Comparing oyster population structure and disease prevalence between a disease‐resistant and transplanted wild population in Barnegat Bay, NJ ( USA )

2022 ◽  
Author(s):  
Christine M. Thompson ◽  
Steve Evert ◽  
Jessica A. Baez
Keyword(s):  
Population Structure ◽  
Wild Population ◽  
Disease Prevalence ◽  
Barnegat Bay ◽  
Oyster Population ◽  
Disease Resistant

scholarly journals Understanding drivers of wild oyster population persistence

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mickael Teixeira Alves ◽  
Nick G. H. Taylor ◽  
Hannah J. Tidbury
Keyword(s):  
Population Density ◽  
Carrying Capacity ◽  
Pacific Oyster ◽  
Wild Population ◽  
Population Persistence ◽  
Oyster Reefs ◽  
Oyster Population ◽  
Northern European ◽  
Age Structured ◽  
The Impact

AbstractPersistence of wild Pacific oyster, Magallana gigas, also known as Crassostrea gigas, has been increasingly reported across Northern European waters in recent years. While reproduction is inhibited by cold waters, recent warm summer temperature has increased the frequency of spawning events. Although correlation between the increasing abundance of Pacific oyster reefs in Northern European waters and climate change is documented, persistence of wild populations may also be influenced by external recruitment from farmed populations and other wild oyster populations, as well as on competition for resources with aquaculture sites. Our understanding of the combined impact of the spawning frequency, external recruitment, and competition on wild population persistence is limited. This study applied an age-structured model, based on ordinary differential equations, to describe an oyster population under discrete temperature-related dynamics. The impact of more frequent spawning events, external recruitment, and changes in carrying capacity on Pacific oyster density were simulated and compared under theoretical scenarios and two case studies in Southern England. Results indicate that long term persistence of wild oyster populations towards carrying capacity requires a high frequency of spawning events but that in the absence of spawning, external recruitment from farmed populations and other wild oyster populations may act to prevent extinction and increase population density. However, external recruitment sources may be in competition with the wild population so that external recruitment is associated with a reduction in wild population density. The implications of model results are discussed in the context of wild oyster population management.

Large-scale comparative genomics of Salmonella enterica to refine the organization of the global Salmonella population structure

2021 ◽  
Author(s):  
Chao Chun Liu ◽  
William W.L. Hsiao
Keyword(s):  
Population Structure ◽  
In Silico ◽  
Salmonella Enterica ◽  
Disease Prevalence ◽  
Controlled Vocabulary ◽  
Antigenic Determinants ◽  
Population Divergence ◽  
Typing Scheme ◽  
Niche Adaptation ◽  
Genomic Studies

1.AbstractSince the introduction of the White-Kauffmann-Le Minor (WKL) scheme for Salmonella serotyping, the nomenclature remains the most widely used for reporting the disease prevalence of Salmonella enterica across the globe. With the advent of whole genome sequencing (WGS), traditional serotyping has been increasingly replaced by in-silico methods that couple the detection of genetic variations in antigenic determinants with sequence-based typing. However, despite the integration of genomic-based typing by in-silico serotyping tools such as SeqSero2 and SISTR, in-silico serotyping in certain contexts remains ambiguous and insufficiently informative due to polyphyletic serovars. Furthermore, in spite of the widespread acknowledgement of polyphyly from genomic studies, the serotyping nomenclature remains unaltered. To prompt refinements to the Salmonella typing nomenclature for disease reporting, we herein performed a systematic characterization of putative polyphyletic serovars and the global Salmonella population structure by comparing 180,098 Salmonella genomes (representing 723 predicted serovars) from GenomeTrakr and PubMLST databases. We identified a range of core genome MLST typing thresholds that result in stable population structure, potentially suitable as the foundation of a genomic-based typing nomenclature for longitudinal surveillance. From the genomic comparisons of hundreds of predicted serovars, we demonstrated that in-silico serotyping classifications do not consistently reflect the population divergence observed at the genomic level. The organization of Salmonella subpopulations based on antigenic determinants can be confounded by homologous recombination and niche adaptation, resulting in shared classification of highly divergent genomes and misleading distinction between highly similar genomes. In consideration of the pivotal role of Salmonella serotyping, a compendium of putative polyphyletic serovars was compiled and made publicly available to provide additional context for future interpretations of in-silico serotyping results in disease surveillance settings. To refine the typing nomenclatures used in Salmonella surveillance reports, we foresee an improved typing scheme to be a hybrid that integrates both genomic and antigenic information such that the resolution from WGS is leveraged to improve the precision of subpopulation classifications while preserving the common names defined by the WKL scheme. Lastly, we stress the importance of controlled vocabulary integration for typing information in open data settings in order for the global Salmonella population dynamics to be fully trackable.2.Impact StatementSalmonella enterica (S. enterica) is a major foodborne pathogen responsible for an annual incidence rate of more than 90 million cases of foodborne illnesses worldwide. To surveil the high order Salmonella lineages, compare disease prevalence across jurisdictions worldwide, and inform risk assessments, in-silico serotyping has been established as the gold standard for typing the bacteria. However, despite previous Salmonella genomic studies reporting discordance between phylogenomic clades and serovars, refinements have yet been made to the serotyping scheme. Here, we analyzed over 180,000 Salmonella genomes representing 723 predicted serovars to subdivide the population into evolutionarily stable clusters in order to propose a stable organization of the Salmonella population structure that can form the basis of a genomic-based typing scheme for the pathogen. We described numerous instances in which genomes between serotypes are more similar than genomes within a serotype to reflect the inconsistencies of subpopulation classifications based on antigenic determinants. Moreover, we found inconsistencies between predicted serovars and reported serovars which highlighted potential errors in existing in-silico serotyping tools and the need to implement controlled vocabularies for reporting Salmonella subtypes in public databases. The findings of our study aim to motivate the future development of a standardized genomic-based typing nomenclature that more accurately captures the natural populations of S. enterica.3.Data SummaryThe assembly accession numbers of the genomes analyzed in this study (n = 204,952) and the associated metadata (e.g. sampling location, collection date, FTP address for retrieval) are documented in Table S1. The GenomeTrakr genomes were retrieved from the National Center for Biological Information GenBank database. The PubMLST genomes were retrieved using the BIGSdb API.

scholarly journals Mitochondrial DNA D-Loop Diversity of the Helmeted Guinea Fowls in Kenya and Its Implications on HSP70 Gene Functional Polymorphism

2018 ◽  
Vol 2018 ◽  
pp. 1-12
Author(s):  
Philip Murunga ◽  
Grace Moraa Kennedy ◽  
Titus Imboma ◽  
Phillista Malaki ◽  
Daniel Kariuki ◽  
...  
Keyword(s):  
Mitochondrial Dna ◽  
Population Structure ◽  
Wild Population ◽  
Profile Analysis ◽  
Demographic History ◽  
Genetic Profile ◽  
Hsp70 Gene ◽  
Functional Polymorphisms ◽  
Mtdna Haplotypes ◽  
D Loop

We analyzed variations in 90 mitochondrial DNA (mtDNA) D-loop and heat shock protein 70 (HSP70) gene sequences from four populations of domesticated helmeted Guinea fowls (70 individuals) and 1 population of wild helmeted Guinea fowls (20 individuals) in Kenya in order to get information about their origin, genetic diversity, and traits associated with heat stress. 90 sequences were assigned to 25 distinct mtDNA and 4 HSP70 haplotypes. Most mtDNA haplotypes of the domesticated helmeted Guinea fowls were grouped into two main haplogroups, HgA and HgB. The wild population grouped into distinct mtDNA haplogroups. Two mtDNA haplotypes dominated across all populations of domesticated helmeted Guinea fowls: Hap2 and Hap4, while the dominant HSP70 haplotype found in all populations was CGC. Higher haplotype diversities were generally observed. The HSP70 haplotype diversities were low across all populations. The nucleotide diversity values for both mtDNA and HSP70 were generally low. Most mtDNA genetic variations occurred among populations for the three hierarchical categories considered while most variations in the HSP70 gene occurred among individuals within population. The lack of population structure among the domestic populations could suggest intensive genetic intermixing. The differentiation of the wild population may be due to a clearly distinct demographic history that shaped its genetic profile. Analysis of the Kenyan Guinea fowl population structure and history based on mtDNA D-loop variations and HSP70 gene functional polymorphisms complimented by archaeological and linguistic insight supports the hypothesis that most domesticated helmeted Guinea fowls in Kenya are related to the West African domesticated helmeted Guinea fowls. We recommend more molecular studies on this emerging poultry species with potential for poverty alleviation and food security against a backdrop of climate change in Africa.

scholarly journals Genetic analysis and population structure of wild and cultivated wishbone flower (Torenia fournieri Lind.) lines related to specific floral color

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11702
Author(s):  
Shikai Guan ◽  
Qian Song ◽  
Jinye Zhou ◽  
Haixia Yan ◽  
Yuxiang Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Variability ◽  
Wild Population ◽  
Wild Populations ◽  
Torenia Fournieri ◽  
Similar Reduction ◽  
Floral Color ◽  
Hybrid Lines

Background The wishbone flower or Torenia fournieri Lind., an annual from tropical Indochina and southern China, is a popular ornamental plant, and many interspecific (T. fournieri × T. concolor) hybrid lines have been bred for the international market. The cultivated lines show a pattern of genetic similarity that correlates with floral color which informs on future breeding strategies. This study aimed to perform genetic analysis and population structure of cultivated hybrid lines comparing with closely related T. concolor wild populations. Methods We applied the retrotransposon based iPBS marker system for genotyping of a total of 136 accessions from 17 lines/populations of Torenia. These included 15 cultivated lines of three series: Duchess (A, B, C); Kauai (D, E, F, G, H, I, J); Little Kiss (K, L, M, N, P) and two wild T. concolor populations (Q and R). PCR products from each individual were applied to estimate the genetic diversity and differentiation between lines/populations. Results Genotyping results showed a pattern of genetic variation differentiating the 17 lines/populations characterized by their specific floral colors. The final PCoA analysis, phylogenetic tree construction, and Bayesian population structural bar plot all showed a clear subdivision of lines/populations analysed. The 15 cultivated hybrid lines and the wild population Q that collected from a small area showed the lowest genetic variability while the other wild population R which sampled from a larger area had the highest genetic variability. Discussion The extremely low genetic variability of 15 cultivated lines indicated that individual line has similar reduction in diversity/heterozygosity from a bottleneck event, and each retained a similar (but different from each other) content of the wild genetic diversity. The genetic variance for the two wild T. concolor populations could be due to our varied sampling methods. The two wild populations (Q, R) and the cultivated hybrid lines (I, K, M, N, P) are genetically more closely related, but strong positive correlations presented in cultivated lines A, C, E, M, and N. These results could be used to guide future Torenia breeding. Conclusions The genetic variation and population structure found in our study showed that cultivated hybrid lines had similar reduction in diversity/heterozygosity from a bottleneck event and each line retained a similar (but different from each other) content of the wild genetic diversity, especially when strong phenotypic selection of floral color overlaps. Generally, environmental factors could induce transposon activation and generate genetic variability which enabled the acceleration of the evolutionary process of wild Torenia species. Our study revealed that wild Torenia populations sampled from broad geographic region represent stronger species strength with outstanding genetic diversity, but selective breeding targeting a specific floral color decreased such genetic variability.

Population structure and changes in body mass and composition of mallards (Anas platyrhynchos) wintering in Edmonton, Alberta

1993 ◽  
Vol 71 (11) ◽  
pp. 2275-2281 ◽  
Author(s):  
Iwona M. Pawlina ◽  
David A. Boag ◽  
Frank E. Robinson
Keyword(s):  
Body Composition ◽  
Population Structure ◽  
Body Mass ◽  
Protein Intake ◽  
Wild Population ◽  
Anas Platyrhynchos ◽  
Age Composition ◽  
The North ◽  
Energy Demands ◽  
In The Wild

The population structure and changes in body mass and body composition of mallards wintering on the North Saskatchewan River in Edmonton, Alberta, were investigated from November 20, 1989 to March 15, 1990. The age composition of the population was biased in favor of juveniles (84%) and in favor of males (71%), possibly because of differential emigration at the onset of winter. Ducks in the wild population lost 22–30% of their live mass over winter. On average, males lost 75–76% of body lipids and 24–29% of proteins. Females lost between 66 and 92% of body lipids and between 18 and 23% of proteins. These losses suggested that mallards wintering in Edmonton in 1989–1990 were insufficiently prepared to meet the energy demands of spring migration and reproduction. Moreover, neither sex was able to maintain the level of protein intake needed to meet the protein costs of molt.

Population Structure of Adult Blue Crabs, Callinectes sapidus, in Relation to Physical Characteristics in Barnegat Bay, New Jersey

2016 ◽  
Vol 40 (1) ◽  
pp. 235-250 ◽  
Author(s):  
Paul R. Jivoff ◽  
Jennifer M. Smith ◽  
Valerie L. Sodi ◽  
Stacy M. VanMorter ◽  
Kathryn M. Faugno ◽  
...  
Keyword(s):  
Population Structure ◽  
New Jersey ◽  
Callinectes Sapidus ◽  
Physical Characteristics ◽  
Blue Crabs ◽  
Barnegat Bay

scholarly journals Genetic diversity and population structure of Cynara cardunculus L. in southern Portugal

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0252792
Author(s):  
Maria Miguel Castro ◽  
Daniela Rosa ◽  
Ana M. Ferro ◽  
Ana Faustino ◽  
Ana Paulino ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Wild Population ◽  
Cynara Cardunculus ◽  
Wild Populations ◽  
Significant Genetic Differentiation ◽  
Southern Portugal ◽  
High Level ◽  
Geographic Group ◽  
Future Management

Cynara cardunculus L. is a cardoon species native to the Mediterranean region, which is composed of three botanical taxa, each having distinct biological characteristics. The aim of this study was to examine wild populations of C. cardunculus established in Portugal, in order to determine their genetic diversity, geographic distribution, and population structure. Based on SSR markers, 121 individuals of C. cardunculus from 17 wild populations of the Portuguese Alentejo region were identified and analysed. Ten SSRs were found to be efficient markers in the genetic diversity analysis. The total number of alleles ranged from 9 to 17 per locus. The expected and observed means in heterozygosity, by population analysed, were 0.591 and 0.577, respectively. The wild population exhibited a high level of genetic diversity at the species level. The highest proportion of genetic variation was identified within a geographic group, while variation was lower among groups. Geographic areas having highest genetic diversity were identified in Alvito, Herdade da Abóboda, Herdade da Revilheira and Herdade de São Romão populations. Moreover, significant genetic differentiation existed between wild populations from North-Alentejo geographic locations (Arraiolos, Évora, Monte da Chaminé) and Centro Hortofrutícola, compared with other populations. This study reports genetic diversity among a representative number of wild populations and genotypes of C. cardunculus from Portugal. These results will provide valuable information towards future management of C. cardunculus germplasm.

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