scholarly journals Evolutionary Ecology of Lizards: Lessons from a Special Issue

Diversity ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 565
Author(s):  
Francisco Javier Zamora-Camacho ◽  
Mar Comas
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Ecology ◽  
Special Issue

Regardless of taxonomical disquisitions on its yet unraveled phylogenetic relationships within and among taxa [...]

Phylogenetic relationships in the monocot order Commelinales, with a focus on PhilydraceaeThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 719-731 ◽  
Author(s):  
Jeffery M. Saarela ◽  
Peter J. Prentis ◽  
Hardeep S. Rai ◽  
Sean W. Graham
Keyword(s):  
Phylogenetic Relationships ◽  
Strong Support ◽  
Sister Group ◽  
Higher Order ◽  
Special Issue ◽  
Likelihood Methods ◽  
The Family ◽  
Selection Of

To characterize higher-order phylogenetic relationships among the five families of Commelinales, we surveyed multiple plastid loci from exemplar taxa sampled broadly from the order, and from other major monocot lineages. Phylogenetic inferences in Commelinales using parsimony and likelihood methods are congruent, and we find strong support for most aspects of higher-order relationship in the order. We obtain moderately strong support for the local placement of Philydraceae, a family whose position has proven particularly difficult to infer in previous studies. Commelinaceae and Hanguanaceae are sister taxa, and together they are the sister group of a clade consisting of Haemodoraceae, Philydraceae, and Pontederiaceae; Haemodoraceae and Pontederiaceae are also sister taxa. Our sampling of Philydraceae includes all three or four genera in the family; we identify Philydrella as the sister group of a Helmholtzia–Philydrum clade, a resolution that is potentially consistent with several aspects of morphology.

scholarly journals Phylogenomic analyses using genomes and transcriptomes do not resolve relationships among major clades in Phrymaceae

2021 ◽  
Author(s):  
Diego F. Morales-Briones ◽  
Nan Lin ◽  
Eileen Y. Huang ◽  
Dena L. Grossenbacher ◽  
James M. Sobel ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Ecology ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Reticulate Evolution ◽  
Small Scale ◽  
Gene Trees ◽  
Network Analyses ◽  
Gene Tree Discordance ◽  
Close Relatives

Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons. Methods: We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events. Key results: Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. Conclusions: We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that genome-scale data do not always fully "resolve" phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.

Species delimitation, phylogenetic relationships, and two new species in the Cuscuta gracillima complex (Convolvulaceae)This paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 670-681 ◽  
Author(s):  
Mihai Costea ◽  
Fiona Aiston ◽  
Saša Stefanović
Keyword(s):  
New Species ◽  
Phylogenetic Relationships ◽  
Species Delimitation ◽  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Conservation Status ◽  
Special Issue ◽  
Dna Sequence Data ◽  
F Region ◽  
Selection Of

Basic morphology, scanning electron microscopy, and DNA sequence data from the plastid trnL–F region and the nuclear internal transcribed spacer (ITS) regions were used to delimit the species of a recently circumscribed clade of Cuscuta (Convolvulaceae) and to investigate their phylogenetic relationships. This clade comprises the Cuscuta gracillima complex from Mexico, Central and northern South America, a group which is characterized by inflorescences that appear to emerge directly from the host stem. Eight lineages are recognized, with two of them described here as new species: Cuscuta punana Costea & Stefanović, sp. nov. from Ecuador and Cuscuta vandevenderi Costea & Stefanović, sp. nov. from Mexico. Cuscuta colombiana Yunck is redefined to include Cuscuta aristeguietae Yunck., and Cuscuta deltoidea Yunck. is broadened to encompass Cuscuta serruloba Yunck. A taxonomic treatment with an identification key, descriptions, and illustrations is provided; the biogeography and conservation status of the eight species are also discussed.

Molecular phylogeny of the North American eurybioid asters (Asteraceae, Astereae) based on the nuclear ribosomal internal and external transcribed spacersThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (8) ◽  
pp. 901-915 ◽  
Author(s):  
Sugirthini Selliah ◽  
Luc Brouillet
Keyword(s):  
Molecular Phylogeny ◽  
Coastal Plain ◽  
North American ◽  
Phylogenetic Relationships ◽  
Special Issue ◽  
Bayesian Analyses ◽  
The North ◽  
Perennial Herbs ◽  
American Clade ◽  
Selection Of

The eurybioid asters Oreostemma , Herrickia , Eurybia , and Triniteurybia form a complex that is part of the North American clade of tribe Astereae. They comprise 31 species of perennial herbs that are widely distributed on the continent. Previous analyses had shown poor resolution among the four genera and among the species, particularly within Eurybia (23 spp.), which includes diploids and polyploids. We investigated phylogenetic relationships within the group using the nuclear ribosomal ITS and ETS regions, in separate and combined parsimony and Bayesian analyses. We detected incongruence between the ITS and ETS regions when polyploids were included, and so only diploids were considered in the combined analyses. Eurybia pygmaea (Lindl.) G.L. Nesom is confirmed as a member of Symphyotrichum ; Eurybia is monophyletic once this species is re-classified. The eurybioids form a paraphyletic grade with Oreostemma, sister to the remaining taxa, followed in succession by Herrickia , Eurybia , and Triniteurybia , and with the latter genus sister to subtribe Machaerantherinae. Thus the xeric Machaerantherinae (x = 6, 5, 4) is nested within the grade of mesic eurybioids (x = 9). Although largely grouping together, the polyploid taxa of Eurybia apparently do not constitute a clade and their relationships to the diploid taxa and to each other could not be assessed further. Among the diploids, two clades emerge: one including the western Eurybia integrifolia (Nutt.) G.L. Nesom and Eurybia sibirica (L.) G.L. Nesom, and the southeastern Eurybia eryngiifolia (Torr. & A. Gray) G.L. Nesom; and a second including the western Eurybia radulina (A. Gray) G.L. Nesom, the eastern cordate-leaved (sect. Eurybia) and the narrow-leaved, mostly coastal plain species of Eurybia. Our analyses, therefore, do not support the current classifications of Eurybia.

Phylogenetic relationships in subtribe Poinae (Poaceae, Poeae) based on nuclear ITS and plastid trnT–trnL–trnF sequencesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (8) ◽  
pp. 938-967 ◽  
Author(s):  
Lynn J. Gillespie ◽  
Robert J. Soreng ◽  
Roger D. Bull ◽  
Surrey W.L. Jacobs ◽  
Nancy F. Refulio-Rodriguez
Keyword(s):  
Phylogenetic Relationships ◽  
Internal Transcribed Spacer ◽  
Close Relationships ◽  
Sequence Data ◽  
New Combination ◽  
Special Issue ◽  
Consensus Tree ◽  
Strict Consensus Tree ◽  
Nuclear Its ◽  
Selection Of

The worldwide temperate subtribe Poinae comprises the largest grass genus, Poa (500+ species), and multiple additional small genera. We explore generic boundaries and relationships among genera of Poinae using nuclear ribosomal internal transcribed spacer data (ITS) and plastid trnT–trnL–trnF (TLF) sequence data. ITS and TLF analyses are mostly congruent with regards to circumscription of genera, and with respect to relationships among Poinae genera, but tree structure is generally better supported among genera in the ITS strict consensus tree. ITS and TLF both support two main Poinae lineages: (i) Poa and (ii) a clade comprising all other sampled Poinae. Nine small genera were nested within the large Poa clade, including Aphanelytrum , Dissanthelium , and Tovarochloa , supporting inclusion of these as sections within Poa. In the second clade, three subclades support close relationships among Nicoraepoa , Hookerochloa , and Arctagrostis ; Arctophila and Dupontia ; and Apera , Bellardiochloa , and Ventenata . Genera of the related subtribes Alopecurinae, Cinninae, and Miliinae were mixed among or in part external to Poinae in different ways in ITS and TLF analyses, and only subtribe Puccinelliinae was strongly supported and monophyletic. ITS analyses supported placement of Catabrosella , Hyalopoa , and Paracolpodium in Puccinelliinae (no TLF data available). The position of Poa subgenus Arctopoa is incongruent between the two analyses: TLF data support inclusion within Poa and ITS data place it outside of Poa. Similarly, TLF data resolves the genus Aniselytron outside of Poa, whereas ITS data place it within Poa. Based on these results and a consideration of morphology, we recognize Arctopoa and Aniselytron as genera, probably of ancient hybrid origins. Nothogenus  × Duarctopoa is coined for Arctopoa × Dupontia, with a single nothospecies  × Duarctopoa labradorica . A new combination is provided for Poa subg. Sylvestres .

Systematics of thePhialophora verrucosacomplex: new insights from analyses of β-tubulin, large subunit nuclear rDNA and ITS sequencesThis paper is one of a selection of papers published in the Special Issue on Systematics Research.

Botany ◽  
2008 ◽  
Vol 86 (7) ◽  
pp. 742-750 ◽  
Author(s):  
Wendy A. Untereiner ◽  
Andrea Angus ◽  
Martina Réblová ◽  
Mary-Jane Orr
Keyword(s):  
Ribosomal Rna ◽  
Phylogenetic Relationships ◽  
Type Species ◽  
Large Subunit ◽  
Lsu Rdna ◽  
Special Issue ◽  
Nuclear Rdna ◽  
Molecular Characters ◽  
Selection Of ◽  
Β Tubulin

Phialophora Medlar, as defined currently, is a genus encompassing melanized, anamorphic Ascomycota that produce one-celled conidia from phialides with distinct, darkened collarettes. The type species, Phialophora verrucosa Medlar, is closely related to Phialophora americana (Nannf.) S. Hughes, the anamorph of Capronia semiimmersa (Candoussau & Sulmont) Untereiner & Naveau (Herpotrichiellaceae, Chaetothyriales). To confirm that P. americana and P. verrucosa are distinct taxa, and to examine their phylogenetic relationships to species of Capronia and other representatives of the Chaetothyriales, we sequenced portions of the β-tubulin gene and nuclear ribosomal RNA cistron (ITS and LSU rDNA). We also compared isolates of P. americana grown on a number of media. Isolates of C. semiimmersa, Capronia svrcekiana Réblová, and P. americana produced phialides bearing deep, vase-shaped collarettes and formed a strongly supported clade that did not include P. verrucosa in a phylogeny inferred from the combined β-tubulin–ITS–LSU dataset. Capronia svrcekiana was found to be conspecific with C. semiimmersa based on the comparison of cultural, micromorphological, and molecular characters. In the LSU phylogeny, three recently described species of Phialophora ( Phialophora europaea de Hoog et al., Phialophora reptans de Hoog, and Phialophora sessilis de Hoog) were grouped outside of the clade containing sampled members of the Herpotrichiellaceae. While the position of these species in the Chaetothyriales remained unresolved, it was evident that P. europaea, P. reptans, and P. sessilis are not members of the P. verrucosa complex.

scholarly journals Special Issue: Evolutionary Ecology of Venom

Toxins ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 310
Author(s):  
Kevin Arbuckle
Keyword(s):  
Evolutionary Ecology ◽  
Special Issue ◽  
Ecological Attributes

This Special Issue of Toxins aims to increase the profile and understanding of how ecology shapes the evolution of venom systems, and also how venom influences the ecological attributes of and interactions among species [...]

Architecture of Radiolitid Rudist (Mollusca) Shell-Wall Structures and its Phylogenetic Implications

1975 ◽  
Vol 33 ◽  
pp. 686-687
Author(s):  
David H. Sturm ◽  
Bob F. Perkins
Keyword(s):  
Phylogenetic Relationships ◽  
Outer Wall ◽  
Shell Microstructure ◽  
Shell Wall ◽  
Wall Structures ◽  
Phylogenetic Implications ◽  
Cellular Wall ◽  
Superfamily Analysis ◽  
Central Texas

Each of the seven families of rudists (Mollusca, Bivalvia, Hippuritacea) is characterized by distinctive shell-wall architectures which reflect phylogenetic relationships within the superfamily. Analysis of the complex, calcareous, cellular wall of the attached valve of the radiolite rudist Eoradiolites davidsoni (Hill) from the Comanche Cretaceous of Central Texas indicates that its wall architecture is an elaboration of the simpler monopleurid rudist wall and supports possible radiolite-monopleurid relationships.Several well-preserved specimens of E. davidsoni were sectioned, polished, etched, and carbon and gold coated for SEM examination. Maximum shell microstructure detail was displayed by etching with a 0.7% HC1 solution from 80 to 100 seconds.The shell of E. davidsoni comprises a large, thick-walled, conical, attached valve (AV) and a small, very thin, operculate, free valve (FV) (Fig. 1a). The AV shell is two-layered with a thin inner wall, in which original structures are usually obliterated by recrystallization, and a thick, cellular, outer wall.

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