Cytochrome b haplotype divergences in West European Apodemus

Reutter, Brigitte A.; Petit, Éric; Brünner, H.; Vogel, Peter

doi:10.1078/1616-5047-00077

Cited by 22 publications

(41 citation statements)

References 27 publications

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“…Both tissue samples were from biopsies of released animals without preserved voucher specimens. Reutter et al (2003) suggested that an unrecognized population of A. fulvipectus might occur in southern Germany. As these sequences were fully coding the authors excluded the presence of a nuclear pseudogene and refuted the possibility of a DNA contamination in their laboratory, as they had never handled samples of A. fulvipectus from the Caucasus before.…”

Section: Introductionmentioning

confidence: 99%

“…A thorough phylogeography of A. sylvaticus, based on the cyt-b (Michaux et al, 2003), highlighted a clear pattern with slightly divergent sub-clades involving different geographic areas such as (i) western, northern and central Europe, (ii) Italy and Balkans, or (iii) Sicily. Interestingly, Reutter et al (2003), based on restricted sampling, found two additional well differentiated sequences of A. sylvaticus (G3.4 and G3.1), both from Karlsruhe in the southern part of Germany, from animals clearly identified as A. sylvaticus in the field. The first one (G3.4) was considered to belong to a lineage that separated very early, before the split separating the Italian animals (Michaux et al, 2003) and animals from the Pyreneans to the Ukraine.…”

Section: Introductionmentioning

confidence: 99%

“…1). For A. alpicola, a species restricted to the alpine region, Michaux et al (2002) and Reutter et al (2003) documented its monophyly. A thorough phylogeography of A. sylvaticus, based on the cyt-b (Michaux et al, 2003), highlighted a clear pattern with slightly divergent sub-clades involving different geographic areas such as (i) western, northern and central Europe, (ii) Italy and Balkans, or (iii) Sicily.…”

Section: Introductionmentioning

confidence: 99%

“…In the present study, we therefore analysed 102 cyt-b sequences of different species and lineages of Apodemus, and compared their DNA and amino-acid compositions in order to explain the presence of three divergent cyt-b lineages of A. sylvaticus in Germany, i.e. (i) the lineage widely distributed in central and northern Europe (Michaux et al 2003), (ii) the unexpected lineage (G3.4) found by Reutter et al (2003), and (iii) the lineage including samples of A. fulvipectus from Germany (Martin et al, 2000;Reutter et al, 2003: G3.1), and A. fulvipectus and A. ponticus from Georgia (Hille et al, 2002).…”

Section: Introductionmentioning

confidence: 99%

“…Martin et al, 2000;Hille et al, 2002;Michaux et al, 2002Michaux et al, , 2003Michaux et al, , 2004Michaux et al, , 2005Reutter et al, 2003;Balakirev et al, 2007;Hoofer et al, 2007;Suzuki et al, 2008) or both mitochondrial and nuclear genes (e.g. Michaux et al, 2002Michaux et al, , 2005Suzuki et al, 2008).…”

Section: Introductionmentioning

confidence: 99%

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False phylogenies on wood mice due to cryptic cytochrome-b pseudogene

Dubey¹,

Michaux²,

Brünner³

et al. 2009

Molecular Phylogenetics and Evolution

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a b s t r a c tThe phylogeny and phylogeography of the Old World wood mice (subgenus Sylvaemus, genus Apodemus, Muridae) are well-documented. Nevertheless, the distributions of species, such as A. fulvipectus and A. ponticus remain dubious, as well as their phylogenetic relationships with A. sylvaticus. We analysed samples of Apodemus spp. across Europe using the mitochondrial cytochrome-b gene (cyt-b) and compared the DNA and amino-acid compositions of previously published sequences. The main result stemming from this study is the presence of a well-differentiated lineage of Sylvaemus including samples of various species (A. sylvaticus, A. fulvipectus, A. ponticus) from distant locations, which were revealed to be nuclear copies of the mitochondrial cyt-b. The presence of this cryptic pseudogene in published sequences is supported by different pathways. This has led to important errors in previous molecular trees and hence to partial misinterpretations in the phylogeny of Apodemus.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

False phylogenies on wood mice due to cryptic cytochrome-b pseudogene

Dubey¹,

Michaux²,

Brünner³

et al. 2009

Molecular Phylogenetics and Evolution

View full text Add to dashboard Cite

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A new fast real‐time PCR method for the identification of three sibling Apodemus species (A. sylvaticus, A. flavicollis, and A. alpicola) in Italy

Sozio

Curini

Pascucci

et al. 2018

Ecology and Evolution

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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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Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers

Jarquín‐Díaz

Balard

Mácová

et al. 2020

Ecology and Evolution

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Intracellular parasites of the genus Eimeria are described as tissue/host‐specific. Phylogenetic classification of rodent Eimeria suggested that some species have a broader host range than previously assumed. We explore whether Eimeria spp. infecting house mice are misclassified by the most widely used molecular markers due to a lack of resolution, or whether, instead, these parasite species are indeed infecting multiple host species. With the commonly used markers (18S/COI), we recovered monophyletic clades of E. falciformis and E. vermiformis from Mus that included E. apionodes identified in other rodent host species (Apodemus spp., Myodes glareolus, and Microtus arvalis). A lack of internal resolution in these clades could suggest the existence of a species complex with a wide host range infecting murid and cricetid rodents. We question, however, the power of COI and 18S markers to provide adequate resolution for assessing host specificity. In addition to the rarely used marker ORF470 from the apicoplast genome, we present multilocus genotyping as an alternative approach. Phylogenetic analysis of 35 nuclear markers differentiated E. falciformis from house mice from isolates from Apodemus hosts. Isolates of E. vermiformis from Mus are still found in clusters interspersed with non‐Mus isolates, even with this high‐resolution data. In conclusion, we show that species‐level resolution should not be assumed for COI and 18S markers in coccidia. Host–parasite cospeciation at shallow phylogenetic nodes, as well as contemporary coccidian host ranges more generally, is still open questions that need to be addressed using novel genetic markers with higher resolution.

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Cytochrome b haplotype divergences in West European Apodemus

Cited by 22 publications

References 27 publications

False phylogenies on wood mice due to cryptic cytochrome-b pseudogene

False phylogenies on wood mice due to cryptic cytochrome-b pseudogene

A new fast real‐time PCR method for the identification of three sibling Apodemus species (A. sylvaticus, A. flavicollis, and A. alpicola) in Italy

Generalist Eimeria species in rodents: Multilocus analyses indicate inadequate resolution of established markers

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