scholarly journals Allele Sorting as a Novel Approach to Resolving the Origin of Allotetraploids Using Hyb-Seq Data: A Case Study of the Balkan Mountain Endemic Cardamine barbaraeoides

2021 ◽  
Vol 12 ◽  
Author(s):  
Marek Šlenker ◽  
Adam Kantor ◽  
Karol Marhold ◽  
Roswitha Schmickl ◽  
Terezie Mandáková ◽  
...  
Keyword(s):  
Phylogenetic Reconstruction ◽  
Balkan Peninsula ◽  
Nuclear Genes ◽  
Nuclear Ribosomal Dna ◽  
Interspecific Gene Flow ◽  
Polyploid Evolution ◽  
Pleistocene Climate ◽  
Novel Approach ◽  
The Rich ◽  
Phylogenomic Analyses

Mountains of the Balkan Peninsula are significant biodiversity hotspots with great species richness and a large proportion of narrow endemics. Processes that have driven the evolution of the rich Balkan mountain flora, however, are still insufficiently explored and understood. Here we focus on a group of Cardamine (Brassicaceae) perennials growing in wet, mainly mountainous habitats. It comprises several Mediterranean endemics, including those restricted to the Balkan Peninsula. We used target enrichment with genome skimming (Hyb-Seq) to infer their phylogenetic relationships, and, along with genomic in situ hybridization (GISH), to resolve the origin of tetraploid Cardamine barbaraeoides endemic to the Southern Pindos Mts. (Greece). We also explored the challenges of phylogenomic analyses of polyploid species and developed a new approach of allele sorting into homeologs that allows identifying subgenomes inherited from different progenitors. We obtained a robust phylogenetic reconstruction for diploids based on 1,168 low-copy nuclear genes, which suggested both allopatric and ecological speciation events. In addition, cases of plastid–nuclear discordance, in agreement with divergent nuclear ribosomal DNA (nrDNA) copy variants in some species, indicated traces of interspecific gene flow. Our results also support biogeographic links between the Balkan and Anatolian–Caucasus regions and illustrate the contribution of the latter region to high Balkan biodiversity. An allopolyploid origin was inferred for C. barbaraeoides, which highlights the role of mountains in the Balkan Peninsula both as refugia and melting pots favoring species contacts and polyploid evolution in response to Pleistocene climate-induced range dynamics. Overall, our study demonstrates the importance of a thorough phylogenomic approach when studying the evolution of recently diverged species complexes affected by reticulation events at both diploid and polyploid levels. We emphasize the significance of retrieving allelic and homeologous variation from nuclear genes, as well as multiple nrDNA copy variants from genome skim data.

scholarly journals Genic evidence that gnetophytes are sister to all other seed plants

2019 ◽  
Author(s):  
Yinzhi Zhang ◽  
Zhiming Liu
Keyword(s):  
Gene Evolution ◽  
Gene Tree ◽  
Phylogenetic Inference ◽  
Nuclear Genes ◽  
Recent Common Ancestor ◽  
Seed Plants ◽  
Most Recent Common Ancestor ◽  
Novel Approach ◽  
Evolution Pattern ◽  
Phylogenomic Analyses

AbstractGnetophytes, comprising three relict genera, Gnetum, Welwitchia and Ephedra, are a morphologically diverse and enigmatic assemblage among seed plants. Despite recent progress on phylogenomic analyses or the insights from the recently decoded Gnetum genome, the relationship between gnetophytes and other seed plant lineages is still one of the outstanding, unresolved questions in plant sciences. Here, we showed that phylogenetic studies from nuclear genes support the hypothesis that places gnetophytes as sister to all other extant seed plants and so this hypothesis should not be ruled out according to phylogenetic inference based on nuclear genes. However, this extraordinarily difficult phylogenetic problem might never be solved by phylogenetic inference based gene tree under various artificial selection. Hence, we adopted a novel approach, comparing gene divergence among different lineages, to solve the conflicts by showing that gnetophytes actually did not gained a set of genes like the most recent common ancestor (MRCA) of other seed plants. This distinct gene evolution pattern could not be explained by random gene lost as in other seed plants but should be interpreted by the early divergence of gnetophytes from rest of seed plants. With such a placement, the gymnosperms are paraphyletic and there should be three distinct groups of living seed plants: gnetophytes, non-gnetophytes gymnosperms and angiosperms.

scholarly journals The design of Lil’Flo, a socially assistive robot for upper extremity motor assessment and rehabilitation in the community via telepresence

2021 ◽  
Vol 8 ◽  
pp. 205566832110018
Author(s):  
Michael J Sobrepera ◽  
Vera G Lee ◽  
Michelle J Johnson
Keyword(s):  
Rural Areas ◽  
Motor Rehabilitation ◽  
Rehabilitation Care ◽  
Rehabilitation Professionals ◽  
Novel Approach ◽  
Assistive Robot ◽  
Care Facilities ◽  
The Rich ◽  
Socially Assistive Robot ◽  
Assistive Robotic

Introduction We present Lil’Flo, a socially assistive robotic telerehabilitation system for deployment in the community. As shortages in rehabilitation professionals increase, especially in rural areas, there is a growing need to deliver care in the communities where patients live, work, learn, and play. Traditional telepresence, while useful, fails to deliver the rich interactions and data needed for motor rehabilitation and assessment. Methods We designed Lil’Flo, targeted towards pediatric patients with cerebral palsy and brachial plexus injuries using results from prior usability studies. The system combines traditional telepresence and computer vision with a humanoid, who can play games with patients and guide them in a present and engaging way under the supervision of a remote clinician. We surveyed 13 rehabilitation clinicians in a virtual usability test to evaluate the system. Results The system is more portable, extensible, and cheaper than our prior iteration, with an expressive humanoid. The virtual usability testing shows that clinicians believe Lil’Flo could be deployed in rural and elder care facilities and is more capable of remote stretching, strength building, and motor assessments than traditional video only telepresence. Conclusions Lil’Flo represents a novel approach to delivering rehabilitation care in the community while maintaining the clinician-patient connection.

scholarly journals Phylogenomic analyses of large-scale nuclear genes provide new insights into the evolutionary relationships within the rosids

2016 ◽  
Vol 105 ◽  
pp. 166-176 ◽  
Author(s):  
Lei Zhao ◽  
Xia Li ◽  
Ning Zhang ◽  
Shu-Dong Zhang ◽  
Ting-Shuang Yi ◽  
...  
Keyword(s):  
Large Scale ◽  
Nuclear Genes ◽  
Evolutionary Relationships ◽  
Phylogenomic Analyses

Molecular systematics of subtribe Banksiinae (Banksia and Dryandra; Proteaceae) Based on cpDNA and nrDNA sequence data: Implications for taxonomy and biogeography

1998 ◽  
Vol 11 (4) ◽  
pp. 321 ◽  
Author(s):  
Austin R. Mast
Keyword(s):  
Sequence Data ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Internal Transcribed Spacers ◽  
Nuclear Ribosomal Dna ◽  
Base Substitution ◽  
Trnl Intron ◽  
Single Root ◽  
Cladistic Analyses ◽  
Molecular Characters

Despite considerable research interest in the subtribe Banksiinae (Banksia L.f. and Dryandra R.Br.), no strongly supported phylogenetic hypothesis for the relationship between the genera exists, nor have molecular characters been sampled for phylogenetic reconstruction at any level. In this study, DNA sequence characters were sampled from chloroplast DNA (cpDNA; the trnL intron, the trnL 3′ exon, and the spacer between the trnL 3′ exon and trnF) and nuclear ribosomal DNA (nrDNA; both internal transcribed spacers) of 18 species of Banksia and five of Dryandra, with six outgroup taxa from the subfamily Grevilleoideae. The molecular characters provided the opportunity to code taxa outside of Banksia for cladistic comparison with the genus—an opportunity not previously provided by morphological characters. Cladistic analyses, using parsimony, explored the effects of various weightings of transition to transversion events and base substitution to insertion and deletion events to determine which relationships in the cladograms were robust. The trnL/trnF and ITS characters strongly supported a paraphyletic Banksia with respect to a monophyletic Dryandra. The molecular results supported a single root for Thiele and Ladiges’(1996) unrooted morphological cladogram along the branch between the Isotylis to B. fuscolutea clade and the Grandes to B. tricuspis clade. George’s (1981) subgenus Banksia and section Banksia appeared dramatically non-monophyletic. The distribution of eastern taxa at derived positions on the molecular cladograms suggested considerable cladogenesis in the the genus prior to the formation of the Nullarbor Plain during the Tertiary.

Comparative Law in Central and Eastern Europe

2019 ◽  
pp. 180-200
Author(s):  
Zdeněk Kühn
Keyword(s):  
Soviet Union ◽  
Eastern Europe ◽  
Central And Eastern Europe ◽  
Comparative Law ◽  
Balkan Peninsula ◽  
The Czech Republic ◽  
The Soviet Union ◽  
History Of ◽  
The Rich ◽  
Rich History

The region of Central and Eastern Europe covers many of the European nations east of Germany. The dominant nation of the region is Russia. Between Russia and Germany there are, first, a number of small nations composing the region known as Central Europe (Poland, Hungary, the Czech Republic, and Slovakia); second, the nations which formed the western part of the Soviet Union; and, third, the states on the Balkan peninsula. This article shows the rich history of comparative law before the installment of communist regimes, such as the era of Stalin, and then discusses comparative law under communism and the role and status of comparative law after the fall of communist rule.

Development of Comparative Law in Central and Eastern Europe

2006 ◽  
pp. 214-236
Author(s):  
Zdeněk Kühn
Keyword(s):  
Soviet Union ◽  
Eastern Europe ◽  
Central And Eastern Europe ◽  
Comparative Law ◽  
Balkan Peninsula ◽  
The Czech Republic ◽  
The Soviet Union ◽  
History Of ◽  
The Rich ◽  
Rich History

The region of Central and Eastern Europe covers many of the European nations east of Germany. The dominant nation of the region is Russia. Between Russia and Germany there are, first, a number of small nations composing the region known as Central Europe (Poland, Hungary, the Czech Republic, and Slovakia); second, the nations which formed the western part of the Soviet Union; and, third, the states on the Balkan peninsula. This article shows the rich history of comparative law before the installment of communist regimes, such as the era of Stalin, and then discusses comparative law under communism and the role and status of comparative law after the fall of communist rule.

Students’ viewpoints on using tableaux to analyse short stories

2018 ◽  
Vol 17 (3) ◽  
pp. 245-256
Author(s):  
Logamurthie Athiemoolam
Keyword(s):  
Short Stories ◽  
Short Story ◽  
Detailed Account ◽  
Content Type ◽  
Written Narratives ◽  
Psychological States ◽  
Novel Approach ◽  
Approach To Teaching ◽  
The Rich ◽  
Phenomenological Design

Purpose The purpose of the paper is to provide a detailed account of pre-service teachers’ viewpoints on the use of tableaux as pedagogy to analyse short stories in secondary schools based on their exposure to the use of tableaux and their active participation in the process of tableau creation. Design/methodology/approach The study adopted a qualitative approach and a phenomenological design as it provides a detailed account of PGCE English Methodology pre-service teachers’ views on the use of tableaux to teach a short story. The data collection method used was written narratives based on the participants’ detailed accounts of their learning during the process of tableau creation and their viewpoints on the use of such an approach in the teaching of literature within secondary school contexts. The “rich, thick data” extracted from the written narratives were analysed thematically. Findings The findings indicated that although pre-service teachers were initially sceptical towards the use of tableaux as a strategy to teach a short story, as they grew in their understanding of the practices involved their insights into the themes, motifs and characters’ emotional, personal and psychological states of being were enhanced. Originality/value Research in the use of tableaux as a strategy for pre-service teachers to critically analyse and engage with short stories is a novel approach to teaching and limited research has been conducted in the field.

Phylogeny of Macronematinae (Trichoptera: Hydropsychidae) based on molecular and morphological analyses

2019 ◽  
Vol 151 (6) ◽  
pp. 696-716 ◽  
Author(s):  
Christine Jewel C. Uy ◽  
Ji Hyoun Kang ◽  
John C. Morse ◽  
Yeon Jae Bae
Keyword(s):  
Phylogenetic Relationships ◽  
Large Subunit ◽  
Phylogenetic Reconstruction ◽  
Morphological Characters ◽  
Nuclear Ribosomal Dna ◽  
Phylogenetic Study ◽  
Base Pairs ◽  
Morphological Findings ◽  
Close Relationship ◽  
Evolutionary Novelties

AbstractThe phylogenetic relationships among the members of Macronematinae (Trichoptera: Hydropsychidae) have long been debated and often revised. Our study based on a large subunit (28S) nuclear ribosomal DNA (D2 expansion fragment; 464 base pairs) of gene sequences found all genera to be monophyletic except for the genus Polymorphanisus Walker, which produced two clades in accordance with its species groups established using morphological characters. Phylogenetic reconstruction based on mitochondrial cytochrome oxidase I (658 base pairs) found the same monophyletic relationships, however, except for the genera Polymorphanisus and Macrostemum Kolenati. The placement of the genus Leptonema Guérin-Méneville as the basal clade in the subfamily was also ruled out, which is consistent with previous morphological findings. The monophyly of two previously recognised tribes (Macronematini and Polymorphanisini) was not supported. We also found that the genera Centromacronema Ulmer, Baliomorpha Neboiss, and Macronema Pictet are most closely related, having three head setal warts on the vertex of the head and unsegmented inferior appendages of male genitalia as their synapomorphies. Our study supported the hypothesis of close relationship of the genera Amphipsyche McLachlan and Protomacronema Ulmer with the morphological synapomorphies: absence of a forewing discoidal cell and the presence of elevated head carinae on the larvae. Some notable evolutionary novelties in the structure of adults in various lineages of this subfamily include reduction of maxillae and labium, reduction and loss of a discoidal cell and evolution of a c-sc crossvein in each forewing, fusion of segments in each male inferior appendage, and evolution of dark colour patterns in the forewings. Also, the head setal warts, which are unique organs in Trichoptera, evolved towards a decreasing number in the subfamily. This first molecular phylogenetic study, covering most genera in Macronematinae and including an interpretation of 12 key evolutionary novelties, provides an important basis for resolving long-standing questions regarding phylogenetic relationships and classification of genera and species and helps lay a stronger foundation for inference of testable hypotheses about functional traits for species of this common and widespread subfamily.

Sign in / Sign up

Export Citation Format

Share Document