Rafael Medina

350 My of Mitochondrial Genome Stasis in Mosses, an Early Land Plant Lineage

Among land plants, angiosperms have the structurally most labile mitochondrial (mt) genomes. In contrast, the so-called early land plants (e.g., mosses) seem to have completely static mt chromosomes. We assembled the complete mt genomes from 12 mosses spanning the moss tree of life, to assess 1) the phylogenetic depth of the conserved mt gene content and order and 2) the correlation between scattered sequence repeats and gene order lability in land plants. The mt genome of most mosses is approximately 100 kb in size, and thereby the smallest among land plants. Based on divergence time estimates, moss mt genome structure has remained virtually frozen for 350 My, with only two independent gene losses and a single gene relocation detected across the macroevolutionary tree. This is the longest period of mt genome stasis demonstrated to date in a plant lineage. The complete lack of intergenic repeat sequences, considered to be essential for intragenomic recombinations, likely accounts for the evolutionary stability of moss mt genomes.

HybPiper: Extracting Coding Sequence and Introns for Phylogenetics from High-Throughput Sequencing Reads Using Target Enrichment

Premise of the study: Using sequence data generated via target enrichment for phylogenetics requires reassembly of high-throughput sequence reads into loci, presenting a number of bioinformatics challenges. We developed HybPiper as a user-friendly platform for assembly of gene regions, extraction of exon and intron sequences, and identification of paralogous gene copies. We test HybPiper using baits designed to target 333 phylogenetic markers and 125 genes of functional significance in Artocarpus (Moraceae). Methods and Results: HybPiper implements parallel execution of sequence assembly in three phases: read mapping, contig assembly, and target sequence extraction. The pipeline was able to recover nearly complete gene sequences for all genes in 22 species of Artocarpus. HybPiper also recovered more than 500 bp of nontargeted intron sequence in over half of the phylogenetic markers and identified paralogous gene copies in Artocarpus. Conclusions: HybPiper was designed for Linux and Mac OS X and is freely available at https://github.com/mossmatters/HybPiper.

New national and regional bryophyte records, 43

1. Acaulon mediterraneum LimprContributor: R. NatchevaBulgaria: Blagoevgrad region, Belasitsa Nature Park, south of the road between the villages of Razdak and Drangovo, on soil in pasture, 41.3981...

Lewinskya, a New Genus to Accommodate the Phaneroporous and Monoicous Taxa of Orthotrichum (Bryophyta, Orthotrichaceae)

Abstract Molecular analyses have consistently evidenced the phylogenetic heterogeneity of Orthotrichum Hedw., and suggested the need to segregate the species with superficial stomata in a separate genus. A recent proposal has been made to accommodate the monoicous species with such stomata in the genus Dorcadion Adans. ex Lindb., which is, however, an illegitimate name according to the current Code of nomenclature of algae, fungi and plants. Consequently a new name is required, and the generic name Lewinskya F.Lara, Garilleti & Goffinet is proposed. New combinations are made for all the species included in the new genus. Given the long history of the genus Orthotrichum and the similarities between this genus and Lewinskya, the morphological and geographic circumscriptions of both genera are provided to define them accurately. The taxa remaining in Orthotrichum s.str. are also listed.

A new look at Orthotrichum scanicum Grönvall (Orthotrichaceae, Bryophyta)

Abstract Orthotrichum scanicum Grönvall has been considered a European endemic whose main range corresponded to the central and northern region of the continent, and it is currently included in the 2007 IUCN World Red List as Vulnerable. However, a large number of recent reports and the examination of herbarium specimens have remarkably expanded the limits of its area in the Mediterranean and Caucasian regions. Additionally, the revision of the original collections of Orthotrichum holmenii from Kazakhstan shows that this taxon is conspecific with O. scanicum. An updated description of the species comprising the known range of its morphological variability is provided, and its exclusion from the World Red List is suggested.

Epiphytic bryophytes in harsh environments: the Juniperus thurifera forests

Abstract The forests of Juniperus thurifera are peculiar ecosystems that typically grow on mountains and highplateaux of the western Mediterranean basin with dry and continental climates. Some previous surveys suggested that these forests house a rather distinctive epiphytic bryophyte flora. Epiphytic bryophyte communities were systematically sampled in 19 representative juniper forests, for the first time spanning all the distribution area of this conifer. The flora consists of 44 species (32 acrocarpous mosses, 10 pleurocarpous mosses and 2 liverworts). Orthotrichum species are the most frequent and abundant in most of the sampled localities, including some uncommon taxa such as Orthotrichum vittii which shows a clear association with J. thurifera. Epiphytic bryophyte communities on this species were highly homogeneous, although they can be arranged into different groups in response to environmental conditions. Typically, the epiphytic communities of the Mediterranean juniper forests comprise a distinct combination of xerophytic taxa that enhances the interest of these ecosystems and provides new fields for their research and conservation.

New national and regional bryophyte records, 27

ub lis he d by M an ey P ub lis hi ng ( c) B rit is h B ry ol og ic al S oc ie ty Bryological Note New national and regional bryophyte records, 27 L T Ellis, A K Asthana, Vinay Sahu, P Bansal, V Nath, P Erzberger, T Hallingback, M Infante, P Lazarevic, L Luis, R Medina, R Ochyra, N Pande, B Papp, V Plasek, M Sabovljevic, J Sawicki, M Sim-Sim, A Stebel, G M Suarez, J van Rooy, N Phephu Department of Botany, The Natural History Museum, London, UK, Bryology Laboratory, National Botanical Research Institute, Lucknow, India, Belziger Str. 37, Berlin, Germany, Swedish University of Agricultural Sciences, Uppsala, Sweden, Museo de Ciencias Naturales de Alava, Vitoria-Gasteiz, Spain, Institute for Nature Conservation of Serbia, Belgrade, Serbia, Faculdade de Ciencias de Lisboa, Universidade de Lisboa, Portugal, Instituto Piaget, Campus Universitario de Santo Andre, Portugal, Universidad Autonoma de Madrid, Spain, Laboratory of Bryology, Institute of Botany, Polish Academy of Sciences, Krakow, Poland, Department of Botany, Kumaun University, Nainital, India, Botanical Department, Hungarian Natural History Museum, Budapest, Hungary, Department of Biology and Ecology, University of Ostrava, Czech Republic, Faculty of Biology, Institute of Botany and Botanical Garden, University of Belgrade, Serbia, Deparment of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Poland, Museu Nacional de Historia Natural, Lisboa, Portugal, Department of Pharmaceutical Botany, Medical University of Silesia in Katowice, Poland, Facultad de Ciencias Naturales, Fundacion Miguel Lillo, Tucuman, Argentina, National Herbarium, South African National Biodiversity Institute, Pretoria, South Africa

New national and regional bryophyte records, 14

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Orthotrichum norrisii (Orthotrichaceae), a new epiphytic Californian moss

Abstract A new Orthotrichum species, O. norrisii, is described from California. The new taxon is recognized by a unique combination of sporophytic characters: capsule narrowly cylindrical and not contracted below mouth when dry, exothecial bands narrow and formed by 2(–3) cell rows, peristome with eight pairs of exostome teeth and eight endostome segments, stomata cryptopore and located in the lower part of the urn, lid plane and rostrate and vaginula hairy. Widely distributed throughout California, the new taxon has been overlooked and confused with O. tenellum.

DNA based revised geographic circumscription of species of Physcomitrella s.l. (Funariaceae): P. patens new to East Asia and P. magdalenae new to East Africa

Abstract Physcomitrella, as traditionally defined, accommodates certain Funariaceae with immersed and cleistocarpous capsules. Recent molecular inferences revealed that the three or four taxa typically recognized within Physcomitrella did not arise from a unique common ancestor, and hence that their morphological similarities likely resulted from convergence, while one potential taxon, P. patens subsp. californica ( = Physcomitridium readeri s.l.), is currently regarded as a polyphyletic entity, making Physcomitridium polyphyletic. Following recent discoveries that would greatly expand the known range of two taxa, we sampled populations of Physcomitrella s.l. from all main geographic regions, and sequenced the nuclear ITS regions and four plastid loci to assess the geographic circumscription of each clade. We recovered three unambiguous monophyletic entities matching the three morphotypes recognized by Fife, each with a distinct geographic range: Physcomitrella patens s.str. with a range in Europe and North America extended to East Asia (China); P. magdalenae with a range from West and Central Africa extended eastwards to Ethiopia; and Physcomitridium (Physcomitrella) readeri from western Europe and western North America to Japan and Australia, plus a doubtful occurrence in China. Although the distinction of P. californica from P. readeri remains doubtful, we reject the hypothesis that Physcomitridium is polyphyletic, arguing that this resulted from a misidentification of the sequenced voucher.