Phylogeny of Paramysis (Crustacea: Mysida) and the origin of Ponto-Caspian endemic diversity: Resolving power from nuclear protein-coding genes

2008 ◽  
Vol 46 (2) ◽  
pp. 738-759 ◽  
Author(s):  
Asta Audzijonyte ◽  
Mikhail E. Daneliya ◽  
Nikolai Mugue ◽  
Risto Väinölä
2005 ◽  
Vol 34 (1) ◽  
pp. 147-158 ◽  
Author(s):  
Jerome C. Regier ◽  
Heather M. Wilson ◽  
Jeffrey W. Shultz

2008 ◽  
Vol 48 (1) ◽  
pp. 359-368 ◽  
Author(s):  
L.M. Tsang ◽  
K.Y. Ma ◽  
S.T. Ahyong ◽  
T.-Y. Chan ◽  
K.H. Chu

2018 ◽  
Author(s):  
Yang Liu ◽  
Simin Liu ◽  
Chia-Fen Yeh ◽  
Nan Zhang ◽  
Guoling Chen ◽  
...  

AbstractMultiple nuclear markers provide genetic polymorphism data for molecular systematics and population genetic studies. They are especially required for the coalescent-based analyses that can be used to accurately estimate species trees and infer population demographic histories. However, in avian evolutionary studies, these powerful coalescent-based methods are hindered by the lack of a sufficient number of markers. In this study, we designed PCR primers to amplify 136 nuclear protein-coding loci (NPCLs) by scanning the published Red Junglefowl (Gallus gallus) and Zebra Finch (Taeniopygia guttata) genomes. To test their utility, we amplified these loci in 41 bird species representing 23 Aves orders. The sixty-three best-performing NPCLs, based on high PCR success rates, were selected which had various mutation rates and were evenly distributed across 17 avian autosomal chromosomes and the Z chromosome. To test phylogenetic resolving power of these markers, we conducted a Neoavian phylogenies analysis using 63 concatenated NPCL markers derived from 48 whole genomes of birds. The resulting phylogenetic topology, to a large extent, is congruence with results resolved by previous whole genome data. To test the level of intraspecific polymorphism in these makers, we examined the genetic diversity in four populations of the Kentish Plover (Charadrius alexandrinus) at 17 of NPCL markers chosen at random. Our results showed that these NPCL markers exhibited a level of polymorphism comparable with mitochondrial loci. Therefore, this set of pan-avian nuclear protein-coding loci has great potential to facilitate studies in avian phylogenetics and population genetics.


2011 ◽  
Vol 61 (3) ◽  
pp. 628-638 ◽  
Author(s):  
Jenny Knapp ◽  
Minoru Nakao ◽  
Tetsuya Yanagida ◽  
Munehiro Okamoto ◽  
Urmas Saarma ◽  
...  

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Christopher E Laumer ◽  
Andreas Hejnol ◽  
Gonzalo Giribet

Flatworms number among the most diverse invertebrate phyla and represent the most biomedically significant branch of the major bilaterian clade Spiralia, but to date, deep evolutionary relationships within this group have been studied using only a single locus (the rRNA operon), leaving the origins of many key clades unclear. In this study, using a survey of genomes and transcriptomes representing all free-living flatworm orders, we provide resolution of platyhelminth interrelationships based on hundreds of nuclear protein-coding genes, exploring phylogenetic signal through concatenation as well as recently developed consensus approaches. These analyses robustly support a modern hypothesis of flatworm phylogeny, one which emphasizes the primacy of the often-overlooked ‘microturbellarian’ groups in understanding the major evolutionary transitions within Platyhelminthes: perhaps most notably, we propose a novel scenario for the interrelationships between free-living and vertebrate-parasitic flatworms, providing new opportunities to shed light on the origins and biological consequences of parasitism in these iconic invertebrates.


BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Liping Yan ◽  
Thomas Pape ◽  
Karen Meusemann ◽  
Sujatha Narayanan Kutty ◽  
Rudolf Meier ◽  
...  

Abstract Background Blowflies are ubiquitous insects, often shiny and metallic, and the larvae of many species provide important ecosystem services (e.g., recycling carrion) and are used in forensics and debridement therapy. Yet, the taxon has repeatedly been recovered to be para- or polyphyletic, and the lack of a well-corroborated phylogeny has prevented a robust classification. Results We here resolve the relationships between the different blowfly subclades by including all recognized subfamilies in a phylogenomic analysis using 2221 single-copy nuclear protein-coding genes of Diptera. Maximum likelihood (ML), maximum parsimony (MP), and coalescent-based phylogeny reconstructions all support the same relationships for the full data set. Based on this backbone phylogeny, blowflies are redefined as the most inclusive monophylum within the superfamily Oestroidea not containing Mesembrinellidae, Mystacinobiidae, Oestridae, Polleniidae, Sarcophagidae, Tachinidae, and Ulurumyiidae. The constituent subfamilies are re-classified as Ameniinae (including the Helicoboscinae, syn. nov.), Bengaliinae, Calliphorinae (including Aphyssurinae, syn. nov., Melanomyinae, syn. nov., and Toxotarsinae, syn. nov.), Chrysomyinae, Luciliinae, Phumosiinae, Rhiniinae stat. rev., and Rhinophorinae stat. rev. Metallic coloration in the adult is shown to be widespread but does not emerge as the most likely ground plan feature. Conclusions Our study provides the first phylogeny of oestroid calyptrates including all blowfly subfamilies. This allows settling a long-lasting controversy in Diptera by redefining blowflies as a well-supported monophylum, and blowfly classification is adjusted accordingly. The archetypical blowfly trait of carrion-feeding maggots most likely evolved twice, and the metallic color may not belong to the blowfly ground plan.


MycoKeys ◽  
2019 ◽  
Vol 47 ◽  
pp. 17-33 ◽  
Author(s):  
Alica Košuthová ◽  
Martin Westberg ◽  
Mónica A.G. Otálora ◽  
Mats Wedin

Here, we test the current generic delimitation of Rostania (Collemataceae, Peltigerales, Ascomycota) utilizing molecular phylogeny and morphological investigations. Using DNA sequence data from the mitochondrial SSU rDNA and two nuclear protein-coding genes (MCM7 and β-tubulin) and utilizing parsimony, maximum likelihood and Bayesian phylogenetic methods, Rostania is shown to be non-monophyletic in the current sense. A new generic delimitation of Rostania is thus proposed, in which the genus is monophyletic, and three species (Rostaniacoccophylla, R.paramensis, R.quadrifida) are excluded and transferred to other genera. Rostaniaoccultata is further non-monophyletic, and a more detailed investigation of species delimitations in Rostania s. str. is needed. The new combinations Leptogiumparamense and Scytiniumquadrifidum are proposed.


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