scholarly journals Tracking of Anopheles stephensi in Ethiopia using mitochondrial DNA reveals pattern of spread

2021 ◽  
Author(s):  
Tamar E Carter ◽  
Solomon Yared ◽  
Dejene Getachew ◽  
Joseph Spear ◽  
Sae Hee Choi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
South Asian ◽  
Anopheles Stephensi ◽  
Phylogenetic Analyses ◽  
Eastern Ethiopia ◽  
Multiple Introductions ◽  
Minimum Spanning Network ◽  
History Of ◽  
Spread Analysis ◽  
The Impact

The recent detection of the South Asian malaria vector Anopheles stephensi in the Horn of Africa (HOA) raises concerns about the impact of this mosquito on malaria transmission in the region. The mode and history of introduction is important for predicting the likelihood of continued introduction and future spread. Analysis of An. stephensi genetic diversity and population structure can provide insight into the history of the mosquito in the HOA. We investigated genetic diversity of An. stephensi in eastern Ethiopia where detection suggests a range expansion to this region to understand the history of this invasive population. We sequenced the cytochrome oxidase subunit I (COI) and cytochrome B gene (CytB) in 187 An. stephensi collected from 10 sites in Ethiopia in 2018. Phylogenetic analyses using a maximum-likelihood approach and minimum spanning network were conducted for Ethiopian sequences. Molecular identification of bloodmeal sources was also performed using universal vertebrate CytB sequencing. Six COI-CytB haplotypes were observed based on five segregating sites, with the highest number of haplotypes in the northeastern sites (Semera, Bati, and Gewana towns) relative to the southeastern sites (Kebridehar, Godey, and Degehabur) in eastern Ethiopia. In the phylogenetic and network analysis, we observed population differentiation based on the distribution of the haplotypes across the northeastern and central sites (Erer Gota, Dire Dawa, and Awash Sebat Kilo) compared to the southeastern sites and evidence of a South Asian origin of the HOA An. stephensi lineages. The presence of the putative South Asian haplotype of origin at sites closest to Ethiopia's northeastern borders support route of introductions into Ethiopia from the northeast. Finally, molecular bloodmeal analysis revealed evidence of feeding on bovines, goats, dogs, and humans, as well as evidence of multiple (mixed) blood meals. In conclusion, we find support for the hypothesis for the recent expansion of An. stephensi into southeastern Ethiopia with multiple introductions. We also find evidence that supports the hypothesis that HOA An. stephensi populations originate from South Asia rather than the Arabian Peninsula. The evidence of both zoophagic and anthropophagic feeding support the potential for livestock movement to play a role in vector spread in this region.

scholarly journals Genetic diversity of Anopheles stephensi in Ethiopia provides insight into patterns of spread

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Tamar E. Carter ◽  
Solomon Yared ◽  
Dejene Getachew ◽  
Joseph Spear ◽  
Sae Hee Choi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Blood Meal ◽  
Anopheles Stephensi ◽  
Arabian Peninsula ◽  
Eastern Ethiopia ◽  
Structure Variation ◽  
Network Analyses ◽  
History Of ◽  
The Impact ◽  
Insight Into

Abstract Background The recent detection of the South Asian malaria vector Anopheles stephensi in the Horn of Africa (HOA) raises concerns about the impact of this mosquito on malaria transmission in the region. Analysis of An. stephensi genetic diversity and population structure can provide insight into the history of the mosquito in the HOA to improve predictions of future spread. We investigated the genetic diversity of An. stephensi in eastern Ethiopia, where detection suggests a range expansion into this region, in order to understand the history of this invasive population. Methods We sequenced the cytochrome oxidase subunit I (COI) and cytochrome B gene (CytB) in 187 An. stephensi collected from 10 sites in Ethiopia in 2018. Population genetic, phylogenetic, and minimum spanning network analyses were conducted for Ethiopian sequences. Molecular identification of blood meal sources was also performed using universal vertebrate CytB sequencing. Results Six An. stephensi COI-CytB haplotypes were observed, with the highest number of haplotypes in the northeastern sites (Semera, Bati, and Gewana towns) relative to the southeastern sites (Kebridehar, Godey, and Degehabur) in eastern Ethiopia. We observed population differentiation, with the highest differentiation between the northeastern sites compared to central sites (Erer Gota, Dire Dawa, and Awash Sebat Kilo) and the southeastern sites. Phylogenetic and network analysis revealed that the HOA An. stephensi are more genetically similar to An. stephensi from southern Asia than from the Arabian Peninsula. Finally, molecular blood meal analysis revealed evidence of feeding on cows, goats, dogs, and humans, as well as evidence of multiple (mixed) blood meals. Conclusion We show that An. stephensi is genetically diverse in Ethiopia and with evidence of geographical structure. Variation in the level of diversity supports the hypothesis for a more recent introduction of An. stephensi into southeastern Ethiopia relative to the northeastern region. We also find evidence that supports the hypothesis that HOA An. stephensi populations originate from South Asia rather than the Arabian Peninsula. The evidence of both zoophagic and anthropophagic feeding support the need for additional investigation into the potential for livestock movement to play a role in vector spread in this region. Graphical Abstract

No Evidence of Low Genetic Diversity Despite High Levels of Inbreeding and Poor Genetic Connectivity Among Tetrastigma loheri (Vitaceae) Populations in Remaining Forest Areas in Cebu, Philippines

2021 ◽  
Vol 46 (4) ◽  
pp. 951-961
Author(s):  
Jasper John A. Obico ◽  
Hemres Alburo ◽  
Julie F. Barcelona ◽  
Marie Hale ◽  
Lisa Paguntalan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Habitat Fragmentation ◽  
Tropical Forests ◽  
Forest Cover ◽  
Genetic Connectivity ◽  
Philippine Island ◽  
Low Genetic Diversity ◽  
History Of ◽  
Gap Data ◽  
The Impact

Abstract— Little is known about the effects of habitat fragmentation on the patterns of genetic diversity and genetic connectivity of species in the remaining tropical forests of Southeast Asia. This is particularly evident in Cebu, a Philippine island that has a long history of deforestation and has lost nearly all of its forest cover. To begin filling this gap, data from 13 microsatellite loci developed for Tetrastigma loheri (Vitaceae), a common vine species in Philippine forests, were used to study patterns of genetic diversity and genetic connectivity for the four largest of the remaining forest areas in Cebu. Evidence of relatively high levels of inbreeding was found in all four areas, despite no evidence of low genetic diversity. The four areas are genetically differentiated, suggesting low genetic connectivity. The presence of inbreeding and low genetic connectivity in a commonly encountered species such as T. loheri in Cebu suggests that the impact of habitat fragmentation is likely greater on rare plant species with more restricted distributions in Cebu. Conservation recommendations for the remaining forest areas in Cebu include the establishment of steppingstone corridors between nearby areas to improve the movement of pollinators and seed dispersers among them.

scholarly journals Phylogenomics reveals a complex evolutionary history of lobed-leaf white oaks in western North America

Genome ◽  
2017 ◽  
Vol 60 (9) ◽  
pp. 733-742 ◽  
Author(s):  
John D. McVay ◽  
Duncan Hauser ◽  
Andrew L. Hipp ◽  
Paul S. Manos
Keyword(s):  
Phylogenetic Analyses ◽  
Introgressive Hybridization ◽  
Sympatric Species ◽  
Robust Estimate ◽  
History Of ◽  
Tree Space ◽  
Quercus Gambelii ◽  
Lobed Leaf ◽  
The Impact ◽  
Historical Range

Species within the genus Quercus (oak) hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q. lobata, and Q. garryana in the context of a broad sampling of allied white oaks (Quercus section Quercus), and particularly the midwestern Q. macrocarpa. We demonstrate that historical introgressive hybridization between once sympatric species affects phylogeny estimation. Historical range expansion during periods of favorable climate likely explains our observations; analyses support genetic exchange between ancestral populations of Q. gambelii and Q. macrocarpa. We conclude that the genomic consequences of introgression caused the attraction of distant lineages in phylogenetic tree space, and that introgressive and divergent signals can be disentangled to produce a robust estimate of the phylogenetic history of the species.

scholarly journals Transnational History and Colonial Records: Locating Bengali Mobility in the British Malaya

2019 ◽  
Vol 3 (2) ◽  
pp. 97
Author(s):  
Gazi Mizanur Rahman
Keyword(s):  
Racial Identity ◽  
South Asian ◽  
Human Mobility ◽  
Transnational History ◽  
British Colonialism ◽  
Migrant Communities ◽  
The Past ◽  
History Of ◽  
British Colonial ◽  
The Impact

By the late 1980s, some historians began to identify their works as transnational history – which dealt with the past human mobility, and the circulation of goods, information, and ideas across the globe. Colonial records are an essential source for reconstructing transnational history. However, some of the colonial census-makers were not aware of the racial identity of transmigrants during the population enumeration. They categorised the transmigrants under different umbrella heads, and due to their stringent systems of cataloguing, the identity of diverse migrants was misplaced or generalised in census reports. Therefore, these certain ambiguities complicate the reconstruction of the transnational history of some specific migrant communities. With the impact of British colonialism in present-day South and Southeast Asia, South Asian multi-ethnic people, including Bengalis, migrated to Malaya. Initially, the British colonial administrators categorised the South Asian multi-racial migrants under different heads including “Bengalis & c.”, “Tamils & c.” and “Indians”. These umbrella terms in colonial records create problems in reconstructing the transnational history of anyone specific race from South Asia, such as the Bengali. Through a reinterpretation of colonial documents, empirical evidence, and oral interviews, this paper attempts to locate the Bengali migrants in British Malaya.

scholarly journals Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic

2021 ◽  
Author(s):  
P.W.G. Mallon ◽  
F. Crispie ◽  
G. Gonzalez ◽  
W. Tinago ◽  
A.A. Garcia Leon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Disease Severity ◽  
Genome Sequencing ◽  
Population Level ◽  
Whole Genome ◽  
Multiple Introductions ◽  
Relative Contribution ◽  
The Impact

AbstractBackgroundWhole-genome sequencing (WGS) of SARS-CoV-2 laboratory-confirmed cases can provide insights into viral transmission and genetic diversity at a population level. However, less is known about the impact of non-pharmaceutical interventions (NPIs), including ‘lockdowns’, on circulating SARS-CoV-2 lineages and variants of concern, the relative contribution of travel to re-emergence of pandemic waves within communities or how different lineages and variants contribute to disease severity.MethodsWe have conducted an analysis within a prospective, multicentre observational study of individuals attending four hospitals in the South-East of Ireland with COVID-19. Samples underwent WGS from which lineages and variants were assigned, lineage frequency was plotted over time and phylogenetic analysis was employed to determine the origin of variants detected post-lockdown. Univariate and multivariate analyses assessed relationships between viral lineage/variant and COVID-19 disease severity.ResultsWe analysed 225 genome sequences across two SARS-CoV-2 waves, 134 (59.6%) from wave 1 (March to June) and 91 (40.4%) from wave 2 (July to December), representing 15.2% of COVID-19 admissions to these hospitals during the sampling periods. Four variants (B.1.1.162, B1.1.70, B.1.1.267 and B.1.1) comprised 68% of variants detected during wave 1. Of these variants, only a single B.1.1.70 sequence was detected in wave 2, while the B.1.177 lineage emerged and contributed to 82.3% of lineages detected. Phylogenetic analysis suggested multiple introductions of wave 2 variants from outside Ireland. We found no consistent association between SARS-CoV-2 lineages and disease severity.ConclusionsThese data suggest elimination of common SARS-CoV-2 lineages from hospitalised cases associated with effective NPIs and that importation of new viral variants through travel was a significant contributor to the re-emergence of the pandemic in the second wave in Ireland. Our findings highlight the importance of genomic surveillance in identifying circulating viral genetic diversity and variants of concern and, also, modelling the disease burden of SARS-CoV-2.

scholarly journals Extensive Genetic Diversity of Polyomaviruses in Sympatric Bat Communities: Host Switching versus Coevolution

2020 ◽  
Vol 94 (9) ◽  
Author(s):  
Zhizhou Tan ◽  
Gabriel Gonzalez ◽  
Jinliang Sheng ◽  
Jianmin Wu ◽  
Fuqiang Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analyses ◽  
Mammalian Species ◽  
Host Switching ◽  
Dna Viruses ◽  
Evolutionary Scheme ◽  
History Of ◽  
Murine Polyomavirus ◽  
Horseshoe Bat ◽  
Multiple Species

ABSTRACT Polyomaviruses (PyVs) are small DNA viruses carried by diverse vertebrates. The evolutionary relationships of viruses and hosts remain largely unclear due to very limited surveillance in sympatric communities. In order to investigate whether PyVs can transmit among different mammalian species and to identify host-switching events in the field, we conducted a systematic study of a large collection of bats (n = 1,083) from 29 sympatric communities across China which contained multiple species with frequent contact. PyVs were detected in 21 bat communities, with 192 PyVs identified in 186 bats from 15 species within 6 families representing at least 28 newly described PyVs. Surveillance results and phylogenetic analyses surprisingly revealed three interfamily PyV host-switching events in these sympatric bat communities: two distinct PyVs were identified in two bat species in restricted geographical locations, while another PyV clustered phylogenetically with PyVs carried by bats from a different host family. Virus-host relationships of all discovered PyVs were also evaluated, and no additional host-switching events were found. PyVs were identified in different horseshoe bat species in sympatric communities without observation of host-switching events, showed high genomic identities, and clustered with each other. This suggested that even for PyVs with high genomic identities in closely related host species, the potential for host switching is low. In summary, our findings revealed that PyV host switching in sympatric bat communities can occur but is limited and that host switching of bat-borne PyVs is relatively rare on the predominantly evolutionary background of codivergence with their hosts. IMPORTANCE Since the discovery of murine polyomavirus in the 1950s, polyomaviruses (PyVs) have been considered highly host restricted in mammals. Sympatric bat communities commonly contain several different bat species in an ecological niche facilitating viral transmission, and they therefore represent a model to identify host-switching events of PyVs. In this study, we screened PyVs in a large number of bats in sympatric communities from diverse habitats across China. We provide evidence that cross-species bat-borne PyV transmission exists, though is limited, and that host-switching events appear relatively rare during the evolutionary history of these viruses. PyVs with close genomic identities were also identified in different bat species without host-switching events. Based on these findings, we propose an evolutionary scheme for bat-borne PyVs in which limited host-switching events occur on the background of codivergence and lineage duplication, generating the viral genetic diversity in bats.

scholarly journals Multiple Introductions of Tomato Pathogen Clavibacter michiganensis subsp. michiganensis into Iran as Revealed by a Global-Scale Phylogeographic Analysis

2019 ◽  
Vol 85 (24) ◽  
Author(s):  
Maryam Ansari ◽  
S. Mohsen Taghavi ◽  
Habiballah Hamzehzarghani ◽  
Miryam Valenzuela ◽  
María Ines Siri ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Housekeeping Genes ◽  
Global Scale ◽  
Phylogenetic Position ◽  
Bacterial Canker ◽  
Clavibacter Michiganensis ◽  
Content Type ◽  
Canker Disease ◽  
Multiple Introductions ◽  
History Of

ABSTRACT Tomato bacterial canker caused by Clavibacter michiganensis subsp. michiganensis is one of the most important seed-borne tomato diseases around the globe. The disease was initially reported in 1993 in Iran, and it became a rising threat for the multibillion dollar tomato industry of the country during the last decade. In this study, using phylogeographic analyses, we determined genetic diversity and geographic distribution of C. michiganensis subsp. michiganensis in Iran. Our field surveys showed that the pathogen is expanding into the southern and eastern areas of the country. Furthermore, multilocus sequence analysis and typing (MLSA/MLST) using the sequences of five housekeeping genes (atpD, gyrB, ppk, recA, and rpoB) revealed that 37 C. michiganensis subsp. michiganensis strains isolated in Iran had high genetic diversity and placed in 15 sequence types (STs), while all the available 184 worldwide C. michiganensis subsp. michiganensis sequences were placed in 43 STs. MLSA divided the worldwide C. michiganensis subsp. michiganensis strains into two phylogroups (I and II). Among the 37 strains isolated in Iran, 30 strains clustered in phylogroup I, while 7 strains clustered in phylogroup II. Phylogeographic data inferred from the allelic profile of the five housekeeping genes suggested multiple introductions of C. michiganensis subsp. michiganensis inoculum into Iran, while the geographic origin of the Iranian C. michiganensis subsp. michiganensis strains remains undetermined. Further analyses using higher numbers of strains are warranted to decipher the evolutionary history of C. michiganensis subsp. michiganensis in Iran. Additionally, stricter seed/transplant inspections are recommended to reduce the risk of pathogen expansion to areas with no history of the disease. IMPORTANCE Clavibacter michiganensis subsp. michiganensis, the causal agent of tomato bacterial canker disease, is one of the economically important pathogens of solanaceous crops (e.g., eggplant, pepper, and tomato) around the world. The disease occurs in many countries, with a particular importance in regions characterized by high precipitation and humid environmental conditions. As a seed-borne pathogen, C. michiganensis subsp. michiganensis is included in the A2 (high risk) list of quarantine pathogens by the European and Mediterranean Plant Protection Organization (EPPO). Bacterial canker disease was reported for the first time in 1993 in Iran, while the geographic distribution, genetic diversity, and phylogenetic position of the causal agent remain undetermined. In this study, using the multilocus sequence analysis and typing (MLSA/MLST) approach, we provided a phylogeographic scheme for the C. michiganensis subsp. michiganensis strains isolated in Iran. Furthermore, global-scale phylogenetic analyses led to determination of phylogenetic position of Iranian C. michiganensis subsp. michiganensis strains among worldwide population of the pathogen. Based on diversity parameters and population structure, we suggest relatively higher genetic diversity of the bacterial canker pathogen in Iran than has so far been observed in the other areas of the world. Results obtained in this study provide a novel insight into the genetic diversity and population structure of the bacterial canker pathogen on a global scale.

scholarly journals Genetic heterogeneity in natural beds of the razor clamEnsis siliquarevealed by microsatellites

2011 ◽  
Vol 92 (1) ◽  
pp. 171-177 ◽  
Author(s):  
Miguel A. Varela ◽  
Andrés Martínez-Lage ◽  
Ana M. González-Tizón
Keyword(s):  
Genetic Diversity ◽  
Oil Spill ◽  
Statistical Power ◽  
Atlantic Coast ◽  
Microsatellite Data ◽  
Prestige Oil Spill ◽  
History Of ◽  
Razor Clams ◽  
Source Populations ◽  
The Impact

The aim of this study was to analyse the genetic diversity and population structure in the razor clamEnsis siliquaalong the European Atlantic coast taking into account their recent history of exploitation and the ‘Prestige' oil spill. To this end we examined the genetic variability of microsatellite markers in 211 razor clams from five populations in Ireland, Portugal and Spain. Microsatellite data revealed a low genetic differentiation between the Spanish and Portuguese populations (FST = 0–0.032) and a moderate differentiation of these populations and the Irish samples (FST = 0.071–0.100). Although we observed changes in genetic diversity in accordance with the level of exploitation and the distribution of the oil spill, these changes were mild and not significant after Bonferroni correction. This could be the result of a genuine low impact, lack of statistical power and/or the capacity of this species to recolonize quickly after the impact of anthropogenic stressors. Supporting the latter argument we found a significant temporal heterogeneity of allelic frequencies in samples coming from the same sampling locality that could be attributed to the movement of adults or larvae from unaffected source populations.

scholarly journals Geographical distribution of Anopheles stephensi in eastern Ethiopia

2019 ◽  
Author(s):  
Meshesha Balkew ◽  
Peter Mumba ◽  
Dereje Dengela ◽  
Gedeon Yohannes ◽  
Dejene Getachew ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
South Asian ◽  
Internal Transcribed Spacer ◽  
Anopheles Stephensi ◽  
Molecular Approach ◽  
Horn Of Africa ◽  
Eastern Ethiopia ◽  
Larval Habitats ◽  
Potential Impact ◽  
Endpoint Assay

ABSTRACTBackgroundThe recent detection of the South Asian malaria vector An. stephensi in Ethiopia and other regions in the Horn of Africa has raised concerns about its potential impact on malaria transmission. We report here findings of survey for this species in eastern Ethiopia using both morphological and molecular methods for species identification.MethodsAdult and larval/pupal collections were conducted at ten sites in eastern Ethiopia and Anopheles specimens’ species were determined using standard morphological keys and genetic analysis.ResultsIn total, 2,231 morphologically identified An. stephensi were collected. A molecular approach incorporating both PCR endpoint assay and sequencing of portions of the internal transcribed spacer 2 (ITS2) and cytochrome oxidase I (COI) loci confirmed the identity of the An. stephensi in most cases (119/124 of the morphologically identified An. stephensi confirmed molecularly). Additionally, we observed Aedes aegypti larvae and pupae at many of the An. stephensi larval habitats.ConclusionsOur findings show that An. stephensi is widely distributed in eastern Ethiopia and highlight the need for further surveillance in the southern, western and northern parts of the country and throughout the Horn of Africa.

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