Lara, Enrique

2007, Lara, Enrique, Heger, Thierry J, Mitchell, Edward, Meisterfeld, Ralf, Ekelund, Flemming

The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a study aiming to fill several important gaps and better understand the relationships among the main euglyphid testate amoebae and the evolutionary steps that led to the present diversity at a higher level. We obtained new SSU rRNA sequences from five genera and seven species. This new phylogeny obtained shows that (1) the clade formed by species of genera Assulina and Placocista branches unambiguously at the base of the subclade of Euglyphida comprising all members of the family Trinematidae and genus Euglypha, (2) family Trinematidae (Trachelocorythion, Trinema, and Corythion) branches as a sister group to genus Euglypha, (3) three newly sequenced Euglypha species (E. cf. ciliata, E. penardi, and E. compressa) form a new clade within the genus. Since our results show that Assulina and Placocista do not belong to the Euglyphidae (unless the Trinematidae are also included in this family), we propose the creation of a new family named Assulinidae. Consequently, we give a family status to the genera Euglypha and (tentatively) Scutiglypha, which become the new family Euglyphidae. The evolutionary pattern suggested by SSU rRNA phylogeny shows a clear tendency towards increasing morphological complexity of the shell characterised by changes in the symmetry (migration of the aperture to a ventral position and/or compression of the shell) and the appearance of specialised scales at the aperture (in families Trinematidae and Euglyphidae). (C) 2007 Elsevier GmbH. All rights reserved.

, Lahr Daniel J. G., Lara, Enrique, Mitchell, Edward

Nomenclature of microbial eukaryotes has been historically relegated to secondary importance. This is a legacy of the traditional classification of life into the most studied multicellular forms (plants, fungi, and animals). Despite the revolution in an understanding of eukaryotic diversity and relationships that has been achieved as a result of the use of molecular techniques, the description of microbial eukaryote genera and species is more difficult today than in the past. Researchers are at liberty to choose between the botanical (in the traditional sense) and zoological codes of nomenclature, although there is no obligation to comply with either. We demonstrate that, by combining the foci of different nomenclature codes with the current knowledge of relationships, a large number of genera and species end up being regulated by two codes (Patterson's ambiregnal taxa) and, in some cases, may even be regulated by none. We briefly present historically proposed types of solutions to this problem, and propose that an elaboration of authoritative guidelines to regulate the nomenclature of microbial eukaryotes by the community of researchers is most appropriate at this time. Most importantly, we plead to the community of researchers to resolve this centuries old outstanding issue.

2007, Lara, Enrique, Heger, Thierry J., Mitchell, Edward, Meisterfeld, Ralf, Ekelund, Flemming

The existing data on the molecular phylogeny of filose testate amoebae from order Euglyphida has revealed contradictions between traditional morphological classification and SSU rRNA phylogeny and, moreover, the position of several important genera remained unknown. We therefore carried out a study aiming to fill several important gaps and better understand the relationships among the main euglyphid testate amoebae and the evolutionary steps that led to the present diversity at a higher level.
We obtained new SSU rRNA sequences from five genera and seven species. This new phylogeny obtained shows that (1) the clade formed by species of genera Assulina and Placocista branches unambiguously at the base of the subclade of Euglyphida comprising all members of the family Trinematidae and genus Euglypha, (2) family Trinematidae (Trachelocorythion, Trinema, and Corythion) branches as a sister group to genus Euglypha, (3) three newly sequenced Euglypha species (E. cf. ciliata, E. penardi, and E. compressa) form a new clade within the genus.
Since our results show that Assulina and Placocista do not belong to the Euglyphidae (unless the Trinematidae are also included in this family), we propose the creation of a new family named Assulinidae. Consequently, we give a family status to the genera Euglypha and (tentatively) Scutiglypha, which become the new family Euglyphidae.
The evolutionary pattern suggested by SSU rRNA phylogeny shows a clear tendency towards increasing morphological complexity of the shell characterised by changes in the symmetry (migration of the aperture to a ventral position and/or compression of the shell) and the appearance of specialised scales at the aperture (in families Trinematidae and Euglyphidae).

, Adl, Sina M., Simpson, Alastair G. B., Lane, Christopher E., Lukeš, Julius, Bass, David, Bowser, Samuel S., Brown, Matthew W., Burki, Fabien, Dunthorn, Micah, Hampl, Vladimir, Heiss, Aaron, Hoppenrath, Mona, Lara, Enrique, le Gall, Line, Lynn, Denis H., McManus, Hilary, Mitchell, Edward, Mozley-Stanridge, Sharon E., Parfrey, Laura W., Pawlowski, Jan, Rueckert, Sonja, Shadwick, Laura, Schoch, Conrad L., Smirnov, Alexey, Spiegel, Frederick W.

This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.

2006, Lara, Enrique, Chatzinotas, Antonis, Simpson, Alastair G. B.

A new heterotrophic flagellate (Andalucia godoyi n. gen. n. sp.) is described from soil. Earlier preliminary 18S rRNA analyses had indicated a relationship with the phylogenetically difficult-to-place jakobid Jakoba incarcerata. Andalucia godoyi is a small (3–5 μm) biflagellated cell with a ventral feeding groove. It has tubular mitochondrial cristae. There are two major microtubular roots (R1, R2) and a singlet root associated with basal body 1 (posterior). The microtubular root R1 is associated with non-microtubular fibres "I,""B," and "A," and divides in two parts, while R2 is associated with a "C" fibre. These structures support the anterior portion of the groove. Several features of A. godoyi are characteristic of jakobids: (i) there is a single dorsal vane on flagellum 2; (ii) the C fibre has the jakobid multilaminate substructure; (iii) the dorsal fan of microtubules originates in very close association with basal body 2; and (iv) there is no "R4" microtubular root associated with basal body 2. Morphological analyses incorporating the A. godoyi data strongly support the monophyly of all jakobids. Our 18S rRNA phylogenies place A. godoyi and J. incarcerata as a strong clade, which falls separately from other jakobids. Statistical tests do not reject jakobid monophyly, but a specific relationship between Jakoba libera and J. incarcerata and/or A. godoyi is rejected. Therefore, we have established a new genus Andalucia n. gen. with the type species Andalucia godoyi n. sp., and transfer Jakoba incarcerata to Andalucia as Andalucia incarcerata n. comb.