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

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.

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

Zootaxa ◽

10.11646/zootaxa.3485.1.1 ◽

2012 ◽

Vol 3485 (1) ◽

pp. 1 ◽

Cited By ~ 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

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Pleioblastus triangulata (Poaceae: Bambusoideae), a new combination for Indosasa triangulata based on morphological and molecular evidence

Phytotaxa ◽

10.11646/phytotaxa.527.4.5 ◽

2021 ◽

Vol 527 (4) ◽

pp. 275-283

Author(s):

ZHENG-YANG NIU ◽

YI-HUA TONG ◽

NIAN-HE XIA

Keyword(s):

Morphological Study ◽

Phylogenetic Analyses ◽

Distinct Species ◽

New Combination ◽

Molecular Evidence ◽

Molecular Phylogenetic

This study aims to end the debate whether Indosasa triangulata belongs to Indosasa or Pleioblastus. The evidence from our morphological study and molecular phylogenetic analyses clearly indicate that Indosasa triangulata should be a member of Pleioblastus, rather than Indosasa, and is a distinct species close to Pleioblastus maculatus and P. oleosus. Thus, it is transferred from Indosasa to Pleioblastus in this study. A detailed description as well as two color plates of this species is also provided.

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Phylogenetic revision of the Late Ordovician orthid brachiopod generaPlaesiomysandHebertellafrom Laurentia

Journal of Paleontology ◽

10.1666/12-083 ◽

2013 ◽

Vol 87 (6) ◽

pp. 1107-1128 ◽

Cited By ~ 10

Author(s):

David F. Wright ◽

Alycia L. Stigall

Keyword(s):

Statistical Approach ◽

Phylogenetic Analyses ◽

Distinct Species ◽

Geographic Range ◽

Late Ordovician ◽

Species Level ◽

Evolutionary Relationships ◽

Marine Communities ◽

Bayesian Methodologies ◽

Phylogenetic Revision

The orthidine brachiopod generaPlaesiomysandHebertellaare significant constituents of Late Ordovician benthic marine communities throughout Laurentia. Species-level phylogenetic analyses were conducted on both genera to inform systematic revisions and document evolutionary relationships. Phylogenetic analyses combined discrete and continuous characters, from which character states were determined using a statistical approach, and utilized both cladistic and Bayesian methodologies.Plaesiomys cutterensis,P. idahoensis, andP. occidentalisare herein recognized as distinct species rather than subspecies ofP. subquadratus. Similarly,Hebertella montoyensisandH. prestonensisare recognized as distinct species separate fromH. occidentalis, andH. richmondensisis recognized as a distinct species rather than a geographical variant ofH. alveata.Hebertella subjugatais removed from its tentative synonymy withH. occidentalisand revalidated.The development of species-level evolutionary hypotheses forPlaesiomysandHebertellaprovides a detailed framework for assessing evolutionary and paleobiogeographic patterns of Late Ordovician brachiopods from Laurentia. The geographic range ofHebertellaexpanded throughout Laurentia during the Richmondian into both intracratonic and marginal basins.Plaesiomys subquadratusparticipated in the Late Ordovician Richmondian Invasion. The recovered phylogenetic topology forPlaesiomyssuggests thatP. subquadratusmay have migrated into the Cincinnati region from a basin situated to the paleo-northeast.

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Senecio kumaonensis (Asteraceae, Senecioneae) is a Synotis based on evidence from karyology and nuclear ITS/ETS sequence data

Phytotaxa ◽

10.11646/phytotaxa.292.1.3 ◽

2017 ◽

Vol 292 (1) ◽

pp. 35 ◽

Cited By ~ 2

Author(s):

TIAN-JING TONG ◽

MING TANG ◽

CHEN REN ◽

QIN-ER YANG

Keyword(s):

Multidisciplinary Approach ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Strong Support ◽

New Combination ◽

Tissue Cell ◽

Close Relationship ◽

Nuclear Its ◽

Micromorphological Characters ◽

Relationship Of

We apply a multidisciplinary approach to settle the dispute over the generic affiliation of the Himalayan species Senecio kumaonensis (based on Cacalia penninervis). Some floral micromorphological characters of this species, including shape of anther bases, configuration of anther collars, and anther endothecial tissue cell wall thickenings, are confirmed to perfectly match those of Senecio and this has obviously resulted in the placement of the species within that genus. Chromosome counts indicate S. kumaonensis has 2n = 40, a number common to Senecio and Synotis but not occurring in Parasenecio (the correct generic name for the Asian species previously referred to Cacalia), which has 2n = 52, 58, and 60. The presence of six subterminal-centromeric (st) chromosomes in the karyotype of S. kumaonensis, however, lends strong support to the close relationship of this species to Synotis. Our phylogenetic analyses based on ITS/ ETS sequences also place S. kumaonensis in Synotis. In this species the anther tail feature, once deemed to be diagnostic for Synotis (anther bases in Synotis with sterile, tailed auricles vs. those in Senecio without such auricles, obtuse to sagittate), has an exception as evidenced from phylogeny. We therefore transfer S. kumaonensis to Synotis and, as the epithet “penninervis” has hitherto never been used in the genus, we propose the new combination Syn. penninervis for this species.

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

Zootaxa ◽

10.11646/zootaxa.4482.3.10 ◽

2018 ◽

Vol 4482 (3) ◽

pp. 591 ◽

Cited By ~ 2

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.

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Unraveling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)

Plants ◽

10.3390/plants9040549 ◽

2020 ◽

Vol 9 (4) ◽

pp. 549 ◽

Cited By ~ 3

Author(s):

Andrew J. Helmstetter ◽

Suzanne Mogue Kamga ◽

Kevin Bethune ◽

Thea Lautenschläger ◽

Alexander Zizka ◽

...

Keyword(s):

Species Delimitation ◽

Morphological Evolution ◽

Phylogenetic Analyses ◽

Construction Material ◽

Distinct Species ◽

Phylogenetic Study ◽

Inflorescence Morphology ◽

Biogeographic History ◽

Snp Data ◽

Exon Capture

Palms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling, and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution, and other eco-evolutionary aspects of this charismatic, socially, and economically important palm genus.

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Unravelling the Phylogenomic Relationships of the Most Diverse African Palm Genus Raphia (Calamoideae, Arecaceae)

10.1101/2020.03.09.984351 ◽

2020 ◽

Author(s):

Andrew J. Helmstetter ◽

Suzanne Mogue Kamga ◽

Kevin Bethune ◽

Thea Lautenschläger ◽

Alexander Zizka ◽

...

Keyword(s):

Species Delimitation ◽

Morphological Evolution ◽

Phylogenetic Analyses ◽

Construction Material ◽

Distinct Species ◽

Phylogenetic Study ◽

Inflorescence Morphology ◽

Biogeographic History ◽

Snp Data ◽

Exon Capture

AbstractPalms are conspicuous floristic elements across the tropics. In continental Africa, even though there are less than 70 documented species, they are omnipresent across the tropical landscape. The genus Raphia has 20 accepted species in Africa and one species endemic to the Neotropics. It is the most economically important genus of African palms with most of its species producing food and construction material. Raphia is divided into five sections based on inflorescence morphology. Nevertheless, the taxonomy of Raphia is problematic with no intra-generic phylogenetic study available. We present a phylogenetic study of the genus using a targeted exon capture approach sequencing of 56 individuals representing 18 out of the 21 species. Our results recovered five well supported clades within the genus. Three sections correspond to those based on inflorescence morphology. R. regalis is strongly supported as sister to all other Raphia species and is placed into a newly described section: Erectae. Overall, morphological based identifications agreed well with our phylogenetic analyses, with 12 species recovered as monophyletic based on our sampling. Species delimitation analyses recovered 17 or 23 species depending on the confidence level used. Species delimitation is especially problematic in the Raphiate and Temulentae sections. In addition, our clustering analysis using SNP data suggested that individual clusters matched geographic distribution. The Neotropical species R. taedigera is supported as a distinct species, rejecting the hypothesis of a recent introduction into South America. Our analyses support the hypothesis that the Raphia individuals from Madagascar are potentially a distinct species different from the widely distributed R. farinifera. In conclusion, our results support the infra generic classification of Raphia based on inflorescence morphology, which is shown to be phylogenetically useful. Classification and species delimitation within sections remains problematic even with our phylogenomic approach. Certain widely distributed species could potentially contain cryptic species. More in-depth studies should be undertaken using morphometrics, increased sampling and more variable markers. Our study provides a robust phylogenomic framework that enables further investigation on the biogeographic history, morphological evolution and other eco-evolutionary aspects of this charismatic, socially and economically important palm genus.

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

Genome Biology and Evolution ◽

10.1093/gbe/evz209 ◽

2019 ◽

Vol 11 (10) ◽

pp. 2824-2849 ◽

Cited By ~ 6

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.

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A refined circumscription of Notobubon striatum and the resurrection of Dregea collina Ecklon & Zeyher (Apiaceae, Apioideae)

Phytotaxa ◽

10.11646/phytotaxa.266.1.4 ◽

2016 ◽

Vol 266 (1) ◽

pp. 27 ◽

Cited By ~ 1

Author(s):

ANTHONY R. MAGEE ◽

ODETTE E. CURTIS ◽

B-E. VAN WYK

Keyword(s):

Conservation Status ◽

Leaf Size ◽

Type Specimen ◽

Distinct Species ◽

Critically Endangered ◽

Type Material ◽

New Combination ◽

Careful Examination ◽

Field Surveys ◽

Extensive Field

Extensive field surveys of the Critically Endangered Central and Eastern Rûens Shale Renosterveld have uncovered that Notobubon striatum, as currently circumscribed, comprises two distinct species. Upon careful examination of the type material it has become clear that names exist for both species. The type specimen of N. striatum clearly matches the lesser known species, a large shrub, ca. 1 m. tall, with a powerful anise-scent and which is restricted to the banks of seasonal rivers and watercourses in the Central and Eastern Rûens Shale Renosterveld. The second and better known entity, with a wider distribution, corresponds to the type material of Dregea collina Ecklon & Zeyher. As such, a new combination, Notobubon collinum (Ecklon & Zeyher) Magee, is here made to accommodate this taxon, restricted to dry quartz and silcrete patches or outcrops in Eastern Rûens Shale Renosterveld. In their revised circumscriptions N. striatum and N. collinum are readily distinguished by habit, scent, leaf size and division, as well as leaf lobe shape and sepal size. Comprehensive descriptions of both species are provided, together with notes on their ecology and conservation status, and the existing key to the species of Notobubon updated. This brings the number of recognised species in the genus to thirteen.

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

Botanical Journal of the Linnean Society ◽

10.1093/botlinnean/boab020 ◽

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.

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