Co-amplification of mitochondrial pseudogenes in Calomys musculinus (Rodentia, Cricetidae): a source of error in phylogeographic studies (original) (raw)
Related papers
2002
In order to contribute to knowledge of colonization patterns in the rodent Calomys musculinus, a natural reservoir of the virus producing Argentine hemorrhagic fever (AHF), we studied the haplotype diversity of the mitochondrial DNA D-loop region in five natural populations from central Argentina. Digestion with eight restriction enzymes (RsaI, MseI, Tsp509I, AluI, AciI, HaeIII, NlaIII, and AseI) revealed polymorphism in the 1300 bp fragment amplified by PCR. Twenty different composite haplotypes were detected. Hierarchical analyses indicated that almost all variation (94%) is contained within local populations. Haplotypes 1 and 2, shared by all populations, were the most frequent. Nonsignificant genetic differentiation was found among populations of the endemic and nonendemic areas of AHF. All locations sampled presented exclusive haplotypes in spite of their geographic proximity, which would support previous observations indicating restricted gene flow among C. musculinus populations.
False phylogenies on wood mice due to cryptic cytochrome-< i> b pseudogene
2009
The 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.
The interpretation of a signal produced by the mtDNA cytb gene as a molecular marker in phylo genetic and population genetic research can be complicated by the cumulative influence of parallel muta tions, i.e., by the entropy of nucleotide sequences that impede differentiation among the effects of the hybrid ization, natural polymorphisms, and artifacts imposed by pseudo genes. We analyzed possible limitations in the use of the mtDNA cytb gene as a molecular marker by the example of the Apodemus genus. For this pur pose, the entropy of nucleotide sequences was calculated and the probable tracts of gene conversion were sought in samples of various Apodemus species from Tibet, Korea, the southern part of the Russian Primorye, and Western Europe. Many haplotypes were identified as containing tracts of gene conversion. A high level of nucleotide sequence variability was found in species from the Tibetian Plateau, particularly, in A. draco, pre sumably due to the influence exercised by the low effective size of populations on the rate of point mutation accumulation and also the role of cytochrome b in the adaptation to unfavorable environment. The effects of hypervariability in the cytb nucleotide sequences of some samplings resulting in the entropy growth, imitating gene conversion when compared to other species of the genus were analyzed. Furthermore, the examples of possible pseudo gene interference among the published cytb sequences are provided. It is suggested that the strategy in the use of the mtDNA cytb gene in population genetics and phylogenetics should be adapted to the degree of gene variability. The emphasis is placed on the necessity of close control over sequencing data at all stages of their analysis.
False phylogenies on wood mice due to cryptic cytochrome-b pseudogene
Molecular Phylogenetics and Evolution, 2009
The 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.
Journal of Mammalogy, 2007
The rodent Calomys musculinus is the reservoir of the Junin virus, which causes Argentine hemorrhagic fever. A phylogeographic approach was used for the analysis of 6 populations from central Argentina based on cytochrome-b sequences from 27 individuals. Thirteen haplotypes were detected, each closely linked in the phylogenetic network; 2 of the most frequent haplotypes were internal, whereas the majority were unique to single populations and presented distal positions in the network. Most of the variance was explained by withinpopulation genetic diversity. Results of a mismatch distribution analysis and the deviation from neutrality confirmed that C. musculinus has experienced a recent range expansion; genetic drift has apparently been the main force acting at present, with low to moderate current gene flow. These results are in agreement with previous studies based on polymerase chain reaction-restriction fragment length polymorphism data of the mitochondrial D-loop region, and they support the reliability of both types of techniques.
Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences
Molecular Biology and Evolution, 1999
Concatenated sequences of all protein-coding genes in mitochondria recovered a known phylogeny of 11 vertebrate species correctly with statistical significance. However, when it was rooted by lampreys or sea urchins, the root of the vertebrate tree was placed between the mammal cluster and the chicken-frog-fish cluster or between the mammalchicken cluster and the frog-fish cluster, depending on the tree-making method used. Although the frog-fish or chicken-frog-fish cluster was biologically incorrect, it was again supported with a significantly high bootstrap value. In this study, we investigated the reasons why this happened. It has been suggested that an incorrect phylogeny may be constructed due to a change of amino acid composition in different lineages or due to homoplasies at sites with hydrophobic amino acids. However, our results indicated that these were not the causes of the incorrect rooting of the vertebrate tree. Rather, it was important to take into account an extensive rate variation across sites and different probabilities of substitution among different amino acids. The substitution rates for mitochondrial sequences vary considerably for different vertebrate lineages. In such a case, it is known to be important to use the model that reflects the actual substitution probability to obtain a correct tree topology. The correct rooting of the vertebrate tree was recovered when rate variation across sites was properly accounted for.
Rabbit mitochondrial DNA: preliminary comparison between some domestic and wild animals
Genetics Selection Evolution, 1987
The map of the restriction endonuclease cleavage sites of rabbit mitochondrial DNA (mtDNA) has been established : 41 sites were mapped using 13 enzymes. This genome, although rather large for a mammalian mtDNA (17 300 bp), is organized in the typical vertebrate fashion. For each of 6 wild and 5 domestic rabbits belonging respectively to the subspecies Oryctolagus cuniculus algirus and Oryctolagus cuniculus cuniculus, mtDNA molecules are heterogeneous in size. The length variations of about 100 bp have been assigned to the main non coding region of the genome. Very curiously, according to these preliminary results the mtDNAs of the two subspecies exhibit similar restriction patterns. However, 2 variants were found among the animals examined, one in each population.
Genetics, 1981
Restriction endonuclease analysis has revealed extensive mtDNA polymorphism in two species of rats, Rattus rattus and Rattus norvegicus. Sequence divergence values for the eight detected R. norvegicus variants range from 0.2% to 1.8% and for the eight R. rattus variants, from 0.2% to 9.6%. Three of the most closely related R. norvegicus mtDNA's appear to differ by deletions/insertions of about 4 base pairs apiece. Restriction sites for seven enzymes have been mapped for 11 of these variants. The 31 intraspecific and 41 interspecific variant sites appear to be evenly distributed on the mtDNA molecule outside of the rRNA cistrons. The location of sites present in all the DNAs suggests that the rRNA genes and possibly the light strand origin of replication may be more highly evolutionarily conserved than other parts of the molecule. The sequence divergences among the mtDNAs of animals whose geographic origins are separated by major barriers, such as oceans, were significantly great...
Sumichrast's harvest mouse (Reithrodontomys sumichrasti) is a montane rodent species widely distributed through the Mesoamerican highlands. We used sequence data from one mitochondrial (cytochrome b) and two nuclear (b-fibrinogen and acid phosphatase type V) genes for a total of 1962 base pairs to estimate genealogical relationships and assess population genetic structure across the range of this taxon. Maximum likelihood and Bayesian approaches using cytochrome b resolved several major clades, revealing considerably more genetic diversity than observed in previous studies. The basal split in the tree topologies corresponded to the geographical separation among samples on either side of the Isthmus of Tehuantepec in México. We estimated an early Pleistocene or late Pliocene divergence between these two groups. We also recovered a well-supported clade south of the Nicaraguan Depression in Central America that we consider a separate biological species. The 12 networks generated using statistical parsimony (TCS) for cytochrome b sequence data were largely concordant with the phylogenetic analyses and we document the co-occurrence of two of these networks in central Veracurz. Phylogenies derived from b-fibrinogen and acid phosphatase type V gene segments revealed less phylogenetic signal and did not separate samples of R. sumichrasti east and west of the Isthmus of Tehuantepec. The phylogeny estimated by combining the mitochondrial and nuclear sequence data was essentially identical to the cytochrome b gene tree.