scholarly journals Taxonomic updates to Artocarpus subgenus Artocarpus (Moraceae) and allied taxa with a particular focus on the species native to Singapore

2021 ◽  
Vol 73 (2) ◽  
pp. 309-374
Author(s):  
E.M. Gardner ◽  
N.J.C. Zerega
Keyword(s):  
Phylogenetic Analyses ◽  
Distinct Species ◽  
Hybrid Origin ◽  
Second Step ◽  
Phylogenetic Position ◽  
Herbarium Specimens ◽  
Field Observations ◽  
Taxonomic Changes ◽  
Artocarpus Elasticus ◽  
Phylogenomic Analyses

The breadfruit genus Artocarpus J.R.Forst. & G.Forst. (Moraceae) has sixteen species in Singapore, fourteen of them native. In this precursory study to the treatment of Artocarpus for the Flora of Singapore, we present updated phylogenomic analyses of Artocarpus subgenus Artocarpus based on 517 nuclear genes. The following taxonomic changes based on recent phylogenetic analyses, review of herbarium specimens, and field observations, are proposed. Artocarpus subg. Cauliflori (F.M.Jarrett) Zerega is reduced to a section within Artocarpus subg. Artocarpus, and Artocarpus sect. Glandulifolium F.M.Jarrett is raised to subgenus status. The new monotypic subgenus Artocarpus subg. Aenigma E.M.Gardner & Zerega is proposed for Artocarpus sepicanus Diels, whose phylogenetic position remains uncertain and may be of ancient hybrid origin. Artocarpus elasticus Reinw. ex Blume, A. scortechinii King and A. corneri Kochummen are recognised as distinct species. Artocarpus clementis Merr. is reinstated as distinct from A. lanceifolius Roxb. Artocarpus calophyllus Kurz and A. melinoxylus Gagnep. are reinstated as distinct from both A. chama Buch.-Ham. and A. rigidus Blume. Artocarpus nigrescens Elmer is reinstated as distinct from A. treculianus Elmer. Keys to the subgenera, the sections of Artocarpus subg. Artocarpus and to the species found in Singapore are presented. A nomenclatural synopsis of subgenera Artocarpus, Aenigma and Glandulifolium is presented with taxonomic notes to aid in identification. Seventeen lectotypes, six of them in a second step, and two neotypes are designated.

Phylogenetic position of Sphaerospora testicularis and Latyspora scomberomori n. gen. n. sp. (Myxozoa) within the marine urinary clade

Parasitology ◽  
2010 ◽  
Vol 138 (3) ◽  
pp. 381-393 ◽  
Author(s):  
PAVLA BARTOŠOVÁ ◽  
MARK A. FREEMAN ◽  
HIROSHI YOKOYAMA ◽  
MONICA CAFFARA ◽  
IVAN FIALA
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dicentrarchus Labrax ◽  
Sensu Stricto ◽  
Phylogenetic Position ◽  
Species Cluster ◽  
The Family ◽  
Sutural Line ◽  
Taxonomic Changes

SUMMARYAn amendment of the family Sinuolineidae (Myxosporea) is proposed in order to include a newly described genus Latyspora n. gen. The type species Latyspora scomberomori n. gen. n. sp. is a coelozoic parasite in the kidney tubules of Scomberomorus guttatus. In addition to the morphological and molecular characterization of L. scomberomori n. gen. n. sp., we also present novel SSU rDNA data on Sphaerospora testicularis, a serious parasite of Dicentrarchus labrax. Performed phylogenetic analyses revealed that both species cluster within the marine urinary clade encompassing the representatives with a shared insertion within their V4 SSU rRNA region and grouping according to the shape of their spores’ sutural line and their similar tissue tropism in the host. Sphaerospora testicularis is the closest relative to Parvicapsula minibicornis within the Parvicapsula subclade and L. scomberomori n. gen. n. sp. is the basal species of the Zschokkella subclade. The phylogenetic position of S. testicularis, outwith the basal Sphaerospora sensu stricto clade, and its morphology suggest it being a non-typical Sphaerospora. The sequence data provided on S. testicularis can help in future revisions of the strongly polyphyletic genus Sphaerospora. We recommend re-sequencing of several sphaerosporids as an essential step before such taxonomic changes are accomplished.

Toward an Updated Taxonomy of the South American Chenopodiaceae I: Subfamilies Betoideae, Camphorosmoideae, and Salsoloideae

2021 ◽  
Vol 106 ◽  
pp. 10-30
Author(s):  
Nicolás F. Brignone ◽  
Silvia S. Denham
Keyword(s):  
South America ◽  
Taxonomic Revision ◽  
Second Step ◽  
Herbarium Specimens ◽  
South American ◽  
Field Observations ◽  
The South ◽  
Type Specimens ◽  
Salsola Kali ◽  
New Synonyms

This paper is the first in a projected series of publications treating the Chenopodiaceae in South America. We present here a taxonomic revision of subfamilies Betoideae, Camphorosmoideae, and Salsoloideae in South America, where all representatives of these subfamilies are introduced. Our research is based on the study of herbarium material, type specimens, digital images, original publications, and field observations. The South American Chenopodiaceae flora includes only Beta vulgaris L. from Betoideae, Bassia hyssopifolia (Pall.) Kuntze, Bassia scoparia (L.) A. J. Scott, and Maireana brevifolia (R. Br.) P. G. Wilson from Camphorosmoideae, and Salsola kali L., Salsola tragus L., and Soda inermis Fourr. from Salsoloideae. Lectotypes for Echinopsilon reuterianus Boiss., Kochia alata Bates, K. parodii Aellen, K. parodii var. elongata Aellen, K. parodii var. densa Aellen, K. parodii var. glabrescens Aellen, and Suaeda sieversiana Pall. are designated here, as well as a second-step lectotype for K. brevifolia R. Br. The distribution of all species is updated based on the revision and proper identification of many herbarium specimens and field observations. The distribution of M. brevifolia in Chile is here expanded. New synonyms for Bassia scoparia are proposed. A preliminary key to the genera of Chenopodiaceae in South America is also presented.

scholarly journals Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Luis Javier Galindo ◽  
Purificación López-García ◽  
Guifré Torruella ◽  
Sergey Karpov ◽  
David Moreira
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Gene Repertoire ◽  
Parasitic Fungi ◽  
Hyphal Morphogenesis ◽  
Specific Proteins ◽  
Phylogenomic Analyses ◽  
Protein Datasets

AbstractCompared to multicellular fungi and unicellular yeasts, unicellular fungi with free-living flagellated stages (zoospores) remain poorly known and their phylogenetic position is often unresolved. Recently, rRNA gene phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and long kinetosomes, the sanchytrids Amoeboradix gromovi and Sanchytrium tribonematis, showed that they formed a monophyletic group without close affinity with known fungal clades. Here, we sequence single-cell genomes for both species to assess their phylogenetic position and evolution. Phylogenomic analyses using different protein datasets and a comprehensive taxon sampling result in an almost fully-resolved fungal tree, with Chytridiomycota as sister to all other fungi, and sanchytrids forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Comparative genomic analyses across fungi and their allies (Holomycota) reveal an atypically reduced metabolic repertoire for sanchytrids. We infer three main independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. Based on sanchytrids’ phylogenetic position and unique traits, we propose the designation of a novel phylum, Sanchytriomycota. In addition, our results indicate that most of the hyphal morphogenesis gene repertoire of multicellular fungi had already evolved in early holomycotan lineages.

Phylogenetic relationships within Cicuta (Apiaceae tribe Oenantheae) inferred from nuclear rDNA ITS and cpDNA sequence data

2006 ◽  
Vol 84 (3) ◽  
pp. 453-468 ◽  
Author(s):  
Chang-Shook Lee ◽  
Stephen R. Downie
Keyword(s):  
North American ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Distinct Species ◽  
Sister Group ◽  
Nuclear Ribosomal Dna ◽  
Hybrid Origin ◽  
Rdna Its ◽  
The North

The genus Cicuta (Apiaceae tribe Oenantheae Dumort.) is the most virulently poisonous group of flowering plants native to the north temperate zone. A recent treatment recognized four species ( C. bulbifera L., C. douglasii (DC.) J.M. Coult. & Rose, C. maculata L., and C. virosa L.), with C. maculata divided into four varieties. We present results of phylogenetic analyses of the nuclear ribosomal DNA (rDNA) internal transcribed spacer (ITS) locus and the region bounded by the chloroplast genes psbI and trnK 5′ exon to determine taxonomic limits and relationships among these taxa, and to assess the taxonomic status of C. douglasii, a polyploid thought to be derived from C. maculata and C. virosa. Cicuta bulbifera and C. virosa are each resolved as monophyletic, the latter is a sister group to all other species. Discordance between the ITS- and plastid-derived phylogenies and lack of resolution in the ITS trees preclude unequivocal hypotheses of relationship; all trees do suggest, however, that the allotetraploid C. douglasii is polyphyletic and possibly polytopic, with all examined accessions but one nested within C. maculata. This single outstanding accession is from California and, pending further study, might warrant recognition as a distinct species. The diploid C. bulbifera may also be of hybrid origin, as revealed by significant discordance between data sets. Within C. maculata, only the western North American var. angustifolia Hook. is resolved in the ITS trees. In the cpDNA trees, C. maculata var. angustifolia comprises a strongly supported clade with C. maculata var. bolanderi (S. Watson) G.A. Mulligan and C. douglasii, both of primarily western North American distribution. The eastern North American taxa, C. maculata vars. maculata and victorinii (Fernald) B. Boivin, also comprise a clade, sister group to C. bulbifera.

scholarly journals Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota

2020 ◽  
Author(s):  
Luis Javier Galindo ◽  
Purificación López-García ◽  
Guifré Torruella ◽  
Sergey Karpov ◽  
David Moreira
Keyword(s):  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
28S Rrna ◽  
Gene Repertoire ◽  
Protein Markers ◽  
Parasitic Fungi ◽  
Molecular Phylogenetic ◽  
Phylogenomic Analyses

AbstractCompared to well-known multicellular fungi and unicellular yeast, unicellular fungi with zoosporic, free-living flagellated stages remain poorly known and their phylogenetic position is often unresolved. Recently, 18S+28S rRNA gene molecular phylogenetic analyses of two atypical parasitic fungi with amoeboid zoospores and record-long simplified kinetosomes, Amoeboradix gromovi and Sanchytrium tribonematis, showed that they formed a monophyletic group without affinity with any known fungal clade. To assess their phylogenetic position and unique trait evolution, we sequenced single-cell genomes for both species. Phylogenomic analyses using 264 protein markers and a comprehensive taxon sampling retrieved and almost fully-resolved fungal tree with these species forming a well-supported, fast-evolving clade sister to Blastocladiomycota. Chytridiomycota branched as sister to all other fungi, and the zoosporic fungus Olpidium bornovanus as sister to non-flagellated fungi. Comparative genomic analyses across Holomycota revealed an atypically reduced metabolic repertoire for sanchytrids given their placement in the tree. We infer four independent flagellum losses from the distribution of over 60 flagellum-specific proteins across Holomycota. The highly reduced sanchytrid flagellar machinery, notably their long kinetosome, might have been retained to support a putative light-sensing lipid organelle. Together with their phylogenetic position, these unique traits justify the erection of the novel phylum Sanchytriomycota. Our results also show that most of the hyphal morphogenesis gene repertoire of multicellular Fungi had already evolved in early holomycotan lineages.

Taxonomic changes in C4 Cyperus (Cypereae, Cyperoideae, Cyperaceae): combining the sedge genera Ascolepis, Kyllinga and Pycreus into Cyperus s.l.

Phytotaxa ◽  
2014 ◽  
Vol 166 (1) ◽  
pp. 33 ◽  
Author(s):  
ISABEL LARRIDON ◽  
KENNETH BAUTERS ◽  
MARC REYNDERS ◽  
WIM HUYGH ◽  
PAUL GOETGHEBEUR
Keyword(s):  
Phylogenetic Analyses ◽  
Single Species ◽  
Herbarium Specimens ◽  
New Combinations ◽  
Phylogenetic Hypothesis ◽  
Generic Level ◽  
Separate Paper ◽  
Molecular Phylogenetic ◽  
Taxonomic Changes ◽  
Sectional Classification

The sedge genera Alinula, Ascolepis, Kyllinga, Lipocarpha, Pycreus, Queenslandiella, Remirea, Sphaerocyperus and Volkiella (Cyperaceae) were recognised at generic level because they possess specialised inflorescence and/or flower characters. However, recent molecular phylogenetic analyses show that these genera are all nested in a paraphyletic Cyperus s.s. and therefore should be viewed as part of a broadly circumscribed genus Cyperus. For all species of Alinula and for the single species of Queenslandiella, Remirea and Sphaerocyperus, Cyperus names were already published by other authors. For the species of Lipocarpha and Volkiella, Cyperus names and a new sectional classification are published in a separate paper including a detailed molecular phylogenetic hypothesis for these taxa. Based on a study of herbarium specimens and literature, in this paper, twenty species of Ascolepis, seventeen species of Kyllinga, and six species of Pycreus, which do not yet have a validly published and legitimate name in Cyperus, are formally included into Cyperus as new combinations or new names. Notes on the synonymy of an African Pycreus species are also included.

On the resurrection of Persicaria puritanorum (Polygonaceae)

Phytotaxa ◽  
2017 ◽  
Vol 308 (1) ◽  
pp. 20
Author(s):  
SANG-TAE KIM ◽  
MICHAEL J. DONOGHUE ◽  
SONIA E. SULTAN
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Leaf Size ◽  
Its Region ◽  
Distinct Species ◽  
Hybrid Origin ◽  
Cape Cod ◽  
Herbarium Specimens ◽  
Maximum Width

Pond populations in Cape Cod described as Persicaria puritanorum (≡ Polygonum puritanorum) have been treated by recent authors as a synonym of P. maculosa (≡ Polygonum persicaria) based on gross morphology. However, consistent differences in leaf and inflorescence features raise the question as to whether this is an extreme phenotype of P. maculosa, an ecotype of that species, or a distinct taxon. In this study, we analyzed nuclear ITS region and chloroplast matK region DNA sequences from 37 populations of 11 species within section Eupersicaria and counted the chromosome number of individuals from the pond populations in question. We also compared leaf size and shape of plants from these populations with those of the typical P. maculosa plants by measuring selected herbarium specimens. Phylogenetic trees inferred from sequence data indicate a separation of pond populations from P. maculosa suggesting to recover P. puritanorum as a distinct species. Chromosome counts of pond population plants (2n = 60) strongly support this result, and furthermore suggest the possibility of a hybrid polyploid origin of P. puritanorum. A leaf morphological trait (greater relative height of the maximum width point from the leaf base) also supports the separation of pond populations from P. maculosa. P. punctata allied to P. hydropiper in the ITS-based tree, and to pond populations as well as P. hydropiperoides and P. opelousana in the matK-based tree, suggesting the possibility of hybrid origin of P. punctata. Our ITS sequence analyses also reveal distinct two lineages in P. lapathifolia but the chloroplast matK region sequences of P. pensylvanica and two lineages of P. lapathifolia are almost identical suggesting cytoplasmic introgression or allopolyploid speciation sharing the maternal lineage.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

scholarly journals Resolving Phylogenetic Relationships within Passeriformes Based on Mitochondrial Genes and Inferring the Evolution of Their Mitogenomes in Terms of Duplications

2019 ◽  
Vol 11 (10) ◽  
pp. 2824-2849 ◽  
Author(s):  
Paweł Mackiewicz ◽  
Adam Dawid Urantówka ◽  
Aleksandra Kroczak ◽  
Dorota Mackiewicz
Keyword(s):  
Phylogenetic Analyses ◽  
Mitochondrial Genes ◽  
The Other ◽  
Phylogenetic Position ◽  
Evolutionary Relationships ◽  
Mitochondrial Genomes ◽  
Ancestral State ◽  
Phylogenetic Information ◽  
Long Time ◽  
Tree Topologies

Abstract Mitochondrial genes are placed on one molecule, which implies that they should carry consistent phylogenetic information. Following this advantage, we present a well-supported phylogeny based on mitochondrial genomes from almost 300 representatives of Passeriformes, the most numerous and differentiated Aves order. The analyses resolved the phylogenetic position of paraphyletic Basal and Transitional Oscines. Passerida occurred divided into two groups, one containing Paroidea and Sylvioidea, whereas the other, Passeroidea and Muscicapoidea. Analyses of mitogenomes showed four types of rearrangements including a duplicated control region (CR) with adjacent genes. Mapping the presence and absence of duplications onto the phylogenetic tree revealed that the duplication was the ancestral state for passerines and was maintained in early diverged lineages. Next, the duplication could be lost and occurred independently at least four times according to the most parsimonious scenario. In some lineages, two CR copies have been inherited from an ancient duplication and highly diverged, whereas in others, the second copy became similar to the first one due to concerted evolution. The second CR copies accumulated over twice as many substitutions as the first ones. However, the second CRs were not completely eliminated and were retained for a long time, which suggests that both regions can fulfill an important role in mitogenomes. Phylogenetic analyses based on CR sequences subjected to the complex evolution can produce tree topologies inconsistent with real evolutionary relationships between species. Passerines with two CRs showed a higher metabolic rate in relation to their body mass.

scholarly journals Nephromyces represents a diverse and novel lineage of the Apicomplexa that has retained apicoplasts

2019 ◽  
Author(s):  
Sergio A Muñoz-Gómez ◽  
Keira Durnin ◽  
Laura Eme ◽  
Christopher Paight ◽  
Christopher E Lane ◽  
...  
Keyword(s):  
Life Style ◽  
Metabolic Pathways ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Phylogenetic Position ◽  
Biosynthetic Pathways ◽  
History Of ◽  
Sea Squirts ◽  
Shed Light ◽  
Apicoplast Genome

Abstract A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to (1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, (2) search for the apicoplast genome of Nephromyces, and (3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the non-photosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.

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