Hybridization and introgression between a rare and a common lady’s slipper orchid, Cypripedium candidum and C. parviflorum (Orchidaceae)

Botany ◽  
2009 ◽  
Vol 87 (11) ◽  
pp. 1054-1065 ◽  
Author(s):  
Anne C. Worley ◽  
Lauren Sawich ◽  
Habibollah Ghazvini ◽  
Bruce A. Ford
Keyword(s):  
Clustering Analysis ◽  
Fragment Length Polymorphism ◽  
Parental Species ◽  
Genetic Data ◽  
Morphological Characters ◽  
Mixed Ancestry ◽  
Bayesian Analyses ◽  
Slipper Orchid ◽  
The Common ◽  
Genetic Profiles

Extinction through hybridization can threaten endangered species when hybrids are vigorous and fertile. We studied hybridization between the endangered small white lady’s slipper ( Cypripedium candidum Muhlenberg ex Willdenow) and the common yellow lady’s slipper ( Cypripedium parviflorum Salisbury var. makasin (Farwell) Sheviak and C. parviflorum var. pubescens (Willdenow) O.W. Knight) in four Manitoban populations. We used 8 morphological characters and 1061 amplified fragment length polymorphism (AFLP) loci to characterize variation in 182 plants. Canonical correlation analysis indicated that morphology was highly predictive of genetic composition. Ordination analyses of morphological and genetic data, and Bayesian clustering analysis of the genetic data, all clearly distinguished the two parental species. The two varieties of C. parviflorum were morphologically divergent but occupied the same genetic cluster in both ordination and Bayesian analyses. Putative hybrids had considerable morphological overlap with parental species but were mostly genetically intermediate. Five of 79 individuals assigned to C. candidum and 15 of 71 individuals assigned to C. parviflorum had genetic profiles consistent with mixed ancestry. These results suggest that some introgression has occurred, but genetic assimilation of endangered C. candidum by the more common C. parviflorum does not seem imminent. The high local abundance of C. candidum may reduce its susceptibility to gene flow from C. parviflorum.

The Power of Matrix Factorization: Methods for Deconvoluting Genetic Heterogeneous Data at Expression Level

2021 ◽  
Vol 15 (8) ◽  
pp. 841-853
Author(s):  
Yuan Liu ◽  
Zhining Wen ◽  
Menglong Li
Keyword(s):  
Artificial Intelligence ◽  
Matrix Factorization ◽  
In Silico ◽  
Genetic Data ◽  
Heterogeneous Data ◽  
Expression Level ◽  
Mathematical Methods ◽  
Challenges And Opportunities ◽  
Factorization Methods ◽  
Genetic Profiles

Background:: The utilization of genetic data to investigate biological problems has recently become a vital approach. However, it is undeniable that the heterogeneity of original samples at the biological level is usually ignored when utilizing genetic data. Different cell-constitutions of a sample could differentiate the expression profile, and set considerable biases for downstream research. Matrix factorization (MF) which originated as a set of mathematical methods, has contributed massively to deconvoluting genetic profiles in silico, especially at the expression level. Objective: With the development of artificial intelligence algorithms and machine learning, the number of computational methods for solving heterogeneous problems is also rapidly abundant. However, a structural view from the angle of using MF to deconvolute genetic data is quite limited. This study was conducted to review the usages of MF methods on heterogeneous problems of genetic data on expression level. Methods: MF methods involved in deconvolution were reviewed according to their individual strengths. The demonstration is presented separately into three sections: application scenarios, method categories and summarization for tools. Specifically, application scenarios defined deconvoluting problem with applying scenarios. Method categories summarized MF algorithms contributed to different scenarios. Summarization for tools listed functions and developed web-servers over the latest decade. Additionally, challenges and opportunities of relative fields are discussed. Results and Conclusion: Based on the investigation, this study aims to present a relatively global picture to assist researchers to achieve a quicker access of deconvoluting genetic data in silico, further to help researchers in selecting suitable MF methods based on the different scenarios.

scholarly journals A Mathematical Study of Barcelona Metro Network

Electronics ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 557
Author(s):  
Irene Mariñas-Collado ◽  
Elisa Frutos Bernal ◽  
Maria Teresa Santos Martin ◽  
Angel Martín del Rey ◽  
Roberto Casado Vara ◽  
...  
Keyword(s):  
Clustering Analysis ◽  
Transportation Network ◽  
Point Of View ◽  
Statistical Point ◽  
Transport Services ◽  
Urban Public Transport ◽  
The Common ◽  
Subway Stations ◽  
Metro Network

The knowledge of the topological structure and the automatic fare collection systems in urban public transport produce many data that need to be adequately analyzed, processed and presented. These data provide a powerful tool to improve the quality of transport services and plan ahead. This paper aims at studying, from a mathematical and statistical point of view, the Barcelona metro network; specifically: (1) the structural and robustness characteristics of the transportation network are computed and analyzed considering the complex network analysis; and (2) the common characteristics of the different subway stations of Barcelona, based on the passenger hourly entries, are identified through hierarchical clustering analysis. These results will be of great help in planning and restructuring transport to cope with the new social conditions, after the pandemic.

scholarly journals Molecular Correlation between Larval, Deutonymph and Adult Stages of the Water Mite Arrenurus (Micruracarus) Novus

Life ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 108
Author(s):  
Pedro María Alarcón-Elbal ◽  
Ricardo García-Jiménez ◽  
María Luisa Peláez ◽  
Jose Luis Horreo ◽  
Antonio G. Valdecasas
Keyword(s):  
Culex Pipiens ◽  
Adult Stage ◽  
Gravid Female ◽  
Morphological Characters ◽  
Species Level ◽  
Life Stages ◽  
Water Mite ◽  
Molecular Correlation ◽  
The Common ◽  
Morphological Transformations

The systematics of many groups of organisms has been based on the adult stage. Morphological transformations that occur during development from the embryonic to the adult stage make it difficult (or impossible) to identify a juvenile (larval) stage in some species. Hydrachnidia (Acari, Actinotrichida, which inhabit mainly continental waters) are characterized by three main active stages—larval, deutonymph and adult—with intermediate dormant stages. Deutonymphs and adults may be identified through diagnostic morphological characters. Larvae that have not been tracked directly from a gravid female are difficult to identify to the species level. In this work, we compared the morphology of five water mite larvae and obtained the molecular sequences of that found on a pupa of the common mosquito Culex (Culex) pipiens with the sequences of 51 adults diagnosed as Arrenurus species and identified the undescribed larvae as Arrenurus (Micruracarus) novus. Further corroborating this finding, adult A. novus was found thriving in the same mosquito habitat. We established the identity of adult and deutonymph A. novus by morphology and by correlating COI and cytB sequences of the water mites at the larval, deutonymph and adult (both male and female) life stages in a particular case of ‘reverse taxonomy’. In addition, we constructed the Arrenuridae phylogeny based on mitochondrial DNA, which supports the idea that three Arrenurus subgenera are ‘natural’: Arrenurus, Megaluracarus and Micruracarus, and the somewhat arbitrary distinction of the species assigned to the subgenus Truncaturus.

Systematics and phylogeography of the Australasian mangrove crabs Parasesarma semperi and P. longicristatum (Decapoda : Brachyura : Sesarmidae) based on morphological and molecular data

2018 ◽  
Vol 32 (1) ◽  
pp. 196 ◽  
Author(s):  
Adnan Shahdadi ◽  
Peter J. F. Davie ◽  
Christoph D. Schubart
Keyword(s):  
Genetic Data ◽  
Morphological Characters ◽  
Molecular Data ◽  
Geographic Range ◽  
The Philippines ◽  
Mitochondrial Genes ◽  
Width Ratio ◽  
Sister Relationship ◽  
Mangrove Crabs ◽  
Morphological And Molecular Data

Parasesarma semperi (Bürger, 1893) was first described from Bohol in the Philippines and is considered to be widely distributed in Southeast Asia. Parasesarma longicristatum (Campbell, 1967) was originally described as a subspecies of P. semperi from Queensland, Australia, and later recognised as a full species. In this study, we re-examine specimens of the two species from across their entire geographic range using genetic markers, a morphometric analysis, and traditional morphological characters. Previous taxonomic species diagnoses were found to be unreliable, but morphometric principle component analyses consistently separate the two species, with the length to width ratio of the propodus of the fourth pereiopod being of particular importance. Genetic data corresponding to the mitochondrial genes COI, ND1 and 16S confirmed a close sister relationship between the two species, forming reciprocally monophyletic groups. Both species have high haplotype diversities and high intraspecific gene flow.

scholarly journals Relationships among Morphological Characters, Isozymes Polymorphism and DNA Variability – the Impact on Lactuca Germplasm Taxonomy

2011 ◽  
Vol 39 (No. 2) ◽  
pp. 59-67 ◽  
Author(s):  
I. Doležalová ◽  
A. Lebeda ◽  
M. Dziechciarková ◽  
E. Křístková ◽  
D. Astley ◽  
...  
Keyword(s):  
Dna Content ◽  
Fragment Length Polymorphism ◽  
Morphological Variability ◽  
Morphological Characters ◽  
Aflp Analysis ◽  
Dapi Staining ◽  
Lactuca Species ◽  
Relative Dna Content ◽  
The Impact

Fifty one accessions of nineteen Lactuca species, the hybrid L. serriola × L. sativa and the related species Mycelis muralis were evaluated for morphological variability, esterase (EST) polymorphism, Amplified Fragment Length Polymorphism (AFLP) and relative DNA content. Sixteen Lactuca accessions were classified taxonomically on the basis of morphology, isozyme analysis and AFLP. Twenty-eight bands (isoforms) of EST were recorded allowing 82% of accessions to be distinguished. The relative DNA content, measured using flow-cytometry (DAPI staining), ranged from 2.02 pg in L. capensis to 17.96 pg in L. canadensis. The results from AFLP analysis and the relative DNA content measurement corresponded well with recent taxonomic classification of the genus Lactuca.  

scholarly journals Current perspectives on the evolution of birds

2008 ◽  
Vol 77 (2) ◽  
pp. 109-116 ◽  
Author(s):  
Per G.P. Ericson
Keyword(s):  
Evolutionary History ◽  
Genetic Data ◽  
Morphological Characters ◽  
Current Understanding ◽  
Sources Of Information ◽  
Theropod Dinosaurs ◽  
History Of ◽  
Evolution Of Birds ◽  
The Many ◽  
Rapid Radiations

The paper summarizes the current understanding of the evolution and diversification of birds. New insights into this field have mainly come from two fundamentally different, but complementary sources of information: the many newly discovered Mesozoic bird fossils and the wealth of genetic analyses of living birds at various taxonomic levels. The birds have evolved from theropod dinosaurs from which they can be defined by but a few morphological characters. The early evolutionary history of the group is characterized by the extinctions of many major clades by the end of the Cretaceous, and by several periods of rapid radiations and speciation. Recent years have seen a growing consensus about the higher-level relationships among living birds, at least as can be deduced from genetic data.

Taxonomic notes on Alpheus inopinatus Holthuis & Gottlieb, 1958 and Alpheus cf. lobidens De Haan, 1849 from Kuwait (Malacostraca: Decapoda: Alpheidae)

Zootaxa ◽  
2020 ◽  
Vol 4851 (1) ◽  
pp. 189-197
Author(s):  
ARTHUR ANKER ◽  
MANAL AL-KANDARI ◽  
SAMMY DE GRAVE
Keyword(s):  
Species Complex ◽  
Morphological Characters ◽  
Colour Pattern ◽  
Similar Species ◽  
Snapping Shrimp ◽  
The Status ◽  
The Common

The status of the common intertidal snapping shrimp, Alpheus inopinatus Holthuis & Gottlieb, 1958, is discussed based on newly collected material from Kuwait. Alpheus inopinatus was previously confused with morphologically very similar species in the Alpheus lobidens De Haan, 1849 species complex, formerly identified as A. crassimanus Heller, 1862 and herein tentatively referred to as A. cf. lobidens. The material herein examined strongly supports the validity of A. inopinatus based on several morphological characters, as well as differences in the colour pattern, compared to other members of the A. lobidens complex. 

Molecular phylogeny of Fordini (Hemiptera: Aphididae: Pemphiginae) inferred from nuclear gene EF-1 α and mitochondrial gene COI

2007 ◽  
Vol 97 (4) ◽  
pp. 379-386 ◽  
Author(s):  
H.C. Zhang ◽  
G.X. Qiao
Keyword(s):  
Phylogenetic Trees ◽  
Host Plants ◽  
Mitochondrial Gene ◽  
Nuclear Gene ◽  
Morphological Characters ◽  
Primary Host ◽  
Gene Coi ◽  
The Common ◽  
Different Parts ◽  
Selection Of

AbstractThe tribe Fordini is a fascinating group because of its complicated life history, primary host specificity and gall-forming characteristic. Different species produce galls with different morphology on different parts of the host plants. The EF-1α-based, COI-based and combined sequences-based phylogenetic trees with three algorithms MP, ML and Bayes all strongly suggest that Fordini is a monophyletic group with two clades corresponding to two subtribes, Fordina and Melaphidina, each also monophyletic. Some important morphological characters and primary host plants of aphids were mapped onto the phylogenetic tree to analyse the division of subtribes and to uncover at which level the aphids correspond to their primary hosts, Pistacia and Rhus. Results suggest that the division of subtribes in Fordini is closely related to host selection of aphids. The evolution of gall morphology and the probable driving force behind it in this tribe were also discussed. The Fordini aphids seem to have evolved towards a better ability to manipulate their host plant, induce strong sinks and gain high reproductive success. Galls in this tribe evolved mainly along two directions to attain this goal: (i) by enlarging the gall from small bag to spherical, even big cauliflower-like, and changing the galls' location or forming two galls in their life cycle (Fordina); (ii) by moving the gall position from midrib, petiole of the leaflet, and eventually to the common petiole of the compound leaf (Melaphidina).

Electrophoretic evidence for the presence of the undescribed ‘Bellinger’ catfish (Tandanus sp.) (Teleostei : Plotosidae) in four New South Wales mid-northern coastal rivers

1997 ◽  
Vol 48 (3) ◽  
pp. 235 ◽  
Author(s):  
Dean R. Jerry ◽  
David J. Woodland
Keyword(s):  
Population Structure ◽  
New South ◽  
New South Wales ◽  
Genetic Data ◽  
Undescribed Species ◽  
Allopatric Populations ◽  
South Wales ◽  
Coastal Rivers ◽  
Allelic Differences ◽  
The Common

Genetic data were collected from eight allopatric populations of the common freshwater catfish, Tandanus tandanus. Catfish sampled from the New South Wales (NSW) mid-northern coastal rivers of the Bellinger, Macleay, Hastings and Manning exhibited fixed allelic differences from T. tandanus from the type locality (Namoi River) at four enzymatic loci (GPI-1*, EST*, UMB-1* and UMB-2*), suggesting that, collectively, catfish from these four river systems constitute an undescribed species of Tandanus. Catfish from the northern coastal rivers of NSW (Tweed, Richmond and Clarence) displayed a complex pattern of population structure that was not fully resolved by the present study. More work is needed on the complex assemblage of populations of eel-tailed catfish in the eastern coastal drainages of Australia.

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