scholarly journals Insect phylogenomics: results, problems and the impact of matrix composition

2012 ◽  
Vol 279 (1741) ◽  
pp. 3282-3290 ◽  
Author(s):  
Harald O. Letsch ◽  
Karen Meusemann ◽  
Benjamin Wipfler ◽  
Kai Schütte ◽  
Rolf Beutel ◽  
...  
Keyword(s):  
Sequence Data ◽  
Morphological Characters ◽  
Data Matrix ◽  
Matrix Composition ◽  
Wide Sense ◽  
Heterogeneous Distribution ◽  
Pediculus Humanus ◽  
Stick Insects ◽  
Phylogenomic Analyses ◽  
The Impact

In this study, we investigated the relationships among insect orders with a main focus on Polyneoptera (lower Neoptera: roaches, mantids, earwigs, grasshoppers, etc.), and Paraneoptera (thrips, lice, bugs in the wide sense). The relationships between and within these groups of insects are difficult to resolve because only few informative molecular and morphological characters are available. Here, we provide the first phylogenomic expressed sequence tags data (‘EST’: short sub-sequences from a c(opy) DNA sequence encoding for proteins) for stick insects (Phasmatodea) and webspinners (Embioptera) to complete published EST data. As recent EST datasets are characterized by a heterogeneous distribution of available genes across taxa, we use different rationales to optimize the data matrix composition. Our results suggest a monophyletic origin of Polyneoptera and Eumetabola (Paraneoptera + Holometabola). However, we identified artefacts of tree reconstruction (human louse Pediculus humanus assigned to Odonata (damselflies and dragonflies) or Holometabola (insects with a complete metamorphosis); mayfly genus Baetis nested within Neoptera), which were most probably rooted in a data matrix composition bias due to the inclusion of sequence data of entire proteomes. Until entire proteomes are available for each species in phylogenomic analyses, this potential pitfall should be carefully considered.

scholarly journals Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

2016 ◽  
Vol 6 (12) ◽  
pp. 3927-3939 ◽  
Author(s):  
Xing-Xing Shen ◽  
Xiaofan Zhou ◽  
Jacek Kominek ◽  
Cletus P Kurtzman ◽  
Chris Todd Hittinger ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Sequence Data ◽  
Data Matrix ◽  
Data Sets ◽  
Codon Positions ◽  
Phylogenomic Analyses ◽  
Genome Scale ◽  
Yeast Genomes ◽  
Yeast Phylogeny ◽  
Data Matrices

Abstract Understanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multilocus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing nine of the 11 known major lineages and 10 nonyeast fungal outgroups to generate a 1233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the nine major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, eight of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and the species Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

scholarly journals Reconstructing the backbone of the Saccharomycotina yeast phylogeny using genome-scale data

2016 ◽  
Author(s):  
Xing-Xing Shen ◽  
Xiaofan Zhou ◽  
Jacek Kominek ◽  
Cletus P. Kurtzman ◽  
Chris Todd Hittinger ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Sequence Data ◽  
Data Matrix ◽  
Data Sets ◽  
Codon Positions ◽  
Phylogenomic Analyses ◽  
Genome Scale ◽  
Yeast Genomes ◽  
Yeast Phylogeny ◽  
Data Matrices

AbstractUnderstanding the phylogenetic relationships among the yeasts of the subphylum Saccharomycotina is a prerequisite for understanding the evolution of their metabolisms and ecological lifestyles. In the last two decades, the use of rDNA and multi-locus data sets has greatly advanced our understanding of the yeast phylogeny, but many deep relationships remain unsupported. In contrast, phylogenomic analyses have involved relatively few taxa and lineages that were often selected with limited considerations for covering the breadth of yeast biodiversity. Here we used genome sequence data from 86 publicly available yeast genomes representing 9 of the 11 major lineages and 10 non-yeast fungal outgroups to generate a 1,233-gene, 96-taxon data matrix. Species phylogenies reconstructed using two different methods (concatenation and coalescence) and two data matrices (amino acids or the first two codon positions) yielded identical and highly supported relationships between the 9 major lineages. Aside from the lineage comprised by the family Pichiaceae, all other lineages were monophyletic. Most interrelationships among yeast species were robust across the two methods and data matrices. However, 8 of the 93 internodes conflicted between analyses or data sets, including the placements of: the clade defined by species that have reassigned the CUG codon to encode serine, instead of leucine; the clade defined by a whole genome duplication; and of Ascoidea rubescens. These phylogenomic analyses provide a robust roadmap for future comparative work across the yeast subphylum in the disciplines of taxonomy, molecular genetics, evolutionary biology, ecology, and biotechnology. To further this end, we have also provided a BLAST server to query the 86 Saccharomycotina genomes, which can be found at http://y1000plus.org/blast.

scholarly journals Multi-locus phylogenetic analysis of lophiostomatoid fungi motivates a broad concept of Lophiostoma and reveals nine new species

2021 ◽  
Author(s):  
M. Andreasen ◽  
I. Skrede ◽  
W.M. Jaklitsch ◽  
H. Voglmayr ◽  
B. Nordén
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Morphological Traits ◽  
Sequence Data ◽  
Intraspecific Variability ◽  
Morphological Characters ◽  
Molecular Data ◽  
Data Matrix ◽  
Multigene Analysis ◽  
Broad Concept

Recent studies on the fungal families Lophiostomataceae and Lophiotremataceae (Pleosporales) have provided varying phylogenetic and taxonomic results concerning constituent genera and species. By adding DNA sequences of 24 new strains of Lophiostomataceae and nine new strains of Lophiotremataceae to a sequence data matrix from international databases, we provide a new understanding of the relationships within these families. Multigene analysis of the four molecular markers ITS, LSU, TEF1-α, and RPB2 reveals that the genera within Lophiotremataceae are phylogenetically well supported. Lophiostoma myriocarpum is recognised as a species of Lophiotrema in contrast to earlier concepts. In Lophiostomataceae, we resurrect a broad generic concept of the genus Lophiostoma and reduce 14 genera to synonymy: Alpestrisphaeria, Biappendiculispora, Capulatispora, Coelodictyosporium, Guttulispora, Lophiohelichrysum, Lophiopoacea, Neopaucispora, Neotrematosphaeria, Platystomum, Pseudocapulatispora, Pseudolophiostoma, Pseudoplatystomum, and Sigarispora. Nine new species are described based on molecular data and in most cases supported by morphological characters: Antealophiotrema populicola, Atrocalyx nordicus, Lophiostoma carpini, Lophiostoma dictyosporium, Lophiostoma erumpens, Lophiostoma fusisporum, Lophiostoma jotunheimenense, Lophiostoma plantaginis, and Lophiostoma submuriforme. Lophiostoma caespitosum and Lophiotrema myriocarpum are lecto- and epitypified to stabilise their species concepts. High intraspecific variability of several morphological traits is common within Lophiostomataceae.

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

Revised circumscription of Nothofagus and recognition of the segregate genera Fuscospora, Lophozonia, and Trisyngyne (Nothofagaceae)

Phytotaxa ◽  
2013 ◽  
Vol 146 (1) ◽  
pp. 1 ◽  
Author(s):  
PETER B. HEENAN ◽  
ROB D. SMISSEN
Keyword(s):  
Phylogenetic Analysis ◽  
South America ◽  
Papua New Guinea ◽  
New Genus ◽  
New Caledonia ◽  
Sequence Data ◽  
Morphological Characters ◽  
New Combinations ◽  
Southern South America ◽  
Dna Sequence Data

The generic taxonomy of the Nothofagaceae is revised. We present a new phylogenetic analysis of morphological characters and map these characters onto a recently published phylogenetic tree obtained from DNA sequence data. Results of these and previous analyses strongly support the monophyly of four clades of Nothofagaceae that are currently treated as subgenera of Nothofagus. The four clades of Nothofagaceae are robust and well-supported, with deep stem divergences, have evolutionary equivalence with other genera of Fagales, and can be circumscribed with morphological characters. We argue that these morphological and molecular differences are sufficient for the four clades of Nothofagaceae to be recognised at the primary rank of genus, and that this classification will be more informative and efficient than the currently circumscribed Nothofagus with four subgenera.        Nothofagus is recircumscribed to include five species from southern South America, Lophozonia and Trisyngyne are reinstated, and the new genus Fuscospora is described. Fuscospora and Lophozonia, with six and seven species respectively, occur in New Zealand, southern South America and Australia. Trisyngyne comprises 25 species from New Caledonia, Papua New Guinea and Indonesia. New combinations are provided where necessary in each of these genera.

A cladistic analysis of the Old World species of Lotus L. (Fabaceae: Loteae)

2000 ◽  
Vol 78 (3) ◽  
pp. 351-360 ◽  
Author(s):  
Ana M Arambarri
Keyword(s):  
Cladistic Analysis ◽  
Morphological Characters ◽  
Comparison Method ◽  
Data Matrix ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
World Species ◽  
Old World ◽  
Species Phylogeny ◽  
The World

The diagnostic characters of the genus Lotus L. are a claw with a thickened infolded margin, diadelphous stamens, and a style hardened from the base. This genus contains about 100 species that are distributed throughout the world. To investigate the phylogeny of the Old World species of Lotus, subgenus Edentolotus, sections Krokeria, Xantholotus, and Erythrolotus, a cladistic analysis was performed using 31 morphological characters. To test the phylogenetic relationships among species of Lotus-Edentolotus and Dorycnium, Pedrosia, and Tetragonolobus, these taxa were included as part of the ingroup. The polarity of the characters was based on the outgroup comparison method, using Anthyllis as one outgroup and Tripodion as another. The analysis with Anthyllis as outgroup yielded eight equally parsimonious trees (with all characters equally weighted), each with 62 steps, a consistency index of 0.53, and a retention index of 0.75. All trees (including the strict consensus tree from the eight initial trees) showed that genus Lotus, subgenus Edentolotus, and sections Xantholotus and Erythrolotus are polyphyletic, with only section Krokeria appearing as monophyletic. On the other hand, the groups of species Lotus angustissimus, Lotus corniculatus, Lotus creticus, and Lotus peregrinus are monophyletic. Identical results were derived from the data matrix using Tripodion as the outgroup. Results are compared with previous cytogenetic and biochemical evidence.Key words: cladistic analysis, Fabaceae, Loteae, Lotus, Old World species, phylogeny.

GEMPROT: visualization of the impact on the protein of the genetic variants found on each haplotype

2018 ◽  
Vol 35 (14) ◽  
pp. 2492-2494
Author(s):  
Tania Cuppens ◽  
Thomas E Ludwig ◽  
Pascal Trouvé ◽  
Emmanuelle Genin
Keyword(s):  
Genetic Variants ◽  
Protein Sequence ◽  
Sequence Data ◽  
Protein Sequences ◽  
Supplementary Information ◽  
Analysis Tool ◽  
Functional Protein ◽  
Key Players ◽  
On Line ◽  
The Impact

Abstract Summary When analyzing sequence data, genetic variants are considered one by one, taking no account of whether or not they are found in the same individual. However, variant combinations might be key players in some diseases as variants that are neutral on their own can become deleterious when associated together. GEMPROT is a new analysis tool that allows, from a phased vcf file, to visualize the consequences of the genetic variants on the protein. At the level of an individual, the program shows the variants on each of the two protein sequences and the Pfam functional protein domains. When data on several individuals are available, GEMPROT lists the haplotypes found in the sample and can compare the haplotype distributions between different sub-groups of individuals. By offering a global visualization of the gene with the genetic variants present, GEMPROT makes it possible to better understand the impact of combinations of genetic variants on the protein sequence. Availability and implementation GEMPROT is freely available at https://github.com/TaniaCuppens/GEMPROT. An on-line version is also available at http://med-laennec.univ-brest.fr/GEMPROT/. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals VARIABILITAS GENETIK DAN HERITABILITAS KARAKTER MORFOLOGIS BEBERAPA GENOTIPE KENTANG

EUGENIA ◽  
2013 ◽  
Vol 19 (2) ◽  
Author(s):  
Ventje Pangemanan ◽  
D. S. Runtunuwu ◽  
J. Pongoh
Keyword(s):  
Genetic Variability ◽  
Leaf Area ◽  
Plant Height ◽  
Narrow Range ◽  
Morphological Characters ◽  
Wide Sense ◽  
Number Of Leaves

ABSTRACT This study aimed to determine the genetic variability and heritability of morphological characters of some genotypes of potato at the Seed Station in Linelean Village, Modoinding of South Minahasa Regency. The results showed that, the relatively narrow range of genotypes variance for all the characters observed. The coefficient of variance genotypes for plant height, at 14, 42 and 56 DAP (Days After Planting) was relatively narrow, whereas at 7, 21, 28, 35 and 42 DAP relatively wide. For the character of the number of leaves at 7 and 14 DAP are wide and at 21, 28, 35, 42 and 49 DAP relatively narrow. For the character of leaf area at 7 and 14 DAP were wide and at 21, 28, 35, 42 and 49 DAP relatively narrow. For the character of the number of harvest tubers per plant and weight per tuber harvest were wide. Wide sense heritability were high for all the characters observed, except for plant height at 7 and 56 DAP were classified as moderate. Keywords: genotype variance, coefficient variance of genotype and heritability ABSTRAK Penelitian ini bertujuan untuk mengetahui variabilitas genetik dan heritabilitas karakter   morfologis beberapa genotipe kentang di Balai Benih Desa Linelean Modoinding Kabupaten Minahasa Selatan. Hasil penelitian menunjukkan bahwa ragam genotipe tergolong sempit untuk semua karakter yang diamati. Koefisien ragam genotipe untuk karakter tinggi tanaman, pada 14, 42 dan 56 HST (Hari Setelah Tanam)  tergolong sempit, sedangkan pada 7, 21, 28, 35 dan 42 HST tergolong luas. Untuk karakter jumlah daun pada 7 dan 14 HST tergolong luas dan pada 21, 28, 35, 42 dan 49 HST tergolong sempit. Untuk karakter luas daun pada 7 dan 14 HST tergolong luas dan pada 21, 28, 35, 42 dan 49 HST tergolong sempit. Untuk karakter jumlah umbi panen per tanaman dan berat per umbi panen tergolong luas. Heritabilitas arti luas semua karakter tergolong tinggi, kecuali untuk karakter tinggi tanaman pada 7 dan 56 HST yang tergolong sedang. Eugenia Volume 19  No. 2  Agustus 2013 Kata kunci: ragam genotipe, koefisien ragam genotipe dan heritabilitas

scholarly journals A new corticolous species of Mycena sect. Viscipelles (Basidiomycota: Agaricales) from the bark of a Living American elm tree in Texas, U.S.A.

2020 ◽  
Vol 14 (2) ◽  
pp. 167-185
Author(s):  
Brian A. Perry ◽  
Harold W. Keller ◽  
Edward D. Forrester ◽  
Billy G. Stone
Keyword(s):  
Sequence Data ◽  
Intermediate Stage ◽  
Morphological Characters ◽  
Morphological Features ◽  
Depth Of Field ◽  
Morphological Development ◽  
Fort Worth ◽  
Moist Chamber ◽  
American Elm ◽  
The North

A  Mycena species new to science was obtained from moist chamber cultures of trunk bark of a living American elm tree (Ulmus americana) located in the Fort Worth Botanic Garden, Tarrant County, Texas. This discovery was part of an ongoing study of corticolous myxomycetes on larger American elm trees occurring in Fort Worth nature parks. More than 15 American elm trees were sampled for trunk bark but only a single tree yielded  Mycena basidiomes. Collections of bark began in the summer of 2017 and continued until the beginning of 2020. Bark samples from the north, south and west side of the tree yielded fruit bodies of the mushroom in moist chamber culture. No fruit bodies were observed in nature nor were early formation stages on the underside of the bark. Crystals previously described in another study were present on the bark surfaces, edges, and undersides. Habit and morphological development were photographed using light microscopy applying multifocal imaging and computer stacking to increase depth of field. Basidiome development was observed and photographed from the earliest primordial beginning stage, the button stage, intermediate stage and the final emerging stalk elongation and mature cap formation stage. Mature mushroom development took from 9 to 21 days after wetting the bark in moist chamber cultures. Scanning electron microscopy was used to illustrate development of the button stage, emerging stalk and pileus stage, and the fully mature pileus, lamellae, and pseudocollarium. Morphological features and DNA sequence data confirmed that this  Mycena species was undescribed and distinct from other  Mycena taxa. Morphological features suggest placement of the novel taxon in  Mycena sect. Viscipelles, distinct from other members based on morphological characters and phylogenetic analysis.

scholarly journals Rapture-ready darters: choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference in Etheostoma

2020 ◽  
Author(s):  
Brendan N. Reid ◽  
Rachel L. Moran ◽  
Christopher J. Kopack ◽  
Sarah W. Fitzpatrick
Keyword(s):  
Reference Genome ◽  
Sequence Data ◽  
Low Cost ◽  
Read Depth ◽  
Model Organisms ◽  
Whole Genome ◽  
Reduced Representation ◽  
Sequence Capture ◽  
Population Genomic ◽  
The Impact

AbstractResearchers studying non-model organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, are still difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genus Etheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.

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