Molecular data place Trypetheliaceae in Dothideomycetes

The phylogenetic position of Trypetheliaceae was studied using partial sequences of the mtSSU and nuLSU rDNA of 100 and 110 ascomycetes, respectively, including 48 newly obtained sequences. Our analysis confirms Trypetheliaceae as monophyletic and places the family in Dothideomycetes. Pyrenulaceae, which were previously classified with Trypetheliaceae in Pyrenulales or Melanommatales, are supported as belonging to Chaetothyriomycetes. Monophyly of Pyrenulales, including Trypetheliaceae is rejected using three independent test methods. Monophyly of Arthopyreniaceae plus Trypetheliaceae, the two families including lichen-forming fungi in Dothideomycetes, is also rejected, as well as a placement of Trypetheliaceae in Pleosporales (incl. Melanommatales).     

Hennig’s orphans revisited: Testing morphological hypotheses in the “Opomyzoidea” (Diptera: Schizophora)

The acalyptrate fly superfamily Opomyzoidea, as currently recognized, is a poorly-known group of 14 families. The composition of this group and relationships among included families have been controversial. Furthermore, the delimitation of two opomyzoid families, Aulacigastridae and Periscelididae, has been unstable with respect to placement of the genera Stenomicra, Cyamops, and Planinasus. To test the monophyly of Opomyzoidea, previously proposed relationships between families, and the position of the three problematic genera, we sequenced over 3300 bp of nucleotide sequence data from the 28S ribosomal DNA and CAD (rudimentary) genes from 29 taxa representing all opomyzoid families, as well as 13 outgroup taxa. Relationships recovered differed between analyses, and only branches supporting well-established monophyletic families were recovered with high support, with a few exceptions. Opomyzoidea and its included subgroup, Asteioinea, were found to be non-monophyletic. Stenomicra, Cyamops, and Planinasus group consistently with Aulacigastridae, contrary to recent classifications. Xenasteiidae and Australimyzidae, two small, monogeneric families placed in separate superfamilies, were strongly supported as sister groups.     

Revised classification of former genus Phoxinellus using nuclear DNA sequences

Molecular data inferred from three nuclear DNA regions were used to re-examine the phylogenetic position and taxonomic status of former Phoxinellus taxa. Using either distance method, maximum likelihood or MCMC, phylogenetic tree revealed statistically well supported clade of Delminichthys adspersus, Delminichthys ghetaldii, Delminichthys jadovensis, and Delminichthys krbavensis occupying a sister position to Pelasgus prespensis; furthermore, Phoxinellus pseudalepidotus emerged as a sister taxon to Delminichthys–Pelasgus group. There was a moderate support for sister relationship between Telestes croaticus and Telestes fontinalis, while the position of Telestes metohiensis varied depending on the region and method used. The topology of taxa within Delminichthys was weakly supported and remained pretty much unresolved. Our results confirm a previous notion that the former genus Phoxinellus is not a monophyletic group but rather a grouping of independent lineages.     

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.     

Phylogenetic relationships of the anamorphic genus <Emphasis Type="Italic">Fusicladium</Emphasis> s. lat. as inferred by ITS nrDNA data

The genus Fusicladium s. lat. (incl. Pollaccia and Spilocaea) was phylogenetically analysed using ITS nrDNA sequences. Pollaccia and Spilocaea did not form monophyletic groups of their own, but were intermingled between Fusicladium species, together with which they formed a monophyletic clade. Thus, Pollaccia and Spilocaea should be included in a wider genus concept of Fusicladium, constituting a morphologically variable genus. Furthermore, all Venturia and Fusicladium isolates clustered together on the bases of available ITS data, providing support for the monophyly of the anamorphic genus Fusicladium and the teleomorphic genus Venturia. Within this clade several subclades can be recognized. All taxa on the host family Salicaceae were found in one subclade. Three other subclades comprised taxa on Rosaceae whereas taxa on other host families all clustered separately. Geographic specializations were not observed. Two examples of host switching could be demonstrated, but these were confined to instances involving host species belonging to the same family. Fusicladium convolvularum and F. effusum, two species with unknown teleomorphs, clustered within the Fusicladium/Venturia clade, supporting the correct placement of these taxa in Fusicladium. The placement of Pseudocladosporium hachijoense within the family Venturiaceae was also supported.     

Phylogenetic relationships among the New World cypresses (Hesperocyparis; Cupressaceae): evidence from noncoding chloroplast DNA sequences

Nearly 5.6?kb of noncoding chloroplast DNA sequence was combined with 9.2?kb of previously published sequence in addressing phylogenetic relationships among Callitropsis, Xanthocyparis, and the New World cypresses (Hesperocyparis; Cupressaceae). Maximum likelihood and Bayesian analyses of aligned nucleotide sequence and coded length mutations provide strong support for several relationships. These include a clade in which Xanthocyparis and Callitropsis are successively nested at the base of a monophyletic Hesperocyparis and identification of H. bakeri as sister to the remaining Hesperocyparis. Two principal clades are recovered within Hesperocyparis; (1) the Arizonica group, which contains taxa sometimes recognized as varieties of H. lusitanica, H. guadalupensis, and H. arizonica, and (2) the Macrocarpa group, which contains H. macrocarpa and H. goveniana and its allies. Our results are equivocal with respect to placement of H. macnabiana, a morphologically distinct species resolved as the sister group to either the Macrocarpa or Arizonica group, depending on the data set analyzed. We discover many instances in which taxa recognized as varieties or closely related species are placed in disparate parts of the phylogeny. These include segregates of H. lusitanica, H. guadalupensis, and H. arizonica, all of which are included in clades with other species. Despite analyzing 14,799?bp of aligned sequence and 230 binary characters, we find poor support for several relationships, especially within the Arizonica group. These results suggest recovery of well-supported relationships among the closely related taxa of Hesperocyparis will require additional sources of evidence (e.g., morphological, biochemical characters). Implications for morphological evolution and taxonomic revision are discussed.     

Papulosa amerospora accommodated in a new family (papulosaceae, sordariomycetes, ascomycota) inferred from morphological and molecular data

To investigate the systematic position of the unitunicate pyremomycetePapulosa amerospora, we performed phylogenetic analyses of SSU rDNA sequences from 37 ascomycetes. Among these sequences were some new ones from taxa that might be related toPapulosa: Hyponectriaceae (Hyponectria buxi, Monographella nivalis), Phyllachorales (Phyllachora graminis), and Xylariales (Barrmaelia melanotes, Poronia punctata). Our results showed 100% bootstrap support for a clade of all unitunicate pyrenomycetes, the class Sordariomycetes. We also found strong support for recognizing the subclasses Hypocreomycetidae and Xylariomycetidae. The remaining taxa, belonging to subclass Sordariomycetidae, appeared as a polyphyletic group in one analysis, but was monophyletic when shorter SSU sequences were used.Barrmaelia melanotes, Poronia punctata, Hyponectria buxi, andMonographella nivalis are members of Xylariomycetidae, but we could not determine whetherMonographella should be included in Hyponectriaceae. The new family Papulosaceae is erected forPapulosa on molecular and morphological bases, but the exact systematic position ofPapulosa within subclass Sordariomycetidae is still uncertain, since the genus did not cluster consistently with any of the included taxa. Phyllachorales are not closely related to Diaporthales, as previously suggested.     

PHYLOGENETIC ANALYSES OF THE BRYOPSIDALES (ULVOPHYCEAE,CHLOROPHYTA) BASED ON RUBISCO LARGE SUBUNIT GENE SEQUENCES1

Current taxonomy of the Bryopsidales recognizes eight families; most of which are further categorized into two suborders, the Bryopsidineae and Halimedineae. This concept was supported by early molecular phylogenetic analyses based on rRNA sequence data, but subsequent cladistic analyses of morphological characters inferred monophyly in only the Halimedineae. These conflicting results prompted the current analysis of 32 taxa from this diverse group of green algae based on plastid‐encoded RUBISCO large subunit (rbcL) gene sequences. Results of these analyses suggested that the Halimedineae and Bryopsidineae are distinct monophyletic lineages. The families Bryopsidaceae, Caulerpaceae, Codiaceae, Derbesiaceae, and Halimediaceae were inferred as monophyletic, however the Udoteaceae was inferred as non‐monophyletic. The phylogenetic position of two taxa with uncertain subordinal affinity, Dichotomosiphon tuberosus Lawson and Pseudocodium floridanum Dawes & Mathieson, were also inferred. Pseudocodium was consistently placed within the halimedinean clade suggesting its inclusion into this suborder, however familial affinity was not resolved. D. tuberosus was the inferred sister taxon of the Halimedineae based on analyses of rbcL sequence data and thus a possible member of this suborder.     

Phylogeny, character evolution, and classification of Sapotaceae (Ericales)

We present the first cladistic study of the largely tropical family Sapotaceae based on both morphological and molecular data. The data were analyzed with standard parsimony and parsimony jackknife algorithms using equally and successive weighted characters. Sapotaceae are confirmed to constitute two main evolutionary lineages corresponding to the tribes Isonandreae‐Mimusopeae‐Sideroxyleae and Chrysophylleae‐Omphalocarpeae. The Sideroxyleae are monophyletic, Isonandreae are polyphyletic as presently circumscribed, and as suggested by the analyses, the subtribe Mimusopeae‐Mimusopinae has evolved within the Mimusopeae‐Manilkarinae, which hence is also paraphyletic. Generic limits must be altered within Sideroxyleae with the current members Argania, Nesoluma and Sideroxylon. Argania cannot be maintained at a generic level unless a narrower generic concept is adopted for Sideroxylon. Nesoluma cannot be upheld in a narrow or broad generic concept of Sideroxylon. The large tribe Chrysophylleae circumscribes genera such as Chrysophyllum, Pouteria, Synsepalum, and Xantolis, but the tribe is monophyletic only if the taxa from Omphalocarpeae are also included. Neither Chrysophyllum nor Pouteria are monophyletic in their current definitions. The results indicate that the African taxa of Pouteria are monophyletic and distinguishable from the South American taxa. Resurrection of Planchonella, corresponding to Pouteria section Oligotheca, is proposed. The African genera Synsepalum and Englerophytum form a monophyletic group, but their generic limits are uncertain. Classification of the Asian genus Xantolis is particularly interesting. Morphology alone is indecisive regarding Xantolis relationships, the combined unweighted data of molecules and morphology indicates a sister position to Isonandreae‐Mimusopeae‐Sideroxyleae, whereas molecular data alone, as well as successive weighted combined data point to a sister position to Chrysophylleae‐Omphalocarpeae. An amended subfamily classification is proposed corresponding to the monophyletic groups: Sarcospermatoideae (Sarcosperma), Sapotoideae (Isonandreae‐Mimusopeae‐Sideroxyleae) and Chrysophylloideae (Chrysophylleae‐Omphalocarpeae), where Sapotoideae circumscribes the tribes Sapoteae and Sideroxyleae as well as two or three as yet unnamed lineages. Morphological characters are often highly homoplasious and unambiguous synapomorphies cannot be identified for subfamilies or tribes, which we believe are the reason for the variations seen between different classifications of Sapotaceae. © The Willi Hennig Society 2005.     

Evolutionary relationships among aquatic anamorphs and teleomorphs: Lemonniera, Margaritispora, and Goniopila

The hypothesis that similar conidial morphologies in aquatic hyphomycetes are a result of convergent evolution was tested using molecular sequence data. Cladistic analyses were performed on partial sequences of 28S rDNA of seven species of Lemonniera, one species of Margaritispora and one species of Goniopila. Lemonniera has tetraradiate conidia with long arms, whereas Margaritispora and Goniopila have typically globose (isodiametric) conidia, with short conical protuberances in a stellate or quadrangular arrangement. Lemonniera and Margaritispora have phialidic conidiogenesis and both produce dark, minute sclerotia in culture whereas Goniopila has holoblastic conidiogenesis and does not produce sclerotia in culture. Goniopila produces a microconidial phialidic synanamorph in culture. All three genera have schizolytic conidial secession. Molecular analyses demonstrate that Lemonniera species are placed in two distinct clades: one within Leotiomycetes; the other within Pleosporales, Dothideomycetes. Margaritispora is placed with Lemonniera species within Leotiomycetes. Goniopila and Lemonniera pseudofloscula are placed within Dothideomycetes. No morphological character was entirely congruent with the molecular derived phylogeny. This suggests that for the group of species studied, conidial shape is not a reliable indicator of phylogeny but more likely the result of convergent evolution in response to the aquatic environment.     

Comprehensive phylogeny of the Cleroidea (Coleoptera: Cucujiformia)

The first thorough molecular phylogeny of the superfamily Cleroidea, represented by 377 taxa, and the first with an emphasis on Trogossitidae, was undertaken. Maximum likelihood and Bayesian analyses were performed on a four‐gene dataset (18S, 28S, cox1, cytb) of 395 taxa (along with 18 outgroups), including all 16 currently recognized families of Cleroidea and all current and formerly recognized tribes of Trogossitidae. The superfamily as a whole received strong support in Bayesian analyses. On the basis of phylogenetic results, 18 families in Cleroidea are recognized, including three taxa elevated to family for the first time and two reinstated families. The former tribe Rentoniini (Trogossitidae: Peltinae) was strongly supported as a monophyletic group apart from the remainder of Trogossitidae, and is herein elevated to family status, Rentoniidae stat.n. Protopeltis was also found to be an isolated lineage and becomes Protopeltidae stat.n. Peltini + Larinotini were recovered as a weakly supported sister grouping; Peltini (including only Peltis) becomes Peltidae stat.rest. The trogossitid subfamily Lophocaterinae, to the exclusion of Decamerini, formed a clade which is here designated Lophocateridae stat.rest. and sensu n. The Trogossitinae tribes Calityini, Egoliini (represented by Egolia) and Larinotini were recovered apart from core Trogossitidae but showed no strong affinities to other taxa or congruence between analyses; they are here conservatively retained in Trogossitidae as Calityinae stat.rest. , Egoliinae stat.rest. and Larinotinae stat.rest. The genus Thymalus of the peltine tribe Thymalini was indicated with moderate to strong support as the sister group of the Decamerini (Trogossitidae: Lophocaterinae); together these represent Thymalidae stat.n. and sensu n. with subfamilies Decamerinae stat.rest. ( new placement ) and Thymalinae stat.n. The remainder of Trogossitinae, the tribes Trogossitini and Gymnochilini, formed a well‐supported clade which comprises the Trogossitidae: Trogossitinae sensu n. The tribe Gymnochilini syn.n. is synonymized with Trogossitini. The monotypic family Phloiophilidae was recovered, contradicting a recent placement within Trogossitidae. The melyrid lineage was recovered with moderate (maximum likelihood) to strong (Bayesian analyses) support and includes the families Phycosecidae, Rhadalidae, Mauroniscidae, Prionoceridae and Melyridae (including Dasytidae and Malachiidae). The genus Dasyrhadus is tentatively transferred from Rhadalidae to Mauroniscidae. The genus Gietella, once proposed as a distinct family but recently placed within Dasytidae, was recovered as strongly sister to Rhadalidae sensu n. , and we transfer it to that family as Gietellinae new placement . Attalomiminae (formerly Attalomimidae) syn.n. is synonymized with Melyridae: Malachiinae: Lemphini sensu n. Melyridae sensu n. includes only Dasytinae, Malachiinae and Melyrinae. Metaxina is returned to the Chaetosomatidae sensu n. , of which Metaxinidae syn.n. becomes a junior synonym. Resolution within Cleridae was generally poor, but a broadly defined Korynetinae stat rest. + Epiclininae received high support (Bayesian analyses). Outside of Trogossitidae, the main focus of this study, major rearrangements of the classification of Cleroidea were not undertaken, despite evidence indicating such changes are needed.     

Molecular and morphological evolution in the Physciaceae (Lecanorales,lichenized Ascomycotina), with special emphasis on the genus Rinodina

Abstract:A phylogenetic hypothesis based on nuclear ITS sequence data is presented for the familyPhysciaceae , based on various representatives of foliose and fruticose groups and a number of species selected from the crustose genera Rinodina and Buellia s.l. The analysis supports the monophyly of the Physcia - and theBuellia -groups. This is in agreement with existing morphological evidence, particularly ascus characters. ThePhyscia group in the analysis includes the genera Anaptychia, Heterodermia, Hyperphyscia,Mobergia , Phaeophyscia, Phaeorrhiza, Physcia, Physconia, Rinodina, andRinodinella , while the Buellia group includes Amandinea, Buellia and Diploicia. The genera Physcia, Phaeophyscia, Phaeorrhiza and Rinodinella were well supported as monophyletic groups. The support for Physconia is low. Rinodina and Buellia are not supported as monophyletic genera. In agreement with ascus and ascospore characters, Buellia lindingeri is placed within the Rinodina group, close to R. lecanorina. The genus Amandinea as currently circumscribed was not supported as a monophyletic group. The analysis confirms results from other lichen families that foliose members have evolved more than once from crustose lichens.Rinodina and Rinodinella species without chemical compounds in their thalli form the sister group toPhaeophyscia , and both groups form a monophyletic assemblage. A more detailed analysis of the Physcia group is presented. Whilst several of the foliose genera were well supported, there is only poor support for traditionally accepted crustose genera. The taxonomic implications of these findings are discussed.     

Phylogeny of drepanosiphine aphids sensu lato (Hemiptera,Aphidoidea) inferred from molecular and morphological data

As the second largest and most diverse group in the superfamily Aphidoidea, the phylogeny of drepanosiphine aphids sensu lato (s.l.) is critical for discussing the evolution of aphids. However, the taxa composition and phylogenetic relationships of drepanosiphine aphids s.l. have not been fully elucidated to date. In this study, based on total-evidence analyses combining 4 molecular genes (3 mitochondrial, COI, tRNA-Leu/COII, and CytB; 1 nuclear, EF-1ɑ) and 64 morphological and biological characteristics, the phylogeny of this group was reconstructed for the first time at the subfamily level using different datasets, parsimonies and model-based methods. All of our phylogenetic inferences clearly indicated that the drepanosiphine aphids s.l. was not a monophyletic group and seemed to support the division of the drepanosiphine aphids s.l. into different groups classified at the subfamily level. Calaphidinae was also not a monophyletic group, and Saltusaphidinae was nested within this subfamily. Drepanosiphinae was not clustered with Chaitophorinae, which was inconsistent with the previous hypothesis of a close relationship between them, illustrating that their phylogeny remains controversial. Overall, some groups of drepanosiphine aphids s.l., including Phyllaphidinae, Macropodaphidinae, Pterastheniinae, Lizeriinae, Drepanosiphinae, Spicaphidinae, Saltusaphidinae, and Calaphidinae, clustered together and might constitute the actual drepanosiphine aphids s.l. To a certain extent, our results clarified the phylogenetic relationships among drepanosiphine aphids s.l. and confirmed their taxonomic status as subfamilies.     

The phylogenetic positions of the conifer genera Amentotaxus,Phyllocladus, and Nageia inferred from 18s rRNA sequences

To determine the evolutionary positions of the conifer genera Amentotaxus, Phyllocladus, and Nageia, we obtained 18S rRNA sequences from 11 new taxa representing the major living orders and families of gymnosperms. With the published Chlamydomonas as an outgroup, phylogenetic analyses of our new data and available sequences indicate that (1) the Gnetales form a monophyletic group, which is an outgroup to the conifers, (2) the conifers are monophyletic, (3) Taxaceae, Cephalotaxaceae, Cupressaceae, and Taxodiaceae form a monophyletic group, (4) Amentotaxus is closer to Torreya than to Cephalotaxus, suggesting that Amentotaxus is better to be classified as a member of Taxaceae, (5) Phyllocladus, Dacrycarpus, Podocarpus, and Nageia form a monophyletic group, and (6) Pinaceae is an outgroup to the other families of conifers. Our finding that Phyllocladus is a sister group of the Podocarpaceae disagrees with the suggestion that the phylloclade of the genus is an ancient structure and that the genus is a terminal taxon within the Podocarpaceae. The genus Nageia is more closely related to Podocarpus than to Dacrycarpus and was derived from within the Podocarpaceae. In conclusion, our data indicate that in conifers, the uniovulate cone occurred independently in Taxacaeae and Cephalotaxaceae, and in Podocarpaceae after the three families separated from Pinaceae, and support the hypothesis that the uniovulate cone is derived from reduction of a multiovulate cone.Correspondence to: S.-M. Chaw     

A phylogenetic overview of the family Pyronemataceae (Ascomycota, Pezizales)

Partial sequences of nuLSU rDNA were obtained to investigate the phylogenetic relationships of Pyronemataceae, the largest and least studied family of Pezizales. The dataset includes sequences for 162 species from 51 genera of Pyronemataceae, and 39 species from an additional 13 families of Pezizales. Parsimony, ML, and Bayesian analyses suggest that Pyronemataceae is not monophyletic as it is currently circumscribed. Ascodesmidaceae is nested within Pyronemataceae, and several pyronemataceous taxa are resolved outside the family. Glaziellaceae forms the sister group to Pyronemataceae in ML analyses, but this relationship, as well as those of Pyronemataceae to the other members of the lineage, are not resolved with support. Fourteen clades of pyronemataceous taxa are well supported and/or present in all recovered trees. Several pyronemataceous genera are suggested to be non-monophyletic, including Anthracobia, Cheilymenia, Geopyxis, Humaria, Lasiobolidium, Neottiella, Octospora, Pulvinula, Stephensia, Tricharina, and Trichophaea. Cleistothecial and truffle or truffle-like ascomata forms appear to have evolved independently multiple times within Pyronemataceae. Results of these analyses do not support previous classifications of Pyronemataceae, and suggest that morphological characters traditionally used to segregate the family into subfamilial groups are not phylogenetically informative above the genus level.     

Probing the Monophyly of the Sphaeropleales (Chlorophyceae) Using Data From Five Genes

Molecular phylogenetic analyses have had a major impact on the classification of the green algal class Chlorophyceae, corroborating some previous evolutionary hypotheses, but primarily promoting new interpretations of morphological evolution. One set of morphological traits that feature prominently in green algal systematics is the absolute orientation of the flagellar apparatus in motile cells, which correlates strongly with taxonomic classes and orders. The order Sphaeropleales includes diverse green algae sharing the directly opposite (DO) flagellar apparatus orientation of their biflagellate motile cells. However, algae across sphaeroplealean families differ in specific components of the DO flagellar apparatus, and molecular phylogenetic studies often have failed to provide strong support for the monophyly of the order. To test the monophyly of Sphaeropleales and of taxa with the DO flagellar apparatus, we conducted a molecular phylogenetic study of 16 accessions representing all known families and diverse affiliated lineages within the order, with data from four plastid genes (psaA, psaB, psbC, rbcL) and one nuclear ribosomal gene (18S). Although single‐gene analyses varied in topology and support values, analysis of combined data strongly supported a monophyletic Sphaeropleales. Our results also corroborated previous phylogenetic hypotheses that were based on chloroplast genome data from relatively few taxa. Specifically, our data resolved Volvocales, algae possessing predominantly biflagellate motile cells with clockwise (CW) flagellar orientation, as the monophyletic sister lineage to Sphaeropleales, and an alliance of Chaetopeltidales, Chaetophorales, and Oedogoniales, orders having multiflagellate motile cells with distinct flagellar orientations involving the DO and CW forms.     

PHYLOGENY OF THE CONJUGATING GREEN ALGAE (ZYGNEMOPHYCEAE) BASED ON rbc L SEQUENCES

Sequences of the gene encoding the large subunit of RUBISCO (rbcL) for 30 genera in the six currently recognized families of conjugating green algae (Desmidiaceae, Gonatozygaceae, Mesotaeniaceae, Peniaceae, and Zygnemataceae) were analyzed using maximum parsimony and maximum likelihood; bootstrap replications were performed as a measure of support for clades. Other Charophyceae sensu Mattox and Stewart and representative land plants were used as outgroups. All analyses supported the monophyly of the conjugating green algae. The Desmidiales, or placoderm desmids, constitute a monophyletic group, with moderate to strong support for the four component families of this assemblage (Closteriaceae, Desmidiaceae, Gonatozygaceae, and Peniaceae). The analyses showed that the two families of Zygnematales (Mesotaeniaceae, Zygnemataceae), which have plesiomorphic, unornamented and unsegmented cell walls, are not monophyletic. However, combined taxa of these two traditional families may constitute a monophyletic group. Partitioning the data by codon position revealed no significant differences across all positions or between partitions of positions one and two versus position three. The trees resulting from parsimony analyses using first plus second positions versus third position differed only in topology of branches with poor bootstrap support. The tree derived from third positions only was more resolved than the tree derived from first and second positions. The rbcL‐based phylogeny is largely congruent with published analyses of small subunit rDNA sequences for the Zygnematales. The molecular data do not support hypotheses of monophyly for groups of extant unicellular and filamentous or colonial desmid genera exhibiting a common cell shape. A trend is evident from simple omniradiate cell shapes to taxa with lobed cell and plastid shapes, which supports the hypothesis that chloroplast shape evolved generally from simple to complex. The data imply that multicellular placoderm desmids are monophyletic. Several anomalous placements of genera were found, including the saccoderm desmid Roya in the Gonatozygaceae and the zygnematacean Entransia in the Coleochaetales. The former is strongly supported, although the latter is not, and Entransia's phylogenetic position warrants further study.