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1. The robustness of the chaos game representation to mutations and its application in free-alignment methods

Author:
Kania, Adrian; Sarapata, Krzysztof
Source:
Genomics 2021 v.113 no.3 pp. 1428-1437
ISSN:
0888-7543
Subject:
phylogeny,   etc   ; bioinformatics; genomics;     Show all 3 Subjects
Abstract:
... Numerical representation of biological sequences plays an important role in bioinformatics and has many practical applications. One of the most popular approaches is the chaos game representation. In this paper, the authors propose a novel look into chaos game construction - an analytical description of this procedure. This type enables to build more general number sequences using different weight ...
DOI:
10.1016/j.ygeno.2021.03.015

2. Further taxonomic notes on vespinae (hymenoptera: vespidae)

Author:
Carpenter, James M.
Source:
Entomologica americana 2021 v.126 no.1-4 pp. 108-111
ISSN:
1947-5144
Subject:
phylogeny,   etc   ; Dolichovespula; lectotypes;     Show all 3 Subjects
Abstract:
... Lectotypes are designated for two species of Vespinae: Dolichovespula arctica (Rohwer) and Vespula intermedia (du Buysson). Dolichovespula albida (Sladen) is diagnostically distinct from D. norwegica (Fabricius), therefore it is a distinct phylogenetic species. This is also the case for Vespula intermedia versus V. rufa (Linnaeus). ...
DOI:
10.1664/1947-5136-126.1.108

3. Heuristics for unrooted, unranked, and ranked anomaly zones under birth-death models

Author:
Kim, Anastasiia; Degnan, James H.
Source:
Molecular phylogenetics and evolution 2021 v.161 pp. 107162
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; genes; probability; topology; trees;     Show all 5 Subjects
Abstract:
... Species trees that can generate a nonmatching gene tree topology that is more probable than the topology matching the species tree are said to be in an anomaly zone. We introduce some heuristic approaches to infer whether species trees are in anomaly zones when it is difficult or impossible to compute the entire distribution of gene tree topologies. Here, probabilities of unrooted, unranked, and r ...
DOI:
10.1016/j.ympev.2021.107162

4. Collapsing dubiously resolved gene-tree branches in phylogenomic coalescent analyses

Author:
Simmons, Mark P.; Gatesy, John
Source:
Molecular phylogenetics and evolution 2021 v.158 pp. 107092
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; data collection; genes; topology;     Show all 4 Subjects
Abstract:
... In two-step coalescent analyses of phylogenomic data, gene-tree topologies are treated as fixed prior to species-tree inference. Although all gene-tree conflict is assumed to be caused by lineage sorting when applying these methods, in empirical datasets much of the conflict can be caused by estimation error. Weakly supported and even arbitrarily resolved clades are important sources of this estim ...
DOI:
10.1016/j.ympev.2021.107092

5. How Many Sipunculan Species Are Hiding in Our Oceans?

Author:
Schulze, Anja; Kawauchi, Gisele Y.
Source:
Diversity 2021 v.13 no.2
ISSN:
1424-2818
Subject:
phylogeny,   etc   ; Annelida; dissection; species diversity;     Show all 4 Subjects
Abstract:
... Sipuncula, long considered a separate phylum, are now commonly included in the Annelida based on phylogenomic analyses. The sipunculan body consists of an unsegmented trunk and a retractable introvert, usually with a set of tentacles at its anterior end. Unlike other annelids, they have no chaetae, but the introvert is often adorned with proteinaceous hooks that can be important taxonomic characte ...
DOI:
10.3390/d13020043

6. A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution

Author:
Orr, R.J.S.; Di Martino, E.; Gordon, D.P.; Ramsfjell, M.H.; Mello, H.L.; Smith, A.M.; Liow, L.H.
Source:
Molecular phylogenetics and evolution 2021 v.161 pp. 107172
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; Bryozoa; bioinformatics; fauna; mitochondria; New Zealand;     Show all 6 Subjects
Abstract:
... Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we allevi ...
DOI:
10.1016/j.ympev.2021.107172

7. Molecular data and phylogenetic analysis of Myxobolus pseudonobilis n. sp. infecting the gill filaments of silver carp, Hypophthalmichthys molitrix Valenciennes, 1844

Author:
Xiang, Yao; Zhang, Jinye; Zhao, Yuanjun
Source:
Parasitology international 2021 v.83 pp. 102314
ISSN:
1383-5769
Subject:
phylogeny,   etc   ; Hypophthalmichthys molitrix; Myxobolus; parasitology; spores; China;     Show all 6 Subjects
Abstract:
... In the present study, we combined morphological and phylogenetic methods to characterize Myxobolus pseudonobilis n. sp. infecting Hypophthalmichthys molitrix Valenciennes, 1844 from Chongqing, China. The morphology and molecular characteristics of M. pseudonobilis n. sp. were distinct from those of other previously described Myxobolus species. Mature myxospores were ovoid in frontal view with spor ...
DOI:
10.1016/j.parint.2021.102314

8. Transmission dynamics and molecular characterization of HIV-1 epidemic among therapeutic failure patients in Santa Catarina state, southern Brazil

Author:
Fritsch, Hegger M.; Tanuri, Amilcar; Pinto, Aguinaldo R.; Gräf, Tiago
Source:
Infection, genetics, and evolution 2021 v.92 pp. 104854
ISSN:
1567-1348
Subject:
phylogeny,   etc   ; databases; genotyping; infection; mortality; therapeutics; Brazil;     Show all 7 Subjects
Abstract:
... The HIV-1 epidemic in southern Brazil is mostly caused by subtype C, which contrasts the dominance of subtype B in the other regions of the country. Santa Catarina (SC), although the smallest state in the southern region, presents one of the highest incidences and mortality rates in Brazil due to AIDS. This work investigated the HIV-1 molecular diversity and phylogenetic transmission networks in S ...
DOI:
10.1016/j.meegid.2021.104854

9. Decoding the genome of superior chapatti quality Indian wheat variety ‘C 306’ unravelled novel genomic variants for chapatti and nutrition quality related genes

Author:
Mishra, Ankita; Singh, Akshay; Mantri, Shrikant; Pandey, Ajay K.; Garg, Monika; Deshmukh, Rupesh; Sonah, Humira; Kandoth, Pramod Kaitheri; Sharma, Tilak Raj; Roy, Joy
Source:
Genomics 2021 v.113 no.4 pp. 1919-1929
ISSN:
0888-7543
Subject:
phylogeny,   etc   ; DNA; genes; genomics; nutrition; wheat;     Show all 6 Subjects
Abstract:
... An Indian wheat variety, ‘C 306’ has good chapatti quality, which is controlled by multiple genes that have not been explored. We report the high quality de novo assembled genome of ‘C 306’ by combining short and long read sequencing data. The hybrid assembly covered 93% of gene space and identified about 142 K coding genes, 34% repetitive DNA and ~ 501 K SSR motifs. The phylogenetic analysis of a ...
DOI:
10.1016/j.ygeno.2021.03.031

10. Amphibian responses in experimental thermal gradients: Concepts and limits for inference

Author:
Navas, Carlos A.; Gouveia, Sidney F.; Solano-Iguarán, Jaiber J.; Vidal, Marcela A.; Bacigalupe, Leonardo D.
Source:
Comparative biochemistry and physiology 2021 v.254 pp. 110576
ISSN:
1096-4959
Subject:
phylogeny,   etc   ; amphibians; biochemistry; models; ontogeny; thermoregulation;     Show all 6 Subjects
Abstract:
... The interpretation of thermal-gradient data depends on the behavioral drives reported or assumed, and on the underlying behavioral models explaining how such drives operate. The best-known example is positive thermotaxis, a thermoregulatory behavioral drive frequently linked to a dual set-point model of thermoregulation around a target range. This behavioral drive is often assumed as dominant amon ...
DOI:
10.1016/j.cbpb.2021.110576

11. Occurrence of flavonoids in different Lamiaceae taxa for a preliminary study on their evolution based on phytochemistry

Author:
Frezza, Claudio; Venditti, Alessandro; Giuliani, Claudia; Foddai, Sebastiano; Cianfaglione, Kevin; Maggi, Filippo; Fico, Gelsomina; Guiso, Marcella; Nicoletti, Marcello; Bianco, Armandodoriano; Serafini, Mauro
Source:
Biochemical systematics and ecology 2021 v.96 pp. 104247
ISSN:
0305-1978
Subject:
phylogeny,   etc   ; Lamiaceae; chemotaxonomy; ecology; flavonoids; iridoids;     Show all 6 Subjects
Abstract:
... In this work, the continuation of the study of the plant evolution based on phytochemistry was presented. Flavonoids were used to draw a Sporne evolution diagram of selected Lamiaceae taxa. From a phytochemical evolution standpoint, results showed similarities and differences with regard to the previous work on iridoids. In addition, analogies and diversities from the phylogenetic tree based on mo ...
DOI:
10.1016/j.bse.2021.104247

12. Origin and diversification of ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) genes in land plants and phylogenetic evidence that the ancestral CER1/3 gene resulted from the fusion of pre-existing domains

Author:
Chaudhary, Komal; Geeta, R.; Panjabi, Priya
Source:
Molecular phylogenetics and evolution 2021 v.159 pp. 107101
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; Archaea; Charophyta; Miozoa; ancestry; genes;     Show all 6 Subjects
Abstract:
... ECERIFERUM1 (CER1) and ECERIFERUM3 (CER3) are key genes in synthesis of alkanes, a major component of cuticular waxes in land plants. The genes share extensive similarity, including the N-terminal (ERG3/FAH) and C-terminal (WAX2) domains. This study, traces the origin, evolutionary history, phylogenetic relationships and variation in copy number of the two genes within and beyond the Viridiplantae ...
DOI:
10.1016/j.ympev.2021.107101

13. A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths

Author:
Kimball, Rebecca T.; Hosner, Peter A.; Braun, Edward L.
Source:
Molecular phylogenetics and evolution 2021 v.158 pp. 107091
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; Galliformes; chickens; exons; introns; mitochondria; models;     Show all 7 Subjects
Abstract:
... Building taxon-rich phylogenies is foundational for macroevolutionary studies. One approach to improve taxon sampling beyond individual studies is to build supermatricies of publicly available data, incorporating taxa sampled across different studies and utilizing different loci. Most existing supermatrix studies have focused on loci commonly sequenced with Sanger technology (“legacy” markers, suc ...
DOI:
10.1016/j.ympev.2021.107091

14. Bryophytes are not early diverging land plants

Author:
McDaniel, Stuart F.
Source:
Thenew phytologist 2021 v.230 no.4 pp. 1300-1304
ISSN:
0028-646X
Subject:
phylogeny,   etc   ; case studies; literacy; plant taxonomy;     Show all 4 Subjects
Abstract:
... Phylogenetic trees have permeated biology. However, an understanding of how to interpret phylogenies has lagged behind, notably in publications outside of evolutionary biology. Here I argue that some language commonly used in plant systematics has contributed to the confusion by describing phylogenetic trees using intuitive but misleading terms reminiscent of Aristotle's Scala Naturae. These terms ...
DOI:
10.1111/nph.17241

15. A new synonym of Polygonatum in China, based on morphological and molecular evidence

Author:
Xia, Maoqin; Liu, Ying; Liu, Jingjing; Chen, Donghong; Shi, Yan; Bai, Zhicong; Xiao, Yu; Peng, Chen; Si, Jinping; Li, Pan; Qiu, Yingxiong
Source:
PhytoKeys 2021 v.175 pp. 137-149
ISSN:
1314-2003
Subject:
phylogeny,   etc   ; Polygonatum; autumn; perianth; spring; China;     Show all 6 Subjects
Abstract:
... PolygonatumkingianumCollett et Hemsl.var.grandifolium D.M. Liu & W.Z. Zeng (1981), which sprouts twice a year, once in spring and once in autumn, differs from Polygonatum kingianum in leaves, bracts, perianth and filaments. Morphological comparison and molecular phylogeny indicate that it is identical to the newly-published Polygonatum hunanense H.H. Liu & B.Z. Wang (2021). Hence, we propose that ...
DOI:
10.3897/phytokeys.175.63383

16. A robust phylogenomic framework for the calamoid palms

Author:
Kuhnhäuser, Benedikt G.; Bellot, Sidonie; Couvreur, Thomas L.P.; Dransfield, John; Henderson, Andrew; Schley, Rowan; Chomicki, Guillaume; Eiserhardt, Wolf L.; Hiscock, Simon J.; Baker, William J.
Source:
Molecular phylogenetics and evolution 2021 v.157 pp. 107067
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; Calamus; genomics; industry; species diversity;     Show all 5 Subjects
Abstract:
... Well-supported phylogenies are a prerequisite for the study of the evolution and diversity of life on earth. The subfamily Calamoideae accounts for more than one fifth of the palm family (Arecaceae), occurs in tropical rainforests across the world, and supports a billion-dollar industry in rattan products. It contains ca. 550 species in 17 genera, 10 subtribes and three tribes, but their phylogene ...
DOI:
10.1016/j.ympev.2020.107067

17. Phylogenetic analysis of hyperaccumulator plant species for heavy metals and polycyclic aromatic hydrocarbons

Author:
Rajput, Vishnu; Minkina, Tatiana; Semenkov, Ivan; Klink, Galya; Tarigholizadeh, Sarieh; Sushkova, Svetlana
Source:
Environmental geochemistry and health 2021 v.43 no.4 pp. 1629-1654
ISSN:
0269-4042
Subject:
phylogeny,   etc   ; ; biotransformation; geochemistry; hyperaccumulators; soil remediation; toxicity;     Show all 7 Subjects
Abstract:
... Increasing concentration of heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) in the soil may impose a serious threat to living organisms due to their toxicity and the ability to accumulate in plant tissues. The present review focuses on the phylogenetic relationships, sources, biotransformation and accumulation potential of hyperaccumulators for the priority HMs and PAHs. This review ...
DOI:
10.1007/s10653-020-00527-0

18. Phylogenomics of Gesneriaceae using targeted capture of nuclear genes

Author:
Ogutcen, Ezgi; Christe, Camille; Nishii, Kanae; Salamin, Nicolas; Möller, Michael; Perret, Mathieu
Source:
Molecular phylogenetics and evolution 2021 v.157 pp. 107068
ISSN:
1055-7903
Subject:
phylogeny,   etc   ; ; Gesneriaceae; flower morphology; genes; statistical analysis;     Show all 6 Subjects
Abstract:
... Gesneriaceae (ca. 3400 species) is a pantropical plant family with a wide range of growth form and floral morphology that are associated with repeated adaptations to different environments and pollinators. Although Gesneriaceae systematics has been largely improved by the use of Sanger sequencing data, our understanding of the evolutionary history of the group is still far from complete due to the ...
DOI:
10.1016/j.ympev.2021.107068

19. Phylogeny and taxonomy of two new Alternaria (Ascomycota: Pleosporaceae) species in section Gypsophilae from China

Author:
He, Lin; Cheng, Hong; Htun, Aye Aye; Ge, Hui; Xia, Zhen Zhou; Guo, Jian Wei; Deng, Jian Xin; Du, Tao
Source:
Mycological progress 2021 v.20 no.4 pp. 355-363
ISSN:
1617-416X
Subject:
phylogeny,   etc   ; Alternaria; Caryophyllaceae; new species; pathogenicity; China;     Show all 6 Subjects
Abstract:
... During investigation of pathogenic Alternaria in China, nine Alternaria isolates were obtained from two Caryophyllaceae plants. Based on morphological and multilocus phylogenetic approaches and pathogenicity tests, three pathogenic species of Alternaria including two new species and a new record in China were identified. Phylogenetically, the present species were confirmed and grouped within two c ...
DOI:
10.1007/s11557-021-01676-x

20. Streptomyces bathyalis sp. nov., an actinobacterium isolated from the sponge in a deep sea

Author:
Risdian, Chandra; Landwehr, Wiebke; Rohde, Manfred; Schumann, Peter; Hahnke, Richard L.; Spröer, Cathrin; Bunk, Boyke; Kämpfer, Peter; Schupp, Peter J.; Wink, Joachim
Source:
Antonie van Leeuwenhoek 2021 v.114 no.4 pp. 425-435
ISSN:
0003-6072
Subject:
phylogeny,   etc   ; Streptomyces; genes; menaquinones; Atlantic Ocean;     Show all 5 Subjects
Abstract:
... A novel actinobacterium, designated ASO4wetᵀ, was isolated from the unidentified sponge (SO4) in the deep sea collected of the North Atlantic Ocean. Study of 16S rRNA gene sequences indicated that strain ASO4wetᵀ is a member of the genus Streptomyces and showed the closest similarities to Streptomyces karpasiensis K413ᵀ (98.87 %), Streptomyces glycovorans YIM M 10366ᵀ (98.38 %), and Streptomyces a ...
DOI:
10.1007/s10482-021-01528-4