scholarly journals Patterns of hybridization and cryptic introgression among one- and four-needled pinyon pines

2020 ◽  
Vol 126 (3) ◽  
pp. 401-411
Author(s):  
Ryan Buck ◽  
Sandra Hyasat ◽  
Alice Hossfeld ◽  
Lluvia Flores-Rentería
Keyword(s):  
Distinct Species ◽  
Hybrid Origin ◽  
Interspecific Mating ◽  
Nucleotide Polymorphisms ◽  
Intermediate Morphology ◽  
The Status ◽  
Number Variation ◽  
Genetic Clusters ◽  
Variable Morphology ◽  
Genetic Contributions

Abstract Background and Aims Pinyon pine hybridization is widely acknowledged, but the frequency of and contributors to such interspecific mating remain largely unstudied. Pinus quadrifolia has three to four needles per fascicle, suggesting that it is a result of hybridization between the five-needled P. juarezensis and the single-needled P. monophylla. In this study we address the taxonomic validity of P. juarezensis, the hybrid origin of P. quadrifolia and the presence of hybridization and intermediate morphology as a result of interspecific hybridization in this complex. Methods We address these questions by combining a genomic and morphological approach. We generated 1868 single nucleotide polymorphisms (SNPs) to detect genetic clusters using principal co-ordinates analyis, discriminant analysis of principal components, fastSTRUCTURE and ADMIXTURE analyses, and performed a morphological analysis of the leaves. Key Results We found that the five-needled pinyons did not differ genetically from the four-needled P. quadrifolia, reducing the status of P. juarezensis to P. quadrifolia. We also found no evidence that P. quadrifolia is of hybrid origin from P. juarezensis × P. monophylla but is instead a genetically distinct species with natural needle number variation that has yet to be explained. Hybridization does occur in this complex, but mostly between P. quadrifolia and P. californiarum, and less commonly between P. quadrifolia and P. monophylla. Interestingly, some hybrid derivatives were detected between both single-needled taxa, P. monophylla and P. californiarum, a hybrid combination that has not yet been proposed. Hybrids have intermediate morphology when they have similar genetic contributions from both parental species; however, when one parent contributes more, hybrid derivatives resemble the parent with higher genetic contribution, resulting in cryptic introgression. Conclusions Our detailed sampling across the distribution of this complex allows us to describe the patterns of hybridization among these taxa, resolves an ancient taxonomic conflict and provides insights into the challenges of exclusively using morphological traits when identifying these taxa with cryptic hybridization and variable morphology.

Status of Family Fissidentaceae in Gujarat

2016 ◽  
Vol 1 (1) ◽  
Author(s):  
D.G. Shah ◽  
D.N. Mehta ◽  
R.V. Gujar
Keyword(s):  
Distinct Species ◽  
The State ◽  
The Other ◽  
Land Plants ◽  
Reproductive Structures ◽  
The Family ◽  
The Status ◽  
Vegetative Characters ◽  
First Time ◽  
Different Parts

Bryophytes are the second largest group of land plants and are also known as the amphibians of the plant kingdom. 67 species of bryophytes have been reported from select locations across the state of Gujrat. The status of family fissidentaceae which is a large moss family is being presented in this paper. Globally the family consists of 10 genera but only one genus, Fissidens Hedw. has been collected from Gujarat. Fissidens is characterized by a unique leaf structure and shows the presence of three distinct lamina, the dorsal, the ventral and the vaginant lamina. A total of 8 species of Fissidens have been reported from the state based on vegetative characters as no sporophyte stages were collected earlier. Species reported from the neighboring states also showed the absence of sporophytes. The identification of different species was difficult due to substantial overlap in vegetative characters. Hence a detailed study on the diversity of members of Fissidentaceae in Gujarat was carried out between November 2013 and February 2015. In present study 8 distinct species of Fissidens have been collected from different parts of the state. Three species Fissidens splachnobryoides Broth., Fissidens zollingerii Mont. and Fissidens curvato-involutus Dixon. have been identified while the other five are still to be identified. Fissidens zollingerii Mont. and Fissidens xiphoides M. Fleisch., which have been reported as distinct species are actually synonyms according to TROPICOS database. The presence of sexual reproductive structures and sporophytes for several Fissidens species are also being reported for the first time from the state.

scholarly journals Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Cooper J. Park ◽  
Nicole A. Caimi ◽  
Debbie C. Buecher ◽  
Ernest W. Valdez ◽  
Diana E. Northup ◽  
...  
Keyword(s):  
New Mexico ◽  
Genetic Manipulation ◽  
Distinct Species ◽  
Biosynthetic Gene Cluster ◽  
Genomic Variation ◽  
Species Variation ◽  
Nucleotide Polymorphisms ◽  
Peptide Synthetases ◽  
Genome Wide ◽  
Diversity Estimates

Abstract Background Antibiotic-producing Streptomyces bacteria are ubiquitous in nature, yet most studies of its diversity have focused on free-living strains inhabiting diverse soil environments and those in symbiotic relationship with invertebrates. Results We studied the draft genomes of 73 Streptomyces isolates sampled from the skin (wing and tail membranes) and fur surfaces of bats collected in Arizona and New Mexico. We uncovered large genomic variation and biosynthetic potential, even among closely related strains. The isolates, which were initially identified as three distinct species based on sequence variation in the 16S rRNA locus, could be distinguished as 41 different species based on genome-wide average nucleotide identity. Of the 32 biosynthetic gene cluster (BGC) classes detected, non-ribosomal peptide synthetases, siderophores, and terpenes were present in all genomes. On average, Streptomyces genomes carried 14 distinct classes of BGCs (range = 9–20). Results also revealed large inter- and intra-species variation in gene content (single nucleotide polymorphisms, accessory genes and singletons) and BGCs, further contributing to the overall genetic diversity present in bat-associated Streptomyces. Finally, we show that genome-wide recombination has partly contributed to the large genomic variation among strains of the same species. Conclusions Our study provides an initial genomic assessment of bat-associated Streptomyces that will be critical to prioritizing those strains with the greatest ability to produce novel antibiotics. It also highlights the need to recognize within-species variation as an important factor in genetic manipulation studies, diversity estimates and drug discovery efforts in Streptomyces.

The North American Allies of Hylobius piceus (De Geer) (Coleoptera: Curculionidae)

1957 ◽  
Vol 89 (1) ◽  
pp. 37-43 ◽  
Author(s):  
Stephen L. Wood
Keyword(s):  
North American ◽  
Distinct Species ◽  
Morphological Characters ◽  
North American Species ◽  
Winged Form ◽  
The North ◽  
The Status ◽  
Field Workers ◽  
Dimorphic Species ◽  
Biological Differences

While investigating the biology of the North American species of Hypomolyx, field workers in Manitoba found a vestigial, or short-winged, and a long-winged form under apparently identical conditions in about equal numbers. Although biological differences were nor then apparent, there was doubt as to whether they were dealing with one dimorphic species or with two distinct species, A search for morphological characters brought to light numerous differences between the two forms, supporting the view that two species were present. These differences, a description the previously unrecognized species, and notes concerning the status of the genera Hylobius and Hypomolyx are reported below.

scholarly journals Molecular and morphological analyses support recognition of Prostanthera volucris (Lamiaceae), a new species from the Central Tablelands of New South Wales

2021 ◽  
Author(s):  
Ryan P. O'Donnell ◽  
Jeremy J. Bruhl ◽  
Ian R.H. Telford ◽  
Trevor C. Wilson ◽  
Heidi C. Zimmer ◽  
...  
Keyword(s):  
New South ◽  
New South Wales ◽  
Evolutionary Relationship ◽  
Distinct Species ◽  
Morphological Characters ◽  
Critically Endangered ◽  
Nucleotide Polymorphisms ◽  
Line Drawings ◽  
South Wales ◽  
Neighbour Network

Research into the systematics of Prostanthera has recently revealed a close evolutionary relationship among P. phylicifolia s. str., the critically endangered P. gilesii, and a population of uncertain identity from the Central Tablelands of New South Wales, Australia. Previous analyses were unable to establish whether genetic boundaries separated these taxa. This study aimed to assess the species boundaries among these three taxa using a combination of single-nucleotide polymorphisms (SNP) sampled at the population-scale and multivariate analysis of morphological characters. Non-parametric and parametric statistics, neighbour-network analysis, phylogenetic analysis, and ancestry coefficient estimates all provided support for discrete genetic differences between the three taxa. Morphological phenetic analysis identified a suite of characters that distinguished each of these taxa. This corroboration of evidence supports the presence of three independently evolving lineages. Prostanthera gilesii and P. phylicifolia s. str. are distinct species independent from the third taxon which is described here as P. volucris R.P.O'Donnell. A detailed description, diagnostic line drawings and photographs are provided. We evaluate P. volucris as satisfying criteria to be considered Critically Endangered.

scholarly journals Predictive role of serum rheumatoid factor in different disease pattern of psoriasis and psoriatic arthritis

2021 ◽  
Vol 33 (1) ◽  
Author(s):  
Enas Zahran ◽  
Ali Youssof ◽  
Wafaa Shehata ◽  
Ahmed Bahgat ◽  
Emad Elshebiny
Keyword(s):  
Rheumatoid Factor ◽  
Signs And Symptoms ◽  
Inflammatory Disorder ◽  
Clinical Pattern ◽  
Positive Rheumatoid Factor ◽  
Disease Patterns ◽  
The Status ◽  
Disease Pattern ◽  
Variable Morphology ◽  
Genetic And Environmental Factors

Abstract Background Psoriasis is a multisystem inflammatory disorder with variable morphology, clinical pattern and multiple comorbidities. Interplay between genetic and environmental factors leading to an aberrant immune response in the skin may contribute to disease development. The assessment for risk factors, signs, and symptoms of potential comorbid diseases is an important component of patient management. The aim of this study is to determine rheumatoid factors (RF) positivity and its levels in psoriasis patients, and describe its relationship with the demographic and clinical characteristics, comorbidities, and disease patterns of psoriasis. Results Rheumatoid factor was positive in psoriatic patients more than control,30% of patients had positive rheumatoid factor while only 10% of control had positive results. Rheumatoid factor level was 63.8 ± 186.7 IU/ml in psoriasis vs. 9.3 ± 12.3 in control. Thirty percent of psoriasis patients have positive rheumatoid factor vs. 10% of control. There was no significant statistical difference between psoriasis patients with or without arthritis as regard rheumatoid factor positivity and titer; rheumatoid factor was positive in 20% in psoriatic patients with arthritis vs. 26% in psoriatic patients without arthritis. In psoriatic patients, the status of rheumatoid factor did not relate to disease severity, onset, course, site of affection, presence of scalp, nail affection, and presence of dactylitis (p value>0.5). Conclusion Psoriasis was associated with higher seropositivity of RF compared to age-matched non-psoriatic healthy controls. Occurrence and level of rheumatoid factor were not associated with severity or clinical pattern of psoriasis.

Abstract 3666: Common Polymorphisms in Familial Vascular Malformation Genes do not Show Association with Sporadic Brain Arteriovenous Malformation

Stroke ◽  
2012 ◽  
Vol 43 (suppl_1) ◽  
Author(s):  
Shantel Weinsheimer ◽  
Nasrine Bendjilali ◽  
Ludmila Pawlikowska ◽  
Pui-Yan Kwok ◽  
Michael T Lawton ◽  
...  
Keyword(s):  
Arteriovenous Malformation ◽  
Vascular Malformation ◽  
Multiple Testing ◽  
Nucleotide Polymorphisms ◽  
Brain Arteriovenous Malformation ◽  
Inherited Disorders ◽  
Venous Circulation ◽  
Snp Association ◽  
Number Variation ◽  
Genome Wide Data

Background: The genetic basis of brain arteriovenous malformation (BAVM), a tangle of abnormal vessels directly shunting blood from the arterial to venous circulation, is unknown. However, there are two rare vascular disorders with known familial mutations in which a subset of patients display a BAVM phenotype: hereditary hemorrhagic telangiectasia ( ACVRL1 , ENG , and SMAD4 mutations) and capillary malformation-arteriovenous malformation ( RASA1 mutations). To investigate whether variants in these four vascular malformation genes are associated with sporadic BAVM, we performed a case-control study, evaluating both single nucleotide polymorphisms (SNPs) and copy number variation (CNV). Methods: We used genome-wide data (Affymetrix SNP 6.0) from 319 cases and 496 healthy controls. There were 27 unlinked SNPs (r 2 <0.8) on the array with minor allele frequency >1% and in Hardy-Weinberg equilibrium (p>0.01) mapping within 20kb of the four genes: ACVRL1 (n=16), ENG (n=6), SMAD4 (n=2), and RASA1 (n=3). Single SNP association was tested using multivariate logistic regression in PLINK, adjusting for age, gender, and top 3 principal components of ancestry (to control for population stratification). The Bonferroni method (p<0.0019) was used to correct for multiple comparisons. CNVs in these genes were called using the PennCNV algorithm. Results: Two SNPs located upstream and downstream of ACVRL1 were associated with BAVM at nominal p<0.05: rs10783480 (OR=0.69, 95% CI=0.50 - 0.96, p=0.029,) and rs11169956 (OR=0.69, 95% CI=0.48 - 0.99, p=0.046). However, these SNPs were not associated with BAVM after correction for multiple testing of all SNPs. Polymorphisms in the RASA1 , ENG , and SMAD4 genes were not significantly associated with BAVM (p>0.05). We observed one CNV, a duplication that mapped to the ACVRL1 gene, in one control. We did not observe any CNVs mapping to RASA1 , ENG , or SMAD4 . Conclusions: Common SNPs and CNVs in four vascular malformation genes associated with inherited disorders displaying BAVM were not significantly associated with sporadic BAVM. A previously reported ACVRL1 intronic SNP (rs2071219) was not on the Affymetrix array and none of the existing ACVRL1 SNPs tagged this SNP. Further, rare polymorphisms in these genes were not genotyped and may contribute to BAVM risk.

scholarly journals Reciprocal hybridization between diploid Ficaria calthifolia and tetraploid Ficaria verna subsp. verna: evidence from experimental crossing, genome size and molecular markers

2019 ◽  
Vol 189 (3) ◽  
pp. 293-310 ◽  
Author(s):  
Ondřej Popelka ◽  
Michal Sochor ◽  
Martin Duchoslav
Keyword(s):  
Genome Size ◽  
Morphological Variability ◽  
Plastid Dna ◽  
Genotypic Diversity ◽  
Hybrid Origin ◽  
Aflp Analysis ◽  
Sympatric Populations ◽  
Aflp Data ◽  
Evolutionary Forces ◽  
Genetic Clusters

Abstract Ficaria is a taxonomically intriguing polyploid complex with high morphological variability. Both hybridization and polyploidization have been suggested as the main evolutionary forces behind the high morphological variability in this genus; however, detailed studies are lacking. In Central Europe, two Ficaria taxa (diploid F. calthifolia and tetraploid F. verna subsp. verna) occasionally co-occur in local sympatry, which might result in hybridization. We investigated sympatric populations of the two Ficaria taxa using flow cytometry, chromosome counts, AFLP analysis and plastid DNA sequencing; we also performed experimental homoploid and heteroploid crosses to determine the frequency and direction of hybrid triploid formation, an alternative route of triploid origin (autopolyploidy) and the possibility of a one-step neoallotetraploid origin. Sympatric populations were composed of three genetic clusters corresponding to diploid F. calthifolia (2n = 16), tetraploid F. verna subsp. verna (2n = 32) and triploid plants (2n = 24). The holoploid genome size and AFLP data suggest a hybrid origin of the triploids, thereby making their formation via autopolyploidization in F. calthifolia unlikely. The triploid populations are monoclonal and of independent origin. In contrast, the parental populations exhibit high genotypic diversity and frequent sexual reproduction, including those of predominantly asexual F. verna subsp. verna. Experimental crossing confirmed that both parental taxa produce fertile seeds via a sexual pathway, but not by apomixis, and that both serve as pollen acceptors in heteroploid crosses, which is consistent with the plastid sequencing. However, hybridization is asymmetric, with maternal-excess crosses being significantly more successful. No signs of neoautotetraploidization or neoallotetraploidization were detected. In summary, recent gene flow between the studied Ficaria taxa is either limited or absent.

Genetics of Schizophrenia and Bipolar Disorder

2017 ◽  
Author(s):  
Alexander Charney ◽  
Pamela Sklar
Keyword(s):  
Bipolar Disorder ◽  
Copy Number ◽  
Psychotic Disorders ◽  
Copy Number Variants ◽  
Nucleotide Polymorphisms ◽  
Common Variants ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Number Variation

Schizophrenia and bipolar disorder are the classic psychotic disorders. Both diseases are strongly familial, but have proven recalcitrant to genetic methodologies for identifying the etiology until recently. There is now convincing genetic evidence that indicates a contribution of many DNA changes to the risk of becoming ill. For schizophrenia, there are large contributions of rare copy number variants and common single nucleotide variants, with an overall highly polygenic genetic architecture. For bipolar disorder, the role of copy number variation appears to be much less pronounced. Specific common single nucleotide polymorphisms are associated, and there is evidence for polygenicity. Several surprises have emerged from the genetic data that indicate there is significantly more molecular overlap in copy number variants between autism and schizophrenia, and in common variants between schizophrenia and bipolar disorder.

The status and distribution of Carex subimpressa (Cyperaceae)

1986 ◽  
Vol 64 (1) ◽  
pp. 227-232 ◽  
Author(s):  
A. A. Reznicek ◽  
P. M. Catling
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Natural Populations ◽  
Field Studies ◽  
Diagnostic Character ◽  
Wide Area ◽  
Hybrid Origin ◽  
The Status ◽  
Specific Rank ◽  
Scanning Electron

Carex subimpressa, originally described as a hybrid of C. hyalinolepsis and C. lanuginosa, has been reported over a wide area and beyond the range of C. hyalinolepis. Consequently it has been accorded specific rank. Various aspects of morphology reflected in scatter diagrams as well as intermediate stomatal structure revealed through scanning electron microscopy and sectioning support the hybrid origin as originally proposed. This is further supported by field studies of natural populations where both putative parents were invariably present. Reports from beyond the range of one or both parents are the result of misidentification. The diagnostic character combination includes sparsely pubescent perigynia 4.2–6.4 mm long, with relatively short beaks, leaves 4.5–11 mm wide, and ligules 1.8–9 mm long.

Single nucleotide polymorphisms (SNPs) analysis of CYP2C8, GSTT1, GSTP1, MDR1(A), MDR1(B) and ERCC1 as predictor of survival after weekly paclitaxel for relapsed advanced head & neck cancer patients (AHNCP)

2007 ◽  
Vol 25 (18_suppl) ◽  
pp. 2540-2540 ◽  
Author(s):  
J. J. Grau ◽  
M. Monzo ◽  
M. Vargas ◽  
S. Jansa ◽  
m. Campayo ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Phase 1 ◽  
High Rate ◽  
Weekly Paclitaxel ◽  
Head Neck Cancer ◽  
Nucleotide Polymorphisms ◽  
Wild Type ◽  
Single Nucleotide ◽  
The Status ◽  
Head Neck

2540 Background: Gene SNPs correlate with survival in cancer patients (pts) treated with chemotherapy (CHM). CYP2C8 and GSTT1, GTSP1 genes are involved in phase 1 and 2 drug cellular metabolisms respectively; MDR1(A) and MDR1(B) are involved in drug membrane transport and ERCC1 in DNA repair Methods: We evaluated the presence of SNPs of these 6 genes and the survival of AHNCP treated with weekly paclitaxel, 80 mg/m2 iv for 6 weeks. Responding pts continue CHM till progression. All pts were cisplatin resistant and no other local therapies were available. We analysed paraffin-embedded biopsies from 47 consecutive AHNCP for SNPs of the mentioned genes. The status of the alleles wild type (wt) or at least 1 SNP was compared with response rate (RR), time to progression (TTP) and overall survival (OS) Results: Of 47 pts, 43 were male and 4 female. The median of age was 57 yr (46–80). RR was 45% (21/47) and the TTP in responders was 5 months of median. OS for all pts was 5.6 months. Wild type vs at least 1 SNPs frequencies according the genes were: CYP2C8 23/24; GSTT1 45/2; GSTP1 36/11; MDR1(A) 21/28; MDR1(B) 13/34; and ERCC1 27/20. OS was significantly better in pts with 2 or more SNPs accumulated (p=0.0455). No other significant differences were observed in RR, TTP or OS in SNPs vs wild type pts. Conclusions: SNPs of CYP2C8, MDR1(A) and MDR1(B) genes were more frequent than wt in our pts. OS was significantly better in pts with 2 or more SNPs accumulated. Paclitaxel provides high rate of responses of short duration in AHNC pts No significant financial relationships to disclose.

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