scholarly journals Phylogeny of Pyrus and their relationships inferred from sequences of nuclear NIA-i3 intron and chloroplast ndhC-trnV and trnR-atpA

2021 ◽  
Author(s):  
Danying Cai ◽  
Shuang Jiang ◽  
Ping Sun ◽  
Xiaoyan Zheng ◽  
Xiaoyan Yue ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Network ◽  
Sequence Divergence ◽  
Nuclear Genes ◽  
Chloroplast Genes ◽  
European Species ◽  
Asian Species ◽  
Chinese White

Abstract Background: Pear (Pyrus L.) belongs to subtribe Malinae, tribe Maleae, family Rosaceae. According to the geography distribution, it could be divided into Oriental pear and Occidental pear. Though the phylogeny of Pyrus was complicate, previous study referring to morphology, nuclear genes and chloroplast genes made the relationships clear gradually. However, they had lower sequence divergence and less information, therefore it hardly solved the phylogeny of Pyrus. Results: A total of 100 accessions from Oriental and Occidental pears were used to elucidate the phylogeny of Pyrus by one nuclear NIA-i3 intron and two chloroplast regions (ndhC-trnV and trnR-atpA) with higher polymorphism. The Neighbor-Net phylogenetic network indicated that the phylogenetic relationships were complicate based on ndhC-trnV and trnR-atpA. Oriental pear and Occidental pear were separated in the tree of NIA-i3, P. betulaforlia, P. pashia (except P. pashia ‘P10-3’_1 and P. pashia ‘P23-4’_1) were monophyly; several P. ussuriensis were closely related with P. xerophila. However, the phylogenetic relationships of Chinese White Pear, P. pyrifolia and some P. ussuriensis still could not be well solved; West Asian species and European species were mingled together. Occidental pear P. caucasica 684，P. pyraster 989，P. elaeagrifolia 2817 might be hybrids between Oriental pear and Occidental pear.Conclusions: The phylogenetic relationships of Pyrus were still complicate because interspecies and intraspecies of Oriental pear and Occidental pear respectively were intercrossed. More genes and more accessions were needed to solve the phylogenetic relationships in Pyrus and to explore the possible parents.

scholarly journals Unraveling phylogenetic relationships, reticulate evolution, and genome composition of polyploid plant complexes by RAD-Seq and Hyb-Seq

2021 ◽  
Author(s):  
Kevin Karbstein ◽  
Salvatore Tomasello ◽  
Ladislav Hodac ◽  
Natascha D. Wagner ◽  
Pia Marincek ◽  
...  
Keyword(s):  
Genome Evolution ◽  
Phylogenetic Relationships ◽  
Species Complex ◽  
Phylogenetic Network ◽  
Reticulate Evolution ◽  
Nuclear Genes ◽  
Omics Data ◽  
Genome Composition ◽  
Bioinformatic Pipeline ◽  
Polyploid Plant

Complex genome evolution of young polyploid complexes is poorly understood. Besides challenges caused by hybridization, polyploidization, and incomplete lineage sorting, bioinformatic analyses are often exacerbated by missing information on progenitors, ploidy, and reproduction modes. By using a comprehensive, self-developed bioinformatic pipeline covering tree, structure, network, and SNP-origin analyses, we for the first time unraveled polyploid phylogenetic relationships and genome evolution within the large Eurasian Ranunculus auricomus species complex comprising more than 840 taxa. Our results rely on 97,312 genomic RADseq loci, target enrichment of 576 nuclear genes (48 phased), and 71 plastid regions (Hybseq; OMICS-data) derived from the 75 most widespread polyploid apomictic taxa and four di- and one tetraploid potential sexual progenitor species. Phylogenetic tree and structure analyses consistently showed 3-5 supported polyploid groups, each containing sexual progenitor species. In total, analyses revealed four diploid sexual progenitors and a one unknown, probably extinct progenitor, contributing to the genome composition of R. auricomus polyploids. Phylogenetic network, structure, and SNP-origin analyses based on RADseq loci and phased nuclear genes completed by plastid data demonstrated predominantly allopolyploid origins, each involving 2-3 different diploid sexual subgenomes. Allotetraploid genomes were characterized by subgenome dominance and large proportions of interspecific, non-hybrid SNPs, indicating an enormous degree of post-origin evolution (i.e., Mendelian segregation of the diploid hybrid generations, back-crossings, and gene flow due to facultative sexuality of apomicts), but only low proportions of lineage-specific SNPs. The R. auricomus model system is the first large European polyploid species complex studied with reduced representation OMICS data. Our bioinformatic pipeline underlines the importance of combining different approaches and datasets to successfully unveil how reticulate evolution and post-origin processes shape the diversity of polyploid plant complexes.

scholarly journals An updated checklist of the European Butterflies (Lepidoptera, Papilionoidea)

ZooKeys ◽  
2018 ◽  
Vol 811 ◽  
pp. 9-45 ◽  
Author(s):  
Martin Wiemers ◽  
Emilio Balletto ◽  
Vlad Dincă ◽  
Zdenek Faltynek Fric ◽  
Gerardo Lamas ◽  
...  
Keyword(s):  
European Country ◽  
Cryptic Species ◽  
Phylogenetic Relationships ◽  
The Other ◽  
Ural Mountains ◽  
Species Status ◽  
Asian Species ◽  
Senior Synonym ◽  
Eastern Border ◽  
New Evidence

This paper presents an updated checklist of the butterflies of Europe, together with their original name combinations, and their occurrence status in each European country. According to this checklist, 496 species of the superfamily Papilionoidea occur in Europe. Changes in comparison with the last version (2.6.2) of Fauna Europaea are discussed. Compared to that version, 16 species are new additions, either due to cryptic species most of which have been discovered by molecular methods (13 cases) or due to discoveries of Asian species on the eastern border of the European territory in the Ural mountains (three cases). On the other hand, nine species had to be removed from the list, because they either do not occur in Europe or lost their species status due to new evidence. In addition, three species names had to be changed and 30 species changed their combination due to new evidence on phylogenetic relationships. Furthermore, minor corrections were applied to some authors’ names and years of publication. Finally, the namePolyommatusottomanusLefèbvre, 1831, which is threatened by its senior synonymLycaenalegeriFreyer, 1830, is declared anomen protectum, thereby conserving its name in the current combinationLycaenaottomana.

A taxonomic revision of the genus Metadrinomyia Shima (Diptera: Tachinidae) with descriptions of two new species

Zootaxa ◽  
2009 ◽  
Vol 2311 (1) ◽  
pp. 55-65
Author(s):  
HYE-WOO BYUN ◽  
HO-YEON HAN
Keyword(s):  
New Species ◽  
South Korea ◽  
Phylogenetic Relationships ◽  
East Asian ◽  
Taxonomic Revision ◽  
Asian Species ◽  
Two New Species

A little known tachinid genus, Metadrinomyia Shima, is revised based on four East Asian species including two new to science: M. flavifrons sp. nov. and M. xanthokolos sp. nov. The majority of the specimens used in this study were collected from low vegetation in the foothills of mountains in South Korea. The new species can be clearly distinguished from their congeners by their pruinosity, chaetotaxy and genitalic structures. A key, descriptions, photographs, and illustrations of the male genitalic structures are provided and the phylogenetic relationships among the species are investigated.

scholarly journals Genetic Divergences and Phylogenetic Relationships Among the Fejervarya limnocharis Complex in Thailand and Neighboring Countries Revealed by Mitochondrial and Nuclear Genes

2008 ◽  
Vol 25 (4) ◽  
pp. 381-390 ◽  
Author(s):  
Manabu Kotaki ◽  
Atsushi Kurabayashi ◽  
Masafumi Matsui ◽  
Wichase Khonsue ◽  
Tjong Hon Djong ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Genes ◽  
Fejervarya Limnocharis

Re: Phylogenetic Relationships in Sphingidae (Insecta: Lepidoptera): Initial Evidence from Two Nuclear Genes

2001 ◽  
Vol 20 (2) ◽  
pp. 311-316 ◽  
Author(s):  
Jerome C. Regier ◽  
Charles Mitter ◽  
Timothy P. Friedlander ◽  
Richard S. Peigler
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Genes

Phylogenetic relationships and divergence times among dormice (Rodentia, Gliridae) based on three nuclear genes

2007 ◽  
Vol 36 (6) ◽  
pp. 537-546 ◽  
Author(s):  
Mitsuo Nunome ◽  
Shumpei P. Yasuda ◽  
Jun J. Sato ◽  
Peter Vogel ◽  
Hitoshi Suzuki
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Genes ◽  
Divergence Times

Genetic divergence and geographic diversification in Nautilus

Paleobiology ◽  
1995 ◽  
Vol 21 (2) ◽  
pp. 220-228 ◽  
Author(s):  
Charles G. Wray ◽  
Neil H. Landman ◽  
W. Bruce Saunders ◽  
James Bonacum
Keyword(s):  
Dna Sequence ◽  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Sequence Divergence ◽  
Distinct Species ◽  
Morphological Characters ◽  
Geographic Diversification ◽  
Isolated Populations ◽  
Systematic Analysis

Despite exhaustive investigation of present-day Nautilus, the phylogenetic relationships of the five or six recognized species within this genus remain unclear. Mitochondrial and nuclear DNA sequence data plus a suite of morphological characters are used to investigate phylogenetic relationships. Systematic analysis of the morphological variation fails to characterize described species as independent lineages. However, DNA sequence analysis indicates that there are three geographically distinct clades consisting of western Pacific, eastern Australian/Papua-New Guinean, and western Australian/Indonesian forms. The morphologically and genetically distinct species Nautilus scrobiculatus falls outside the three geographically recognized assemblages. Members of the genus Nautilus also exhibit low levels of sequence divergence. All these data suggest that Nautilus is currently undergoing diversification, which may have begun only several million years ago. These data also suggest that some of the morphological features used to define Nautilus species may simply represent fixed variations in isolated populations within the same species.

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