique for subtribes Daucinae and Torilidinae and may develop into wings or spines [anatomical and morphological nomenclature according to Kljuykov et al. (2004)]. ...
... We sequenced three markers, one nuclear (ITS) and two chloroplast (rbcL and rps16 intron), used in phylogenetic inference in Apiaceae at various taxonomic levels (e.g., Banasiak et al., 2016;Downie et al., 2000;Downie & Katz-Downie, 1999;Panahi et al., 2015;Piwczyński et al., 2015;Plunkett et al., 1997). N-nc18S10 and C26A primers were used to amplify the ITS region (Wen & Zimmer, 1996), whereas chloroplast markers were amplified using a_f and a_r (Kress & Erickson, 2007; Table S3 therein) and s16exF and s16exR (Panahi et al., 2015) primers for rbcL and rps16 ...
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The angiosperm Apiaceae tribe Scandiceae includes four major clades—subtribes Daucinae, Ferulinae, Torilidinae and Scandicinae—that separated c. 20 Mya. Although all four subtribes are highly supported in molecular analyses, and morphological data indicate a sister relationship between Daucinae and Torilidinae, their branching order has not been resolved using standard Sanger multilocus data. Therefore, in this study, we test the utility of genomic RAD‐seq data in resolving deep phylogenetic relationships (up to 20 Mya) in Apiaceae subfamily Apioideae with special emphasis on tribe Scandiceae using 12 representative species. We used two bioinformatic pipelines, pyRAD and RADIS (based on STACKS), to assemble RAD‐seq data and we tested the influence of various combinations of parameters on the robustness of the inferred tree topologies. Although different data processing approaches produced alignments with various amounts of missing data, they converged to two well‐supported topologies irrespective of the phylogenetic method applied. Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups confirming, therefore, the relationship inferred from morphology. We conclude that the RAD‐seq method can be successfully used to resolve deep relationships as old as 20 Mya, within Apiaceae. We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.
... villosum complex is positioned in section Chrysocarpum, together with the clade C. aureum. The species of our interest, C. coloratum also belongs to section Chrysocarpum, clade C. aureum and is grouped within clade comprising C. aromaticum, C. atlanticum, C. azoricum, C. creticum and C. bulbosum (Piwczyński et al., 2015). ...
... Plant anatomy of C. coloratum is almost not studied. Details of the fruit structure are reported in the paper of Kowal and Latowki (1973) and Piwczyński et al. (2015). In 1971, Kowal et al. pointed out the anatomical diagnostic features of the Chaerophyllum species occurring in Poland (C. ...
... Anatomical characters of C. coloratum (own measurements) and six previously studied species: C. aromaticum, C. astrantiae, C. aureum, C. bulbosum, C. coloratum, C. hirsutum and C. temulum (Kowal et al., 1971;Yilmaz and Tekin, 2013;Piwczyński et al., 2015) was subjected to cluster analysis (UPGMA, Euclidean distance) using SynTax 2000 (Podani, 2001). The data set of 33 parameters were used: 1) average size of secretory cavities in root, 2) the ratio of the width of secondary xylem (SX) and surrounding tissues (ST) in the root, 3) size of secretory ducts in the cortex of the stem, 4) number (No) of glandular cells in secretory ducts in the cortex of stem, 5) No vascular bundles in stem, 6) No of vessels in bigger vascular bundles in stem, 7) size of secretory ducts in the pith of stem, below the bigger vascular bundles, 8) No of glandular cells in secretory ducts in the pith of stem, below the bigger vascular bundles, 9) No of subepidermal bands of collenchyma in inflorescence rays, 10) No of cell layers in collenchyma in inflorescence rays, 11) No of chlorenchyma layers in inflorescence rays, 12) parenchyma layers in inflorescence rays, 13) position of secretory ducts in the cortex of inflorescence rays, 14) size of secretory ducts in the cortex in inflorescence rays, 15) No of glandular cells in secretory ducts in the cortex in inflorescence rays, 16) size of secretory ducts in the cortex in inflorescence rays, between the ribs, 17) No of glandular cells in secretory ducts in the cortex in inflorescence rays, between the ribs, 18) No of vascular bundles in inflorescence rays, 19) presence of secretory ducts in the pith of inflorescence rays, 20) size of secretory ducts in the pith of inflorescence rays, 21) No of glandular cells in secretory ducts in the pith of inflorescence rays, 22) size of bigger secretory ducts in leaf blade, 23) size of smaller secretory ducts in leaf blade, 24) No of glandular cells in the secretory ducts in leaf blade, 25) stomata type in leaf blade, 26) No of vascular bundles in leaf petiole, 27) size of secretory ducts in leaf petiole below the collenchyma, 28) No of glandular cells in secretory ducts in leaf petiole below the collenchyma, 29) size of secretory ducts in leaf petiole next to the phloem caps below the bundles, 30) No of glandular cells in secretory ducts in leaf petiole next to the phloem caps below the bundles, 31) No of vascular bundles in leaf sheet, 32) No of cells surrounding secretory ducts in leaf sheets below the collenchyma, 33) size of secretory ducts in fruit. ...
... All but one are vertebrates. The sole exception is the fruit length, a fitness related trait, data for 33 Chaerophyllum species [Piwczyński et al., 2015]. Ten datasets from the animal kingdom are looked into. ...
... [Pabijan et al., 2012] 2 Brownian motion 3 Ornstein-Uhlenbeck with α < 0 4 Ornstein-Uhlenbeck with α > 0 5[Piwczyński et al., 2015] 6 [Diniz-Filho and Tôrres, 2002, Pavoine et al., 2005a] 7[Dray and Durfor, 2007, Garland, T., Jr. et al., 1993 8 [datasets in GEIGER R packageHarmon et al., 2008] ...
Preprint
In this paper I address the question — how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein–Uhlenbeck processes — the regression effective sample size . I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AIC c is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.
... All but one are vertebrates. The sole exception is the fruit length, a fitness related trait, data for 33 Chaerophyllum species (Piwczyński et al., 2015). Ten datasets from the animal kingdom are looked into. ...
... Hence these dynamics on the scale of the phylogeny are indistinguishable from a BM. Piwczyński et al. (2015). f Diniz-Filho and Tôrres (2002) and Pavoine et al. (2005a). ...
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Carpological anatomical characters are important in the taxonomy of Apiaceae. At present, it is necessary to include them in any critical revision of taxa of every rank, to characterize species and genera and to identify groups of related taxa. To create standardized descriptions of these taxa, we have compiled a list of taxonomically important fruit anatomical characters. This list includes 15 characters and 79 character states. Fruit anatomical characters are often constant in genera and can characterize genera or groups of closely related genera. However, the same anatomical character can occur in distant taxa. All anatomical characters are illustrated on schematic transverse sections of mericarps or in photographs.
... We only include representative samples of subtribes Scandicinae and Ferulinae. The former was subject of our earlier studies of fruit evolution ( Piwczyński et al. 2015;Spalik et al. 2001) while the latter includes only anemochorous species (Korovin 1947) and therefore does not represent any notable variation in dispersal strategy. ...
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... N-nc18S10 and C26A primers were used to am- plify the ITS region (Wen and Zimmer 1996). Details of the DNA extraction, PCR amplification and sequencing are pro- vided elsewhere ( Piwczyñski et al. 2015). BLAST searches were performed against the GenBank database at NCBI for each new DNA sequence to determine its similarity with deposited sequences. ...
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We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized. [Bayes factor; Coleoptera; Dytiscidae; marginal likelihood; model testing; posterior odds; reversible-jump MCMC; stepping-stone sampling.]
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The results of phylogenetic analyses of 1240 nrDNA ITS sequences of Apiaceae subfamily Apioideae, representing 292 genera and 959 species from all major clades of the subfamily except those most basally branching, were compared to a preexisting phylogenetic classification for the group based on several molecular markers and a smaller sampling of taxa. This was done to confirm previously defined tribal and generic limits and to identify additional major clades and genera whose monophyly and relationships can be tested in future studies. All species for which ITS data are available in Gen-Bank plus newly obtained sequences for 53 additional taxa were considered for inclusion in this study and their simultaneous analysis permitted misidentifications and other problematic sequences to be revealed. Analyses of these ITS data, in conjunction with results of recently published molecular studies, identified 41 major clades in Apioideae, of which 21 have already been recognized at the tribal or subtribal rank. No major changes to the preexisting phylogenetic classification of Apioideae are proposed, other than the recognition of additional major clades and the expansion of others to accommodate increased sampling. As noted in previous studies, many genera are not monophyletic; indeed, 18 genera are highly polyphyletic, with their members occurring in 2 to 7 major clades. Each of the 1240 accessions examined can be unambiguously assigned to a particular major clade. Resolution of relationships, as well as the formal recognition of several major clades, must await supporting data, such as that from the cpDNA trnQ(UUG)−5' trnK(UUU) intergenic spacer region. An ITS-based classification of the subfamily is proposed that enables direct and precise references to specific groups and facilitates sampling and hypothesis testing in future systematic studies.
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Of the 455 known genera in Apiaceae (Umbelliferae), 41% are monotypic and 26% comprise only two or three species each. Similarly, of the 16 genera constituting Scandiceae Spreng, subtribe Scandicinae Tausch, seven (Balansaea Boiss. & Reut., Kozlovia Lipsky, Krasnovia Schischk., Myrrhis Mill., Myrrhoides Fabr., Sphallerocarpus DC. and Todaroa Pari.) are monotypic, and two (Neoconopodium Pimenov & Kljuykov and Tinguarra Parl.) are bitypic. Phylogenetic analysis of the subtribe, using molecular (rDNA ITS), morphological and anatomical data, indicates that the number of genera may be reduced with only three, Todaroa, Sphallerocarpus and Myrrhis, retained as monotypic. Remaining taxa form eight clades that are supported by high bootstrap values and are morphologically distinct. Four of these clades (Anthriscus Pers., Geocaryum Coss., Osmorhiza Raf. and Scandix L.) are equivalent to currently recognized genera. Kozlovia, Krasnovia and Neoconopodium form a well-supported clade that may be recognized as the single genus Kozlovia, and Myrrhoides is grouped with Chaerophyllum L. Tinguarra and Athamanta L. form a monophyletic group that is well supported by analyses of morphology, fruit anatomy, and combined morphological, anatomical and ITS sequence data; however, this group is not maintained in separate analyses of ITS sequences. Similarly, the group formed by Conopodium W. D. J. Koch and Balansaea is monophyletic in morphological, anatomical, and combined analyses, but is not supported by the separate analyses of ITS sequence data. All of these groups are well delimited on the basis of fruit characters that have long been regarded as essential in umbellifer taxonomy. One new combination is proposed: Athamanta montana (Webb ex H. Christ.) Spalik, A. Wojew. & S. R. Downie.
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Background and aims Fruit structural characters have traditionally been important in the taxonomy of the family Apiaceae. Previous investigations using a limited number of taxa have shown that the carpophore may be especially useful in helping to circumscribe subfamily Azorelloideae. The present study examines, for the first time, carpophore structure in 92 species from 43 genera, representing all subfamilies of Apiaceae, and including all genera assigned to subfamily Azorelloideae. Phylogenetic interpretations are made for the first time, using all available information, and a standard terminology is proposed to describe the various character states found in carpophores.
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A phylogenetic study of Oxypolis and Ptilimnium, two small genera of tribe Oenantheae (Apiaceae: subfamily Apioideae), was carried out. Generic circumscriptions and infrageneric and infraspecific relationships were investigated through parsimony and Bayesian inference analyses of nuclear rDNA ITS and cpDNA trnQ-5′rps16 and 3′rps16-5′trnK intergenic spacer sequences. Fruit anatomical characters were also examined and used in conjunction with leaf morphology to corroborate the results of the phylogenetic analyses. Each genus as currently delimited has both compound-leaved and rachis-leaved species. Results of the phylogenetic analyses show that neither Oxypolis nor Ptilimnium is monophyletic; each genus is split into two strongly supported clades that correspond to differences in leaf morphology within the groups. Fruit anatomical characters support these splits. The fruits of compound-leaved and rachis-leaved Oxypolis species differ in the number of commissural vittae per mericarp, the branching of the vittae, and the lignification of mericarp around the seed. The fruits of compoundleaved and rachis-leaved Ptilimnium species differ in the compression of the mericarps and the development of the marginal ribs. The fruits of rachis-leaved Oxypolis and rachis-leaved Ptilimnium species also differ in the compression of the mericarps and the development of the marginal ribs. Based on analyses of molecular data and corroboration with morphological and fruit anatomical data, new circumscriptions for the genera Oxypolis and Ptilimnium are formalized. Each of the two polyphyletic genera (Oxypolis and Ptilimnium) is split, two genera (Tiedemannia and Harperella) are resurrected, and three new combinations are made.
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Generic circumscriptions and phylogenetic relationships of the Cape genera Capnophyllum , Dasispermum, and Sonderina are explored through parsimony and Bayesian inference analyses of nrDNA ITS and cpDNA rps16 intron sequences, morphology, and combined molecular and morphological data. The relationship of these genera with the North African genera Krubera and Stoibrax is also assessed. Analyses of both molecular data sets place Capnophyllum , Dasispermum , Sonderina, and the only southern African species of Stoibrax ( S. capense ) within the newly recognized Lefebvrea clade of tribe Tordylieae. Capnophyllum is strongly supported as monophyletic and is distantly related to Krubera . The monotypic genus Dasispermum and Stoibrax capense are embedded within a paraphyletic Sonderina . This complex is distantly related to the North African species of Stoibrax in tribe Apieae, in which the type species, Stoibrax dichotomum , occurs. Consequently, Dasispermum is expanded to include both Sonderina and Stoibrax capense . New combinations are formalized for Dasispermum capense , D. hispidum , D. humile , and D. tenue . An undescribed species from the Tanqua Karoo in South Africa is also closely related to Capnophyllum and the Dasispermum – Sonderina complex. The genus Scaraboides is described herein to accommodate the new species, S. manningii . This monotypic genus shares the dorsally compressed fruit and involute marginal wings with Capnophyllum, but is easily distinguished by its erect branching habit, green leaves, scabrous umbels, and fruit with indistinct median and lateral ribs, additional solitary vittae in each marginal wing, and parallel, closely spaced commissural vittae. Despite the marked fruit similarities with Capnophyllum , analyses of DNA sequence data place Scaraboides closer to the Dasispermum – Sonderina complex, with which it shares the erect habit, green (nonglaucous) leaves, and scabrous umbels.
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The Cape endemic genus Capnophyllum Gaertn. is revised. As a result of valuable recent collections and extensive fieldwork, this hitherto neglected genus was found to comprise four annual species, two of which are newly described, namely C. lutzeyeri Magee and B.-E.van Wyk, and C. macrocarpum Magee and B.-E.van Wyk. The four species are distinguished from one another by their fruit morphology (relative length of the styles, the shape and position of the stylopodium, fruit size, surface sculpturing, and the presence or absence of a sterile apical portion) and fruit anatomy (marginal wings slightly or prominently involute and secondary ribs present or absent). A comprehensive key to the species, their complete nomenclature and typification, together with complete descriptions and known geographical distributions for all the species are presented and illustrated.
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A taxonomic revision of the recircumscribed South African endemic genus Dasispermum Raf. is presented, including keys to the species, complete nomenclature, typifications, descriptions, and geographical distributions. In addition, two new species, D. grandicarpum Magee & B.-E.van Wyk and D. perennans Magee & B.-E.van Wyk, are described. Seven species of Dasispermum are now recognised and can be distinguished from one another by their habit (life history and growth form), leaf morphology (leaf texture, leaf colour and width of the ultimate leaflet segments), inflorescence structure (length of the peduncle, presence or absence and division of involucral and involucel bracts), fruit morphology (relative length of the styles, fruit size and the prominence and relative orientation of the ribs) and fruit anatomy (shape of the cells external to the vittae).
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Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.
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Theories of ecological diversification make predictions about the timing and ordering of character state changes through history. These theories are testable by "reconstructing" ancestor states using phylogenetic trees and measurements of contemporary species. Here we use maximum likelihood to estimate and evaluate the accuracy of ancestor reconstructions. We present likelihoods of discrete ancestor states and derive probability distributions for continuous ancestral traits. The methods are applied to several examples: diets of ancestral Darwin's finches; origin of inquilinism in gall wasps; microhabitat partitioning and body size evolution in scrubwrens; digestive enzyme evolution in artiodactyl mammals; origin of a sexually selected male trait, the sword, in platies and swordtails; and evolution of specialization in Anolis lizards. When changes between discrete character states are rare, the maximum-likelihood results are similar to parsimony estimates. In this case the accuracy of estimates is often high, with the exception of some nodes deep in the tree. If change is frequent then reconstructions are highly uncertain, especially of distant ancestors. Ancestor states for continuous traits are typically highly uncertain. We conclude that measures of uncertainty are useful and should always be provided, despite simplistic assumptions about the probabilistic models that underlie them. If uncertainty is too high, reconstruction should be abandoned in favor of approaches that fit different models of trait evolution to species data and phylogenetic trees, taking into account the range of ancestor states permitted by the data.
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The phenomenon of correlation pleiades, i.e., the presence of correlations between some quantitative characteristics of certain parts of an organism and at the same time by the absence of correlations between these and the other parts demonstrates the independence of certain developmental processes with respect to other processes within the organism. The study of correlation sets makes it possible to establish the degree of such independence. The adoption of a quantitative criterion provides an adequate basis for the comparative method in the study of stabilizing selection. Nineteen species of herbaceous plants have been studied in order to determine the variability in the degree of dependence between the dimensions of different parts of an organism. It has been established that twelve species have correlation pleiades, while seven species have no correlation pleiades with respect to the dimensions of analogous parts. In all the instances of existence of pleiades it was the flower that had become free of the correlation interdependences within the plant organism. Existence of correlation pleiades is associated with the mode of pollen transfer, involving the presence of specific insect pollinators, with adaptations to localize the pollen deposit on some definite part of the body of the pollinating insect, and with at least one of the structural features providing for such localization (zygomorphism, presence of tubular parts, lateral position of flowers, oligomerization and a rigid fixation of the number of homologous parts of a flower). Insects were the selective factor stabilizing the dimensions of those parts of flowers which participate in the process of the precise localization of pollen on the insect body. Stabilizing selection of flower dimensions created correlation pleiades for reproductive organs, as well as for vegetative parts of the same organism. The general principle underlying the origin of developmental homeostasis in the process of evolution is the discrepancy between the agencies participating in the formation of the character and the selective forces determining its function. The same principle is responsible for the origin of correlation pleiades.
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— We studied sequence variation in 16S rDNA in 204 individuals from 37 populations of the land snail Candidula unifasciata (Poiret 1801) across the core species range in France, Switzerland, and Germany. Phylogeographic, nested clade, and coalescence analyses were used to elucidate the species evolutionary history. The study revealed the presence of two major evolutionary lineages that evolved in separate refuges in southeast France as result of previous fragmentation during the Pleistocene. Applying a recent extension of the nested clade analysis (Templeton 2001), we inferred that range expansions along river valleys in independent corridors to the north led eventually to a secondary contact zone of the major clades around the Geneva Basin. There is evidence supporting the idea that the formation of the secondary contact zone and the colonization of Germany might be postglacial events. The phylogeographic history inferred for C. unifasciata differs from general biogeographic patterns of postglacial colonization previously identified for other taxa, and it might represent a common model for species with restricted dispersal.
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Article
Modern phylogenetic comparative biology uses data from the relationships between species (phylogeny) combined with comparative information for phenotypic traits to draw model‐based statistical inferences about the evolutionary past. Recent years have seen phylogeny methods for evolutionary inference become central in the study of organic evolution.Here, I present two different graphical methods for visualizing phenotypic evolution on the tree. Method 1 is a new approach for plotting the posterior density of stochastically mapped character histories for a binary (two‐state) phenotypic trait on a phylogeny. Method 2 is a closely related technique that uses ancestral character estimation to visualize historical character states for a continuous trait along the branches of a tree.One shortcoming of Method 2 is that by mapping the point estimates of ancestral states along the branches of the tree, we have effectively ignored the uncertainty associated with ancestral character estimation of continuous traits. To alleviate this issue, I propose a new method for visualizing ancestral state uncertainty using a type of projection of the tree into morphospace called a ‘traitgram.’All of these approaches should prove useful in summarizing complex comparative inferences about ancestral character reconstruction. They are implemented in the freely available and open‐source R phylogenetics package ‘phytools.’
Article
1. Here, I present a new, multifunctional phylogenetics package, phytools, for the R statistical computing environment. 2. The focus of the package is on methods for phylogenetic comparative biology; however, it also includes tools for tree inference, phylogeny input/output, plotting, manipulation and several other tasks. 3. I describe and tabulate the major methods implemented in phytools, and in addition provide some demonstration of its use in the form of two illustrative examples. 4. Finally, I conclude by briefly describing an active web-log that I use to document present and future developments for phytools. I also note other web resources for phylogenetics in the R computational environment.
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Apiaceae (Umbelliferae) is a large angiosperm family that includes many medicinally important species. The ability to identify these species and their adulterants is important, yet difficult to do so because of their subtle fruit morphological differences and often lack of diagnostic features in preserved specimens. Moreover, dried roots are often the official medical organs, making visual identification to species almost impossible. DNA barcoding has been proposed as a powerful taxonomic tool for species identification. The Consortium for the Barcode of Life (CBOL) Plant Working Group has recommended the combination of rbcL+matK as the core plant barcode. Recently, the China Plant BOL Group proposed that the nuclear ribosomal DNA internal transcribed spacer (ITS), as well as a subset of this marker (ITS2), be incorporated alongside rbcL+matK into the core barcode for seed plants, particularly angiosperms. In this study, we assess the effectiveness of these four markers plus psbA-trnH as Apiaceae barcodes. A total of 6,032 sequences representing 1,957 species in 385 diverse genera were sampled, of which 211 sequences from 50 individuals (representing 7 species) were newly obtained. Of these five markers, ITS and ITS2 showed superior results in intra- and interspecific divergence and DNA barcoding gap assessments. For the matched dataset (173 samples representing 45 species in 5 genera), the ITS locus had the highest identification efficiency (73.3%), yet ITS2 also performed relatively well with 66.7% identification efficiency. The identification efficiency increased to 82.2% when using an ITS+psbA-trnH marker combination (ITS2+psbA-trnH was 80%), which was significantly higher than that of rbcL+matK (40%). For the full sample dataset (3,052 ITS sequences, 3,732 ITS2 sequences, 1,011 psbA-trnH sequences, 567 matK sequences, and 566 rbcL sequences), ITS, ITS2, psbA-trnH, matK, and rbcL had 70.0%, 64.3%, 49.5%, 38.6%, and 32.1% discrimination abilities, respectively. These results confirm that ITS or its subset ITS2 be incorporated into the core barcode for Apiaceae and that the combination of ITS/ITS2+psbA-trnH has much potential value as a powerful, standard DNA barcode for Apiaceae identification.This article is protected by copyright. All rights reserved.
Article
Speciation is a fundamental evolutionary process, the knowledge of which is crucial for understanding the origins of biodiversity. Genomic approaches are an increasingly important aspect of this research field. We review current understanding of genome-wide effects of accumulating reproductive isolation and of genomic properties that influence the process of speciation. Building on this work, we identify emergent trends and gaps in our understanding, propose new approaches to more fully integrate genomics into speciation research, translate speciation theory into hypotheses that are testable using genomic tools and provide an integrative definition of the field of speciation genomics.
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Two new species from the eastern Himalaya are described, one in Physospermopsis and one in Sinocarum. Additionally, new combinations are proposed for the Indian area in Bupleurum. Schulzia, Meeboldia, Sinocarum, Pimpinellu, and Angelica. © 1991, Trustees of the Royal Botanic Garden Edinburgh. All rights reserved.
Article
Marlothiella gummifera is a small perennial shrublet endemic to the Skeleton Coast of Namibia. Surprisingly it was found that the general fruit morphology agrees with that typically found in Saniculoideae and other basally diverging taxa. It is remarkable in the combination of a compound umbellate inflorescence, slightly heteromorphic fruits and dispersed crystals (typical of basally divergent genera of the subfamily Apioideae) with several characters typical of the subfamily Saniculoideae: large rib ducts, no vittae, unicellular stellate trichomes (not yet observed in any other genus of the family), and ventral vascular bundles that are poorly developed or absent. New insights into the morphology and possible systematic affinities of this poorly known monotypic genus are presented, together with a detailed taxonomic revision.
Article
Theories of ecological diversification make predictions about the timing and ordering of character state changes through history. These theories are testable by "reconstructing" ancestor states using phylogenetic trees and measurements of contemporary species. Here we use maximum likelihood to estimate and evaluate the accuracy of ancestor reconstructions. We present likelihoods of discrete ancestor states and derive probability distributions for continuous ancestral traits. The methods are applied to several examples: diets of ancestral Darwin's finches; origin of inquilinism in gall wasps; microhabitat partitioning and body size evolution in scrubwrens; digestive enzyme evolution in artiodactyl mammals; origin of a sexually selected male trait, the sword, in platies and swordtails; and evolution of specialization in Anolis lizards. When changes between discrete character states are rare, the maximum likelihood results are similar to parsimony estimates. In this case the accuracy of estimates is often high, with the exception of some nodes deep in the tree. If change is frequent then reconstructions are highly uncertain, especially of distant ancestors. Ancestor states for continuous traits are typically highly uncertain. We conclude that measures of uncertainty are useful and should always be provided, despite simplistic assumptions about the probabilistic models that underlie them. If uncertainty is too high, reconstruction should be abandoned in favor of approaches that fit different models of trait evolution to species data and phylogenetic trees, taking into account the range of ancestor states permitted by the data.
Article
The mericarps of Eryngium (Apiaceae-Saniculoideae) differ in the locations of the oil ducts, which are dorsal/lateral in subg. Eryngium and dorsal/ventral in all other subgenera. For subg. Eryngium, a conspicuous lignified ventral band of the mericarp is characteristic. Fruit wings are present in subg. Eryngium and subg. Monocotyloidea. In subg. Eryngium, they consist of an oil duct, vascular bundles, the lateral part of the lignified ventral band, and parenchymatic carpel tissue. In subg. Monocotyloidea, the fruit wings are formed by lateral scales and consist mainly of parenchymatic tissue without oil ducts or lignifications. The scales are unequal in the subgg. Eryngium, Monocotyloidea, and Semiaquatica, and equal in most species of subg. Foetida and in subg. Ilicifolia. The latter has extremely specialized fruits with the oil ducts located in the ribs and the wings. The petals conspicuously differ in subg. Eryngium from the other subgenera. A distinct type was found in subg. Foetida. The subg. Eryngium is separated in nearly all character groups and may deserve generic rank. From the other subgenera, subg. Monocotyloidea is well defined, whereas subgg. Semiaquatica and Foetida are less clearly delimited from each other. A comparison with molecular results supports the two lineages and the delimitation of subg. Monocotyloidea.
Article
Aim Four genera of the plant family Apiaceae subfamily Apioideae –Apium, Chaerophyllum, Daucus and Lilaeopsis– are characterized by amphitropic and amphiantarctic distribution patterns, and in Australasia the subfamily is also represented by the tribe Aciphylleae. We infer the molecular ages of achieving amphitropic distribution for these lineages, reconstruct the biogeographical histories of Apium, Chaerophyllum, Daucus and Lilaeopsis, and identify the sister group of Aciphylleae. Location Worldwide, with an emphasis on South America and Australasia. Methods Divergence times were estimated employing a Bayesian approach (beast) with fossil pollen of basal apioids as calibration points and using a data set of nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) sequences from 284 accessions of Apioideae. Additionally, maximum-likelihood analyses were performed for data subsets comprising Apium, Daucus and Lilaeopsis. For Chaerophyllum, maximum-likelihood and beast analyses were carried out using combined chloroplast DNA and ITS data. Biogeographical scenarios were inferred using diva and lagrange. Results The sister group to Aciphylleae is the Sino-Himalayan Acronema clade and the divergence between these two lineages is dated at 34.8 Ma, whereas the radiation of Aciphylleae started 11.0 Ma. A Northern Hemispheric origin was inferred for Apium, Chaerophyllum and Daucus, whereas Lilaeopsis probably originated in South America following a dispersal of its ancestor from North America. Chaerophyllum, Daucus and Lilaeopsis dispersed to the Southern Hemisphere at 5.3, 7.0 and 27.9 Ma, respectively. For Apium, two dispersals from Europe were inferred: to South America at 6.3 Ma, and to southern Africa at 3.9 Ma. The taxa migrated along the land masses of North and South America (Daucus, Lilaeopsis) and Africa (Apium) or by direct transoceanic dispersals through the Atlantic (Apium) or the Pacific (Chaerophyllum). Within the Southern Hemisphere they dispersed both westwards (Apium, Daucus, Lilaeopsis) and eastwards (Chaerophyllum, Lilaeopsis). For Chaerophyllum and Lilaeopsis, subsequent dispersal events to the Northern Hemisphere were also inferred. Main conclusions Similar timing, contrasted with the diversity of migration routes, suggests that the dispersal events of these umbellifer taxa (and many other amphitropic amphiantarctic genera) were facilitated by favourable ecological conditions in the Southern Hemisphere (climatic cooling of the late Palaeogene/early Neogene) rather than by increased dispersal opportunities.
Article
We investigated the anatomical expression of leaf traits in hybrids between evergreen Vaccinium vitis-idaea and deciduous V. myrtillus. We compared parents from four populations with their respective F1 hybrids and tested whether (i) transgression can be the source of novel anatomical traits in hybrids; (ii) expression of transgressive traits is more probable for traits with similar values in parents and intermediate for more distinct values, as predicted by theory; and (iii) independent origin of hybrids leads to identical trait expression profiles among populations. We found that anatomical leaf traits can be divided into four categories based on their similarity to parents: intermediate, parental-like, transgressive and non-significant. Contrary to the common view, parental-like trait values were equally important in shaping the hybrid profile, as were intermediate traits. Transgression was revealed in 17/144 cases and concerned mainly cell and tissue sizes. As predicted by theory, we observed transgressive segregation more often when there was little phenotypic divergence, but intermediate values when parental traits were differentiated. It is likely that cell and tissue sizes are phylogenetically more conserved due to stabilising selection, whereas traits such as leaf thickness and volume fraction of the intercellular spaces, showing a consistent intermediate pattern across populations, are more susceptible to directional selection. Hybrid populations showed little similarity in expression profile, with only three traits identically expressed across all populations. Thus local adaptation of parental species and specific genetic background may be of importance.
Article
Burr size is the major factor affecting variation in the intensity of predation by two species of insect on the seeds of the cocklebur, Xanthium strumarium. Mean burr size varied among 10 adjacent local populations studied over three years, as did intensity of seed predation. Seed predation was more intense in populations with low mean burr length and declined linearly with increasing burr length under field and experimental conditions. Seed predation thus is a selective factor influencing the evolution of both burr size and correlated protective characteristics such as burr spine length and wall thickness. As in some other plants, morphological rather than chemical features appear to pose the major barrier to attack by host-specific seed predators. The advantage of more highly developed tissues protecting seeds may occur at the expense of total seed production.
Article
Species boundaries and phylogenetic relationships of 17 taxa ofAnthriscus (Apiaceae), with special emphasis on the critical sect.Cacosciadium, were explored using morphological data with principal component analysis, phenetics, and phylogenetics. The analyses did not provide satisfactory resolution of taxa from sect.Cacosciadium and only four species were retained. The total number of species was reduced to nine. Sect.Cacosciadium is distinguished by only two synapomorphies while sects.Anthriscus andCaroides are better supported. Present geographic and ecological variation suggests that the radiation ofAnthriscus occurred through divergence of peripheral isolated populations adapting to different habitats: high montane meadows and screes, shady climax forests, and seasonally dry habitats at lower altitudes. The adaptive significance of particular morphological traits is discussed.
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Unlabelled: Reflecting its continuously increasing versatility and functionality, the popularity of the ape (analysis of phylogenetics and evolution) software package has grown steadily over the years. Among its features, it has a strong distance-based component allowing the user to compute distances from aligned DNA sequences based on most methods from the literature and also build phylogenetic trees from them. However, even data generated with modern genomic approaches can fail to give rise to sufficiently reliable distance estimates. One way to overcome this problem is to exclude such estimates from data analysis giving rise to an incomplete distance data set (as opposed to a complete one). So far their analysis has been out of reach for ape. To remedy this, we have incorporated into ape several methods from the literature for phylogenetic inference from incomplete distance matrices. In addition, we have also extended ape's repertoire for phylogenetic inference from complete distances, added a new object class to efficiently encode sets of splits of taxa, and extended the functionality of some of its existing functions. Availability: ape is distributed through the Comprehensive R Archive Network: http://cran.r-project.org/web/packages/ape/index.html Further information may be found at http://ape.mpl.ird.fr/pegas/
Article
Low temperature was found to induce the accumulation of anthocyanins in Japanese parsley (Oenanthe stolonifera, DC.), and cyanidin was identified as their major component. Among three cultivars, cv. Jizeri responded most strongly to low-temperature stress, accumulating four-fold higher anthocyanin levels in leaves of plants grown at 12 °C compared with those at 25 °C. RNA gel-blot analysis showed that expression of the dihydroflavonol 4-reductase gene (dfr) was especially affected by low temperature. In the cv. Jizeri, the dfr transcripts were rapidly induced 6 to 7 days after transfer to low-temperature conditions, whereas dfr expression was scarcely observed in the non-pigmented cultivar (cv. Matsuemidori). The phenylalanine ammonia-lyase gene (pal) and chalcone synthase gene (chs) seemed to be expressed coordinately at both 12 °C and 25 °C in both cultivars. The pal and chs genes comprised multigene families, while the dfr gene was detected as being unique. These results suggest that the mechanism regulating dfr expression differs from those for pal and chs expression in Japanese parsley, and that dfr expression is a key step in the regulation by low-temperature stress in the temperature-sensitive cultivars of Japanese parsley.
Article
Herbivore damage is generally detrimental to plant fitness, and the evolu- tionary response of plant populations to damage can involve either increased resistance or increased tolerance. While characters that contribute to resistance, such as secondary chem- icals and trichomes, are relatively well understood, characters that contribute to a plant's ability to tolerate damage have received much less attention. Using Helianthus annuus (wild sunflower) and simulated damage of Haplorhynchites aeneus (head-clipping weevil) as a model system, we examined morphological characters and developmental processes that contribute to compensatory ability. We performed a factorial experiment that included three levels of damage (none, the first two, or the first four inflorescences were clipped with scissors) and eight sires each mated to four dams. We found that plants compensated fully for simulated head-clipper damage and that there was no variation among plant families in compensatory ability: seed production and mean seed mass did not vary among treat- ments, and sire X treatment interactions were not significant. Plants used four mechanisms to compensate for damage: (1) Clipped plants produced significantly more inflorescences than unclipped plants. Plants produced these additional inflorescences on higher order branches at the end of the flowering season. (2) Clipped plants filled significantly more seeds in their remaining heads than did unclipped plants. (3) Clipped plants, because they effectively flowered later than unclipped plants, were less susceptible to damage by seed- feeding herbivores other than Haplorhynchites. (4) In later heads, seed size was greater on clipped plants, which allowed mean seed size to be maintained in clipped plants. Although there was genetic variation among the families used in this experiment for most of the characters associated with compensation for damage (seed number, mean seed size, mean flowering date, length of the flowering period, and branching morphology), in analyses of these characters, no sire X treatment interactions were significant indicating that all of the families relied on similar mechanisms to compensate for damage.