Evgeny V. Mavrodiev

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae).

Polyploidy, or whole genome duplication, has played a major role in the evolution of many eukaryotic lineages. Although the prevalence of polyploidy in plants is well documented, the molecular and cytological consequences are understood largely from newly formed polyploids (neopolyploids) that have been grown experimentally. Classical cytological and molecular cytogenetic studies both have shown that experimental neoallopolyploids often have meiotic irregularities, producing chromosomally variable gametes and progeny; however, little is known about the extent or duration of chromosomal variation in natural neoallopolyploid populations. We report the results of a molecular cytogenetic study on natural populations of a neoallopolyploid, Tragopogon miscellus, which formed multiple times in the past 80 y. Using genomic and fluorescence in situ hybridization, we uncovered massive and repeated patterns of chromosomal variation in all populations. No population was fixed for a particular karyotype; 76% of the individuals showed intergenomic translocations, and 69% were aneuploid for one or more chromosomes. Importantly, 85% of plants exhibiting aneuploidy still had the expected chromosome number, mostly through reciprocal monosomy-trisomy of homeologous chromosomes (1:3 copies) or nullisomy-tetrasomy (0:4 copies). The extensive chromosomal variation still present after ca. 40 generations in this biennial species suggests that substantial and prolonged chromosomal instability might be common in natural populations after whole genome duplication. A protracted period of genome instability in neoallopolyploids may increase opportunities for alterations to genome structure, losses of coding and noncoding DNA, and changes in gene expression.

Molecular phylogeny of Atripliceae (Chenopodioideae, Chenopodiaceae): Implications for systematics, biogeography, flower and fruit evolution, and the origin of C4 photosynthesis.

UNLABELLED PREMISE OF THE STUDY Atripliceae (Chenopodiaceae), including Atriplex (300 spp.) as the largest genus of the family, are an ecologically important group of steppes and semideserts worldwide. Relationships in Atripliceae are poorly understood due to obscure and potentially convergent morphological characters. • METHODS Using sequence variation of two chloroplast markers (rbcL gene, atpB-rbcL spacer) and one nrDNA marker (ITS) analyzed with BEAST, we investigated the systematics and biogeography of Atripliceae. We surveyed flower morphology and fruit anatomy to study the evolution of flowers and fruits in the tribe. • KEY RESULTS Female flowers with persistent foliar cover (the diagnostic character of traditional Atripliceae) evolved three times in Chenopodioideae, in Atripliceae s.s., Axyrideae, and Spinacia. Atripliceae s.s. started to diversify during the Early Miocene in Eurasia, separating into the Archiatriplex and the Atriplex clades. The former consists of eight species-poor, disjunct, and morphologically heterogeneous genera and is likely a relictual lineage. The Atriplex clade comprises the majority of species and evolved one C(4) lineage 14.1-10.5 Ma, which diversified rapidly worldwide. The C(4) Atriplex entered North America during the Middle/Late Miocene and spread to South America subsequently. Australia was colonized by two C(4) lineages both arriving during the Late Miocene. One of them diversified rapidly, giving rise to most Australian Atriplex species. • CONCLUSIONS Atripliceae s.s. comprise Archiatriplex, Atriplex, Exomis, Extriplex, Grayia, Halimione, Holmbergia, Manochlamys, Proatriplex, and Stutzia. Microgynoecium is included based on morphology but only weak molecular support. Axyris, Krascheninnikovia, and Ceratocarpus (here described as Axyrideae) and Spinacia are excluded from Atripliceae.

ITS and ETS Sequence Data and Phylogeny Reconstruction in Allopolyploids and Hybrids

Abstract The impact of unknowingly including a hybrid or an allopolyploid in which rDNA homogenization (via gene loss, concerted evolution, or some other mechanism) has not occurred to completion in a phylogenetic analysis of internal transcribed spacer (ITS) or external transcribed spacer (ETS) sequences is unclear. To investigate the impact of polymorphic sites on phylogeny reconstruction, we used ITS and ETS sequence data for diploids and allotetraploids in Tragopogon, as well as ITS data for diploid and allopolyploid species of Paeonia and Glycine, and for diploids and their hybrids in Rubus. Only very general predictions can be made regarding the placement of these polymorphic sequences. The polymorphic sequences of hybrids and allopolyploids appear (1) with a diploid parent (but not necessarily the one with which it shares more apomorphies), (2) at or near the base of the clade containing one or both parents, or (3) in a basal position relative to all other ingroup taxa in the data set. The inclusion of a polymorphic sequence may be accompanied by an increase in the number of shortest trees, less resolution in the strict consensus, and a decrease in bootstrap support for some nodes; CI and RI values are little, if at all, affected. In no case did the addition of a sequence from a hybrid or allopolyploid alter the overall topology in a major way. Our results generally parallel those of phylogenetic studies that include F1 hybrids and their parents and use morphology.

Are polyploids really evolutionary dead-ends (again)? A critical reappraisal of Mayrose et al. (2011)

Throughout the past century, hybridization and polyploidization have variously been viewed as drivers of biodiversity (e.g. Arnold, 1997) or evolutionary noise, unimportant to the main processes of evolution (e.g. Stebbins, 1950; Wagner, 1970). Wagner (1970) argued that while polyploids have always existed, they have never diversified or played a major role in the evolution of plants, and that the study of polyploidy (as well as inbreeding, apomixis, and hybridization) has led researchers to be ‘carried away with side branches and blind alleys that go nowhere’. However, the use of molecular tools revolutionized the study of polyploidy, revealing that a given polyploid species often forms multiple times (reviewed in Soltis & Soltis, 1993, 1999, 2000, 2009). The realization that recurrent polyploidization from genetically differentiated parents is the rule that shattered the earlier perceptions of polyploids as genetically depauperate (Stebbins, 1950; Wagner, 1970). Because of multiple origins, polyploid species can maintain high levels of segregating genetic variation through the incorporation of genetic diversity from multiple populations of their diploid progenitors (e.g. Soltis & Soltis, 1993, 1999, 2000; Tate et al., 2005). Numerous studies have also shown that polyploid genomes are highly dynamic, with enormous potential for generating novel genetic variation (e.g. Gaeta et al., 2007; Doyle et al., 2008; Leitch & Leitch, 2008; Flagel & Wendel, 2009; Hawkins et al., 2009; Chester et al., 2012; Hao et al., 2013; Roulin et al., 2013). Furthermore, genomic studies have also revealed numerous ancient polyploidy events across the angiosperms (e.g. Vision et al., 2000; Bowers et al., 2003; Blanc &Wolfe, 2004; Paterson et al., 2004; Schlueter et al., 2004; Van de Peer & Meyer, 2005; Cannon et al., 2006; Cui et al., 2006; Tuskan et al., 2006; Jaillon et al., 2007; Barker et al., 2008, 2009; Lyons et al., 2008; Ming et al., 2008; Shi et al., 2010; Van de Peer, 2011; Jiao et al., 2012; McKain et al., 2012; Tayale & Parisod, 2013; reviewed in Soltis et al., 2009); all angiosperms have undergone at least one round of polyploidy (e.g. Jiao et al., 2011; Amborella Genome Consortium, 2013). Polyploidy is now viewed not as a mere side branch of evolution, but as a major mechanism of evolution and diversification.

Synthetic polyploids of Tragopogon miscellus and T. mirus (Asteraceae): 60 Years after Ownbey’s discovery

In plants, polyploidy has been a significant evolutionary force on both recent and ancient time scales. In 1950, Ownbey reported two newly formed Tragopogon allopolyploids in the northwestern United States. We have made the first synthetic lines of T. mirus and T. miscellus using T. dubius, T. porrifolius, and T. pratensis as parents and colchicine treatment of F(1) hybrids. We also produced allotetraploids between T. porrifolius and T. pratensis, which are not known from nature. We report on the crossability between the diploids, as well as the inflorescence morphology, pollen size, meiotic behavior, and fertility of the synthetic polyploids. Morphologically, the synthetics resemble the natural polyploids with short- and long-liguled forms of T. miscellus resulting when T. pratensis and T. dubius are reciprocally crossed. Synthetic T. mirus was also formed reciprocally, but without any obvious morphological differences resulting from the direction of the cross. Of the 27 original crosses that yielded 171 hybrid individuals, 18 of these lineages have persisted to produce 386 S(1) progeny; each of these lineages has produced S(2) seed that are viable. The successful generation of these synthetic polyploids offers the opportunity for detailed comparative studies of natural and synthetic polyploids within a nonmodel system.

Phylogenetic relationships and character evolution analysis of Saxifragales using a supermatrix approach

UNLABELLED PREMISE OF THE STUDY We sought novel evolutionary insights for the highly diverse Saxifragales by constructing a large phylogenetic tree encompassing 36.8% of the species-level biodiversity. • METHODS We built a phylogenetic tree for 909 species of Saxifragales and used this hypothesis to examine character evolution for annual or perennial habit, woody or herbaceous habit, ovary position, petal number, carpel number, and stamen to petal ratio. We employed likelihood approaches to investigate the effect of habit and life history on speciation and extinction within this clade. • KEY RESULTS Two major shifts occurred from a woody ancestor to the herbaceous habit, with multiple secondary changes from herbaceous to woody. Transitions among superior, subinferior, and inferior ovaries appear equiprobable. A major increase in petal number is correlated with a large increase in carpel number; these increases have co-occurred multiple times in Crassulaceae. Perennial or woody lineages have higher rates of speciation than annual or herbaceous ones, but higher probabilities of extinction offset these differences. Hence, net diversification rates are highest for annual, herbaceous lineages and lowest for woody perennials. The shift from annuality to perenniality in herbaceous taxa is frequent. Conversely, woody perennial lineages to woody annual transitions are infrequent; if they occur, the woody annual state is left immediately. • CONCLUSIONS The large tree provides new insights into character evolution that are not obvious with smaller trees. Our results indicate that in some cases the evolution of angiosperms might be conditioned by constraints that have been so far overlooked.

How to Handle Speciose Clades? Mass Taxon-Sampling as a Strategy towards Illuminating the Natural History of Campanula (Campanuloideae)

Background Speciose clades usually harbor species with a broad spectrum of adaptive strategies and complex distribution patterns, and thus constitute ideal systems to disentangle biotic and abiotic causes underlying species diversification. The delimitation of such study systems to test evolutionary hypotheses is difficult because they often rely on artificial genus concepts as starting points. One of the most prominent examples is the bellflower genus Campanula with some 420 species, but up to 600 species when including all lineages to which Campanula is paraphyletic. We generated a large alignment of petD group II intron sequences to include more than 70% of described species as a reference. By comparison with partial data sets we could then assess the impact of selective taxon sampling strategies on phylogenetic reconstruction and subsequent evolutionary conclusions. Methodology/Principal Findings Phylogenetic analyses based on maximum parsimony (PAUP, PRAP), Bayesian inference (MrBayes), and maximum likelihood (RAxML) were first carried out on the large reference data set (D680). Parameters including tree topology, branch support, and age estimates, were then compared to those obtained from smaller data sets resulting from “classification-guided” (D088) and “phylogeny-guided sampling” (D101). Analyses of D088 failed to fully recover the phylogenetic diversity in Campanula, whereas D101 inferred significantly different branch support and age estimates. Conclusions/Significance A short genomic region with high phylogenetic utility allowed us to easily generate a comprehensive phylogenetic framework for the speciose Campanula clade. Our approach recovered 17 well-supported and circumscribed sub-lineages. Knowing these will be instrumental for developing more specific evolutionary hypotheses and guide future research, we highlight the predictive value of a mass taxon-sampling strategy as a first essential step towards illuminating the detailed evolutionary history of diverse clades.

PHYLOGENY OF TRAGOPOGON L. (ASTERACEAE) BASED ON INTERNAL AND EXTERNAL TRANSCRIBED SPACER SEQUENCE DATA

Tragopogon L. (Lactuceae, Cichorioideae, Scorzonerinae) is an Old World genus of ca. 150 species. To elucidate relationships in this poorly understood genus, we analyzed internal and external transcribed spacer sequences (ITS and ETS, respectively) from 59 species from 14 of the 17 sections recognized by Borisova. Podospermum and Lactuca were used as outgroups. ITS and ETS sequence data provide strong support for the monophyly of Tragopogon under parsimony optimality criteria. Sequence data also support the monophyly of several of the recognized sections within Tragopogon, including the sections Tragopogon, Majores, Hebecarpus, Chromopappus, and Collini. However, the circumscriptions of these groups are often altered from the taxonomic treatment of Borisova. Most members of the recognized sections Brevirostres and Profundisulcati appear within the Brevirostres and Profundisulcati clades, respectively. Species of section Nikitinia are also included in the Brevirostres clade. Sequence data also provide evidence for an Angustissimi clade of T. pusillus, T. filifolius, diploid T. latifolius ( \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape

Does Phylogenetic Distance Between Parental Genomes Govern the Success of Polyploids

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