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Martinů J, Tarabai H, Štefka J, Hypša V. Highly Resolved Genomes of Two Closely Related Lineages of the Rodent Louse Polyplax serrata with Different Host Specificities. Genome Biol Evol 2024; 16:evae045. [PMID: 38478715 PMCID: PMC10972687 DOI: 10.1093/gbe/evae045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2024] [Indexed: 04/01/2024] Open
Abstract
Sucking lice of the parvorder Anoplura are permanent ectoparasites with specific lifestyle and highly derived features. Currently, genomic data are only available for a single species, the human louse Pediculus humanus. Here, we present genomes of two distinct lineages, with different host spectra, of a rodent louse Polyplax serrata. Genomes of these ecologically different lineages are closely similar in gene content and display a conserved order of genes, with the exception of a single translocation. Compared with P. humanus, the P. serrata genomes are noticeably larger (139 vs. 111 Mbp) and encode a higher number of genes. Similar to P. humanus, they are reduced in sensory-related categories such as vision and olfaction. Utilizing genome-wide data, we perform phylogenetic reconstruction and evolutionary dating of the P. serrata lineages. Obtained estimates reveal their relatively deep divergence (∼6.5 Mya), comparable with the split between the human and chimpanzee lice P. humanus and Pediculus schaeffi. This supports the view that the P. serrata lineages are likely to represent two cryptic species with different host spectra. Historical demographies show glaciation-related population size (Ne) reduction, but recent restoration of Ne was seen only in the less host-specific lineage. Together with the louse genomes, we analyze genomes of their bacterial symbiont Legionella polyplacis and evaluate their potential complementarity in synthesis of amino acids and B vitamins. We show that both systems, Polyplax/Legionella and Pediculus/Riesia, display almost identical patterns, with symbionts involved in synthesis of B vitamins but not amino acids.
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Affiliation(s)
- Jana Martinů
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Hassan Tarabai
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Central European Institute of Technology (CEITEC), University of Veterinary Sciences, Brno, Czech Republic
| | - Jan Štefka
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Václav Hypša
- Department of Parasitology, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Institute of Parasitology, Biology Centre, The Czech Academy of Sciences, České Budějovice, Czech Republic
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Lunghi E, Bilandžija H. Telomere length and dynamics in Astyanax mexicanus cave and surface morphs. PeerJ 2024; 12:e16957. [PMID: 38435987 PMCID: PMC10908260 DOI: 10.7717/peerj.16957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/25/2024] [Indexed: 03/05/2024] Open
Abstract
Background Telomeres are non-coding DNA repeats at the chromosome ends and their shortening is considered one of the major causes of aging. However, they also serve as a biomarker of environmental exposures and their length and attrition is affected by various stressors. In this study, we examined the average telomere length in Astyanax mexicanus, a species that has both surface-dwelling and cave-adapted populations. The cave morph descended from surface ancestors and adapted to a markedly different environment characterized by specific biotic and abiotic stressors, many of which are known to affect telomere length. Our objective was to explore whether telomere length differs between the two morphs and whether it serves as a biological marker of aging or correlates with the diverse environments the morphs are exposed to. Methods We compared telomere length and shortening between laboratory-reared Pachón cavefish and Rio Choy surface fish of A. mexicanus across different tissues and ages. Results Astyanax mexicanus surface fish exhibited longer average telomere length compared to cavefish. In addition, we did not observe telomere attrition in either cave or surface form as a result of aging in adults up to 9 years old, suggesting that efficient mechanisms prevent telomere-mediated senescence in laboratory stocks of this species, at least within this time frame. Our results suggest that telomere length in Astyanax may be considered a biomarker of environmental exposures. Cavefish may have evolved shorter and energetically less costly telomeres due to the absence of potential stressors known to affect surface species, such as predator pressure and ultra-violet radiation. This study provides the first insights into telomere dynamics in Astyanax morphs and suggests that shorter telomeres may have evolved as an adaptation to caves.
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Affiliation(s)
- Enrico Lunghi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | - Helena Bilandžija
- Division of Molecular Biology, Ruder Bošković Institute, Zagreb, Croatia
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Yu Q, Hu J, Hu X, Zhou Y, Wang F, Jiang S, Wang Y. Demographic patterns of two related desert shrubs with overlapping distributions in response to past climate changes. FRONTIERS IN PLANT SCIENCE 2024; 15:1345624. [PMID: 38450397 PMCID: PMC10915042 DOI: 10.3389/fpls.2024.1345624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/05/2024] [Indexed: 03/08/2024]
Abstract
Numerous studies have revealed that past geological events and climatic fluctuations had profoundly affected the genetic structure and demographic patterns of species. However, related species with overlapping ranges may have responded to such environmental changes in different ways. In this study, we compared the genetic structure and population dynamics of two typical desert shrubs with overlapping distributions in northern China, Nitraria tangutorum and Nitraria sphaerocarpa, based on chloroplast DNA (cpDNA) variations and species distribution models. We sequenced two cpDNA fragments (trnH-trnA and atpH-atpI) in 633 individuals sampled from 52 natural populations. Twenty-four chlorotypes, including eight rare chlorotypes, were identified, and a single dominant haplotype (H4) widely occurred in the entire geographical ranges of the two species. There were also a few distinctive chlorotypes fixed in different geographical regions. Population structure analyses suggested that the two species had significantly different levels of total genetic diversity and interpopulation differentiation, which was highly likely correlated with the special habitat preferences of the two species. A clear phylogeographic structure was identified to exist among populations of N. sphaerocarpa, but not exist for N. tangutorum. The neutral tests, together with the distribution of pairwise differences revealed that N. tangutorum experienced a sudden demographic expansion, and its expansion approximately occurred between 21 and 7 Kya before present, while a rapid range expansion was not identified for N. sphaerocarpa. The ecological niche modeling (ENM) analysis indicated that the potential ranges of two species apparently fluctuated during the past and present periods, with obvious contraction in the Last Glacial Maximum (LGM) and recolonization in the present, respectively, comparing to the Last Interglacial (LIG). These findings suggest that the two species extensively occurred in the Northwest of China before the Quaternary, and the current populations of them originated from a few separated glacial refugia following their habitat fragmentation in the Quarternary. Our results provide new insights on the impact of past geological and climatic fluctuations on the population dynamics of desert plants in northwestern China, and further enforce the hypothesis that there were several independent glacial refugia for these species during the Quaternary glaciations.
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Affiliation(s)
- Qiushi Yu
- Xinglongshan Forest Ecosystem National Positioning Observation and Research Station, Gansu Research Academy of Forestry Science and Technology, Lanzhou, China
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
- Key Laboratory of Biodiversity Formation Mechanism and Comprehensive Utilization of the Qinghai-Tibet Plateau in Qinghai Province, Qinghai Normal University, Xining, China
| | - Jing Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Xiaoke Hu
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Yongfeng Zhou
- Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fanglin Wang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Shengxiu Jiang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
| | - Yuqi Wang
- State Key Laboratory Breeding Base of Desertification and Aeolian Sand Disaster Combating, Gansu Desert Control Research Institute, Lanzhou, China
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Bakker JW, Pascoe EL, van de Water S, van Keulen L, de Vries A, Woudstra LC, Esser HJ, Pijlman GP, de Boer WF, Sprong H, Kortekaas J, Wichgers Schreur PJ, Koenraadt CJM. Infection of wild-caught wood mice (Apodemus sylvaticus) and yellow-necked mice (A. flavicollis) with tick-borne encephalitis virus. Sci Rep 2023; 13:21627. [PMID: 38062065 PMCID: PMC10703896 DOI: 10.1038/s41598-023-47697-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
The distribution of tick-borne encephalitis virus (TBEV) is expanding to Western European countries, including the Netherlands, but the contribution of different rodent species to the transmission of TBEV is poorly understood. We investigated whether two species of wild rodents native to the Netherlands, the wood mouse Apodemus sylvaticus and the yellow-necked mouse Apodemus flavicollis, differ in their relative susceptibility to experimental infection with TBEV. Wild-caught individuals were inoculated subcutaneously with the classical European subtype of TBEV (Neudoerfl) or with TBEV-NL, a genetically divergent TBEV strain from the Netherlands. Mice were euthanised and necropsied between 3 and 21 days post-inoculation. None of the mice showed clinical signs or died during the experimental period. Nevertheless, TBEV RNA was detected up to 21 days in the blood of both mouse species and TBEV was also isolated from the brain of some mice. Moreover, no differences in infection rates between virus strains and mouse species were found in blood, spleen, or liver samples. Our results suggest that the wood mouse and the yellow-necked mouse may equally contribute to the transmission cycle of TBEV in the Netherlands. Future experimental infection studies that include feeding ticks will help elucidate the relative importance of viraemic transmission in the epidemiology of TBEV.
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Affiliation(s)
- Julian W Bakker
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands.
| | - Emily L Pascoe
- Laboratory of Entomology, Wageningen University & Research, Wageningen, The Netherlands
- Conservation Genomics Research Unit, Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
| | - Sandra van de Water
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Lucien van Keulen
- Department of Bacteriology, Host-Pathogen Interaction and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - Ankje de Vries
- National Institute of Public Health and the Environment (RIVM), Utrecht, The Netherlands
| | - Lianne C Woudstra
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Helen J Esser
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Gorben P Pijlman
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands
| | - Willem F de Boer
- Wildlife Ecology and Conservation Group, Wageningen University & Research, Wageningen, The Netherlands
| | - Hein Sprong
- National Institute of Public Health and the Environment (RIVM), Utrecht, The Netherlands
| | - Jeroen Kortekaas
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
- Laboratory of Virology, Wageningen University & Research, Wageningen, The Netherlands
- Boehringer Ingelheim Animal Health, Saint Priest, France
| | - Paul J Wichgers Schreur
- Department of Virology and Molecular Biology, Wageningen Bioveterinary Research, Lelystad, The Netherlands
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Kaminskienė E, Radzijevskaja J, Griciuvienė L, Stanko M, Snegiriovaitė J, Mardosaitė-Busaitienė D, Paulauskas A. Molecular Identification and Phylogenetic Analysis of Laelapidae Mites (Acari: Mesostigmata). Animals (Basel) 2023; 13:2185. [PMID: 37443981 DOI: 10.3390/ani13132185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
The family Laelapidae (Dermanyssoidea) is morphologically and ecologically the most diverse group of Mesostigmata mites. Although molecular genetic data are widely used in taxonomic identification and phylogenetic analysis, most classifications in Mesostigmata mites are based solely on morphological characteristics. In the present study, eight species of mites from the Laelapidae (Dermanyssoidea) family collected from different species of small rodents in Lithuania, Norway, Slovakia, and the Czech Republic were molecularly characterized using the nuclear (28S ribosomal RNA) and mitochondrial (cytochrome oxidase subunit I gene) markers. Obtained molecular data from 113 specimens of mites were used to discriminate between species and investigate the phylogenetic relationships and genetic diversity among Laelapidae mites from six genera. This study provides new molecular data on Laelaps agilis, Laelaps hilaris, Laelaps jettmari, Haemogamasus nidi, Eulaelaps stabularis, Hyperlaelaps microti, Myonyssus gigas, and Hirstionyssus sp. mites collected from different rodent hosts and geographical regions in Europe.
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Affiliation(s)
- Evelina Kaminskienė
- Faculty of Natural Sciences, Vytautas Magnus University, Donelaičio Str. 58, LT-44248 Kaunas, Lithuania
| | - Jana Radzijevskaja
- Faculty of Natural Sciences, Vytautas Magnus University, Donelaičio Str. 58, LT-44248 Kaunas, Lithuania
| | - Loreta Griciuvienė
- Faculty of Natural Sciences, Vytautas Magnus University, Donelaičio Str. 58, LT-44248 Kaunas, Lithuania
| | - Michal Stanko
- Department of Vector-Borne Diseases, Institute of Parasitology, Slovak Academy of Sciences, Hlinkova 3, 04001 Košice, Slovakia
| | - Justina Snegiriovaitė
- Faculty of Natural Sciences, Vytautas Magnus University, Donelaičio Str. 58, LT-44248 Kaunas, Lithuania
| | | | - Algimantas Paulauskas
- Faculty of Natural Sciences, Vytautas Magnus University, Donelaičio Str. 58, LT-44248 Kaunas, Lithuania
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Bondaryuk AN, Kulakova NV, Belykh OI, Bukin YS. Dates and Rates of Tick-Borne Encephalitis Virus-The Slowest Changing Tick-Borne Flavivirus. Int J Mol Sci 2023; 24:2921. [PMID: 36769238 PMCID: PMC9917962 DOI: 10.3390/ijms24032921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
We evaluated the temporal signal and substitution rate of tick-borne encephalitis virus (TBEV) using 276 complete open reading frame (ORF) sequences with known collection dates. According to a permutation test, the TBEV Siberian subtype (TBEV-S) data set has no temporal structure and cannot be applied for substitution rate estimation without other TBEV subtypes. The substitution rate obtained suggests that the common clade of TBEV (TBEV-common), including all TBEV subtypes and louping-ill virus (LIV), is characterized by the lowest rate (1.87 × 10-5 substitutions per site per year (s/s/y) or 1 nucleotide substitution per ORF per 4.9 years; 95% highest posterior density (HPD) interval, 1.3-2.4 × 10-5 s/s/y) among all tick-borne flaviviruses previously assessed. Within TBEV-common, the TBEV European subtype (TBEV-E) has the lowest substitution rate (1.3 × 10-5 s/s/y or 1 nucleotide substitution per ORF per 7.5 years; 95% HPD, 1.0-1.8 × 10-5 s/s/y) as compared with TBEV Far-Eastern subtype (3.0 × 10-5 s/s/y or 1 nucleotide substitution per ORF per 3.2 years; 95% HPD, 1.6-4.5 × 10-5 s/s/y). TBEV-common representing the species tick-borne encephalitis virus diverged 9623 years ago (95% HPD interval, 6373-13,208 years). The TBEV Baikalian subtype is the youngest one (489 years; 95% HPD, 291-697 years) which differs significantly by age from TBEV-E (848 years; 95% HPD, 596-1112 years), LIV (2424 years; 95% HPD, 1572-3400 years), TBEV-FE (1936 years, 95% HPD, 1344-2598 years), and the joint clade of TBEV-S (2505 years, 95% HPD, 1700-3421 years) comprising Vasilchenko, Zausaev, and Baltic lineages.
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Affiliation(s)
- Artem N. Bondaryuk
- Laboratory of Natural Focal Viral Infections, Irkutsk Antiplague Research Institute of Siberia and the Far East, 664047 Irkutsk, Russia
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Nina V. Kulakova
- Department of Biodiversity and Biological Resources, Siberian Institute of Plant Physiology and Biochemistry, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Olga I. Belykh
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
| | - Yurij S. Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, 664033 Irkutsk, Russia
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7
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Polic D, Yıldırım Y, Lee KM, Franzén M, Mutanen M, Vila R, Forsman A. Linking large-scale genetic structure of three Argynnini butterfly species to geography and environment. Mol Ecol 2022; 31:4381-4401. [PMID: 35841126 PMCID: PMC9544544 DOI: 10.1111/mec.16594] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/17/2022] [Accepted: 06/29/2022] [Indexed: 12/04/2022]
Abstract
Understanding which factors and processes are associated with genetic differentiation within and among species remains a major goal in evolutionary biology. To explore differences and similarities in genetic structure and its association with geographical and climatic factors in sympatric sister species, we conducted a large‐scale (>32° latitude and >36° longitude) comparative phylogeographical study on three Argynnini butterfly species (Speyeria aglaja, Fabriciana adippe and F. niobe) that have similar life histories, but differ in ecological generalism and dispersal abilities. Analyses of nuclear (ddRAD‐sequencing derived SNP markers) and mitochondrial (COI sequences) data revealed differences between species in genetic structure and how genetic differentiation was associated with climatic factors (temperature, solar radiation, precipitation, wind speed). Geographical proximity accounted for much of the variation in nuclear and mitochondrial structure and evolutionary relationships in F. adippe and F. niobe, but only explained the pattern observed in the nuclear data in S. aglaja, for which mitonuclear discordance was documented. In all species, Iberian and Balkan individuals formed genetic clusters, suggesting isolation in glacial refugia and limited postglacial expansion. Solar radiation and precipitation were associated with the genetic structure on a regional scale in all species, but the specific combinations of environmental and geographical factors linked to variation within species were unique, pointing to species‐specific responses to common environments. Our findings show that the species share similar colonization histories, and that the same ecological factors, such as niche breadth and dispersal capacity, covary with genetic differentiation within these species to some extent, thereby highlighting the importance of comparative phylogeographical studies in sympatric sister species.
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Affiliation(s)
- Daniela Polic
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
| | - Yeşerin Yıldırım
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Kyung Min Lee
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Markus Franzén
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Marko Mutanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Anders Forsman
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, Sweden
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8
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Nazarizadeh M, Martinů J, Nováková M, Stanko M, Štefka J. Phylogeography of the parasitic mite Laelaps agilis in Western Palearctic shows lineages lacking host specificity but possessing different demographic histories. BMC ZOOL 2022; 7:15. [PMID: 37170127 PMCID: PMC10127304 DOI: 10.1186/s40850-022-00115-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
Abstract
Background
Laelaps agilis C.L. Koch, 1836 is one the most abundant and widespread parasitic mite species in the Western Palearctic. It is a permanent ectoparasite associated with the Apodemus genus, which transmits Hepatozoon species via the host’s blood. Phylogenetic relationships, genealogy and host specificity of the mite are uncertain in the Western Palearctic. Here, we investigated the population genetic structure of 132 individual mites across Europe from their Apodemus and Clethrionomys hosts. Phylogenetic relationships and genetic variation of the populations were analyzed using cytochrome c oxidase subunit I (COI) gene sequences.
Results
We recovered three main mtDNA lineages within L. agilis in the Western Palearctic, which differentiated between 1.02 and 1.79 million years ago during the Pleistocene period: (i) Lineage A, including structured populations from Western Europe and the Czech Republic, (ii) Lineage B, which included only a few individuals from Greece and the Czech Republic; and (iii) Lineage C, which comprised admixed populations from Western and Eastern Europe. Contrary to their population genetic differentiation, the lineages did not show signs of specificity to different hosts. Finally, we confirmed that the sympatric congener L. clethrionomydis is represented by a separated monophyletic lineage.
Conclusion
Differences in the depth of population structure between L. agilis Lineages A and C, corroborated by the neutrality tests and demographic history analyses, suggested a stable population size in the structured Lineage A and a rapid range expansion for the geographically admixed Lineage C. We hypothesized that the two lineages were associated with hosts experiencing different glaciation histories. The lack of host specificity in L. agilis lineages was in contrast to the co-occurring highly host-specific lineages of Polyplax serrata lice, sharing Apodemus hosts. The incongruence was attributed to the differences in mobility between the parasites, allowing mites to switch hosts more often.
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Kujawska M, Raulo A, Millar M, Warren F, Baltrūnaitė L, Knowles SCL, Hall LJ. Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential. ISME COMMUNICATIONS 2022; 2:20. [PMID: 37938745 PMCID: PMC9723756 DOI: 10.1038/s43705-022-00102-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 01/30/2022] [Accepted: 02/09/2022] [Indexed: 11/09/2023]
Abstract
Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania). Members of Bifidobacterium castoris, Bifidobacterium animalis and Bifodobacterium pseudolongum were detected in wild mice (Apodemus sylvaticus, Apodemus agrarius and Apodemus flavicollis), but not voles or shrews. B. castoris constituted the most commonly recovered Bifidobacterium (78% of all isolates), with the majority of strains only detected in a single population, although populations frequently harboured multiple co-circulating strains. Phylogenetic analysis revealed that the mouse-associated B. castoris clades were not specific to a particular location or host species, and their distribution across the host phylogeny was consistent with regular host shifts rather than host-microbe codiversification. Functional analysis, including in vitro growth assays, suggested that mouse-derived B. castoris strains encoded an extensive arsenal of carbohydrate-active enzymes, including putative novel glycosyl hydrolases such as chitosanases, along with genes encoding putative exopolysaccharides, some of which may have been acquired via horizontal gene transfer. Overall, these results provide a rare genome-level analysis of host specificity and genomic capacity among important gut symbionts of wild animals, and reveal that Bifidobacterium has a labile relationship with its host over evolutionary time scales.
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Affiliation(s)
- Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Aura Raulo
- Department of Zoology, University of Oxford, Mansfield Road, Oxford, UK
| | - Molly Millar
- Food Innovation and Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK
| | - Fred Warren
- Food Innovation and Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK
| | | | - Sarah C L Knowles
- Department of Zoology, University of Oxford, Mansfield Road, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, Hawkshead Lane, Hatfield, Herfordshire, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Biosciences, Norwich Research Park, Norwich, UK.
- Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, UK.
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Arif S, Gerth M, Hone-Millard WG, Nunes MDS, Dapporto L, Shreeve TG. Evidence for multiple colonisations and Wolbachia infections shaping the genetic structure of the widespread butterfly Polyommatus icarus in the British Isles. Mol Ecol 2021; 30:5196-5213. [PMID: 34402109 DOI: 10.1111/mec.16126] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 07/30/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022]
Abstract
The paradigm of isolation in southern refugia during glacial periods followed by expansions during interglacials, producing limited genetic differentiation in northern areas, dominates European phylogeography. However, the existence of complex structured populations in formerly glaciated areas, and islands connected to mainland areas during glacial maxima, call for alternative explanations. We reconstructed the mtDNA phylogeography of the widespread Polyommatus Icarus butterfly with an emphasis on the formerly glaciated and connected British Isles. We found distinct geographical structuring of CO1 haplogroups, with an ancient lineage restricted to the marginal European areas, including Northern Scotland and Outer Hebrides. Population genomic analyses, using ddRADSeq genomic markers, also reveal substantial genetic structuring within Britain. However, there is negligble mito-nuclear concordance consistent with independent demographic histories of mitochondrial versus nuclear DNA. While mtDNA-Wolbachia associations in northern Britain could account for the geographic structuring of mtDNA across most of the British Isles, for nuclear DNA markers (derived from ddRADseq data) butterflies from France cluster between northern and southern British populations - an observation consistent with a scenario of multiple recolonisation. Taken together our results suggest that contemporary mtDNA structuring in the British Isles (and potentially elsewhere in Europe) largely results from Wolbachia infections, however, nuclear genomic structuring suggests a history of at least two distinct colonisations. This two-stage colonisation scenario has previously been put forth to explain genetic diversity and structuring in other British flora and fauna. Additionally, we also present preliminary evidence for potential Wolbachia-induced feminization in the Outer Hebrides.
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Affiliation(s)
- Saad Arif
- Centre for Functional Genomics, Oxford Brookes University, Oxford, UK.,Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Michael Gerth
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | | | - Maria D S Nunes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Leonardo Dapporto
- ZEN Laboratory, Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Timothy G Shreeve
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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11
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Escalante MA, Horníková M, Marková S, Kotlík P. Niche differentiation in a postglacial colonizer, the bank vole Clethrionomys glareolus. Ecol Evol 2021; 11:8054-8070. [PMID: 34188871 PMCID: PMC8216960 DOI: 10.1002/ece3.7637] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 03/30/2021] [Accepted: 04/13/2021] [Indexed: 01/25/2023] Open
Abstract
Species-level environmental niche modeling has been crucial in efforts to understand how species respond to climate variation and change. However, species often exhibit local adaptation and intraspecific niche differences that may be important to consider in predicting responses to climate. Here, we explore whether phylogeographic lineages of the bank vole originating from different glacial refugia (Carpathian, Western, Eastern, and Southern) show niche differentiation, which would suggest a role for local adaptation in biogeography of this widespread Eurasian small mammal. We first model the environmental requirements for the bank vole using species-wide occurrences (210 filtered records) and then model each lineage separately to examine niche overlap and test for niche differentiation in geographic and environmental space. We then use the models to estimate past [Last Glacial Maximum (LGM) and mid-Holocene] habitat suitability to compare with previously hypothesized glacial refugia for this species. Environmental niches are statistically significantly different from each other for all pairs of lineages in geographic and environmental space, and these differences cannot be explained by habitat availability within their respective ranges. Together with the inability of most of the lineages to correctly predict the distributions of other lineages, these results support intraspecific ecological differentiation in the bank vole. Model projections of habitat suitability during the LGM support glacial survival of the bank vole in the Mediterranean region and in central and western Europe. Niche differences between lineages and the resulting spatial segregation of habitat suitability suggest ecological differentiation has played a role in determining the present phylogeographic patterns in the bank vole. Our study illustrates that models pooling lineages within a species may obscure the potential for different responses to climate change among populations.
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Affiliation(s)
- Marco A. Escalante
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
| | - Michaela Horníková
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
- Department of ZoologyFaculty of ScienceCharles UniversityPragueCzech Republic
| | - Silvia Marková
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
| | - Petr Kotlík
- Laboratory of Molecular EcologyInstitute of Animal Physiology and Genetics of the Czech Academy of SciencesLiběchovCzech Republic
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12
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Lavrinienko A, Hämäläinen A, Hindström R, Tukalenko E, Boratyński Z, Kivisaari K, Mousseau TA, Watts PC, Mappes T. Comparable response of wild rodent gut microbiome to anthropogenic habitat contamination. Mol Ecol 2021; 30:3485-3499. [PMID: 33955637 DOI: 10.1111/mec.15945] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 04/07/2021] [Accepted: 04/29/2021] [Indexed: 12/11/2022]
Abstract
Species identity is thought to dominate over environment in shaping wild rodent gut microbiota, but it remains unknown whether the responses of host gut microbiota to shared anthropogenic habitat impacts are species-specific or if the general gut microbiota response is similar across host species. Here, we compare the influence of exposure to radionuclide contamination on the gut microbiota of four wild mouse species: Apodemus flavicollis, A. sylvaticus, A. speciosus and A. argenteus. Building on the evidence that radiation impacts bank vole (Myodes glareolus) gut microbiota, we hypothesized that radiation exposure has a general impact on rodent gut microbiota. Because we sampled (n = 288) two species pairs of Apodemus mice that occur in sympatry in habitats affected by the Chernobyl and Fukushima nuclear accidents, these comparisons provide an opportunity for a general assessment of the effects of exposure to environmental contamination (radionuclides) on gut microbiota across host phylogeny and geographical areas. In general agreement with our hypothesis, analyses of bacterial 16S rRNA gene sequences revealed that radiation exposure alters the gut microbiota composition and structure in three of the four species of Apodemus mice. The notable lack of an association between the gut microbiota and soil radionuclide contamination in one mouse species from Fukushima (A. argenteus) probably reflects host "radiation escape" through its unique tree-dwelling lifestyle. The finding that host ecology can modulate effects of radiation exposure offers an interesting counterpoint for future analyses into effects of radiation or any other toxic exposure on host and its associated microbiota. Our data show that exposure to radionuclide contamination is linked to comparable gut microbiota responses across multiple species of rodents.
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Affiliation(s)
- Anton Lavrinienko
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Anni Hämäläinen
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.,Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| | | | - Eugene Tukalenko
- Ecology and Genetics, University of Oulu, Oulu, Finland.,National Research Center for Radiation Medicine of the National Academy of Medical Science, Kyiv, Ukraine
| | - Zbyszek Boratyński
- CIBIO-InBIO Associate Laboratory, Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, Portugal
| | - Kati Kivisaari
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Timothy A Mousseau
- Department of Biological Sciences, University of South Carolina, Columbia, SC, USA.,SURA/LASSO/NASA, ISS Utilization and Life Sciences Division, Kennedy Space Center, Cape Canaveral, FL, USA
| | - Phillip C Watts
- Ecology and Genetics, University of Oulu, Oulu, Finland.,Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - Tapio Mappes
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
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13
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García-Rodríguez A, Guarnizo CE, Crawford AJ, Garda AA, Costa GC. Idiosyncratic responses to drivers of genetic differentiation in the complex landscapes of Isthmian Central America. Heredity (Edinb) 2021; 126:251-265. [PMID: 33051599 PMCID: PMC8027409 DOI: 10.1038/s41437-020-00376-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 11/08/2022] Open
Abstract
Isthmian Central America (ICA) is one of the most biodiverse regions in the world, hosting an exceptionally high number of species per unit area. ICA was formed <25 million years ago and, consequently, its biotic assemblage is relatively young and derived from both colonization and in situ diversification. Despite intensive taxonomic work on the local fauna, the potential forces driving genetic divergences and ultimately speciation in ICA remain poorly studied. Here, we used a landscape genetics approach to test whether isolation by distance, topography, habitat suitability, or environment drive the genetic diversity of the regional frog assemblage. To this end, we combined data on landscape features and mitochondrial DNA sequence variation for nine codistributed amphibian species with disparate life histories. In five species, we found that at least one of the factors tested explained patterns of genetic divergence. However, rather than finding a general pattern, our results revealed idiosyncratic responses to historical and ecological processes, indicating that intrinsic life-history characteristics may determine the effect of different drivers of isolation on genetic divergence in ICA. Our work also suggests that the convergence of several factors promoting isolation among populations over a heterogeneous landscape might maximize genetic differentiation, despite short geographical distances. In conclusion, abiotic factors and geographical features have differentially affected the genetic diversity across the regional frog assemblage. Much more complex models (i.e., considering multiple drivers), beyond simple vicariance of Caribbean and Pacific lineages, are needed to better understand the evolutionary history of ICA's diverse biotas.
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Affiliation(s)
- Adrián García-Rodríguez
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, AP 70-153, Ciudad Universitaria, CP, 04510, Ciudad de México, México.
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, 59078-900, RN, Brazil.
- Escuela de Biología, Universidad de Costa Rica, San Pedro, 11501-2060, San José, Costa Rica.
| | - Carlos E Guarnizo
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia
| | - Andrew J Crawford
- Departamento de Ciencias Biológicas, Universidad de los Andes, Bogotá, 111711, Colombia
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Panamá, Republic of Panama
| | - Adrian A Garda
- Departamento de Ecologia, Universidade Federal do Rio Grande do Norte, Natal, 59078-900, RN, Brazil
| | - Gabriel C Costa
- Department of Biology and Environmental Sciences, Auburn University at Montgomery, Montgomery, AL, 36124, USA
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14
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Amshokova A, Tembotova F, Kononenko E. Assessment differentiation degree cryptic species of the genus Apodemus in the Northern Caucasus based on non-metric cranial characters. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213500004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A phenetic analysis of non-metric cranial traits of two genetically identified cryptic species of the genus Apodemus in different ecological conditions of the North Caucasus was carried out. The maximum distance obtained between cryptic species did not exceed the level of subspecies differences. The phenetic distance between A. uralensis and A. flavicollis, which inhabit symbiotopically and sympatrically in the Western Caucasus, is almost 2 times lower. The smaller value of phenetic differences is probably related to the habitat of both species in similar land-scapebiotopic and climatic conditions, which contributes to the development of phenotypic similarity. In general, the obtained results indicate weak morphological differentiation of the studied species according to the studied phenetic characters (cranial foramen), although according to the results of molecular genetic analysis of the cyt b gene site, the genetic distance between the studied taxa is 10% and corresponds to the level of interspecific differences. Based on the above, reliable diagnosis of the studied species in the Caucasus is possible only by molecular genetic methods.
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15
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Bennett AJ, Paskey AC, Ebinger A, Pfaff F, Priemer G, Höper D, Breithaupt A, Heuser E, Ulrich RG, Kuhn JH, Bishop-Lilly KA, Beer M, Goldberg TL. Relatives of rubella virus in diverse mammals. Nature 2020; 586:424-428. [PMID: 33029010 PMCID: PMC7572621 DOI: 10.1038/s41586-020-2812-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 07/17/2020] [Indexed: 12/17/2022]
Abstract
Since 1814, when rubella was first described, the origins of the disease and its causative agent, rubella virus (Matonaviridae: Rubivirus), have remained unclear1. Here we describe ruhugu virus and rustrela virus in Africa and Europe, respectively, which are, to our knowledge, the first known relatives of rubella virus. Ruhugu virus, which is the closest relative of rubella virus, was found in apparently healthy cyclops leaf-nosed bats (Hipposideros cyclops) in Uganda. Rustrela virus, which is an outgroup to the clade that comprises rubella and ruhugu viruses, was found in acutely encephalitic placental and marsupial animals at a zoo in Germany and in wild yellow-necked field mice (Apodemus flavicollis) at and near the zoo. Ruhugu and rustrela viruses share an identical genomic architecture with rubella virus2,3. The amino acid sequences of four putative B cell epitopes in the fusion (E1) protein of the rubella, ruhugu and rustrela viruses and two putative T cell epitopes in the capsid protein of the rubella and ruhugu viruses are moderately to highly conserved4-6. Modelling of E1 homotrimers in the post-fusion state predicts that ruhugu and rubella viruses have a similar capacity for fusion with the host-cell membrane5. Together, these findings show that some members of the family Matonaviridae can cross substantial barriers between host species and that rubella virus probably has a zoonotic origin. Our findings raise concerns about future zoonotic transmission of rubella-like viruses, but will facilitate comparative studies and animal models of rubella and congenital rubella syndrome.
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Affiliation(s)
- Andrew J Bennett
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Leidos, Reston, VA, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Arnt Ebinger
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Florian Pfaff
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Grit Priemer
- State Office for Agriculture, Food Safety and Fisheries, Rostock, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Angele Breithaupt
- Department of Experimental Animal Facilities and Biorisk Management, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Elisa Heuser
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Insel Riems, Greifswald-Insel Riems, Germany
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Frederick, MD, USA
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
| | - Tony L Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
- Global Health Institute, University of Wisconsin-Madison, Madison, WI, USA.
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16
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Martin Cerezo ML, Kucka M, Zub K, Chan YF, Bryk J. Population structure of Apodemus flavicollis and comparison to Apodemus sylvaticus in northern Poland based on RAD-seq. BMC Genomics 2020; 21:241. [PMID: 32183700 PMCID: PMC7079423 DOI: 10.1186/s12864-020-6603-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 02/21/2020] [Indexed: 02/08/2023] Open
Abstract
Background Mice of the genus Apodemus are one the most common mammals in the Palaearctic region. Despite their broad range and long history of ecological observations, there are no whole-genome data available for Apodemus, hindering our ability to further exploit the genus in evolutionary and ecological genomics context. Results Here we present results from the double-digest restriction site-associated DNA sequencing (ddRAD-seq) on 72 individuals of A. flavicollis and 10 A. sylvaticus from four populations, sampled across 500 km distance in northern Poland. Our data present clear genetic divergence of the two species, with average p-distance, based on 21377 common loci, of 1.51% and a mutation rate of 0.0011 - 0.0019 substitutions per site per million years. We provide a catalogue of 117 highly divergent loci that enable genetic differentiation of the two species in Poland and to a large degree of 20 unrelated samples from several European countries and Tunisia. We also show evidence of admixture between the three A. flavicollis populations but demonstrate that they have negligible average population structure, with largest pairwise FST<0.086. Conclusion Our study demonstrates the feasibility of ddRAD-seq in Apodemus and provides the first insights into the population genomics of the species.
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Affiliation(s)
- Maria Luisa Martin Cerezo
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.,AVIAN Behavioural Genomics and Physiology Group, IFM Biology, Department of Zoology, Linköping University, Linköping, Sweden
| | - Marek Kucka
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Karol Zub
- The Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | | | - Jarosław Bryk
- School of Applied Sciences, University of Huddersfield, Quennsgate, Huddersfield, UK.
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17
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Álvarez-Castañeda ST, Nájera-Cortazar LA. Do island populations differ in size and shape compared to mainland counterparts? J Mammal 2019. [DOI: 10.1093/jmammal/gyz193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
AbstractAdaptation and evolution of terrestrial vertebrates inhabiting islands have been the topic of many studies, particularly those seeking to identify trends or patterns in body size in mammals, albeit not necessarily in shape, in relation to mainland populations. The spiny pocket mouse, Chaetodipus spinatus, is distributed in the Baja California peninsula and its surrounding islands. Insular populations became isolated ~12,000 due to changes in sea level; these populations’ matrilinear (mitochondrial) DNA shows minor interpopulation variation. We tested the hypothesis that adaptation and evolution in these island populations involve variation in both skull size and skull shape (using geometric morphometrics) relative to mainland populations, rather than only in size as previously assumed. A total of 363 specimens from 15 insular and peninsular populations were used in analysis of the skull length and geometric morphometric analyses. Our findings revealed significant differences related to skull size among population. The skull shape analyses showed two significantly different morphotypes: one for all island specimens and one for all mainland samples. Our analyses support the hypothesis that insular populations may not only vary in size relative to mainland populations, but may also show variations in shape, regardless of differing conditions across islands.
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Affiliation(s)
- Sergio Ticul Álvarez-Castañeda
- Centro de Investigaciones Biológicas del Noroeste, S. C., Instituto Politécnico Nacional 195, Baja California Sur, México
| | - Laura A Nájera-Cortazar
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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18
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Morphological and genetic characterization of Mount Kenya brush-furred rats (Lophuromys Peters 1874); relevance to taxonomy and ecology. MAMMAL RES 2019. [DOI: 10.1007/s13364-019-00470-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Okulova NM, Bogdanov AS, Baskevich MI, Orlov VN, Popova YV, Antonets NV, Lavrenchenko LA. Skull Sizes and Proportions in Western Palearctic Wood Mice (Sylvaemus, Muridae, Rodentia) from Eastern Europe: 2. Intraspecific Variability. BIOL BULL+ 2019. [DOI: 10.1134/s1062359019080119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Comparative phylogeography of two hemipteran species (Geisha distinctissima and Megacopta cribraria) in the Zhoushan Archipelago of China reveals contrasting genetic structures despite concordant historical demographies. Heredity (Edinb) 2019; 124:207-222. [PMID: 31501533 DOI: 10.1038/s41437-019-0265-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 11/08/2022] Open
Abstract
Continental islands are useful models to explore the roles of shared historical factors in the evolution of sympatric species. However, China's largest continental group of islands, the Zhoushan Archipelago, was neglected by most studies focusing on biodiversity hotspots. Here we investigated the phylogeographic patterns and the historical demography of two sympatric hemipteran insects (Geisha distinctissima and Megacopta cribraria), which shared historical factors in the Zhoushan Archipelago. The results based on mtDNA (COX1, COX2-COX3, and CYTB) and nDNA (28S and ITS2) showed that G. distinctissima diverged into three genetic lineages (L1-L3) ~8.9-13.7 thousand years ago (kya), which coincided with the period of island isolation. However, the three lineages exhibit no clear phylogeographic patterns for frequent asymmetrical gene flow (starting around 5 kya) from the mainland and adjacent islands to other distant islands due to subsequent human activities. In contrast, only one genetic lineage exists for M. cribraria, without any phylogeographic structures. The ancestral range in the mainland as well as in neighboring islands, together with the frequent asymmetrical gene flow of M. cribraria (from the mainland and neighboring islands to more distant islands) within the last 5000 years suggests that human activities may have lead to the colonization of this species in the Zhoushan Archipelago. The contrasting genetic structures indicate shared historical factors but independent evolutionary histories for the two sympatric species in the Zhoushan Archipelago. Our demographic analysis clearly showed that both species underwent population expansion before 5 kya during the post-LGM (Last Glacial Maximum), which indicates that the two species shared concordant historical demographies. This result suggests that the population size of the two species was affected similarly by the climatic oscillations of post-LGM in Eastern China. Together, our findings reveal that the two insect species in the Zhoushan Archipelago exhibit contrasting genetic structures despite concordant historical demographies, which provides an important framework for the exploration of the evolution patterns of sympatric species in the continental island.
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21
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Michelitsch A, Wernike K, Klaus C, Dobler G, Beer M. Exploring the Reservoir Hosts of Tick-Borne Encephalitis Virus. Viruses 2019; 11:E669. [PMID: 31336624 PMCID: PMC6669706 DOI: 10.3390/v11070669] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/17/2019] [Accepted: 07/19/2019] [Indexed: 12/20/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is an important arbovirus, which is found across large parts of Eurasia and is considered to be a major health risk for humans. Like any other arbovirus, TBEV relies on complex interactions between vectors, reservoir hosts, and the environment for successful virus circulation. Hard ticks are the vectors for TBEV, transmitting the virus to a variety of animals. The importance of these animals in the lifecycle of TBEV is still up for debate. Large woodland animals seem to have a positive influence on virus circulation by providing a food source for adult ticks; birds are suspected to play a role in virus distribution. Bank voles and yellow-necked mice are often referred to as classical virus reservoirs, but this statement lacks strong evidence supporting their highlighted role. Other small mammals (e.g., insectivores) may also play a crucial role in virus transmission, not to mention the absence of any suspected reservoir host for non-European endemic regions. Theories highlighting the importance of the co-feeding transmission route go as far as naming ticks themselves as the true reservoir for TBEV, and mammalian hosts as a mere bridge for transmission. A deeper insight into the virus reservoir could lead to a better understanding of the development of endemic regions. The spatial distribution of TBEV is constricted to certain areas, forming natural foci that can be restricted to sizes of merely 500 square meters. The limiting factors for their occurrence are largely unknown, but a possible influence of reservoir hosts on the distribution pattern of TBE is discussed. This review aims to give an overview of the multiple factors influencing the TBEV transmission cycle, focusing on the role of virus reservoirs, and highlights the questions that are waiting to be further explored.
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Affiliation(s)
- Anna Michelitsch
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Kerstin Wernike
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany
| | - Christine Klaus
- Institute for Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Naumburger Str. 96a, 07743 Jena, Germany
| | - Gerhard Dobler
- Bundeswehr Institute of Microbiology, German Center of Infection Research (DZIF) partner site Munich, Neuherbergstraße 11, 80937 München, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Südufer 10, 17493 Greifswald-Insel Riems, Germany.
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22
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Czarnomska SD, Niedziałkowska M, Borowik T, Jędrzejewska B. Winter temperature correlates with mtDNA genetic structure of yellow-necked mouse population in NE Poland. PLoS One 2019; 14:e0216361. [PMID: 31067251 PMCID: PMC6505929 DOI: 10.1371/journal.pone.0216361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/18/2019] [Indexed: 11/19/2022] Open
Abstract
We analysed a fragment (247 bp) of cytochrome b of mitochondrial DNA sequenced using 353 samples of yellow-necked mice Apodemus flavicollis trapped in seven forests and along three woodlot transects in north-eastern Poland. Our aims were to identify the phylogeographic pattern and mtDNA structure of the population and to evaluate the role of environmental conditions in shaping the spatial pattern of mtDNA diversity. We found out that three European haplogroups occurred sympatrically in north-eastern Poland. Inferences based on mtDNA haplotype distribution and frequency defined five subpopulations. The mtDNA-based structure of mice significantly correlated with winter temperature: frequency of Haplogroup 1 was positively, and that of Haplogroup 3 negatively correlated to mean temperature of January in the year of trapping. Synthesis of the published pan-European data on the species phylogeography also showed that the possibly 'thermophilous' Haplogroup 1 has the westernmost occurrence, whereas the more 'cold-resistant' Haplogroup 3 occurs much further to north-east than the other haplogroups. The observed patter may be a byproduct of the tight coevolution with nuclear genes, as we have earlier found that - in mice population in NE Poland - the spatial pattern of nuclear DNA was best explained by January temperature. Alternatively, the observed association of mitochondrial genetic variation with temperature is possible to be adaptive as cytochrome b is involved in the process of ATP production via oxidative phosphorylation.
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Affiliation(s)
| | | | - Tomasz Borowik
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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23
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Michaux JR, Hürner H, Krystufek B, Sarà M, Ribas A, Ruch T, Vekhnik V, Renaud S. Genetic structure of a European forest species, the edible dormouse ( Glis glis): a consequence of past anthropogenic forest fragmentation? Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- J R Michaux
- Conservation Genetics Laboratory, Institut de Botanique, Chemin de la Vallée, Liège, Belgium
- CIRAD/INRA UMR117 ASTRE, Campus International de Baillarguet, Montpellier Cedex 5, France
| | - H Hürner
- Conservation Genetics Laboratory, Institut de Botanique, Chemin de la Vallée, Liège, Belgium
| | - B Krystufek
- Slovenian Museum of Natural History, Presernova, Ljubljana, Slovenia
| | - M Sarà
- Dipartimento STEBICEF, Via Archirafi, Palermo, Italy
| | - A Ribas
- Museu de Granollers-Ciències Naturals C/Francesc Macià, Granollers, Spain
| | - T Ruch
- Institute for Cell Biology and Neuroscience, Johann Wolfgang-Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
| | - V Vekhnik
- Zhiguli State Nature Reserve, Bakhilova Polyana Village, Samara Oblast, Russia
| | - S Renaud
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, Université Lyon, CNRS, Villeurbanne, France
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24
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Microsatellite-based genetic diversity of Dermacentor reticulatus in Europe. INFECTION GENETICS AND EVOLUTION 2018; 66:200-209. [DOI: 10.1016/j.meegid.2018.09.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/27/2018] [Accepted: 09/30/2018] [Indexed: 01/28/2023]
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25
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Martinů J, Hypša V, Štefka J. Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice. Ecol Evol 2018; 8:10008-10022. [PMID: 30397443 PMCID: PMC6206178 DOI: 10.1002/ece3.4424] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 07/03/2018] [Accepted: 07/09/2018] [Indexed: 12/29/2022] Open
Abstract
A degree of host specificity, manifested by the processes of host-parasite cospeciations and host switches, is assumed to be a major determinant of parasites' evolution. To understand these patterns and formulate appropriate ecological hypotheses, we need better insight into the coevolutionary processes at the intraspecific level, including the maintenance of genetic diversity and population structure of parasites and their hosts. Here, we address these questions by analyzing large-scale molecular data on the louse Polyplax serrata and its hosts, mice of the genus Apodemus, across a broad range of European localities. Using mitochondrial DNA sequences and microsatellite data, we demonstrate the general genetic correspondence of the Apodemus/Polyplax system to the scenario of the postglacial recolonization of Europe, but we also show several striking discrepancies. Among the most interesting are the evolution of different degrees of host specificity in closely related louse lineages in sympatry, or decoupled population structures of the host and parasites in central Europe. We also find strong support for the prediction that parasites with narrower host specificity possess a lower level of genetic diversity and a deeper pattern of interpopulation structure as a result of limited dispersal and smaller effective population size.
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Affiliation(s)
- Jana Martinů
- Biology Centre CASInstitute of ParasitologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Václav Hypša
- Biology Centre CASInstitute of ParasitologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Jan Štefka
- Biology Centre CASInstitute of ParasitologyČeské BudějoviceCzech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
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26
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Czarnomska SD, Niedziałkowska M, Borowik T, Jędrzejewska B. Regional and local patterns of genetic variation and structure in yellow-necked mice - the roles of geographic distance, population abundance, and winter severity. Ecol Evol 2018; 8:8171-8186. [PMID: 30250693 PMCID: PMC6145024 DOI: 10.1002/ece3.4291] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/01/2018] [Accepted: 05/29/2018] [Indexed: 02/03/2023] Open
Abstract
The goal of this study, conducted in seven large woodlands and three areas with small woodlots in northeastern Poland in 2004-2008, was to infer genetic structure in yellow-necked mouse Apodemus flavicollis population and to evaluate the roles of environmental and population ecology variables in shaping the spatial pattern of genetic variation using 768 samples genotyped at 13 microsatellite loci. Genetic variation was very high in all studied regions. The primal genetic subdivision was observed between the northern and the southern parts of the study area, which harbored two major clusters and the intermediate area of highly admixed individuals. The probability of assignment of individual mice to the northern cluster increased significantly with lower temperatures of January and July and declined in regions with higher proportion of deciduous and mixed forests. Despite the detected structure, genetic differentiation among regions was very low. Fine-scale structure was shaped by the population density, whereas higher level structure was mainly shaped by geographic distance. Genetic similarity indices were highly influenced by mouse abundance (which positively correlated with the share of deciduous forests in the studied regions) and exhibited the greatest change between 0 and 1 km in the forests, 0 and 5 km in small woodlots. Isolation by distance pattern, calculated among regions, was highly significant but such relationship between genetic and geographic distance was much weaker, and held the linearity at very fine scale (~1.5 km), when analyses were conducted at individual level.
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Affiliation(s)
- Sylwia D. Czarnomska
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Present address:
Institute of Biochemistry and Biophysics of the Polish Academy of Sciences (IBB PAS)WarszawaPoland
| | | | - Tomasz Borowik
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
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27
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Boratyński JS, Iwińska K, Bogdanowicz W. Body temperature variation in free-living and food-deprived yellow-necked mice sustains an adaptive framework for endothermic thermoregulation. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0392-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Yalkovskaya LE, Sibiryakov PA, Zykov SV. Genetic Variability in the Yellow-Necked Field Mouse (Sylvaemus flavicollis Melch., 1834, Muridae, Rodentia) at the Eastern Border of the Range. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Balasanyan V, Yavruyan E, Somerová B, Abramjan A, Landová E, Munclinger P, Frynta D. High Diversity of mtDNA Haplotypes Confirms Syntopic Occurrence of Two Field Mouse Species Apodemus uralensis and A. witherbyi (Muridae: Apodemus) in Armenia. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Mysteries of host switching: Diversification and host specificity in rodent-coccidia associations. Mol Phylogenet Evol 2018; 127:179-189. [PMID: 29753710 DOI: 10.1016/j.ympev.2018.05.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 05/09/2018] [Accepted: 05/09/2018] [Indexed: 11/21/2022]
Abstract
Recent studies show that host switching is much more frequent than originally believed and constitutes an important driver in evolution of host-parasite associations. However, its frequency and ecological mechanisms at the population level have been rarely investigated. We address this issue by analyzing phylogeny and population genetics of an extensive sample, from a broad geographic area, for commonly occurring parasites of the genus Eimeria within the abundant rodent genera Apodemus, Microtus and Myodes, using two molecular markers. At the most basal level, we demonstrate polyphyletic arrangement, i.e. multiple origin, of the rodent-specific clusters within the Eimeria phylogeny, and strong genetic/phylogenetic structure within these lineages determined at least partially by specificities to different host groups. However, a novel and the most important observation is a repeated occurrence of host switches among closely related genetic lineages which may become rapidly fixed. Within the studied model, this phenomenon applies particularly to the switches between the eimerians from Apodemus flavicollis/Apodemus sylvaticus and Apodemus agrarius groups. We show that genetic differentiation and isolation between A. flavicollis/A. sylvaticus and A. agrarius faunas is a secondary recent event and does not reflect host-parasite coevolutionary history. Rather, it provides an example of rapid ecology-based differentiation in the parasite population.
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31
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Sozio G, Curini V, Pascucci I, Cammà C, Di Domenico M. A new fast real-time PCR method for the identification of three sibling Apodemus species ( A. sylvaticus, A. flavicollis, and A. alpicola) in Italy. Ecol Evol 2018; 8:4807-4814. [PMID: 29876059 PMCID: PMC5980278 DOI: 10.1002/ece3.4026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 01/31/2018] [Accepted: 02/26/2018] [Indexed: 11/23/2022] Open
Abstract
The identification of field mice Apodemus flavicollis, Apodemus sylvaticus, and Apodemus alpicola represents a challenge for field scientists due to their highly overlapping morphological traits and habitats. Here, we propose a new fast real-time PCR method to discriminate the three species by species-specific TaqMan assays. Primers and probes were designed based on the alignment of 54 cyt-b partial sequences from 25 different European countries retrieved from GenBank. TaqMan assays were then tested on 133 samples from three different areas of Italy. Real-time PCR analysis showed 92 samples classified as A. flavicollis, 13 as A. sylvaticus, and 28 as A. alpicola. We did not observe any double amplification and DNA sequencing confirmed species assignment obtained by the TaqMan assays. The method is implementable on different matrices (ear tissues, tail, and blood). It can be used on dead specimens or on alive animals with minimally invasive sampling, and given the high sensitivity, the assay may be also suitable for degraded or low-DNA samples. The method proved to work well to discriminate between the species analyzed. Furthermore, it gives clear results (amplified or not) and it does not require any postamplification handling of PCR product, reducing the time needed for the analyses and the risk of carryover contamination. It therefore represents a valuable tool for field ecologists, conservationists, and epidemiologists.
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Affiliation(s)
- Giulia Sozio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Valentina Curini
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Ilaria Pascucci
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale”TeramoItaly
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32
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Bego F, Saçdanaku E, Pacifici M, Rondinini C. Small terrestrial mammals of Albania: distribution and diversity (Mammalia, Eulipotyphla, Rodentia). Zookeys 2018:127-163. [PMID: 29670434 PMCID: PMC5904422 DOI: 10.3897/zookeys.742.22364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 02/14/2018] [Indexed: 11/12/2022] Open
Abstract
In this paper new records are reported for 23 species of small terrestrial mammals (STM) of Albania collected during the field work campaigns organised in the framework of the project “Strengthening capacity in National Nature Protection – preparation for Natura 2000 network” (NaturAL) in Albania during the summer and autumn of 2016 and 2017 Data on small mammals were primarily collected through Sherman live-trapping campaigns in six high priority protected areas of Albania: Korab-Koritnik, Bredhi i Hotovës, Tomorri, Llogara-Karaburun, Divjakë-Karavasta, Liqeni i Shkodrës (Skadar lake), Lëpushë-Vermosh. Other data were obtained by analysis of owl pellets or by direct observation of individuals (dead or alive) in the field. For 21 species Erinaceusroumanicus, Neomysanomalus, Crocidurasuaveolens, Crociduraleucodon, Suncusetruscus, Talpastankovici/caeca, Myocastorcoypus, Sciurusvulgaris, Glisglis, Dryomysnitedula, Muscardinusavellanarius, Microtuslevis/arvalis, Microtussubterraneus, Microtusthomasi, Microtusfelteni, Myodesglareolus, Apodemussylvaticus, Apodemusflavicollis, Apodemusepimelas, Musmusculus, and Musmacedonicus additional records are provide and their distributions reviewed, while the presence of two new species of shrews (Sorexaraneus and Sorexminutus) for Albania is reported for the first time. A comprehensive review of the published and unpublished distribution records of STM species of the country is made, together with an updated checklist and distribution maps of the species.
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Affiliation(s)
- Ferdinand Bego
- Department of Biology, Faculty of Natural Sciences, University of Tirana, Albania
| | - Enerit Saçdanaku
- Research Centre for Flora and Fauna, Faculty of Natural Sciences, University of Tirana, Albania
| | - Michela Pacifici
- Global Mammal Assessment programme, Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Italy
| | - Carlo Rondinini
- Global Mammal Assessment programme, Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Italy
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33
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Urgoiti J, Muñoz A, Espelta JM, Bonal R. Distribution and space use of seed-dispersing rodents in central Pyrenees: implications for genetic diversity, conservation and plant recruitment. Integr Zool 2018; 13:307-318. [PMID: 29316239 DOI: 10.1111/1749-4877.12301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The function and conservation of many forest ecosystems depend on the distribution and diversity of the community of rodents that consume and disperse seeds. The habitat preferences and interactions are especially relevant in alpine systems where such granivorous rodents reach the southernmost limit of their distribution and are especially sensitive to global warming. We analyzed the community of granivorous rodents in the Pyrenees, one of the southernmost mountain ranges of Europe. Rodent species were identified by DNA with particular attention to the Apodemus species, which are prominent seed-dispersing rodents in Europe. We confirmed for the first time the presence of the yellow-necked mouse, Apodemus flavicollis, in central Pyrenees, a typical Eurosiberian species that reaches its southernmost distribution limit in this area. We also found the wood mouse, Apodemus sylvaticus, a related species more tolerant to Mediterranean environments. Both rodents were spatially segregated by altitude. A. sylvaticus was rare at high altitudes, which might cause the genetic differentiation between populations of the different valleys reported here. We also found other seed consumers like dormice, Elyomis quercinus, and voles, Myodes glareolus, with marked habitat preferences. We suggest that population isolation among valleys may increase the genetic diversity of rodents, like A. sylvaticus. We also highlight the potential threat that global warming may represent for species linked to high-altitude refuges at the southern edge of its distribution, like Apodemus flavicollis. Finally, we discuss how this threat may have a dimension in the conservation of alpine forests dispersed by these rodent populations.
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Affiliation(s)
- Jon Urgoiti
- CREAF, Cerdanyola del Vallés, Catalonia, Spain
| | - Alberto Muñoz
- Department of Didactics of Experimental Sciences, Faculty of Education, University Complutense of Madrid, Madrid, Spain
| | | | - Raúl Bonal
- Forest Research Group, INDEHESA, University of Extremadura, Plasencia, Spain.,DITEG Research Group, University of Castilla-La Mancha, Toledo, Spain.,Research group of Genetic and Cultural Biodiversity, Research centre for Cinegetic Resources (CSIC-UCLM-JCCM), Ciudad Real, Spain
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34
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Lebedev VS, Bannikova AA, Lu L, Snytnikov EA, Adiya Y, Solovyeva EN, Abramov AV, Surov AV, Shenbrot GI. Phylogeographical study reveals high genetic diversity in a widespread desert rodent, Dipus sagitta (Dipodidae: Rodentia). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/blx090] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Vladimir S Lebedev
- Zoological Museum, Moscow State University, B.Nikitskaya, Moscow, Russia
| | - Anna A Bannikova
- Lomonosov Moscow State University, Vorobievy Gory, Moscow, Russia
| | - Liang Lu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Centre of Disease Control and Prevention, Beijing, China
| | | | - Yansanjav Adiya
- Institute of General and Experimental Biology of Mongolian Academy of Science, Ulaanbaatar, Mongolia
| | | | - Alexei V Abramov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya nab., St. Petersburg, Russia
| | - Alexei V Surov
- Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Leninskii pr., Moscow, Russia
| | - Georgy I Shenbrot
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
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35
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André A, Millien V, Galan M, Ribas A, Michaux JR. Effects of parasite and historic driven selection on the diversity and structure of a MHC-II gene in a small mammal species (Peromyscus leucopus) undergoing range expansion. Evol Ecol 2017. [DOI: 10.1007/s10682-017-9898-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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36
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Knitlová M, Horáček I. Late Pleistocene-Holocene paleobiogeography of the genus Apodemus in Central Europe. PLoS One 2017; 12:e0173668. [PMID: 28282422 PMCID: PMC5345881 DOI: 10.1371/journal.pone.0173668] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/25/2017] [Indexed: 11/20/2022] Open
Abstract
Wood mice of the genus Apodemus are an essential component of small mammal communities throughout Europe. Molecular data suggest the postglacial colonization of current ranges from south European glacial refugia, different in particular species. Yet, details on the course of colonization and Holocene history of particular species are not available, partly because of a lack of reliable criteria for species identification in the fossil record. Using a sample of extant species, we analyzed variation patterns and between-species overlaps for a large set of metric and non-metric dental variables and established the criteria enabling the reliable species identification of fragmentary fossil material. The corresponding biometrical analyses were undertaken with fossil material of the genus (2528 items, 747 MNI) from 22 continuous sedimentary series in the Czech Republic and Slovakia, from LGM to Recent. In Central Europe, the genus is invariantly absent in LGM assemblages but regularly appears during the Late Vistulian. All the earliest records belong to A. flavicollis, the species clearly predominating in the fossil record until the Late Holocene. A. uralensis accompanied it in all regions until the late Boreal when disappeared from the fossil record (except for Pannonia). A few items identified as A. sylvaticus had already appeared in the early Holocene assemblages, first in the western part of the region, yet the regular appearance of the species is mostly in the post-Neolithic age. A. agrarius appeared sparsely from the Boreal with a maximum frequency during the post-Neolithic period. The results conform well to the picture suggested by molecular phylogeography but demonstrate considerable differences among particular species in dynamic of the range colonization. Further details concerning Holocene paleobiogeography of individual species in the medium latitude Europe are discussed.
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Affiliation(s)
- Markéta Knitlová
- Department of Zoology, Charles University, Viničná 7, Praha 2, Czech Republic
| | - Ivan Horáček
- Department of Zoology, Charles University, Viničná 7, Praha 2, Czech Republic
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37
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Demanche C, Deville M, Michaux J, Barriel V, Pinçon C, Aliouat-Denis CM, Pottier M, Noël C, Viscogliosi E, Aliouat EM, Dei-Cas E, Morand S, Guillot J. Correction: What Do Pneumocystis Organisms Tell Us about the Phylogeography of Their Hosts? The Case of the Woodmouse Apodemus sylvaticus in Continental Europe and Western Mediterranean Islands. PLoS One 2017; 12:e0171282. [PMID: 28182721 PMCID: PMC5300120 DOI: 10.1371/journal.pone.0171282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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38
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Herman JS, Jóhannesdóttir F, Jones EP, McDevitt AD, Michaux JR, White TA, Wójcik JM, Searle JB. Post-glacial colonization of Europe by the wood mouse,Apodemus sylvaticus: evidence of a northern refugium and dispersal with humans. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12882] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Jeremy S. Herman
- National Museums of Scotland; Chambers Street Edinburgh EH1 1JF UK
| | - Fríđa Jóhannesdóttir
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
| | | | - Allan D. McDevitt
- Ecosystems and Environment Research Centre; School of Environment and Life Sciences; University of Salford; Salford M5 4WT UK
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Johan R. Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège; 4000 Liège Belgique
| | - Thomas A. White
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
- Lancaster Environment Centre; Lancaster University; Lancaster LA1 4YQ UK
| | - Jan M. Wójcik
- Mammal Research Institute; Polish Academy of Sciences; 17-230 Białowieża Poland
| | - Jeremy B. Searle
- Department of Ecology and Evolutionary Biology; Cornell University; Corson Hall Ithaca NY 14853-2701 USA
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39
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Ancillotto L, Mori E, Sozio G, Solano E, Bertolino S, Russo D. A novel approach to field identification of cryptic
Apodemus
wood mice: calls differ more than morphology. Mamm Rev 2016. [DOI: 10.1111/mam.12076] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Leonardo Ancillotto
- Wildlife Research Unit Laboratorio di Ecologia Applicata Sezione di Biologia e Protezione dei Sistemi Agrari e Forestali Dipartimento di Agraria Università degli Studi di Napoli Federico II via Università 100, Portici Napoli 80055 Italy
| | - Emiliano Mori
- Dipartimento di Scienze Agrarie, Forestali e Alimentari Università di Torino Largo Paolo Braccini 2 Grugliasco Torino 10095 Italy
| | - Giulia Sozio
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise “G. Caporale” Campo Boario Teramo 64100 Italy
| | - Emanuela Solano
- Department of Biology and Biotechnology “Charles Darwin” “La Sapienza” University of Rome Via Borelli 50 Rome 00161 Italy
| | - Sandro Bertolino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari Università di Torino Largo Paolo Braccini 2 Grugliasco Torino 10095 Italy
| | - Danilo Russo
- Wildlife Research Unit Laboratorio di Ecologia Applicata Sezione di Biologia e Protezione dei Sistemi Agrari e Forestali Dipartimento di Agraria Università degli Studi di Napoli Federico II via Università 100, Portici Napoli 80055 Italy
- School of Biological Sciences University of Bristol 24 Tyndall Ave Bristol BS8 1TH UK
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40
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Wasimuddin, Bryja J, Ribas A, Baird SJE, Piálek J, Goüy de Bellocq J. Testing parasite 'intimacy': the whipworm Trichuris muris in the European house mouse hybrid zone. Ecol Evol 2016; 6:2688-701. [PMID: 27064973 PMCID: PMC4798833 DOI: 10.1002/ece3.2022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 01/25/2016] [Accepted: 01/27/2016] [Indexed: 01/01/2023] Open
Abstract
Host‐parasite interaction studies across hybrid zones often focus on host genetic variation, treating parasites as homogeneous. ‘Intimately’ associated hosts and parasites might be expected to show similar patterns of genetic structure. In the literature, factors such as no intermediate host and no free‐living stage have been proposed as ‘intimacy’ factors likely constraining parasites to closely follow the evolutionary history of their hosts. To test whether the whipworm, Trichuris muris, is intimately associated with its house mouse host, we studied its population genetics across the European house mouse hybrid zone (HMHZ) which has a strong central barrier to gene flow between mouse taxa. T. muris has a direct life cycle and nonmobile free stage: if these traits constrain the parasite to an intimate association with its host we expect a geographic break in the parasite genetic structure across the HMHZ. We genotyped 205 worms from 56 localities across the HMHZ and additionally T. muris collected from sympatric woodmice (Apodemus spp.) and allopatric murine species, using mt‐COX1, ITS1‐5.8S‐ITS2 rDNA and 10 microsatellites. We show four haplogroups of mt‐COX1 and three clear ITS1‐5.8S‐ITS2 clades in the HMHZ suggesting a complex demographic/phylogeographic history. Microsatellites show strong structure between groups of localities. However, no marker type shows a break across the HMHZ. Whipworms from Apodemus in the HMHZ cluster, and share mitochondrial haplotypes, with those from house mice. We conclude Trichuris should not be regarded as an ‘intimate’ parasite of the house mouse: while its life history might suggest intimacy, passage through alternate hosts is sufficiently common to erase signal of genetic structure associated with any particular host taxon.
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Affiliation(s)
- Wasimuddin
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic; Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Josef Bryja
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic; Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - Alexis Ribas
- Biodiversity Research Group Faculty of Science Udon Thani Rajabhat University Udon Thani Thailand
| | - Stuart J E Baird
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
| | - Jaroslav Piálek
- Institute of Vertebrate Biology of the Czech Academy of Sciences Brno Czech Republic
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41
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Missoup AD, Nicolas V, Eiseb S, Chung EK, Denys C. Phylogenetic position of the endemic Mount Oku rat,Lamottemys okuensis(Rodentia: Muridae), based on molecular and morphological data. Zool J Linn Soc 2015. [DOI: 10.1111/zoj.12361] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Alain Didier Missoup
- Department of Animal Biology Organisms; Faculty of Science; the University of Douala; PO Box: 24157 Douala Cameroon
- Institut de Systématique, Evolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Violaine Nicolas
- Institut de Systématique, Evolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Seth Eiseb
- University of Namibia; Private Bag 13301 Windhoek Namibia
| | | | - Christiane Denys
- Institut de Systématique, Evolution, Biodiversité, ISYEB UMR 7205 - CNRS, MNHN, UPMC, EPHE, Museum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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Mattucci F, Oliveira R, Lyons LA, Alves PC, Randi E. European wildcat populations are subdivided into five main biogeographic groups: consequences of Pleistocene climate changes or recent anthropogenic fragmentation? Ecol Evol 2015; 6:3-22. [PMID: 26811770 PMCID: PMC4716505 DOI: 10.1002/ece3.1815] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 10/14/2015] [Accepted: 10/14/2015] [Indexed: 02/03/2023] Open
Abstract
Extant populations of the European wildcat are fragmented across the continent, the likely consequence of recent extirpations due to habitat loss and over‐hunting. However, their underlying phylogeographic history has never been reconstructed. For testing the hypothesis that the European wildcat survived the Ice Age fragmented in Mediterranean refuges, we assayed the genetic variation at 31 microsatellites in 668 presumptive European wildcats sampled in 15 European countries. Moreover, to evaluate the extent of subspecies/population divergence and identify eventual wild × domestic cat hybrids, we genotyped 26 African wildcats from Sardinia and North Africa and 294 random‐bred domestic cats. Results of multivariate analyses and Bayesian clustering confirmed that the European wild and the domestic cats (plus the African wildcats) belong to two well‐differentiated clusters (average ФST = 0.159, rst = 0.392, P > 0.001; Analysis of molecular variance [AMOVA]). We identified from c. 5% to 10% cryptic hybrids in southern and central European populations. In contrast, wild‐living cats in Hungary and Scotland showed deep signatures of genetic admixture and introgression with domestic cats. The European wildcats are subdivided into five main genetic clusters (average ФST = 0.103, rst = 0.143, P > 0.001; AMOVA) corresponding to five biogeographic groups, respectively, distributed in the Iberian Peninsula, central Europe, central Germany, Italian Peninsula and the island of Sicily, and in north‐eastern Italy and northern Balkan regions (Dinaric Alps). Approximate Bayesian Computation simulations supported late Pleistocene–early Holocene population splittings (from c. 60 k to 10 k years ago), contemporary to the last Ice Age climatic changes. These results provide evidences for wildcat Mediterranean refuges in southwestern Europe, but the evolution history of eastern wildcat populations remains to be clarified. Historical genetic subdivisions suggest conservation strategies aimed at enhancing gene flow through the restoration of ecological corridors within each biogeographic units. Concomitantly, the risk of hybridization with free‐ranging domestic cats along corridor edges should be carefully monitored.
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Affiliation(s)
- Federica Mattucci
- Laboratorio di Genetica Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) 40064 Ozzano dell'Emilia Bologna Italy
| | - Rita Oliveira
- InBio - Laboratório Associado Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) Universidade do Porto Campus de Vairão 4485-661 Vairão Portugal; Departamento de Biologia Faculdade de Ciências da Universidade do Porto 4099-002 Porto Portugal
| | - Leslie A Lyons
- Department of Veterinary Medicine & Surgery College of Veterinary Medicine University of Missouri-Columbia Columbia 65211 Missouri USA
| | - Paulo C Alves
- InBio - Laboratório Associado Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) Universidade do Porto Campus de Vairão 4485-661 Vairão Portugal; Departamento de Biologia Faculdade de Ciências da Universidade do Porto 4099-002 Porto Portugal; Wildlife Biology Program Department of Ecosystem and Conservation Sciences University of Montana Missoula 59812 Montana USA
| | - Ettore Randi
- Laboratorio di Genetica Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA) 40064 Ozzano dell'Emilia BolognaItaly; Department 18/Section of Environmental Engineering Aalborg University 9000 Aalborg Denmark
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Lalis A, Leblois R, Liefried S, Ouarour A, Reddy Beeravolu C, Michaux J, Hamani A, Denys C, Nicolas V. New molecular data favour an anthropogenic introduction of the wood mouse (Apodemus sylvaticus
) in North Africa. J ZOOL SYST EVOL RES 2015. [DOI: 10.1111/jzs.12111] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Aude Lalis
- Institut de Systématique, Evolution; Biodiversité ISYEB UMR 7205 - CNRS MNHN UMPC EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | | | - Sohaib Liefried
- Laboratoire de Biologie et Santé; Faculté des Sciences; Université Abdelmalek Essaâdi; Tétouan Maroc
| | - Ali Ouarour
- Laboratoire de Biologie et Santé; Faculté des Sciences; Université Abdelmalek Essaâdi; Tétouan Maroc
| | | | - Johan Michaux
- Unité de génétique de la conservation; Institut de Botanique; Université de Liège (Sart Tilman); Liège Belgique
| | - Adel Hamani
- Laboratoire d'Ornithologie; Département de Zoologie; ENSA El Harrach; Alger Algeria
| | - Christiane Denys
- Institut de Systématique, Evolution; Biodiversité ISYEB UMR 7205 - CNRS MNHN UMPC EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
| | - Violaine Nicolas
- Institut de Systématique, Evolution; Biodiversité ISYEB UMR 7205 - CNRS MNHN UMPC EPHE; Muséum National d'Histoire Naturelle; Sorbonne Universités; Paris France
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Phylogenetic Relationships of Apodemus Kaup, 1829 (Rodentia: Muridae) Species in the Eastern Mediterranean Inferred from Mitochondrial DNA, with Emphasis on Iranian Species. J MAMM EVOL 2015. [DOI: 10.1007/s10914-015-9294-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Demanche C, Deville M, Michaux J, Barriel V, Pinçon C, Aliouat-Denis CM, Pottier M, Noël C, Viscogliosi E, Aliouat EM, Dei-Cas E, Morand S, Guillot J. What do Pneumocystis organisms tell us about the phylogeography of their hosts? The case of the woodmouse Apodemus sylvaticus in continental Europe and western Mediterranean islands. PLoS One 2015; 10:e0120839. [PMID: 25830289 PMCID: PMC4382281 DOI: 10.1371/journal.pone.0120839] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 02/11/2015] [Indexed: 12/02/2022] Open
Abstract
Pneumocystis fungi represent a highly diversified biological group with numerous species, which display a strong host-specificity suggesting a long co-speciation process. In the present study, the presence and genetic diversity of Pneumocystis organisms was investigated in 203 lung samples from woodmice (Apodemus sylvaticus) collected on western continental Europe and Mediterranean islands. The presence of Pneumocystis DNA was assessed by nested PCR at both large and small mitochondrial subunit (mtLSU and mtSSU) rRNA loci. Direct sequencing of nested PCR products demonstrated a very high variability among woodmouse-derived Pneumocystis organisms with a total number of 30 distinct combined mtLSU and mtSSU sequence types. However, the genetic divergence among these sequence types was very low (up to 3.87%) and the presence of several Pneumocystis species within Apodemus sylvaticus was considered unlikely. The analysis of the genetic structure of woodmouse-derived Pneumocystis revealed two distinct groups. The first one comprised Pneumocystis from woodmice collected in continental Spain, France and Balearic islands. The second one included Pneumocystis from woodmice collected in continental Italy, Corsica and Sicily. These two genetic groups were in accordance with the two lineages currently described within the host species Apodemus sylvaticus. Pneumocystis organisms are emerging as powerful tools for phylogeographic studies in mammals.
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Affiliation(s)
- Christine Demanche
- Laboratoire de Parasitologie (EA4547), Faculté de Pharmacie, Université de Lille, Lille, France; Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Inserm U1019, UMR CNRS 8204, Université de Lille, BioPôle d'Alfort, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France
| | - Manjula Deville
- ENVA, UPEC, Research group Dynamyc, Ecole Nationale Vétérinaire d'Alfort, 94704, Maisons-Alfort Cedex, France
| | - Johan Michaux
- CBGP (Centre de Biologie et de Gestion des Populations), UMR INRA/IRD/Cirad/Montpellier SupAgro, Campus international de Baillarguet, CS 30016, 34988, Montferrier-sur-Lez cedex, France; Institut de Botanique (B22), University of Liège, 4000, Liège, (Sart Tilman), Belgium
| | - Véronique Barriel
- Muséum national d'histoire naturelle, CR2P-UMR 7207 CNRS, MNHN, Univ Paris06, Paris, France
| | - Claire Pinçon
- Departement of Biostatistics (EA2694), Université de Lille, Lille, France
| | - Cécile Marie Aliouat-Denis
- Laboratoire de Parasitologie (EA4547), Faculté de Pharmacie, Université de Lille, Lille, France; Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Inserm U1019, UMR CNRS 8204, Université de Lille, BioPôle d'Alfort, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France
| | - Muriel Pottier
- Laboratoire de Parasitologie (EA4547), Faculté de Pharmacie, Université de Lille, Lille, France; Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Inserm U1019, UMR CNRS 8204, Université de Lille, BioPôle d'Alfort, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France
| | - Christophe Noël
- Geneius Laboratories Ltd, INEX Business Centre, Newcastle upon Tyne, United Kingdom
| | - Eric Viscogliosi
- Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Inserm U1019, UMR CNRS 8204, Université de Lille, BioPôle d'Alfort, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France
| | - El Moukhtar Aliouat
- Laboratoire de Parasitologie (EA4547), Faculté de Pharmacie, Université de Lille, Lille, France; Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Inserm U1019, UMR CNRS 8204, Université de Lille, BioPôle d'Alfort, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France
| | - Eduardo Dei-Cas
- Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Inserm U1019, UMR CNRS 8204, Université de Lille, BioPôle d'Alfort, Biologie et Diversité des Pathogènes Eucaryotes Emergents, Lille, France; Parasitologie-Mycologie (EA4547) Faculté de Médecine, Université de Lille, CHRU, Lille, France
| | - Serge Morand
- Institut des Sciences de l'Evolution, UMR CNRS-IRD-UM2, Université de Montpellier 2, F-34093, Montpellier, France; CIRAD-CNRS, Centre d'Infectiologie Christophe Mérieux du Laos, Vientiane, Lao PDR
| | - Jacques Guillot
- ENVA, UPEC, Research group Dynamyc, Ecole Nationale Vétérinaire d'Alfort, 94704, Maisons-Alfort Cedex, France
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Mayer F, Piel FB, Cassel-Lundhagen A, Kirichenko N, Grumiau L, Økland B, Bertheau C, Grégoire JC, Mardulyn P. Comparative multilocus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation. Mol Ecol 2015; 24:1292-310. [PMID: 25655781 DOI: 10.1111/mec.13104] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 02/02/2015] [Accepted: 02/02/2015] [Indexed: 12/01/2022]
Abstract
While phylogeographic patterns of organisms are often interpreted through past environmental disturbances, mediated by climate changes, and geographic barriers, they may also be strongly influenced by species-specific traits. To investigate the impact of such traits, we focused on two Eurasian spruce bark beetles that share a similar geographic distribution, but differ in their ecology and reproduction. Ips typographus is an aggressive tree-killing species characterized by strong dispersal, whereas Dendroctonus micans is a discrete inbreeding species (sib mating is the rule), parasite of living trees and a poor disperser. We compared genetic variation between the two species over both beetles' entire range in Eurasia with five independent gene fragments, to evaluate whether their intrinsic differences could have an influence over their phylogeographic patterns. We highlighted widely divergent patterns of genetic variation for the two species and argue that the difference is indeed largely compatible with their contrasting dispersal strategies and modes of reproduction. In addition, genetic structure in I. typographus divides European populations in a northern and a southern group, as was previously observed for its host plant, and suggests past allopatric divergence. A long divergence time was estimated between East Asian and other populations of both species, indicating their long-standing presence in Eurasia, prior to the last glacial maximum. Finally, the strong population structure observed in D. micans for the mitochondrial locus provides insights into the recent colonization history of this species, from its native European range to regions where it was recently introduced.
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Affiliation(s)
- François Mayer
- Lutte Biologique et Ecologie Spatiale, Université Libre de Bruxelles, Brussels, Belgium
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Schmidt S, Essbauer SS, Mayer-Scholl A, Poppert S, Schmidt-Chanasit J, Klempa B, Henning K, Schares G, Groschup MH, Spitzenberger F, Richter D, Heckel G, Ulrich RG. Multiple infections of rodents with zoonotic pathogens in Austria. Vector Borne Zoonotic Dis 2014; 14:467-75. [PMID: 24915446 PMCID: PMC4098071 DOI: 10.1089/vbz.2013.1504] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Rodents are important reservoirs for a large number of zoonotic pathogens. We examined the occurrence of 11 viral, bacterial, and parasitic agents in rodent populations in Austria, including three different hantaviruses, lymphocytic choriomeningitis virus, orthopox virus, Leptospira spp., Borrelia spp., Rickettsia spp., Bartonella spp., Coxiella burnetii, and Toxoplasma gondii. In 2008, 110 rodents of four species (40 Clethrionomys glareolus, 29 Apodemus flavicollis, 26 Apodemus sylvaticus, and 15 Microtus arvalis) were trapped at two rural sites in Lower Austria. Chest cavity fluid and samples of lung, spleen, kidney, liver, brain, and ear pinna skin were collected. We screened selected tissue samples for hantaviruses, lymphocytic choriomeningitis virus, orthopox viruses, Leptospira, Borrelia, Rickettsia, Bartonella spp., C. burnetii, and T. gondii by RT-PCR/PCR and detected nucleic acids of Tula hantavirus, Leptospira spp., Borrelia afzelii, Rickettsia spp., and different Bartonella species. Serological investigations were performed for hantaviruses, lymphocytic choriomeningitis virus, orthopox viruses, and Rickettsia spp. Here, Dobrava-Belgrade hantavirus-, Tula hantavirus-, lymphocytic choriomeningitis virus-, orthopox virus-, and rickettsia-specific antibodies were demonstrated. Puumala hantavirus, C. burnetii, and T. gondii were neither detected by RT-PCR/PCR nor by serological methods. In addition, multiple infections with up to three pathogens were shown in nine animals of three rodent species from different trapping sites. In conclusion, these results show that rodents in Austria may host multiple zoonotic pathogens. Our observation raises important questions regarding the interactions of different pathogens in the host, the countermeasures of the host's immune system, the impact of the host-pathogen interaction on the fitness of the host, and the spread of infectious agents among wild rodents and from those to other animals or humans.
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Affiliation(s)
- Sabrina Schmidt
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | - Sandra S. Essbauer
- Bundeswehr Institute of Microbiology, Department of Virology & Rickettsiology, Munich, Germany
| | | | - Sven Poppert
- Institute of Medical Microbiology, Justus-Liebig-University Giessen, Giessen, Germany
| | - Jonas Schmidt-Chanasit
- Bernhard Nocht Institute for Tropical Medicine, WHO Collaborating Centre for Arbovirus and Hemorrhagic Fever Reference and Research, Hamburg, Germany and German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel, Hamburg, Germany
| | - Boris Klempa
- Institute of Virology, Slovak Academy of Science, Bratislava, Slovakia, and Institute of Virology, Charité Medical School, Berlin, Germany
| | - Klaus Henning
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Jena, Germany
| | - Gereon Schares
- Friedrich-Loeffler-Institut, Institute of Epidemiology, Greifswald-Insel Riems, Germany
| | - Martin H. Groschup
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
| | | | - Dania Richter
- Environmental Systems Analysis, Institute of Geoecology, Technical University of Braunschweig, Germany
| | - Gerald Heckel
- Computational and Molecular Population Genetics (CMPG), Institute of Ecology and Evolution, University of Bern and Swiss Institute of Bioinformatics, Genopode, Lausanne, Switzerland
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Institute for Novel and Emerging Infectious Diseases, Greifswald–Insel Riems, Germany
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Xue H, Zhong M, Xu J, Xu L. Geographic distance affects dispersal of the patchy distributed greater long-tailed hamster (Tscherskia triton). PLoS One 2014; 9:e99540. [PMID: 24911266 PMCID: PMC4049827 DOI: 10.1371/journal.pone.0099540] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 05/16/2014] [Indexed: 11/30/2022] Open
Abstract
Dispersal is a fundamental process in ecology influencing the genetic structure and the viability of populations. Understanding how variable factors influence the dispersal of the population is becoming an important question in animal ecology. To date, geographic distance and geographic barriers are often considered as main factors impacting dispersal, but their effects are variable depending on different conditions. In general, geographic barriers affect more significantly than geographic distance on dispersal. In rapidly expanding populations, however, geographic barriers have less effect on dispersal than geographic distance. The effects of both geographic distance and geographic barriers in low-density populations with patchy distributions are poorly understood. By using a panel of 10 microsatellite loci we investigated the genetic structure of three patchy-distributed populations of the Greater long-tailed hamster (Tscherskia triton) from Raoyang, Guan and Shunyi counties of the North China Plain. The results showed that (i) high genetic diversity and differentiation exist in three geographic populations with patchy distributions; (ii) gene flow occurs among these three populations with physical barriers of Beijing city and Hutuo River, which potentially restricted the dispersal of the animal; (iii) the gene flow is negatively correlated with the geographic distance, while the genetic distance shows the positive correlation. Our results suggest that the effect of the physical barriers is conditional-dependent, including barrier capacity or individual potentially dispersal ability. Geographic distance also acts as an important factor affecting dispersal for the patchy distributed geographic populations. So, gene flow is effective, even at relatively long distances, in balancing the effect of geographic barrier in this study.
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Affiliation(s)
- Huiliang Xue
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Min Zhong
- Department of Biological Sciences, Auburn University, Auburn, Alabama, United States of America
| | - Jinhui Xu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
| | - Laixiang Xu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong, China
- * E-mail:
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Jojić V, Bugarski-Stanojević V, Blagojević J, Vujošević M. Discrimination of the sibling species Apodemus flavicollis and A. sylvaticus (Rodentia, Muridae). ZOOL ANZ 2014. [DOI: 10.1016/j.jcz.2014.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Kowalski K, Eichert U, Bogdziewicz M, Rychlik L. Differentiation of flea communities infesting small mammals across selected habitats of the Baltic coast, central lowlands, and southern mountains of Poland. Parasitol Res 2014; 113:1725-34. [PMID: 24619068 PMCID: PMC4544664 DOI: 10.1007/s00436-014-3817-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 02/11/2014] [Indexed: 11/29/2022]
Abstract
Only a few studies comparing flea composition on the coast and in the mountains have been conducted. We investigated differences in flea communities infesting small mammals in selected habitats in northern, central, and southern Poland. We predicted (1) a greater number of flea species in the southeastern Poland and a lower number in the north, (2) a greater number of flea species in fertile and wet habitats than in poor and arid habitats, and (3) a low similarity of flea species between flea communities in western and eastern Poland. We found a negative effect of increasing latitude on flea species richness. We suppose that the mountains providing a variety of environments and the limits of the geographic ranges of several flea subspecies in southeastern Poland result in a higher number of flea species. There was a positive effect of increasing wetness of habitat on flea species richness. We found a high diversity in flea species composition between western and eastern Poland (beta diversity = 11) and between central and eastern Poland (beta diversity = 12). Re-colonization of Poland by small mammals and their ectoparasites from different (western and eastern) refugees can affect on this high diversity of flea species.
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Affiliation(s)
- Krzysztof Kowalski
- Department of Systematic Zoology, Institute of Environmental Biology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznań, 61-614, Poland,
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