scholarly journals Molecular Characterization of the Common Snook, Centropomus undecimalis (Bloch, 1792) in the Usumacinta Basin

Diversity ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 347
Author(s):  
Jazmín Terán-Martínez ◽  
Rocío Rodiles-Hernández ◽  
Marco A. A. Garduño-Sánchez ◽  
Claudia Patricia Ornelas-García
Keyword(s):  
Molecular Characterization ◽  
Conservation Status ◽  
Nuclear Data ◽  
Important Species ◽  
Common Snook ◽  
Mitochondrial Data ◽  
Haplotypic Diversity ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters ◽  
The Common

The common snook is one of the most abundant and economically important species in the Usumacinta basin in the Gulf of Mexico, which has led to overfishing, threatening their populations. The main goal of the present study was to assess the genetic diversity and structure of the common snook along the Usumacinta River in order to understand the population dynamics and conservation status of the species. We characterized two mitochondrial markers (mtCox1 and mtCytb) and 11 microsatellites in the Usumacinta basin, which was divided into three zones: rainforest, floodplain and river delta. The mitochondrial data showed very low diversity, showing some haplotypic diversity differences between the rainforest and delta zones. In contrast, we consistently recovered two genetic clusters in the Usumacinta River basin with the nuclear data in both the DAPC and STRUCTURE analyses. These results were consistent with the AMOVA analyses, which showed significant differences among the genetic clusters previously recovered by DAPC and STRUCTURE. In terms of diversity distribution, the floodplain zone corresponded to the most diverse zone according to the mitochondrial and nuclear data, suggesting that this is a transition zone in the basin. Our results support the relevance of the molecular characterization and monitoring of the fishery resources at the Usumacinta River to better understand their connectivity, which could help in their conservation and management.

Boswellia socotrana: One or Two Taxa?

2020 ◽  
Vol 28 (1) ◽  
pp. 17-23 ◽  
Author(s):  
Samuel Lvončík ◽  
Radomír Řepka
Keyword(s):  
Endemic Species ◽  
Conservation Status ◽  
Important Species ◽  
Socotra Island ◽  
Distribution And Ecology ◽  
Morphological Differences

There are seven endemic species of Boswellia Roxb. ex Colebr. on Socotra Island, Yemen. Boswellia socotrana Balf. f. is a culturally, economically, and ecologically important species on the island. The name Odina aspleniifolia Balf. f. has been considered as a synonym, but there are morphological differences between the two taxa sufficient to justify their distinction at subspecific rank. Therefore, O. aspleniifolia is transferred to Boswellia as B. socotrana subsp. aspleniifolia (Balf. f.) Lvončik. A lectotype is designated for O. aspleniifolia. The distribution and ecology of both subspecies are discussed, as is their conservation status.

scholarly journals Phylogenetic Position of the New World Quail (Odontophoridae): Eight Nuclear Loci and Three Mitochondrial Regions Contradict Morphology and the Sibley-Ahlquist Tapestry

The Auk ◽  
2007 ◽  
Vol 124 (1) ◽  
pp. 71-84 ◽  
Author(s):  
W. Andrew Cox ◽  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
New World ◽  
Sequence Data ◽  
Evolutionary Relationship ◽  
Strong Support ◽  
Nuclear Data ◽  
Morphological Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Mitochondrial Data ◽  
Nuclear Loci

Abstract The evolutionary relationship between the New World quail (Odontophoridae) and other groups of Galliformes has been an area of debate. In particular, the relationship between the New World quail and guineafowl (Numidinae) has been difficult to resolve. We analyzed >8 kb of DNA sequence data from 16 taxa that represent all major lineages of Galliformes to resolve the phylogenetic position of New World quail. A combined data set of eight nuclear loci and three mitochondrial regions analyzed with maximum parsimony, maximum likelihood, and Bayesian methods provide congruent and strong support for New World quail being basal members of a phasianid clade that excludes guineafowl. By contrast, the three mitochondrial regions exhibit modest incongruence with each other. This is reflected in the combined mitochondrial analyses that weakly support the Sibley-Ahlquist topology that placed the New World quail basal in relation to guineafowl and led to the placement of New World quail in its own family, sister to the Phasianidae. However, simulation-based topology tests using the mitochondrial data were unable to reject the topology suggested by our combined (mitochondrial and nuclear) data set. By contrast, similar tests using our most likely topology and our combined nuclear and mitochondrial data allow us to strongly reject the Sibley-Ahlquist topology and a topology based on morphological data that unites Old and New World quail. Posición Filogenética de las Codornices del Nuevo Mundo (Odontophoridae): Ocho Loci Nucleares y Tres Regiones Mitocondriales Contradicen la Morfología y la Filogenia de Sibley y Ahlquist

scholarly journals Molecular Characterization of Pathogenicity Locus (PaLoc) and tcdC Genetic Diversity Among tcdA+B+ Clostridioides Difficile Clinical Isolates in Tehran, Iran

2020 ◽  
Author(s):  
Mansoor Kodori ◽  
Zohreh Ghalavand ◽  
Abbas Yadegar ◽  
Gita Eslami ◽  
Masoumeh Azimirad ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Molecular Characterization ◽  
Disease Severity ◽  
Genetic Variants ◽  
Rflp Analysis ◽  
Clostridioides Difficile ◽  
Pcr Rflp ◽  
The Common ◽  
Healthcare Associated

Abstract Background: Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs).Methods: Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene.Results: Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene.Conclusions: The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/ toxinotype 0 and the RT 126/ toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.

scholarly journals Determining population trends and conservation status of the common quail (Coturnix coturnix) in Western Europe

2012 ◽  
Vol 35 (2) ◽  
pp. 343-352
Author(s):  
M. Puigcerver ◽  
◽  
F. Sardà–Palomera ◽  
J. D. Rodriguez-Teijeiro ◽  
◽  
...  
Keyword(s):  
Western Europe ◽  
Conservation Status ◽  
Population Trends ◽  
Distribution Model ◽  
Breeding Period ◽  
Distribution Models ◽  
Winter Cereal ◽  
Coturnix Coturnix ◽  
The Common ◽  
Common Quail

In this paper we review the conservation status and population trends of the common quail (Coturnix coturnix) from 1900 to the present. Data are sometimes contradictory with regard to the status of this species as it has some features that make it difficult to produce reliable population estimates. Recent data clearly suggest, either at a local scale or at a trans–national scale, that the Atlantic common quail populations have remained stable in the last two decades, and that restocking practices with farm–reared quails (hybrids with the Japanese quail, Coturnix japonica) do not affect our estimates. The complex movement patterns showed by this species require special attention. Analysis of ring recoveries can give important information, especially about the nomadic movement of quails in search of suitable habitats after the destruction of winter cereal crops due to harvesting. Thus, when developing a breeding distribution model for this species, continuously updated information on seasonal habitat and weather must be included for optimal prediction. Including fortnightly data of vegetation indices in distribution models, for example, has shown good results. Obtaining reliable predictions about changes in species distribution and movements during the breeding period could provide useful knowledge about the conservation status and population trends and would help in the design of future management measures.

scholarly journals Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247586
Author(s):  
Christine E. Edwards ◽  
Brooke C. Tessier ◽  
Joel F. Swift ◽  
Burgund Bassüner ◽  
Alexander G. Linan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Plant Species ◽  
Genetic Drift ◽  
Rare Species ◽  
Ex Situ ◽  
Ouachita Mountains ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

Tapesia evilescens. [Descriptions of Fungi and Bacteria].

2013 ◽  
Author(s):  
D. W. Minter
Keyword(s):  
Geographical Distribution ◽  
Phragmites Australis ◽  
Conservation Status ◽  
Common Reed ◽  
The Common

Abstract A description is provided for Tapesia evilescens, a saprobe on dead stems of grasses, particularly the common reed (Phragmites australis). Some information on its substrata, habitat, dispersal and transmission and conservation status is given, along with details of its geographical distribution (Europe (Finland, Netherlands, Ukraine, UK)).

Transport and cryopreservation of sperm of the common snook, Centropomus undecimalis (Bloch)

2004 ◽  
Vol 35 (3) ◽  
pp. 278-288 ◽  
Author(s):  
T R Tiersch ◽  
W R Wayman ◽  
D P Skapura ◽  
C L Neidig ◽  
H J Grier
Keyword(s):  
Centropomus Undecimalis ◽  
Common Snook ◽  
The Common

scholarly journals Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 126 ◽  
Author(s):  
Wilson X. Guillory ◽  
Morgan R. Muell ◽  
Kyle Summers ◽  
Jason L. Brown
Keyword(s):  
Bayesian Methods ◽  
Evolutionary History ◽  
Conservation Status ◽  
Nuclear Data ◽  
Nuclear Markers ◽  
Poison Frog ◽  
Sequence Capture ◽  
Genome Wide ◽  
Frog Species ◽  
History Of

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study.

scholarly journals Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

Diversity ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 154 ◽  
Author(s):  
Lucia Lioi ◽  
Diana L. Zuluaga ◽  
Stefano Pavan ◽  
Gabriella Sonnante
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Genotyping By Sequencing ◽  
Fixation Index ◽  
Most Probable Number ◽  
Probable Number ◽  
Individual Snps ◽  
Starting Point ◽  
Genetic Diversity And Structure ◽  
The Common

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

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