Taxonomic revisions within Embiotocidae (Teleostei, Perciformes) based on molecular phylogenetics

Zootaxa ◽  
2018 ◽  
Vol 4482 (3) ◽  
pp. 591 ◽  
Author(s):  
GARY C. LONGO ◽  
GIACOMO BERNARDI ◽  
ROBERT N. LEA
Keyword(s):  
Natural History ◽  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Eastern Pacific ◽  
Interspecific Relationship ◽  
Interspecific Relationships ◽  
Full Resolution ◽  
Molecular Phylogenetic ◽  
Pacific Species

Embiotocidae, a unique family within the Perciformes that has evolved a complex viviparous natural history, has lacked full resolution and strong support in several interspecific relationships until recently. Here we propose three taxonomic revisions within embiotocid surfperches based on recent molecular phylogenetic analyses that robustly resolve all interspecific relationship in the Eastern Pacific species: Hypsurus caryi (Agassiz, 1853) resurrected to its original name Embiotoca caryi Agassiz, 1853, Rhacochilus vacca (Girard, 1855) shifted into the genus Phanerodon Girard, 1854, and Hyperprosopon anale Agassiz, 1861 separated into the available genus Hypocritichthys Gill, 1862. The proposed changes would leave three previously paraphyletic groups monophyletic (Embiotoca, Hyperprosopon, and Phanerodon) and would maintain the current number of genera at 13. 

Tracing the origins of hybrids through history: monstrous cultivars and Napoléon Bonaparte’s exiled paper daisies (Asteraceae; Gnaphalieae)

2021 ◽  
Author(s):  
Timothy L Collins ◽  
Jeremy J Bruhl ◽  
Alexander N Schmidt-Lebuhn ◽  
Ian R H Telford ◽  
Rose L Andrew
Keyword(s):  
Gene Flow ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Napoleon Bonaparte ◽  
Snp Data ◽  
Cast Doubt ◽  
Molecular Phylogenetic ◽  
St Helena ◽  
New Evidence

Abstract Golden everlasting paper daisies (Xerochrysum, Gnaphalieae, Asteraceae) were some of the earliest Australian native plants to be cultivated in Europe. Reputedly a favourite of Napoléon Bonaparte and Empress Joséphine, X. bracteatum is thought to have been introduced to the island of St Helena in the South Atlantic during Napoléon’s exile there. Colourful cultivars were developed in the 1850s, and there is a widely held view that these were produced by crossing Xerochrysum with African or Asian Helichrysum spp. Recent molecular phylogenetic analyses and subtribal classification of Gnaphalieae cast doubt on this idea. Using single-nucleotide polymorphism (SNP) data, we looked for evidence of gene flow between modern cultivars, naturalized paper daisies from St Helena and four Xerochrysum spp. recorded in Europe in the 1800s. There was strong support for gene flow between cultivars and X. macranthum. Paper daisies from St Helena were genotypically congruent with X. bracteatum and showed no indications of ancestry from other species or from the cultivars, consistent with the continuous occurrence of naturalized paper daisies introduced by Joséphine and Napoléon. We also present new evidence for the origin of colourful Xerochrysum cultivars and hybridization of congeners in Europe from Australian collections.

Molecular phylogenetics of the Onobrychis genus (Fabaceae: Papilionoideae) using ITS and trnL–trnF DNA sequence data

2014 ◽  
Vol 62 (3) ◽  
pp. 235 ◽  
Author(s):  
S. Safaei Chaei Kar ◽  
F. Ghanavati ◽  
M. R. Naghavi ◽  
H. Amirabadi-zade ◽  
R. Rabiee
Keyword(s):  
Dna Sequence ◽  
Molecular Phylogenetics ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Group I ◽  
Molecular Phylogenetic ◽  
Nuclear Its ◽  
Cultivated Species ◽  
Relationship Of

Onobrychis, comprising more than 130 species, is a genus of the family Fabaceae. At this time, the interspecies relationship of this biologically important genus is still a subject of great discussion and debate. To help resolve this disagreement, we used molecular phylogeny to analyse internal transcribed spacer (ITS) and trnL–trnF sequences of 76 species of Onobrychis. Bayesian interference, maximum parsimony and maximum likelihood analyses of nuclear ITS and plastid trnL–trnF DNA sequence data generated trees with strong posterior probability for two groups: Onobrychis subgen. Sisyrosema (including: Heliobrychis, Hymenobrychis, Afghanicae and Anthyllium sections) along with Laxiflorae section in Group I and Onobrychis subgen. Onobrychis (except Laxiflorae section) in the other (Group II). The Laxiflorae section roots back to the ancestral node for Sisyrosema subgen. O. viciifolia (cultivated species), which is closely associated with O. cyri var. cyri, suggesting that the latter may be a wild progenitor of O. viciifolia. The present study supported the paraphyly of subgenera Onobrychis and Sisyrosema. The study proposed the paraphyletic nature of the sections Onobrychis, Dendrobrychis, Heliobrychis and Hymenobrychis. Together with our molecular phylogenetic analyses we present a review of Onobrychis morphology and discuss and compare our results with those of earlier morphological and molecular phylogenetic analyses.

A revision of the soft coral genus, Eunephthya Verrill, 1869 (Anthozoa: Octocorallia: Nephtheidae), with a description of four new species from South Africa

Zootaxa ◽  
2012 ◽  
Vol 3485 (1) ◽  
pp. 1 ◽  
Author(s):  
CATHERINE S. MCFADDEN ◽  
LEEN P. VAN OFWEGEN
Keyword(s):  
South Africa ◽  
New Species ◽  
Type Species ◽  
Molecular Phylogenetics ◽  
Soft Coral ◽  
Phylogenetic Analyses ◽  
28S Rdna ◽  
New Combination ◽  
Coral Genus ◽  
Molecular Phylogenetic

Based on the results of morphological and molecular phylogenetic analyses of newly collected material, we reinstate thesoft coral genus Eunephthya Verrill, 1869 for a group of species endemic to South Africa. Eunephthya is morphologicallyand phylogenetically distinct from the zooxanthellate, tropical genus Capnella Gray, 1869 with which it had been synon-ymized. In Eunephthya the polyp sclerites include unilaterally spinose or leaf spindles, and the sclerites of the stalk surfaceand interior (when present) are small radiates and spheroids. In contrast, C. imbricata, the type species of Capnella, hasleaf clubs and leaf-capstans in the polyps and stalk surface, and large ovals and irregular forms in the interior. We describefour new species of Eunephthya from Algoa Bay, South Africa—E. celata, E. ericius, E. granulata, and E. shirleyae— and propose a new combination, E. susanae.Keywords. Molecular phylogenetics, Capnella, mtMutS, COI, 28S rDNA, endemism

Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae)

2016 ◽  
Vol 29 (3) ◽  
pp. 185 ◽  
Author(s):  
Charles S. P. Foster ◽  
David J. Cantrill ◽  
Elizabeth A. James ◽  
Anna E. Syme ◽  
Rebecca Jordan ◽  
...  
Keyword(s):  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Distinct Species ◽  
Flowering Plants ◽  
New Combination ◽  
Evolutionary Relationships ◽  
Toxic Compounds ◽  
Biogeographic History ◽  
Plastid Markers

Pimelea Banks & Sol. ex Gaertn. is a genus of flowering plants comprising an estimated 90 species in Australia and ~35 species in New Zealand. The genus is economically important, with the inflorescences of some species having floricultural applications, and the presence of toxic compounds in several species proving poisonous to livestock. Pimelea grows in a variety of habitats ranging from arid to alpine, suggesting a complicated biogeographic history. The relationships within Pimelea remain largely uncertain, despite previous attempts at clarification using molecular phylogenetics. However, it is clear that Pimelea is closely related to Thecanthes Wikstr., with the two genera comprising the subtribe Pimeleinae. We used Bayesian and maximum-likelihood phylogenetic analyses of four plastid markers (matK, rbcL, rps16, trnL–F) and one nuclear ribosomal marker (ITS) to examine the evolutionary relationships within Pimeleinae. We found strong support for the monophyly of Pimeleinae but, similar to previous studies, Pimelea was paraphyletic with respect to Thecanthes. Our results also indicated that P. longiflora R.Br. subsp. longiflora and P. longiflora subsp. eyrei (F.Muell.) Rye are best considered as distinct species. Therefore, we reduce Thecanthes to synonymy with Pimelea, making the necessary new combination Pimelea filifolia (Rye) C.S.P.Foster et M.J.Henwood (previously Thecanthes filifolia Rye), and also reinstate Pimelea eyrei F.Muell.

scholarly journals Phylogeny, classification, and character evolution of tribe Citharexyleae (Verbenaceae)

2020 ◽  
Author(s):  
Laura A. Frost ◽  
Nataly O’Leary ◽  
Laura P. Lagomarsino ◽  
David C. Tank ◽  
Richard G. Olmstead
Keyword(s):  
Phylogenetic Analyses ◽  
Strong Support ◽  
Flower Color ◽  
Fruit Color ◽  
Unique Combination ◽  
Inflorescence Architecture ◽  
Distinct Genus ◽  
Molecular Phylogenetic ◽  
Nuclear Loci ◽  
Good Support

AbstractPremise of the studyTribe Citharexyleae comprises three genera: Baillonia, Citharexylum, and Rehdera. While there is good support for these genera as a clade, relationships between genera remain unresolved due to low sampling of the largest genus, Citharexylum. A molecular phylogenetic approach was taken to resolve intergeneric relationships in Citharexyleae and infrageneric relationships in Citharexylum.MethodsSeven chloroplast regions, two nuclear ribosomal spacers, and six low-copy nuclear loci were analyzed for 64 species of Citharexyleae. Phylogenetic analyses were conducted using maximum likelihood, Bayesian inference, and Bayesian multi-species coalescent approaches. Habit, presence/absence of thorns, inflorescence architecture, flower color, fruit color, and geography were examined to identify diagnostic characters for clades within Citharexylum.Key resultsIntergeneric relationships resolved Rehdera as sister to Citharexylum and Baillonia nested within Citharexylum. Two species, C. oleinum and C. tetramerum, fell outside of Citharexyleae close to tribe Duranteae. There is strong support for seven clades within Citharexylum, each characterized by a unique combination of geography, fruit color/maturation, and inflorescence architecture.ConclusionsBaillonia is included in Citharexylum; Rehdera is retained as a distinct genus. A subgeneric classification for Citharexylum is proposed.

scholarly journals ULASAN Kajian Filogenetika Molekuler dan Peranannya dalam Menyediakan Informasi Dasar untuk Meningkatkan Kualitas Sumber Genetik Anggrek

2016 ◽  
Vol 4 (1) ◽  
pp. 35 ◽  
Author(s):  
Topik Hidayat ◽  
Adi Pancoro
Keyword(s):  
Dna Sequences ◽  
Molecular Phylogenetics ◽  
Phylogenetic Analyses ◽  
Molecular Data ◽  
Biochemical Properties ◽  
Intergeneric Hybrids ◽  
Basic Knowledge ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
Ornamental Crops

<p>Early information<br />resulted from molecular phylogenetic studies of many important<br />ornamental crops is often less attention to many<br />growers and farmers. Phylogenetics is one of the most preferable<br />method in systematics to reconstruct evolutionary<br />relationships of groups of biological organisms in order to<br />understand their biodiversities. This has been revolutionized<br />by DNA sequences data. In this method, a group of organisms<br />that shares many identical characteristics are considered<br />to be closely related; deriving from a common<br />ancestor and is assumed to have similar genetic patterns<br />and biochemical properties. By these basic principles,<br />molecular phylogenetics plays important roles in revealing a<br />basic knowledge on pattern of relationships to which<br />genetic resources can be improved. Over the past decade,<br />botanists have done several thousand phylogenetic analyses<br />based on molecular data of economically and horticulturally<br />important crops. Orchids are the best example for this.<br />There is no doubt that most orchid plants had played roles in<br />horticulture and hybridization. At present, many infrageneric<br />and intergeneric hybrids are available commercially. Successful<br />hybridization can be achieved if two or more individual<br />plants understudy are closely related in respect to their<br />genetics and evolution.</p>

scholarly journals Molecular phylogeny of porcelain crabs (Porcellanidae:Petrolisthesand allies) from the south eastern Pacific: the generaAllopetrolisthesandLiopetrolisthesare not natural entities

PeerJ ◽  
2016 ◽  
Vol 4 ◽  
pp. e1805 ◽  
Author(s):  
J. Antonio Baeza
Keyword(s):  
Molecular Phylogeny ◽  
Nuclear Dna ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Eastern Pacific ◽  
Total Evidence ◽  
The South ◽  
South Eastern ◽  
Single Marker ◽  
Porcelain Crabs

Porcelain crabs from the closely related generaPetrolisthes,Liopetrolisthes, andAllopetrolisthesare known for their diversity of lifestyles, habitats, and coloration. The evolutionary relationships among the species belonging to these three genera is not fully resolved. A molecular phylogeny of the group may help to resolve the long-standing taxonomic question about the validity of the generaAllopetrolisthesandLiopetrolisthes. Using both ‘total evidence’ and single-marker analyses based on a 362-bp alignment of the 16S rRNA mitochondrial DNA and a 328-bp alignment of the Histone 3 nuclear DNA, the phylogenetic relationships among 11 species fromPetrolisthes(6 species),Liopetrolisthes(2 species), andAllopetrolisthes(3 species), all native to the south eastern Pacific, were examined. The analyses supported three pairs of sister species:L. mitra+L. patagonicus,P. tuberculatus+P. tuberculosus, andA. angulosus+A. punctatus. No complete segregation of species, according to genera, was evident from tree topologies. Bayesian-factor analyses revealed strong support for the unconstrained tree instead of an alternative tree in which monophyly of the three genera was forced. Thus, the present molecular phylogeny does not support the separation of the species within this complex into the generaPetrolisthes,Liopetrolisthes, andAllopetrolisthes. Taking into account the above and other recent molecular phylogenetic analyses focused on other representatives from the family Porcellanidae, it is tentatively proposed to eliminate the generaLiopetrolisthesandAllopetrolisthes, and to transfer their members to the genusPetrolisthes.

Molecular phylogenetics of Pterocyclus (Apiaceae) based on nrDNA ITS sequences: revised circumscription with a restored species

Phytotaxa ◽  
2021 ◽  
Vol 498 (2) ◽  
pp. 131-138
Author(s):  
JING ZHOU ◽  
JIN WEI ◽  
JUNMEI NIU ◽  
XIAOLI LIU ◽  
ZHENWEN LIU
Keyword(s):  
Phylogenetic Analysis ◽  
Molecular Phylogenetics ◽  
Identification Key ◽  
Its Sequences ◽  
Molecular Phylogenetic Analysis ◽  
Nrdna Its ◽  
Interspecific Relationships ◽  
Molecular Phylogenetic ◽  
Independent Species

The genus Pterocyclus Klotzsch, along with many others, constituted the taxonomically complex Pleurospermum s.l. To delimit its circumscription and clarify its interspecific relationships, molecular phylogenetic analysis and detailed specimen examination were carried out. Its status as an independent genus was confirmed, with four species recognized. Pterocyclus wolffianus, the synonymous species of Pterocyclus forrsetii should be restored as an independent species. A new taxonomic account for Pterocyclus and an identification key to its four species, are provided.

Trechispora yunnanensis sp. nov. (Hydnodontaceae, Basidiomycota) from China

Phytotaxa ◽  
2019 ◽  
Vol 424 (4) ◽  
pp. 253-261 ◽  
Author(s):  
TAI-MIN XU ◽  
YU-HUI CHEN ◽  
CHANG-LIN ZHAO
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Strong Support ◽  
Morphological Characteristics ◽  
Molecular Data ◽  
Fungal Species ◽  
Monophyletic Lineage ◽  
Molecular Phylogenetic ◽  
Inference Methods

A new wood-inhabiting fungal species, Trechispora yunnanensis sp. nov., is proposed based on morphological characteristics and molecular phylogenetic analyses. The species is characterized by resupinate basidiomata, rigid and fragile up on drying, cream to pale greyish hymenial surface; a monomitic hyphal system with generative hyphae bearing clamp connections, IKI-, CB-; ellipsoid, hyaline, thick-walled, ornamented, IKI-, CB- basidiospores measuring as 7–8.5 × 5–5.5 µm. The internal transcribed spacer (ITS) and the large subunit (LSU) regions of nuclear ribosomal RNA gene sequences of the studied samples were generated, and phylogenetic analyses were performed with maximum likelihood (ML), maximum parsimony (MP) and bayesian inference methods (BPP). The phylogenetic analyses based on molecular data of ITS+nLSU sequences showed that T. yunnanensis formed a monophyletic lineage with a strong support (100% ML, 100% MP, 1.00 BPP) and was closely related to T. byssinella and T. laevis. Both morphological characteristics and results of molecular phylogenetic analyses confirmed the placement of the new species in Trechispora.

scholarly journals Two Complete Mitogenomes of Chalcididae (Hymenoptera: Chalcidoidea): Genome Description and Phylogenetic Implications

Insects ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1049
Author(s):  
Huifeng Zhao ◽  
Ye Chen ◽  
Zitong Wang ◽  
Haifeng Chen ◽  
Yaoguang Qin
Keyword(s):  
Stop Codon ◽  
Phylogenetic Analyses ◽  
Strong Support ◽  
Sister Group ◽  
Nucleotide Composition ◽  
Start Codon ◽  
Protein Coding ◽  
Phylogenetic Implications ◽  
Molecular Phylogenetic ◽  
Rna Genes

The complete mitochondrial genomes of two species of Chalcididae were newly sequenced: Brachymeria lasus and Haltichella nipponensis. Both circular mitogenomes are 15,147 and 15,334 bp in total length, respectively, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), and 22 transfer RNA genes (tRNAs) and an A+T-rich region. The nucleotide composition indicated a strong A/T bias. All PCGs of B. lasus and H. nipponensis began with the start codon ATD, except for B. lasus, which had an abnormal initiation codon TTG in ND1. Most PCGs of the two mitogenomes are terminated by a codon of TAR, and the remaining PCGs by the incomplete stop codon T or TA (ATP6, COX3, and ND4 in both species, with an extra CYTB in B. lasus). Except for trnS1 and trnF, all tRNAs can be folded into a typical clover structure. Both mitogenomes had similar control regions, and two repeat units of 135 bp were found in H. nipponensis. Phylogenetic analyses based on two datasets (PCG123 and PCG12) covering Chalcididae and nine families of Chalcidoidea were conducted using two methods (maximum likelihood and Bayesian inference); all the results support Mymaridae as the sister group of the remaining Chalcidoidea, with Chalcididae as the next successive group. Only analyses of PCG123 generated similar topologies of Mymaridae + (Chalcididae + (Agaonidae + remaining Chalcidoidea)) and provided one relative stable clade as Eulophidae + (Torymidae + (Aphelinidae + Trichogrammatidae)). Our mitogenomic phylogenetic results share one important similarity with earlier molecular phylogenetic efforts: strong support for the monophyly of many families, but a largely unresolved or unstable “backbone” of relationships among families.

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