Initial description of the phylogeography, population structure and genetic diversity of Atlantic spotted dolphins from Brazil and the Caribbean, inferred from analyses of mitochondrial and nuclear DNA

Abstract Common ash (Fraxinus excelsior L.) has a widespread distribution throughout Europe, and Latvia is almost at the north eastern edge of the distribution range. In Europe, ash is threatened by ash dieback, a disease caused by the introduced ascomycete Hymenoscyphus fraxineus. Chloroplast and nuclear DNA markers have been used to study the genetic diversity and population structure of ash both in a broader pan-European context as well as in more restricted regions. Some of the markers analysed in these previously published reports were also utilised in this study, enabling comparisons of the genetic parameters calculated from the nuclear SSR marker data and of the haplotypes identified with the chloroplast markers. Analysis of chloroplast markers revealed one dominant haplotype in Latvian stands, which corresponds to the haplotype previously found in Eastern Europe and Scandinavia. A second haplotype, corresponding to a previously reported central European haplotype was found in all individuals from the Ķemeri stand, indicating that this stand was naturally established from introduced germplasm, which was planted in a neighbouring park. The nuclear SSR markers revealed low levels of differentiation of Latvian F. excelsior stands, probably due efficient pollen flow between stands. The analysis of both chloroplast and nuclear DNA markers has revealed different aspects of the structure and provenance of Latvian F. excelsior populations.

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Genetic Variation in Anastrepha obliqua (Diptera: Tephritidae) in a Highly Diverse Tropical Environment in the Mexican State of Veracruz

Journal of Economic Entomology ◽

10.1093/jee/toz223 ◽

2019 ◽

Vol 112 (6) ◽

pp. 2952-2965

Author(s):

Raul Ruiz-Arce ◽

Md-Sajedul Islam ◽

Martin Aluja ◽

Bruce A McPheron

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Microsatellite Markers ◽

Population Biology ◽

Nuclear Dna ◽

Fruit Flies ◽

Tropical Environment ◽

Fine Scale ◽

Mexican State ◽

Anastrepha Obliqua

Abstract There has been considerable interest in understanding biological, ecological, historical, and evolutionary processes that contribute to the diversification of species and populations among tephritid fruit flies. Only a limited number of studies have examined the genetic diversity and population biology of species belonging to the genus Anastrepha considering fine-scale differentiations associated to locality as well as hosts over an entire fruiting season. To expand our understanding of population structure and genetic diversity in one of the critical Anastrepha fruit flies populations in a highly diverse tropical environment we analyzed Anastrepha obliqua (Macquart) (Diptera: Tephritidae) in the Mexican state of Veracruz from five host fruit species and 52 geographic collections using sequence data from mtDNA and microsatellite markers from nuclear DNA. Indeed, we examined the population structure of this pest in a micro-geographic region and report on relationships and historical processes for individuals collected within a small portion of the geographic range of its distribution. Analyses of 1055 bp mtDNA sequences from CO1and ND1genes across 400 individuals detected 34 haplotypes. Haplotype and nucleotide diversity was low, with 53% of the individuals exhibiting a single haplotype (OBV1). Host association and fine-scale differentiation at 17 microsatellite markers across 719 individuals from 32 of the 52 geographic collections reveal fragmented A. obliqua populations. These findings have important implications for the implementation of the Sterile Insect Technique (SIT) and other pest management programs used to control this pestiferous fruit fly.

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Population Structure and Genetic Diversity among Isolates of Coccidioides posadasii in Venezuela and Surrounding Regions

mBio ◽

10.1128/mbio.01976-19 ◽

2019 ◽

Vol 10 (6) ◽

Cited By ~ 5

Author(s):

Marcus M. Teixeira ◽

Primavera Alvarado ◽

Chandler C. Roe ◽

George R. Thompson ◽

José S. L. Patané ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

South America ◽

North American ◽

Arid Regions ◽

Caribbean Sea ◽

Coccidioides Posadasii ◽

The North ◽

The Caribbean ◽

Recent Bottleneck

ABSTRACT Coccidioides posadasii is a pathogenic fungus that causes coccidioidomycosis in many arid regions of the Americas. One of these regions is bordered by the Caribbean Sea, and the surrounding landscape may play an important role in the dispersion of C. posadasii across South America through southeastern Mexico, Honduras, Guatemala, and Venezuela. Comparative phylogenomic analyses of C. posadasii reveal that clinical strains from Venezuela are genetically distinct from the North American populations found in (i) Arizona and (ii) Texas, Mexico, and the rest of South America (TX/MX/SA). We find evidence for admixture between the Venezuela and the North American populations of C. posadasii in Central America. Additionally, the proportion of Venezuelan alleles in the admixed population decreases as latitude (and distance from Venezuela) increases. Our results indicate that the population in Venezuela may have been subjected to a recent bottleneck and shows a strong population structure. This analysis provides insight into potential for Coccidioides spp. to invade new regions. IMPORTANCE Valley Fever is a fungal disease caused by two species of fungi: Coccidioides immitis and C. posadasii. These fungi are found throughout the arid regions of North and South America; however, our understanding of genetic diversity and disease in South America is limited. In this report, we analyze 10 new genomes of Coccidioides posadasii from regions bordering the Caribbean Sea. We show that these populations are distinct and that isolates from Venezuela are likely a result of a recent bottleneck. These data point to patterns that might be observed when investigating recently established populations.

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Genetic diversity, population structure and historical demography of the two-spined yellowtail stargazer (Uranoscopus cognatus)

Scientific Reports ◽

10.1038/s41598-021-92905-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Nur Ilham Syahadah Mohd Yusoff ◽

Tun Nurul Aimi Mat Jaafar ◽

Veera Vilasri ◽

Siti Azizah Mohd Nor ◽

Ying Giat Seah ◽

...

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Resource Management ◽

Nuclear Dna ◽

Incomplete Lineage Sorting ◽

Dna Recombination ◽

Haplotype Diversity ◽

Population Expansion ◽

Management Program ◽

Sampling Station

AbstractBenthic species, though ecologically important, are vulnerable to genetic loss and population size reduction due to impacts from fishing trawls. An assessment of genetic diversity and population structure is therefore needed to assist in a resource management program. To address this issue, the two-spined yellowtail stargazer (Uranoscopus cognatus) was collected within selected locations in the Indo-West Pacific (IWP). The partial mitochondrial DNA cytochrome c oxidase subunit 1 and the nuclear DNA recombination activating gene 1 were sequenced. Genetic diversity analyses revealed that the populations were moderately to highly diversified (haplotype diversity, H = 0.490–0.900, nucleotide diversity, π = 0.0010–0.0034) except sampling station (ST) 1 and 14. The low diversity level, however was apparent only in the matrilineal marker (H = 0.118–0.216; π = 0.0004–0.0008), possibly due to stochastic factors or anthropogenic stressors. Population structure analyses revealed a retention of ancestral polymorphism that was likely due to incomplete lineage sorting in U. cognatus, and prolonged vicariance by the Indo-Pacific Barrier has partitioned them into separate stock units. Population segregation was also shown by the phenotypic divergence in allopatric populations, regarding the premaxillary protrusion, which is possibly associated with the mechanism for upper jaw movement in biomechanical feeding approaches. The moderate genetic diversity estimated for each region, in addition to past population expansion events, indicated that U. cognatus within the IWP was still healthy and abundant (except in ST1 and 14), and two stock units were identified to be subjected to a specific resource management program.

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