A worldwide molecular phylogeny and classification of the leafy spurges, Euphorbia subgenus Esula (Euphorbiaceae)

The leafy spurges, Euphorbia subg. Esula, make up one of four main lineages in Euphorbia. The subgenus comprises about 480 species, most of which are annual or perennial herbs, but with a small number of dendroid shrubs and nearly leafless, pencilâ stemmed succulents as well. The subgenus constitutes the primary northern temperate radiation in Euphorbia. While the subgenus is most diverse from central Asia to the Mediterranean region, members of the group also occur in Africa, in the Indoâ Pacific region, and in the New World. We have assembled the largest worldwide sampling of the group to date (273 spp.), representing most of the taxonomic and geographic breadth of the subgenus. We performed phylogenetic analyses of sequence data from the nuclear ribosomal ITS and plastid ndhF regions. Our individual and combined analyses produced wellâ resolved phylogenies that confirm many of the previously recognized clades and also establish a number of novel groupings and placements of previously enigmatic species. Euphorbia subg. Esula has a clear Eurasian center of diversity, and we provide evidence for four independent arrivals to the New World and three separate colonizations of tropical and southern Africa. One of the latter groups further extends to Madagascar and New Zealand, and to more isolated islands such as Réunion and Samoa. Our results confirm that the dendroid shrub and stemâ succulent growth forms are derived conditions in E. subg. Esula. Stemâ succulents arose twice in the subgenus and dendroid shrubs three times. Based on the molecular phylogeny, we propose a new classification for E. subg. Esula that recognizes 21 sections (four of them newly described and two elevated from subsectional rank), and we place over 95% of the accepted species in the subgenus into this new classification.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/146962/1/tax6221.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/146962/2/tax6221-sup-004-pdf.pd

Estudis filogenètics i filogeogràfics de la tribu Cardueae i el gènere Euphorbia

[cat] La tesi doctoral té com a eixos vertebradors la sistemàtica molecular, la biogeografia i la filogeografia molecular. S’han seleccionat dos grups de plantes per les interessants qüestions que presenten per resoldre i perquè ens han permès aplicar els mètodes més actuals i contrastar els resultats amb les propostes tradicionals basades en caràcters morfològics. Els grups seleccionats són: una part del gènere Euphorbia (Euphorbiaceae) i la tribu Cardueae (Compositae). En el cas del gènere Euphorbia, s’ha investigat el subgènere Esula i en concret el grup Pachycladae. La circumscripció i les afinitats filogenètiques d’aquest grup amb d’altres espècies relacionades s’han resolt en el primer article de la tesis mitjançant els mètodes de Màxima Parsimònia i Inferència Bayesiana d’anàlisi de seqüències nuclears i cloroplàstiques. Es redefineix la secció Aphyllis incloent les espècies de l’est i sud d’Àfrica i la península Aràbiga tradicionalment classificades en la secció Tirucalli dins el complex d’E. mauritanica i les espècies macaronèsiques del grup Pachycladae. La distribució dijunta presentada per la secció Aphyllis és un exemple més del patró fitogeogràfic anomenat Rand Flora, que comprèn grups de plantes amb una distribució disjunta entre la Macaronèsia, l’est i sud d’Àfrica i el sud de la península Aràbiga. En el cas de la secció Aphyllis, aquesta disjunció s’explica per un fenòmen de vicariança produït per la fragmentació d’una flora continua al nord d’Àfrica causada per l’aridificació del medi durant el Miocè-Pliocè. En un segon article, s’ha realitzat un estudi filogeogràfic i taxonòmic de les 11 espècies macaronèsiques de la secció Aphyllis utilitzant els marcadors AFLP. Excloent E. tuckeyana, obtenim una estructura genètica clara en dos grups que corresponen a dos complexes prèviament definits per caràcters morfològics i preferències ecològiques: els complexes d’E. atropurpurea i E. lamarckii. Euphorbia aphylla es resol com a basal dels dos complexes, suggerint una direcció de la dispersió per la Macaronesia de sud a nord, des de les Illes Canàries. Diversos fenòmens de colonització posterior cap al continent expliquen la presència d’E. regis-jubae a la costa atlàntica del Marroc i d’ E. pedroi a la costa atlàntica de Portugal. Totes les anàlisis realitzades revelen que E. pedroi forma part del patrimoni genètic d’E. regis-jubae. Tot i així, recomanem mantenir l’entitat taxonòmica d’E. pedroi per la seva diferenciació morfològica i el seu aïllament geogràfic respecte les poblacions d’E. regis-jubae. En el cas de la tribu Cardueae, diferents filogènies moleculars prèviament publicades no arribaven a resoldre les relacions filogenètiques entre les seves subtribus. El tercer article de la tesis té com a objectius construir una nueva filogènia molecular incloent més marcadors moleculars i un mostreig més exhaustiu per tal de resoldre les relacions filogenètiques entre les subtribus. La subtribu Cardopatiinae es resol com a grup germana a la resta, amb la subtribu Carlininae divergint en segon lloc, seguida per la subtribu Echinopsinae. La darrera clada està formada pel complex Carduinae-Centaureinae. S’ha realitzat també una datació molecular i una reconstrucció biogeogràfica de la tribu, per tal d’estimar l’edat de divergència dels principals fenòmens d’especiació i per tal d’inferir les àrees ancestrals de distribució de la tribu, que presenta una distribució subcosmopolita amb diferents exemples interessants de disjuncions entre àrees llunyanes i per tal de conèixer les principals vies de migració d’aquest grup. Aquest treball inclou nombroses novetats metodològiques com són l’ús de fòssils recentment descoberts, l’ús del concepte del rellotge molecular relaxat i de mètodes bayesians de reconstrucció biogeogràfica. Dins la tribu Cardueae, s’ha explorat de manera particular el gènere Plectocephalus, amb una espectacular disjunció entre l’Àfrica i Amèrica del sud. En el quart article de la tesis, s’ha realitzat la filogènia molecular del grup per tal de verificar la monofilia de Plectocephalus i les seves afinitats amb el gènere Centaurodendron i diverses espècies de Centaurea d’Amèrica del sud, resoldre les relacions filogenètiques del grup amb els grups basals de la subtribu a la qual pertanyen (Centaureinae) i es proposa com a origen de la seva distribució disjunta una migració es del Caucas i Anatòlia cap al continent americà pel pont terrestre de Bering durant el Miocè-Pliocè.[eng] The main items of this thesis are molecular systematics, biogeography and molecular phylogeography. Two main plant groups were chosen due to the several unresolved issues inolving their systematics and evolution: tribe Cardueae (Compositae) and Euphorbia genus (Euphorbiaceae). Regarding Euphorbia, we have focused on subgenus Esula and more particularly in the group Pachycladae. Phylogenetic relationships within species of this group and allies have been investigated using Maximum Parsimony and Bayesian Inference analyses of DNA sequences from nuclear and chloroplast genomes in a first paper. The group has been recircumscribed as section Aphyllis, including the East/South African and Arabian elements of section Tirucalli comprised in the E. mauritanica complex and the Macaronesian Pachycladae core clade and excluding the Mediterranean E. dendroides and the two Macaronesian species E. mellifera and E. stygiana. With this circumscripcion, section Aphyllis is another exemple of the phytogeographic pattern known as the Rand Flora, with a disjoint distribution between Macaronesia, East and West Africa, South Africa and the Arabian Peninsula. In the case of section Aphyllis, this distribution is explained by a vicariance event, resulting from fragmentation of a wider distribution area in North Africa caused by the aridification of the climate during the late Miocene-Pliocene. Subsection Macaronesicae, comprised in section Aphyllis, includes 11 species distributed in four of the five Macaronesian archipelagos and in two Macaronesian enclaves in mainland, in Portugal and Morocco. This clade was analyzed by AFLP fingerptinting techinque in order to study its phylogeography and taxonomy in a second paper. Excluding E. tuckeyana, we obtained a clear genetic structure in two groups which correspond to two complexes previously defined by morphological characters and ecological preferences: the E. atropurpurea and E. lamarckii complexes. Euphorbia aphylla is basal to the two complexes, suggesting a northwards direction of dispersal of the group in the Macaronesia from the Canary Islands. A back colonisation to the continent can explain the presence of E. regis-jubae in the Atlantic coast of Morocco and the presence of E. pedroi en Portugal. All the analyses performed reveal that E. pedroi makes part of the genetic pool of E. regis-jubae. However, we recommend maintaining its taxonomic status since E. pedroi is morphologically differentiated from E. regis-jubae and this differentiation could be further promoted by its geographical isolation. Regarding tribe Cardueae, several published phylogenies lacked a complete sampling and did not resolve the phylogenetic relationships of basal clades. The third paper of this thesis includes a new molecular phylogeny of the tribe with improved sampling and more molecular markers revealing main phylogenetic relationships between Cardueae subtribes and several systematical issues. Moreover, a molecular dating and a biogeographic recontruction to estimate divergence times for the main diversification events and to infer the ancestral areas and main migration events within Cardueae were performed to explain how it attained such a widespread and disjoint distribution. Within tribe Cardueae, we investigated in a fourth paper the interesting genus Plectocehaplus, with a striking disjoint distribution in Africa and South America, to test its monophyly and to determine the systematic position of several South American Centaurea species related to it, the phylogenetic relationships of Centaurodendron and Plectocephalus and their affinities with the basal genera of the Centaureinae

Phylogeography and character evolution of Euphorbia sect. Aphyllis subsect. Macaronesicae (Euphorbiaceae)

19 p., mapas, tablas, ilustracionesThe Macaronesian species of Euphorbia sect. Aphyllis subsect. Macaronesicae are distributed in four of the five archipelagos of Macaronesia and two mainland enclaves in Portugal and Morocco. The aims of this study are to investigate the biogeographic history of this group with AFLP and cpDNA markers, and to identify taxonomic entities within subsect. Macaronesicae based on genetic data, characterize them morphologically and infer the evolution of their diagnostic characters based on the reconstruction of ancestral character states. A continuous spatial diffusion analysis of AFLP data implicated Tenerife (central Canary Islands) as the area of origin of the group, followed by colonization of other Canarian islands and other Macaronesian archipelagos. Two dispersal events back to the mainland were also inferred. Our phylogenetic network, neighbour-joining clustering and Structure analyses of AFLP data demonstrated that species are genetically well delimited and suggested that they may have originated from a combination of allopatric speciation at broad scales (among islands) and fine scales (within islands), or possibly sympatric ecological speciation followed by more recent inter-island dispersal events. Ancestral character state reconstructions of morphological characters suggested that the ancestor of subsect. Macaronesicae was adapted to arid or mesic habitats, and traits associated with adaptation to humid habitats were acquired later. The central Canary Islands harbour the highest species diversity of this group in the Archipelago, and the highest nuclear and plastid genetic diversity. With regards to taxonomy, phylogenetic analyses and neighbour-joining clustering analyses based on AFLPs showed two clearly differentiated genetic groups, sister to each other, which correspond to the E. atropurpurea and E. lamarckii complexes formerly recognised based on morphology. Euphorbia aphylla is recovered as sister to the rest of the species, supporting its exclusion from the two complexes. Euphorbia tuckeyana is excluded from the E. lamarckii complex.This study was supported by the Ministry of Education and Science, Spanish Government (project CGL2010-18631/BOS, CGL2009-13322-C03-03, MEC-CSIC (200730i1035) and BES-2007-14260 (Ph.D. grant to L. Barres) and the Catalan Government (“Ajuts a grups consolidats” 2009/SGR/00439 and 2014/SGR/514).Peer reviewe

Molecular phylogeny of Euphorbia subg. Esula sect. Aphyllis (Euphorbiaceae) inferred from nrDNA and cpDNA markers with biogeographic insights.

16p., il. col., tablas y grafs.Euphorbia subg. Esula (Euphorbiaceae) has recently been shown, using molecular analyses, to contain a clade with a disjunct distribution in Macaronesia, South Africa and the Eritreo-Arabian region, and being primarily made up of members of sect. Tithymalus subsect. Pachycladae and sect. Tirucalli. To delimitate this disjoint group, we carried out phylogenetic analyses of the internal transcribed spacer (nrITS) using a broad sampling, with emphasis on subg. Esula. Subsequently, we carried out phylogenetic analyses focused on this clade using nuclear (ITS, ETS) and chloroplast (trnL-trnF, psbA-trnH, ycf3-trnS, trnG, atpB-rbcL, trnK-matK, trnT-trnL) markers, with the aim of resolving the phylogenetic relationships within the group and reconstructing its biogeographic history. Our results showed that sect. Tithymalus subsect. Pachycladae and sect. Tirucalli are polyphyletic. Section Aphyllis is recircumscribed to comprise the Pachycladae core clade and part of sect. Tirucalli. Low resolution within sect. Aphyllis and incongruences between nuclear and chloroplast phylogenies may be due to hybridization. Section Aphyllis should have originated in the Mediterranean area; its disjunct distribution is probably due to vicariance, resulting from fragmentation of a wider distribution area in North Africa caused by the aridification of the climate during the late Miocene-Pliocene.This work was supported by the Ministry of Education and Science, Spanish Government (project CGL2006-01765/BOS, CGL2009- 13322-C03-03 and BES-2007-14260 Ph.D. grant to L. Barres) and the Catalan Government (‘Ajuts a grups consolidats’ 2009/SGR/00439). We acknowledge the Euphorbia Planetary Biodiversity Inventory Project, which provided material and strongly supports our research. Special thanks are due to A. Moller and J. Morawetz, who kindly provided some photographs for Figure 3. The National Science Foundation Planetary Biodiversity Inventory Grant (DEB-0616533) additionally supported this workPeer reviewe

Allopolyploid origin of highly invasive Centaurea stoebe s.l. (Asteraceae)

Spotted knapweed (Centaurea stoebe) occurs from Western Asia to Western Europe both as diploid and tetraploid cytotypes, predominantly in single-cytotype populations with higher frequency of diploid populations. Interestingly, only tetraploids have been recorded so far from its introduced range in North America where they became highly invasive. We performed phylogenetic and network analyses of more than 40 accessions of the C. stoebe and C. paniculata groups and other related taxa using cloned internal transcribed spacer (ITS) and sequences of the chloroplast trnT–trnL and atpBrbcL regions to (i) assess the evolutionary origin of tetraploid C. stoebe s.l., and (ii) uncover the phylogeny of the C. stoebe group. Both issues have not been studied so far and thus remained controversial. Cloned ITS sequences showed the presence of two slightly divergent ribotypes occurring in tetraploid cytotype, while only one major ribotype was present in diploid C. stoebe s.str. This pattern suggests an allopolyploid origin of tetraploids with contribution of the diploid C. stoebe s.str. genome. Although we were not able to detect the second parental taxon, we hypothesize that hybridization might have triggered important changes in morphology and life history traits, which in turn may explain the colonization success of the tetraploid taxon. Bayesian relaxed clock estimations indicate a relatively recent – Pleistocene origin of the tetraploid C. stoebe s.l. Furthermore, our analyses showed a deep split between the C. paniculata and C. stoebe groups, and a young diversification of the taxa within the C. stoebe group. In contrast to nrDNA analyses, the observed pattern based on two cpDNA regions was inconclusive with respect to the origin and phylogeny of the studied taxa, most likely due to shared ancient polymorphism and frequent homoplasies

Reconstructing the Evolution and Biogeographic History of Tribe Cardueae (Compositae)

16 p.Premise of the study: Tribe Cardueae (thistles) forms one of the largest tribes in the family Compositae (2400 species), with representatives in almost every continent. The greatest species richness of Cardueae occurs in the Mediterranean region where it forms an important element of its flora. New fossil evidence and a nearly resolved phylogeny of Cardueae are used here to reconstruct the spatiotemporal evolution of this group. Methods: We performed maximum parsimony and Bayesian phylogenetic inference based on nuclear ribosomal DNA and chloroplast DNA markers. Divergence times and ancestral area reconstructions for main lineages were estimated using penalized likelihood and dispersal–vicariance analyses, respectively, and integrated over the posterior distribution of the phylogeny from the Bayesian Markov chain Monte Carlo analysis to accommodate uncertainty in phylogenetic relationships. Key results: The phylogeny shows that subtribe Cardopatiinae is sister to the remaining subtribes, and subtribes Carlininae and Echinopsinae appear as consecutive sister-clades to the Carduinae/Centaureinae. Tribe Cardueae is inferred to have originated around the Mid Eocene in West Asia, which is also the ancestral area of most subtribes within Cardueae. Diversification within each subtribe began during the Oligocene-Miocene period. Conclusions: Most diversification events within Cardueae are related to the continuous cycles of area connection and division between the Anatolian microplate and the western Mediterranean Basin during the Oligocene-Miocene and with the uplift of the Himalayan range from the Miocene onward. From these two regions, thistles dispersed and colonized the rest of the continents (e.g., the New World, Africa, and Australia), most likely during the colder Pliocene-Pleistocene period.The authors thank the Ministry of Education and Science of the Spanish Government (projects CGL2006-01765/BOS and CGL2009-13322-C03-03/BOS, CGL2009-13322-C03-01/BOS, CGL2010-18631 and grant BES-2007-14260 to L.B.) and the Catalan Government (‘Ajuts a grups consolidats’ 2009/SGR/00439) for financial support. S.B. and C.L.A. were supported by postdoctoral grants at RJB from the Swiss National Science Foundation grant (PBNEP3-129903) and the Swedish Research Council, respectively.Peer reviewe

Lessons from Plectocephalus (Compositae, Cardueae-Centaureinae): ITS disorientation in annuals and Beringian dispersal as revealed by molecular analyses

-Background and Aims: The geographic distribution of the genus Plectocephalus comprises a single species in Ethiopia, two in North America and possibly four more in South America, in a striking disjunction that is exceptional for genera of the tribe Cardueae. The enormity of this disjunction cast doubts on the precise taxonomic delineation of the genus, which is not unanimously recognized as a natural entity. Our aims were to define the generic boundaries of Plectocephalus and to formulate a hypothesis that would explain its natural range. -Methods: A combined molecular approach, using nuclear ITS and ETS and plastid trnL-trnL-F, rpl32-trnLUAG and ndhF markers, was chosen for phylogenetic reconstruction by maximum parsimony and Bayesian inference. Key Results: Phylogenetic analysis shows that Plectocephalus is a natural genus that includes the African species P. varians, together with all the native South American species, currently classified as Centaurea, C. cachinalensis, C. floccosa and C. tweediei. The recognition of Centaurodendron as an independent genus, which we consider appropriate, would make Plectocephalus paraphyletic. Affinities of Plectocephalus should lie with eastern representatives of Centaureinae. Geographic disjunction is explained as a consequence of dispersal via the Bering Land Bridge during the Miocene-Pliocene. The phylogeny of the basal grade of Centaureinae differs from previous phylogenies, and artifacts resulting from differences in mutation rates of annual and perennial taxa are confirmed. Sensitivity of ITS to these differences was the highest observed for all DNA regions used in this study. Conclusions: The natural status of the genus Plectocephalus is confirmed and several nomenclatural combinations are proposed. New evidence contributes to the debate concerning problems posed by the use of ITS in the phylogenetic reconstruction of groups that differ in terms of their life cycles. Dispersal from the Caucasus and Anatolia along the Siberian route and then across the Bering Land Bridge follows a route previously proposed for other taxonomic groups.This work was supported by the Ministry of Science and Innovation of Spain [projects CGL2006-01765/BOS and CGL2009-13322-C03-03] and the Generalitat de Catalunya ["Ajuts a Grups de Recerca Consolidats" 2009-SGR-439].Peer reviewe

A worldwide molecular phylogeny and classification of the leafy spurges, Euphorbia subgenus Esula (Euphorbiaceae)

The leafy spurges, Euphorbia subg. Esula, make up one of four main lineages in Euphorbia. The subgenus comprises about 480 species, most of which are annual or perennial herbs, but with a small number of dendroid shrubs and nearly leafless, pencil-stemmed succulents as well. The subgenus constitutes the primary northern temperate radiation in Euphorbia. While the subgenus is most diverse from central Asia to the Mediterranean region, members of the group also occur in Africa, in the Indo-Pacific region, and in the New World. We have assembled the largest worldwide sampling of the group to date (273 spp.), representing most of the taxonomic and geographic breadth of the subgenus. We performed phylogenetic analyses of sequence data from the nuclear ribosomal ITS and plastid ndhF regions. Our individual and combined analyses produced well-resolved phylogenies that confirm many of the previously recognized clades and also establish a number of novel groupings and placements of previously enigmatic species. Euphorbia subg. Esula has a clear Eurasian center of diversity, and we provide evidence for four independent arrivals to the New World and three separate colonizations of tropical and southern Africa. One of the latter groups further extends to Madagascar and New Zealand, and to more isolated islands such as Réunion and Samoa. Our results confirm that the dendroid shrub and stem-succulent growth forms are derived conditions in E. subg. Esula. Stem-succulents arose twice in the subgenus and dendroid shrubs three times. Based on the molecular phylogeny, we propose a new classification for E. subg. Esula that recognizes 21 sections (four of them newly described and two elevated from subsectional rank), and we place over 95% of the accepted species in the subgenus into this new classification.Funding was made available by the U.S. National Science Foundation through a Planetary Biodiversity Inventory Grant (DEB-0616533) to P.E. Berry, by the Spanish Ministry of Education and Science through project CGL2009-13322-C03-03 to L. Barres and J. Molero, and by the Russian Foundation for Basic Research through project 10-04-00290-а to D. Geltman and A. Kryukov.Peer reviewe