Global distribution of a chlorophyll f cyanobacterial marker

Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype’s distribution

Origin and evolution of water oxidation before the last common ancestor of the Cyanobacteria

Photosystem II, the water oxidizing enzyme, altered the course of evolution by filling the atmosphere with oxygen. Here, we reconstruct the origin and evolution of water oxidation at an unprecedented level of detail by studying the phylogeny of all D1 subunits, the main protein coordinating the water oxidizing cluster (Mn4CaO5) of Photosystem II. We show that D1 exists in several forms making well-defined clades, some of which could have evolved before the origin of water oxidation and presenting many atypical characteristics. The most ancient form is found in the genome of Gloeobacter kilaueensis JS-1 and this has a C-terminus with a higher sequence identity to D2 than to any other D1. Two other groups of early evolving D1 correspond to those expressed under prolonged far-red illumination and in darkness. These atypical D1 forms are characterized by a dramatically different Mn4CaO5 binding site and a Photosystem II containing such a site may assemble an unconventional metal cluster. The first D1 forms with a full set of ligands to the Mn4CaO5 cluster are grouped with D1 proteins expressed only under low oxygen concentrations and the latest evolving form is the dominant type of D1 found in all cyanobacteria and plastids. In addition, we show that the plastid ancestor had a D1 more similar to those in early branching Synechococcus. We suggest each one of these forms of D1 originated from transitional forms at different stages towards the innovation and optimization of water oxidation before the last common ancestor of all known cyanobacteria

A fresh look at the evolution and diversification of photochemical reaction centers

In this review, I reexamine the origin and diversification of photochemical reaction centers based on the known phylogenetic relations of the core subunits, and with the aid of sequence and structural alignments. I show, for example, that the protein folds at the C-terminus of the D1 and D2 subunits of Photosystem II, which are essential for the coordination of the water-oxidizing complex, were already in place in the most ancestral Type II reaction center subunit. I then evaluate the evolution of reaction centers in the context of the rise and expansion of the different groups of bacteria based on recent large-scale phylogenetic analyses. I find that the Heliobacteriaceae family of Firmicutes appears to be the earliest branching of the known groups of phototrophic bacteria; however, the origin of photochemical reaction centers and chlorophyll synthesis cannot be placed in this group. Moreover, it becomes evident that the Acidobacteria and the Proteobacteria shared a more recent common phototrophic ancestor, and this is also likely for the Chloroflexi and the Cyanobacteria. Finally, I argue that the discrepancies among the phylogenies of the reaction center proteins, chlorophyll synthesis enzymes, and the species tree of bacteria are best explained if both types of photochemical reaction centers evolved before the diversification of the known phyla of phototrophic bacteria. The primordial phototrophic ancestor must have had both Type I and Type II reaction centers

Terrestrial invasion of pomatiopsid gastropods in the heavy-snow region of the Japanese Archipelago

<p>Abstract</p> <p>Background</p> <p>Gastropod mollusks are one of the most successful animals that have diversified in the fully terrestrial habitat. They have evolved terrestrial taxa in more than nine lineages, most of which originated during the Paleozoic or Mesozoic. The rissooidean gastropod family Pomatiopsidae is one of the few groups that have evolved fully terrestrial taxa during the late Cenozoic. The pomatiopsine diversity is particularly high in the Japanese Archipelago and the terrestrial taxa occur only in this region. In this study, we conducted thorough samplings of Japanese pomatiopsid species and performed molecular phylogenetic analyses to explore the patterns of diversification and terrestrial invasion.</p> <p>Results</p> <p>Molecular phylogenetic analyses revealed that Japanese Pomatiopsinae derived from multiple colonization of the Eurasian Continent and that subsequent habitat shifts from aquatic to terrestrial life occurred at least twice within two Japanese endemic lineages. Each lineage comprises amphibious and terrestrial species, both of which are confined to the mountains in heavy-snow regions facing the Japan Sea. The estimated divergence time suggested that diversification of these terrestrial lineages started in the Late Miocene, when active orogenesis of the Japanese landmass and establishment of snowy conditions began.</p> <p>Conclusions</p> <p>The terrestrial invasion of Japanese Pomatiopsinae occurred at least twice beside the mountain streamlets of heavy-snow regions, which is considered the first case of this event in the area. Because snow coverage maintains stable temperatures and high humidity on the ground surface, heavy-snow conditions may have paved the way for these organisms from freshwater to land via mountain streamlets by preventing winter desiccation in mountain valleys. The fact that the terrestrialization of Pomatiopsidae occurred only in year-round wet environments, but not in seasonally dried regions, provides new insight into ancient molluscan terrestrialization.</p

Systematics, Phylogeny, and Distribution of Acer (maples) in the Cenozoic of Western North America

The known fossil fruits and leaves of Acer from western North America represent 91 species and 28 sections, 12 of which are extinct and are described as new sections of Acer. Sixty-four species are described as new, 2 new combinations are proposed, and 6 species are left unnamed; 21 have been previously described. The most diverse sections of Acer in the Tertiary of western North America are the extinct Glabroidea (at least 13 species), Negundo (9 species), Macrophylla (8 species), and Eriocarpa (8 species), Descriptions of almost all the species are presented, and all species are illustrated. Although Aceraceae are considered to be derivatives of an early, extinct group of Sapindaceae, Paullinieae (rather than Harpullieae) are considered 10 be the extant tribe of Sapindaceae most closely related 10 Aceraceae. A cladistic analysis of Aceraceae and of Acer includes Sapindaceae, Dipteronia, and the "Acer" arcticum complex, which is thought to represent an extinct genus of Aceraceae. The cladistic analysis based on extant Acer results in the subdivision of Acer into 4 informal groups: Spicata Group, Macrantha Group, Macrophylla Group (including section Acer and allies), and the Platanoidea Group. Timing of first appearances of the various groups and sections in the fossil record generally parallel the cladistic analysis. The Spicata Group is the oldest (latest Paleocene); this group includes three extinct sections in the early middle Eocene, all of which became extinct by the late middle Eocene. First known in the early middle Eocene are extinct sections of the Macrantha and Macrophylla groups; extant sections of these groups appear by the late middle to early late Eocene. The Platanoidea Group appeared in the late middle Eocene, and extant sections appeared by the latest Eocene. A fifth group, the Orba Group, is known only as fossil and represents sections that diverged between the divergences of the Macrantha and Macrophylla groups. Diversification of Acer at the sectional level appears to have taken place in a volcanic upland region in western North America during the Eocene. Although possibly a mesothermal genus during the late Paleocene and early Eocene, Acer diversified greatly during the middle and late Eocene as microthermal climates increased in area. During the early middle Eocene, 10 sections (all extinct) and 11 species of Acer are known. During the late middle to late Eocene, Acer reached maximal diversity in western North America: at least 34 species and 15 sections are known, and occurrences of other species and sections can be inferred. Acer, however, was apparently a very minor element in Eocene microthermal vegetation. Sectional diversification of Acer was largely completed by the end of the Eocene, although a few derivative sections may be of post-Eocene age. Acer reached maximum abundance in western North America during the early and middle Miocene: at least 29 species and 10 sections are known. Following the middle Miocene, Acer underwent a major decline in diversity and abundance in western North America; this decline was due primarily to declining summer temperatures at high latitudes and increasing aridity at middle latitudes. Present distributions of sections and species of Acer have resulted from a complex history of dispersals and vicariant events, most of which are related to climate. Probable origin of many extant Asian sections of Acer in western North America during the Eocene implies many dispersals from North America to Asia during the Eocene. Many extinct and extant sections of Acer became extinct on North America during the late Eocene and early Oligocene; some of these extant sections re-entered North America during the late Oligocene and Miocene but again became extinct during the Miocene. Cladistic relationships of series Saccharodendron strongly indicate an origin in western Eurasia. Appearance of this section in North America during the early Miocene and absence of a Beringian fossil record indicate long-distance dispersal across the Atlantic Ocean. Absence of a Tertiary record in western North America of Palmata indicates a long-distance dispersal from eastern Asia

United States Geological Survey Report 1026

Abstract: Examination of previously described and some undescribed leaves of Ulmus and Zelkova from the later Oligocene, Miocene, and Pliocene of western North America indicates that at least eight species of Ulmus and two species of Zelkova are represented. Three new species are described: Ulmus chaneyi, U. knowltoni, and Zelkova browni