Impact of Landscape on Host–Parasite Genetic Diversity and Distribution Using the Puumala orthohantavirus–Bank Vole System

In nature, host specificity has a strong impact on the parasite’s distribution, prevalence, and genetic diversity. The host’s population dynamics is expected to shape the distribution of host-specific parasites. In turn, the parasite’s genetic structure is predicted to mirror that of the host. Here, we study the tandem Puumala orthohantavirus (PUUV)–bank vole system. The genetic diversity of 310 bank voles and 33 PUUV isolates from 10 characterized localities of Northeast France was assessed. Our findings show that the genetic diversity of both PUUV and voles, was positively correlated with forest coverage and contiguity of habitats. While the genetic diversity of voles was weakly structured in space, that of PUUV was found to be strongly structured, suggesting that the dispersion of voles was not sufficient to ensure a broad PUUV dissemination. Genetic diversity of PUUV was mainly shaped by purifying selection. Genetic drift and extinction events were better reflected than local adaptation of PUUV. These contrasting patterns of microevolution have important consequences for the understanding of PUUV distribution and epidemiology.

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The spatial genetic structure of bank vole (Myodes glareolus) and yellow-necked mouse (Apodemus flavicollis) populations: The effect of distance and habitat barriers

Animal Biology ◽

10.1163/157075609x437691 ◽

2009 ◽

Vol 59 (2) ◽

pp. 169-187 ◽

Cited By ~ 19

Author(s):

Michal Kozakiewicz ◽

Alicja Gryczyńska–Siemiątkowska ◽

Hanna Panagiotopoulou ◽

Anna Kozakiewicz ◽

Robert Rutkowski ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Bank Vole ◽

Microsatellite Loci ◽

Myodes Glareolus ◽

Apodemus Flavicollis ◽

Island Populations ◽

Local Populations ◽

Bank Vole Myodes Glareolus ◽

Yellow Necked Mouse

AbstractHabitat barriers are considered to be an important factor causing the local reduction of genetic diversity by dividing a population into smaller sections and preventing gene flow between them. However, the “barrier effect” might be different in the case of different species. The effect of geographic distance and water barriers on the genetic structure of populations of two common rodent species – the yellow-necked mouse (Apodemus flavicollis) and the bank vole (Myodes glareolus) living in the area of a lake (on its islands and on two opposite shores) was investigated with the use of microsatellite fragment analysis. The two studied species are characterised by similar habitat requirements, but differ with regard to the socio-spatial structure of the population, individual mobility, capability to cross environmental barriers, and other factors. Trapping was performed for two years in spring and autumn in north-eastern Poland (21°E, 53°N). A total of 160 yellow-necked mouse individuals (7 microsatellite loci) and 346 bank vole individuals (9 microsatellite loci) were analysed. The results of the differentiation analyses (FST and RST) have shown that both the barrier which is formed by a ca. 300 m wide belt of water (between the island and the mainland) and the actual distance of approximately 10 km in continuous populations are sufficient to create genetic differentiation within both species. The differences between local populations living on opposite lake shores are the smallest; differences between any one of them and the island populations are more distinct. All of the genetic diversity indices (the mean number of alleles, mean allelic richness, as well as the observed and expected heterozygosity) of the local populations from the lakeshores were significantly higher than of the small island populations of these two species separated by the water barrier. The more profound “isolation effect” in the case of the island populations of the bank vole, in comparison to the yellow-necked mouse populations, seems to result not only from the lower mobility of the bank vole species, but may also be attributed to other differences in the animals' behaviour.

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Accumulation of point mutations and reassortment of genomic RNA segments are involved in the microevolution of Puumala hantavirus in a bank vole (Myodes glareolus) population

Journal of General Virology ◽

10.1099/vir.0.2008/001248-0 ◽

2008 ◽

Vol 89 (7) ◽

pp. 1649-1660 ◽

Cited By ~ 41

Author(s):

Maria Razzauti ◽

Angelina Plyusnina ◽

Heikki Henttonen ◽

Alexander Plyusnin

Keyword(s):

Genetic Diversity ◽

Bank Vole ◽

Local Population ◽

Point Mutations ◽

Myodes Glareolus ◽

Stabilizing Selection ◽

Genetic Lineage ◽

Nucleotide Substitutions ◽

Bank Voles ◽

L Segment

The genetic diversity of Puumala hantavirus (PUUV) was studied in a local population of its natural host, the bank vole (Myodes glareolus). The trapping area (2.5×2.5 km) at Konnevesi, Central Finland, included 14 trapping sites, at least 500 m apart; altogether, 147 voles were captured during May and October 2005. Partial sequences of the S, M and L viral genome segments were recovered from 40 animals. Seven, 12 and 17 variants were detected for the S, M and L sequences, respectively; these represent new wild-type PUUV strains that belong to the Finnish genetic lineage. The genetic diversity of PUUV strains from Konnevesi was 0.2–4.9 % for the S segment, 0.2–4.8 % for the M segment and 0.2–9.7 % for the L segment. Most nucleotide substitutions were synonymous and most deduced amino acid substitutions were conservative, probably due to strong stabilizing selection operating at the protein level. Based on both sequence markers and phylogenetic clustering, the S, M and L sequences could be assigned to two groups, ‘A’ and ‘B’. Notably, not all bank voles carried S, M and L sequences belonging to the same group, i.e. SAMALA or SBMBLB. A substantial proportion (8/40, 20 %) of the newly characterized PUUV strains possessed reassortant genomes such as SBMALA, SAMBLB or SBMALB. These results suggest that at least some of the PUUV reassortants are viable and can survive in the presence of their parental strains.

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Microevolution of bank voles (Myodes glareolus) at neutral and immune-related genes during multiannual dynamic cycles: Consequences for Puumala hantavirus epidemiology

10.1101/048082 ◽

2016 ◽

Author(s):

Dubois Adelaïde ◽

Maxime Galan ◽

Jean-François Cosson ◽

Bertrand Gauffre ◽

Heikki Henttonen ◽

...

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Bank Vole ◽

Hemorrhagic Fever ◽

Research Area ◽

Density Fluctuations ◽

Myodes Glareolus ◽

Bank Voles ◽

Active Research ◽

Immune Related Genes

ABSTRACTUnderstanding how host dynamics, including variations of population size and dispersal, may affect the epidemiology of infectious diseases through ecological and evolutionary processes is an active research area. Here we focus on a bank vole (Myodes glareolus) metapopulation surveyed in Finland between 2005 and 2009. Bank vole is the reservoir of Puumala hantavirus (PUUV), the agent of nephropathia epidemica (NE, a mild form of hemorrhagic fever with renal symptom) in humans.M glareoluspopulations experience multiannual density fluctuations that may influence the level of genetic diversity maintained in bank voles, PUUV prevalence and NE occurrence. We examine bank vole metapopulation genetics at presumably neutral markers and immune-related genes involved in susceptibility to PUUV (Tnf-promoter,Mhc-Drb, Tlr4,Tlr7andMx2gene) to investigate the links between population dynamics, microevolutionary processes and PUUV epidemiology. We show that genetic drift slightly and transiently affects neutral and adaptive genetic variability within the metapopulation. Gene flow seems to counterbalance its effects during the multiannual density fluctuations. The low abundance phase may therefore be too short to impact genetic variation in the host, and consequently viral genetic diversity. Environmental heterogeneity does not seem to affect vole gene flow, which might explain the absence of spatial structure previously detected in PUUV in this area. Besides, our results suggest the role of vole dispersal on PUUV circulation through sex-specific and density-dependent movements. We find little evidence of selection acting on immune-related genes within this metapopulation. Footprint of positive selection is detected atTlr-4gene in 2008 only. We observe marginally significant associations betweenMhc-Drbhaplotypes and PUUV serology, and betweenMx2genotype and PUUV genogroups. These results show that microevolutionary changes and PUUV epidemiology in this metapopulation are mainly driven by neutral processes, although the relative effects of neutral and adaptive forces could vary temporally with density fluctuations.

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Geographical Distribution and Genetic Diversity of Bank Vole Hepaciviruses in Europe

Viruses ◽

10.3390/v13071258 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1258

Author(s):

Julia Schneider ◽

Bernd Hoffmann ◽

Cristina Fevola ◽

Marie Luisa Schmidt ◽

Christian Imholt ◽

...

Keyword(s):

Genetic Diversity ◽

Geographical Distribution ◽

Bank Vole ◽

Isolation By Distance ◽

Diagnostic Methods ◽

Clethrionomys Glareolus ◽

Myodes Glareolus ◽

Population Fluctuations ◽

Mammal Species ◽

Bank Voles

The development of new diagnostic methods resulted in the discovery of novel hepaciviruses in wild populations of the bank vole (Myodes glareolus, syn. Clethrionomys glareolus). The naturally infected voles demonstrate signs of hepatitis similar to those induced by hepatitis C virus (HCV) in humans. The aim of the present research was to investigate the geographical distribution of bank vole-associated hepaciviruses (BvHVs) and their genetic diversity in Europe. Real-time reverse transcription polymerase chain reaction (RT-qPCR) screening revealed BvHV RNA in 442 out of 1838 (24.0%) bank voles from nine European countries and in one of seven northern red-backed voles (Myodes rutilus, syn. Clethrionomys rutilus). BvHV RNA was not found in any other small mammal species (n = 23) tested here. Phylogenetic and isolation-by-distance analyses confirmed the occurrence of both BvHV species (Hepacivirus F and Hepacivirus J) and their sympatric occurrence at several trapping sites in two countries. The broad geographical distribution of BvHVs across Europe was associated with their presence in bank voles of different evolutionary lineages. The extensive geographical distribution and high levels of genetic diversity of BvHVs, as well as the high population fluctuations of bank voles and occasional commensalism in some parts of Europe warrant future studies on the zoonotic potential of BvHVs.

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Dispersal responses override density effects on genetic diversity during post-disturbance succession

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2015.2934 ◽

2016 ◽

Vol 283 (1827) ◽

pp. 20152934 ◽

Cited By ~ 12

Author(s):

Annabel L. Smith ◽

Erin L. Landguth ◽

C. Michael Bull ◽

Sam C. Banks ◽

Michael G. Gardner ◽

...

Keyword(s):

Genetic Diversity ◽

Population Dynamics ◽

Genetic Structure ◽

Population Density ◽

Population Expansion ◽

Spatial Population ◽

Explicit Simulation ◽

Landscape Genetic ◽

Habitat Succession ◽

Spatial Population Dynamics

Dispersal fundamentally influences spatial population dynamics but little is known about dispersal variation in landscapes where spatial heterogeneity is generated predominantly by disturbance and succession. We tested the hypothesis that habitat succession following fire inhibits dispersal, leading to declines over time in genetic diversity in the early successional gecko Nephrurus stellatus . We combined a landscape genetics field study with a spatially explicit simulation experiment to determine whether successional patterns in genetic diversity were driven by habitat-mediated dispersal or demographic effects (declines in population density leading to genetic drift). Initial increases in genetic structure following fire were likely driven by direct mortality and rapid population expansion. Subsequent habitat succession increased resistance to gene flow and decreased dispersal and genetic diversity in N. stellatus . Simulated changes in population density alone did not reproduce these results. Habitat-mediated reductions in dispersal, combined with changes in population density, were essential to drive the field-observed patterns. Our study provides a framework for combining demographic, movement and genetic data with simulations to discover the relative influence of demography and dispersal on patterns of landscape genetic structure. Our results suggest that succession can inhibit connectivity among individuals, opening new avenues for understanding how disturbance regimes influence spatial population dynamics.

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Genetic diversity and genetic structure of the rare and endangered species, Primula ranunculoides

Biodiversity Science ◽

10.3724/sp.j.1003.2013.09098 ◽

2014 ◽

Vol 21 (5) ◽

pp. 601-609

Author(s):

Wang Deyun ◽

Peng Jie ◽

Chen Yajing ◽

Lü Guosheng ◽

Zhang Xiaoping ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Endangered Species ◽

Rare And Endangered Species ◽

Rare And Endangered

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The Patterns and Puzzles of Genetic Diversity of Endangered Freshwater Mussel Unio crassus Philipsson, 1788 Populations from Vistula and Neman Drainages (Eastern Central Europe)

Life ◽

10.3390/life10070119 ◽

2020 ◽

Vol 10 (7) ◽

pp. 119

Author(s):

Adrianna Kilikowska ◽

Monika Mioduchowska ◽

Anna Wysocka ◽

Agnieszka Kaczmarczyk-Ziemba ◽

Joanna Rychlińska ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Spatial Scales ◽

Freshwater Mussel ◽

Its Region ◽

Strong Relationship ◽

Mantel Test ◽

Freshwater Ecosystems ◽

Hierarchical Organization ◽

Anthropogenic Factors

Mussels of the family Unionidae are important components of freshwater ecosystems. Alarmingly, the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species identifies almost 200 unionid species as extinct, endangered, or threatened. Their decline is the result of human impact on freshwater habitats, and the decrease of host fish populations. The Thick Shelled River Mussel Unio crassus Philipsson, 1788 is one of the examples that has been reported to show a dramatic decline of populations. Hierarchical organization of riverine systems is supposed to reflect the genetic structure of populations inhabiting them. The main goal of this study was an assessment of the U. crassus genetic diversity in river ecosystems using hierarchical analysis. Different molecular markers, the nuclear ribosomal internal transcribed spacer ITS region, and mitochondrial DNA genes (cox1 and ndh1), were used to examine the distribution of U. crassus among-population genetic variation at multiple spatial scales (within rivers, among rivers within drainages, and between drainages of the Neman and Vistula rivers). We found high genetic structure between both drainages suggesting that in the case of the analyzed U. crassus populations we were dealing with at least two different genetic units. Only about 4% of the mtDNA variation was due to differences among populations within drainages. However, comparison of population differentiation within drainages for mtDNA also showed some genetic structure among populations within the Vistula drainage. Only one haplotype was shared among all Polish populations whereas the remainder were unique for each population despite the hydrological connection. Interestingly, some haplotypes were present in both drainages. In the case of U. crassus populations under study, the Mantel test revealed a relatively strong relationship between genetic and geographical distances. However, in detail, the pattern of genetic diversity seems to be much more complicated. Therefore, we suggest that the observed pattern of U. crassus genetic diversity distribution is shaped by both historical and current factors i.e. different routes of post glacial colonization and history of drainage systems, historical gene flow, and more recent habitat fragmentation due to anthropogenic factors.

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Rodent host population dynamics drive zoonotic Lyme Borreliosis and Orthohantavirus infections in humans in Northern Europe

Scientific Reports ◽

10.1038/s41598-021-95000-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mahdi Aminikhah ◽

Jukka T. Forsman ◽

Esa Koskela ◽

Tapio Mappes ◽

Jussi Sane ◽

...

Keyword(s):

Population Dynamics ◽

Lyme Borreliosis ◽

Bank Vole ◽

Myodes Glareolus ◽

Northern Europe ◽

Time Lags ◽

Rodent Population ◽

Vole Cycles ◽

Infection Dynamics ◽

Abundance Fluctuations

AbstractZoonotic diseases, caused by pathogens transmitted between other vertebrate animals and humans, pose a major risk to human health. Rodents are important reservoir hosts for many zoonotic pathogens, and rodent population dynamics affect the infection dynamics of rodent-borne diseases, such as diseases caused by hantaviruses. However, the role of rodent population dynamics in determining the infection dynamics of rodent-associated tick-borne diseases, such as Lyme borreliosis (LB), caused by Borrelia burgdorferi sensu lato bacteria, have gained limited attention in Northern Europe, despite the multiannual abundance fluctuations, the so-called vole cycles, that characterise rodent population dynamics in the region. Here, we quantify the associations between rodent abundance and LB human cases and Puumala Orthohantavirus (PUUV) infections by using two time series (25-year and 9-year) in Finland. Both bank vole (Myodes glareolus) abundance as well as LB and PUUV infection incidence in humans showed approximately 3-year cycles. Without vector transmitted PUUV infections followed the bank vole host abundance fluctuations with two-month time lag, whereas tick-transmitted LB was associated with bank vole abundance ca. 12 and 24 months earlier. However, the strength of association between LB incidence and bank vole abundance ca. 12 months before varied over the study years. This study highlights that the human risk to acquire rodent-borne pathogens, as well as rodent-associated tick-borne pathogens is associated with the vole cycles in Northern Fennoscandia, yet with complex time lags.

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Impact of cyclones on hard coral and metapopulation structure, connectivity and genetic diversity of coral reef fish

Coral Reefs ◽

10.1007/s00338-021-02096-9 ◽

2021 ◽

Author(s):

Gabriele Gerlach ◽

Philipp Kraemer ◽

Peggy Weist ◽

Laura Eickelmann ◽

Michael J. Kingsford

Keyword(s):

Genetic Diversity ◽

Coral Reef ◽

Genetic Structure ◽

Reef Fish ◽

Coral Reef Fish ◽

Population Genetic Study ◽

Hard Coral ◽

Great Loss ◽

Metapopulation Structure ◽

The Impact

AbstractCyclones have one of the greatest effects on the biodiversity of coral reefs and the associated species. But it is unknown how stochastic alterations in habitat structure influence metapopulation structure, connectivity and genetic diversity. From 1993 to 2018, the reefs of the Capricorn Bunker Reef group in the southern part of the Great Barrier Reef were impacted by three tropical cyclones including cyclone Hamish (2009, category 5). This resulted in substantial loss of live habitat-forming coral and coral reef fish communities. Within 6–8 years after cyclones had devastated, live hard corals recovered by 50–60%. We show the relationship between hard coral cover and the abundance of the neon damselfish (Pomacentrus coelestis), the first fish colonizing destroyed reefs. We present the first long-term (2008–2015 years corresponding to 16–24 generations of P. coelestis) population genetic study to understand the impact of cyclones on the meta-population structure, connectivity and genetic diversity of the neon damselfish. After the cyclone, we observed the largest change in the genetic structure at reef populations compared to other years. Simultaneously, allelic richness of genetic microsatellite markers dropped indicating a great loss of genetic diversity, which increased again in subsequent years. Over years, metapopulation dynamics were characterized by high connectivity among fish populations associated with the Capricorn Bunker reefs (2200 km2); however, despite high exchange, genetic patchiness was observed with annual strong genetic divergence between populations among reefs. Some broad similarities in the genetic structure in 2015 could be explained by dispersal from a source reef and the related expansion of local populations. This study has shown that alternating cyclone-driven changes and subsequent recovery phases of coral habitat can greatly influence patterns of reef fish connectivity. The frequency of disturbances determines abundance of fish and genetic diversity within species.

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Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

Virology Journal ◽

10.1186/s12985-020-01466-z ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Edith Khamonya Avedi ◽

Adedapo Olutola Adediji ◽

Dora Chao Kilalo ◽

Florence Mmogi Olubayo ◽

Isaac Macharia ◽

...

Keyword(s):

Genetic Diversity ◽

Selection Pressure ◽

Management Strategies ◽

Purifying Selection ◽

Tomato Leaf ◽

Amino Acid Sequences ◽

Virus Population ◽

Tomato Production ◽

Tomato Leaf Curl ◽

Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

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