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1.
Infect Genet Evol ; 52: 10-18, 2017 08.
Article in English | MEDLINE | ID: mdl-28412525

ABSTRACT

Microbiome studies generally focus on the gut microbiome, which is composed of a large proportion of commensal bacteria. Here we propose a first analysis of the liver microbiome using next generation sequencing as a tool to detect potentially pathogenic strains. We used Peromyscus leucopus, the main reservoir host species of Lyme disease in eastern North America, as a model and sequenced V5-V6 regions of the 16S gene from 18 populations in southern Quebec (Canada). The Lactobacillus genus was found to dominate the liver microbiome. We also detected a large proportion of individuals infected by Bartonella vinsonii arupensis, a human pathogenic bacteria responsible for endocarditis, as well as Borrelia burgdorferi, the pathogen responsible for Lyme disease in North America. We then compared the microbiomes among two P. leucopus genetic clusters occurring on either side of the St. Lawrence River, and did not detect any effect of the host genotype on their liver microbiome assemblage. Finally, we report, for the first time, the presence of B. burgdorferi in a small mammal host from the northern side of the St. Lawrence River, in support of models that have predicted the northern spread of Lyme disease in Canada.


Subject(s)
Disease Reservoirs/microbiology , Liver/microbiology , Microbiota , Peromyscus/microbiology , Sequence Analysis, DNA/methods , Animals , Bartonella/isolation & purification , Borrelia burgdorferi/isolation & purification , Canada , DNA, Ribosomal/analysis , Lactobacillus/isolation & purification , North America , RNA, Ribosomal, 16S/analysis
2.
Mol Ecol ; 20(6): 1176-90, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21244536

ABSTRACT

Human-mediated global change will probably increase the rates of natural hybridization and genetic introgression between closely related species, and this will have major implications for conservation of the taxa involved. In this study, we analyse both mitochondrial and nuclear data to characterize ongoing hybridization and genetic introgression between two sympatric sister species of mustelids, the endangered European mink (Mustela lutreola) and the more abundant polecat (M. putorius). A total of 317 European mink, 114 polecats and 15 putative hybrid individuals were collected from different localities in Europe and genotyped with 13 microsatellite nuclear markers. Recently developed Bayesian methods for assigning individuals to populations and identifying admixture proportions were applied to the genetic data. To identify the direction of hybridization, we additionally sequenced mtDNA and Y chromosomes from 78 individuals and 29 males respectively. We found that both hybridization and genetic introgression occurred at low levels (3% and 0.9% respectively) and indicated that hybridization is asymmetric, as only pure polecat males mate with pure European mink females. Furthermore, backcrossing and genetic introgression was detected only from female first-generation (F1) hybrids of European mink to polecats. This latter result implies that Haldane's rule may apply. Our results suggest that hybridization and genetic introgression between the two species should be considered a rather uncommon event. However, the current low densities of European mink might be changing this trend.


Subject(s)
Bayes Theorem , Ferrets/genetics , Hybridization, Genetic/physiology , Mink/genetics , Animals , DNA, Mitochondrial/genetics , Female , Ferrets/physiology , Hybridization, Genetic/genetics , Male , Microsatellite Repeats/genetics , Mink/physiology , Molecular Sequence Data , Y Chromosome/genetics
3.
Infect Genet Evol ; 11(2): 334-42, 2011 Mar.
Article in English | MEDLINE | ID: mdl-21093612

ABSTRACT

Stomoxys calcitrans (Diptera: Muscidae: Stomoxyini), a synanthropic fly with a worldwide distribution, is recognized to have an important medical and veterinary impact. We conducted a phylogeographic analysis based on several populations from five major zoogeographic regions of the world in order to analyse population genetic structure of S. calcitrans and to trace its global dispersion. Results from mitochondrial (COI, Cyt-b and ND1-16S) and nuclear (ITS2) DNA show a substantial differentiation of Oriental populations (first lineage) from the Afrotropical, Palearctic, Nearctic, Neotropical and Oceanian populations (second lineage). The divergence time analyses suggest the separation between the two lineages approximately in mid-Pleistocene. Oriental populations are isolated and would not have participated in the colonization of other regions, unlike the Afrotropical one which seems to be the source of S. calcitrans dispersion towards other regions. Demographic analyses indicate that Oriental, Afrotropical and Palearctic regions have undergone a population expansion during late Pleistocene-early Holocene. The expansion time of this cosmopolitan species could have been influenced by continental human expansions and by animal domestication.


Subject(s)
DNA, Mitochondrial/genetics , DNA, Ribosomal Spacer/genetics , Muscidae/genetics , Animals , Base Sequence , Cell Nucleus/genetics , Demography , Genes, Insect , Genes, rRNA , Genetic Markers , Genetic Variation , Haplotypes , Humans , Mitochondria/genetics , Molecular Sequence Data , Phylogeography , Sequence Analysis, DNA
4.
BMC Genet ; 11: 53, 2010 Jun 18.
Article in English | MEDLINE | ID: mdl-20565868

ABSTRACT

BACKGROUND: Chickens represent an important animal genetic resource and the conservation of local breeds is an issue for the preservation of this resource. The genetic diversity of a breed is mainly evaluated through its nuclear diversity. However, nuclear genetic diversity does not provide the same information as mitochondrial genetic diversity. For the species Gallus gallus, at least 8 maternal lineages have been identified. While breeds distributed westward from the Indian subcontinent usually share haplotypes from 1 to 2 haplogroups, Southeast Asian breeds exhibit all the haplogroups. The Vietnamese Ha Giang (HG) chicken has been shown to exhibit a very high nuclear diversity but also important rates of admixture with wild relatives. Its geographical position, within one of the chicken domestication centres ranging from Thailand to the Chinese Yunnan province, increases the probability of observing a very high genetic diversity for maternal lineages, and in a way, improving our understanding of the chicken domestication process. RESULTS: A total of 106 sequences from Vietnamese HG chickens were first compared to the sequences of published Chinese breeds. The 25 haplotypes observed in the Vietnamese HG population belonged to six previously published haplogroups which are: A, B, C, D, F and G. On average, breeds from the Chinese Yunnan province carried haplotypes from 4.3 haplogroups. For the HG population, haplogroup diversity is found at both the province and the village level (0.69).The AMOVA results show that genetic diversity occurred within the breeds rather than between breeds or provinces. Regarding the global structure of the mtDNA diversity per population, a characteristic of the HG population was the occurrence of similar pattern distribution as compared to G. gallus spadiceus. However, there was no geographical evidence of gene flow between wild and domestic populations as observed when microsatellites were used. CONCLUSIONS: In contrast to other chicken populations, the HG chicken population showed very high genetic diversity at both the nuclear and mitochondrial levels. Due to its past and recent history, this population accumulates a specific and rich gene pool highlighting its interest and the need for conservation.


Subject(s)
Chickens/genetics , Genetic Variation , Animals , Base Sequence , China , DNA, Mitochondrial , Genetics, Population , India , Vietnam
5.
Mol Ecol Resour ; 9(3): 885-7, 2009 May.
Article in English | MEDLINE | ID: mdl-21564778

ABSTRACT

We isolated and characterized 10 dinucleotide microsatellite loci in the edible dormouse, Glis glis (Linnaeus). Four multiplex panels were developed. Loci were amplified in samples from two geographically distant populations (Torgny in Belgium and Montseny in Spain). All loci were polymorphic in Spain but four were monomorphic in Belgium. Individuals from Belgium and Spain exhibited an average allelic diversity of 1.9 and 3.3 and an observed heterozygosity ranging from 0.08 to 0.47 and from 0.04 to 0.72, respectively.

6.
Mol Phylogenet Evol ; 49(2): 435-44, 2008 Nov.
Article in English | MEDLINE | ID: mdl-18762260

ABSTRACT

This study details the phylogeographic pattern of the white-throated dipper (Cinclus cinclus), a Palearctic, temperate, passerine bird that is exclusively associated with flowing water. Our results reveal a complex phylogeographic structure with at least five distinct lineages for the Western Palearctic region. As for many species of the Western Palearctic fauna and flora, this genetic structure is probably linked to the isolation of populations in different southern refuges during glacial periods. Furthermore, the isolation of populations in Scandinavia and/or Eastern regions, but also in Morocco and probably in Corsica, was accentuated by ecological and biogeographic barriers during Quaternary interglacial periods. During glacial periods, Italy, Sicily and the Balkano-Carpathian region acted as major refuge zones for the dipper. At the end of the last ice age, Western Europe was repopulated by dippers from an Italian refuge, while Eastern Europe was recolonised by Balkano-Carpathian birds. A large contact zone between these two lineages was evidenced and extends from Luxembourg to Hungary. Finally, our results indicate the need to clarify the taxonomic status of the dipper, especially concerning the European subspecies whose validity appears uncertain.


Subject(s)
Genetics, Population , Passeriformes/classification , Passeriformes/genetics , Phylogeny , Animals , Cytochromes b/genetics , DNA, Mitochondrial/genetics , Europe , Evolution, Molecular , Genes, Mitochondrial , Genetic Markers , Genetic Variation , Geography , Likelihood Functions , Mitochondria/genetics , Sequence Alignment , Sequence Analysis, DNA
7.
Mol Phylogenet Evol ; 47(2): 538-54, 2008 May.
Article in English | MEDLINE | ID: mdl-18346916

ABSTRACT

The co-evolution between hosts and parasites has long been recognized as a fundamental driver of macro-evolutionary patterns of diversification. The effect of co-differentiation on parasite diversification is, however, often confounded by underlying geographic patterns of host distribution. In order to disentangle the confounding effects of allopatric versus host speciation, the mitochondrial cytochrome b (cyt b) gene was sequenced in seventy individuals of the parasitic nematode genus Heligmosomoides sampled in the six Apodemus mice species common in the western Palearctic region. The nuclear internal transcribed spacers (ITS) 1 and 2 were also sequenced in fifteen parasites to confirm the mitochondrial data. All lineages differentiated according to a geographic pattern and independently from the sampled host species. This suggests that host speciation did not involve concurrent parasite speciation. However, the geographic distribution range of some parasite lineages mirrors that of A. sylvaticus lineages in SW Europe, and that of A. flavicollis lineages in the Balkans and in the Middle East. Thus, regional co-differentiation likely occurred between the parasite and the two sister Apodemus hosts in different parts of their distribution range. We suggest that differences in regional abundances of A. sylvaticus and A. flavicollis are responsible for generating this pattern of regional co-differentiation. This study highlights the importance of integrating both geography and biogeographic information from potential hosts to better understand their parasite phylogeography.


Subject(s)
Geography , Heligmosomatoidea/genetics , Parasites/genetics , Phylogeny , Animals , Base Sequence , Consensus Sequence , Cytochromes b/genetics , Genetic Variation , Murinae/parasitology , Time Factors
9.
Mol Ecol ; 14(8): 2373-88, 2005 Jul.
Article in English | MEDLINE | ID: mdl-15969721

ABSTRACT

In species of great conservation concern, special attention must be paid to their phylogeography, in particular the origin of animals for captive breeding and reintroduction. The endangered European mink lives now in at least three well-separated populations in northeast, southeast and west Europe. Our aim is to assess the genetic structure of these populations to identify 'distinct population segments' (DPS) and advise captive breeding programmes. First, the mtDNA control region was completely sequenced in 176 minks and 10 polecats. The analysis revealed that the western population is characterized by a single mtDNA haplotype that is closely related to those in eastern regions but nevertheless, not found there to date. The northeast European animals are much more variable (pi = 0.012, h = 0.939), with the southeast samples intermediate (pi = 0.0012, h = 0.469). Second, 155 European mink were genotyped using six microsatellites. The latter display the same trends of genetic diversity among regions as mtDNA [gene diversity and allelic richness highest in northeast Europe (H(E) = 0.539, R(S) = 3.76), lowest in west Europe (H(E) = 0.379, R(S) = 2.12)], and provide evidences that the southeast and possibly the west populations have undergone a recent bottleneck. Our results indicate that the western population derives from a few animals which recently colonized this region, possibly after a human introduction. Microsatellite data also reveal that isolation by distance occurs in the western population, causing some inbreeding because related individuals mate. As genetic data indicate that the three populations have not undergone independent evolutionary histories for long (no phylogeographical structure), they should not be considered as distinct DPS. In conclusion, the captive breeding programme should use animals from different parts of the species' present distribution area.


Subject(s)
Demography , Genetic Variation , Genetics, Population , Mink/genetics , Phylogeny , Animals , Base Sequence , Bayes Theorem , Breeding/methods , Cluster Analysis , Conservation of Natural Resources , DNA Primers , DNA, Mitochondrial/genetics , Europe , Founder Effect , Gene Frequency , Geography , Haplotypes/genetics , Likelihood Functions , Microsatellite Repeats/genetics , Models, Genetic , Molecular Sequence Data , Sequence Analysis, DNA
10.
Mol Ecol ; 14(5): 1473-83, 2005 Apr.
Article in English | MEDLINE | ID: mdl-15813785

ABSTRACT

The spatial genetic structure of common hamsters (Cricetus cricetus) was investigated using three partial mitochondrial (mt) genes and 11 nuclear microsatellite loci. All marker systems revealed significant population differentiation across Europe. Hamsters in central and western Europe belong largely to two allopatric mitochondrial lineages south and northwest of the Carpathian and Sudetes. The southern group, 'Pannonia', comprises populations inside the Carpathian basin (Czech Republic, Hungary) while the second group, 'North', includes hamsters from Belgium, the Netherlands, France, and Germany. Isolation of the lineages is maintained by a combination of geographical and ecological barriers. Both main phylogeographical groups show signs of further subdivision. North is separated into highly polymorphic central German and less polymorphic western populations, which most likely split during late glacial expansion (15,000-10,000 bp). Clock estimates based on haplotype distributions predict a divergence of the two major lineages 85,000-147,000 bp. Expansion times fall during the last glaciation (115,000-10,000 bp) corroborating fossil data, which identify Cricetus cricetus as characteristic of colder climatic phases. Despite the allopatry of mt haplotypes, there is an overlap of nuclear microsatellite alleles between phylogeographical units. Although there are strong evidence that Pannonian hamsters have persisted inside the Carpathian basin over the last 50,000 years, genetic differentiation among European hamsters has mainly been caused by immigration from different eastern refugia. Possible source populations are likely to be found in the Ukrainian and the southern Russian plains--core areas of hamster distribution. From there, hamsters have repeatedly expanded during the Quaternary.


Subject(s)
Cricetinae/genetics , Demography , Evolution, Molecular , Genetic Variation , Genetics, Population , Animals , Base Sequence , Cluster Analysis , DNA Primers , DNA, Mitochondrial/genetics , Europe , Gene Frequency , Geography , Microsatellite Repeats/genetics , Molecular Sequence Data , Population Dynamics , Sequence Analysis, DNA
11.
Mol Ecol ; 14(6): 1727-39, 2005 May.
Article in English | MEDLINE | ID: mdl-15836645

ABSTRACT

This study details the phylogeographic pattern of the bank vole, Clethrionomys glareolus, a European rodent species strongly associated with forest habitat. We used sequences of 1011 base pairs of the mitochondrial DNA cytochrome b gene from 207 bank voles collected in 62 localities spread throughout its distribution area. Our results reveal the presence of three Mediterranean (Spanish, Italian and Balkan) and three continental (western, eastern and 'Ural') phylogroups. The endemic Mediterranean phylogroups did not contribute to the post-glacial recolonization of much of the Palaearctic range of species. Instead, the major part of this region was apparently recolonized by bank voles that survived in glacial refugia in central Europe. Moreover, our phylogeographic analyses also reveal differentiated populations of bank voles in the Ural mountains and elsewhere, which carry the mitochondrial DNA of another related vole species, the ruddy vole (Clethrionomys rutilus). In conclusion, this study demonstrates a complex phylogeographic history for a forest species in Europe which is sufficiently adaptable that, facing climate change, survives in relict southern and northern habitats. The high level of genetic diversity characterizing vole populations from parts of central Europe also highlights the importance of such regions as a source of intraspecific genetic biodiversity.


Subject(s)
Arvicolinae/genetics , Demography , Environment , Genetic Variation , Genetics, Population , Phylogeny , Analysis of Variance , Animals , Base Sequence , Climate , Cluster Analysis , DNA Primers , DNA, Mitochondrial/genetics , Europe , Geography , Haplotypes/genetics , Molecular Sequence Data , Paleontology , Sequence Analysis, DNA
12.
Mol Ecol ; 14(3): 765-79, 2005 Mar.
Article in English | MEDLINE | ID: mdl-15723668

ABSTRACT

This study establishes the continental phylogeographical pattern of a European nematode, Heligmosomoides polygyrus (Dujardin, 1845; Heligmosomoidea). We sequenced 687 base pairs of the mitochondrial DNA (mtDNA) cyt b gene for 136 individuals collected in 22 localities. The results revealed that H. polygyrus populations are separated into five major units corresponding to the Italian, northern European (Denmark and Ireland), Iberian, western European, and Balkan populations. Different subclades were also observed within the first two groups. Based on the rate of molecular evolution of H. polygyrus cyt b gene-estimated to 3.5%-3.7% divergence per million years (Myr) in a previous study--the isolation time of the five clades was estimated between 2.5 +/- 0.24 and 1.5 +/- 0.23 million years ago. Moreover, H. polygyrus presents a higher genetic variability in the Mediterranean peninsulas as compared to northwestern Europe, highlighting the role of these regions as refuge areas. Like its specific host, the wood mouse Apodemus sylvaticus, H. polygyrus' pattern of postglacial recolonization of northwestern Europe was initiated from Iberian populations, while Italian and Balkan populations did not expand to the north. The results also suggest the existence of forested and temperate refuges in the southern British Isles during the Quaternary. Finally, the genetic diversity as well as the level of genetic divergence between the lineages of H. polygyrus are compared to those observed in other vertebrate and invertebrate phylogeographical studies: the existence of highly differentiated lineages in H. polygyrus (5%-10% of genetic divergence) highlights that the effects of Pleistocene climate changes on free-living organisms are also reflected in their obligate parasites.


Subject(s)
Demography , Evolution, Molecular , Genetic Variation , Genetics, Population , Mice/parasitology , Phylogeny , Trichostrongyloidea/genetics , Animals , Base Sequence , Cluster Analysis , DNA, Mitochondrial/genetics , Europe , Geography , Haplotypes/genetics , Molecular Sequence Data , Population Dynamics , Sequence Analysis, DNA
13.
Bull Mem Acad R Med Belg ; 160(5-6): 311-8, 2005.
Article in French | MEDLINE | ID: mdl-16465786

ABSTRACT

The destiny of Bartók is closely related to that of his native land, Hungary. His life endured History's hazards and destiny's whims. It was a trip strewn with obstacles and marked by afflicting health problems; it went through boisterous conflicts and captivating passions, met the injuries of lack of understanding and the bruises of the unvoiced comment. This particular course opened the musician to the ethnomusicology and led him to the creation of original musical works. The exile towards the new world generated difficulties and creativity. An insidious disease mortgaged the future of this uprooted and, in several stages, led him to death. The periods of respite animated his creative genius and generated immortal works.


Subject(s)
Music , History, 19th Century , History, 20th Century , Humans , Hungary , Loneliness , Male , United States
14.
Heredity (Edinb) ; 94(1): 52-63, 2005 Jan.
Article in English | MEDLINE | ID: mdl-15329664

ABSTRACT

In Europe, concordant geographical distribution among genetic lineages within different species is rare, which suggests distinct reactions to Quaternary ice ages. This study aims to determine whether such a discrepancy also affects a pair of sympatric species, which are morphologically and taxonomically closely related but which have slight differences in their ecological habits. The phylogeographic structures of two European rodents, the Yellow-necked fieldmouse (A. flavicollis) and the woodmouse (Apodemus sylvaticus) were, therefore, compared on the basis of mitochondrial DNA cytochrome b (mtDNA cyt b) sequences (965 base pairs) from 196 specimens collected from 59 European localities spread throughout the species distributions. The results indicate that the two species survived in different ways through the Quaternary glaciations. A. sylvaticus survived in the Iberian Peninsula from where it recolonized almost all Europe at the end of the last glaciation. Conversely, the refuge from which A. flavicollis recolonized Europe, including northern Spain, during the Holocene corresponds to the Italo-Balkan area, where A. sylvaticus suffered a serious genetic bottleneck. This study confirms that even closely related species may have highly different phylogeographic histories and shows the importance of ecological plasticity of the species for their survival through climate change. Finally, it suggests that phylogeographic distinctiveness may be a general feature of European species.


Subject(s)
Cytochromes b/genetics , DNA, Mitochondrial/genetics , Demography , Haplotypes , Muridae/genetics , Animals , Europe , Evolution, Molecular , Genetic Variation , Genetics, Population , Phylogeny
15.
Proc Biol Sci ; 271(1557): 2559-68, 2004 Dec 22.
Article in English | MEDLINE | ID: mdl-15615681

ABSTRACT

This study compares the continental phylogeographic patterns of two wild European species linked by a host-parasite relationship: the field mouse Apodemus sylvaticus and one of its specific parasites, the nematode Heligmosomoides polygyrus. A total of 740 base pairs (bp) of the mitochondrial cytochrome b (cyt b) gene were sequenced in 122 specimens of H. polygyrus and compared with 94 cyt b gene sequences (974 bp) previously acquired for A. sylvaticus. The results reveal partial spatial and temporal congruences in the differentiation of both species' lineages: the parasite and its host present three similar genetic and geographical lineages, i.e. Western European, Italian and Sicilian, and both species recolonized northwestern Europe from the Iberian refuge at the end of the Pleistocene. However, H. polygyrus presents three particular differentiation events. The relative rate of molecular evolution of the cyt b gene was estimated to be 1.5-fold higher in the parasite than in its host. Therefore, the use of H. polygyrus as a biological magnifying glass is discussed as this parasite may highlight previously undetected historical events of its host. The results show how incorporating phylogeographic information of an obligate associate can help to better understand the phylogeographic pattern of its host.


Subject(s)
Demography , Evolution, Molecular , Muridae/parasitology , Phylogeny , Rhabditida/physiology , Analysis of Variance , Animals , Bayes Theorem , Cluster Analysis , Cytochromes b/genetics , DNA Primers , Europe , Geography , Host-Parasite Interactions , Models, Genetic , Muridae/genetics , Muridae/physiology , Rhabditida/genetics , Sequence Analysis, DNA , Species Specificity
16.
Mol Phylogenet Evol ; 32(3): 788-98, 2004 Sep.
Article in English | MEDLINE | ID: mdl-15288056

ABSTRACT

The exact location of glacial refugia and the patterns of postglacial range expansion of European mammals are not yet completely elucidated. Therefore, further detailed studies covering a large part of the Western Palearctic region are still needed. In this order, we sequenced 972 bp of the mitochondrial DNA cytochrome b (mtDNA cyt b) from 124 yellow-necked fieldmice (Apodemus flavicollis) collected from 53 European localities. The aims of the study were to answer the following questions: Did the Mediterranean peninsulas act as the main refuge for yellow-necked fieldmouse or did the species also survive in more easterly refugia (the Caucasus or the southern Ural) and in Central Europe? What is the role of Turkey and Near East regions as Quaternary glacial refuges for this species and as a source for postglacial recolonisers of the Western Palearctic region? The results provide a clear picture of the impact of the quaternary glaciations on the genetic and geographic structure of the fieldmouse. This species survived the ice ages in two main refuges, the first one in the Italo-Balkan region; the second one in Turkey and the Near East regions. It is from the Balkan refuge that it recolonised all European regions at the end of the last glaciation. The Turkish and Near East populations are distinct from the European ones and they did not recolonise the Palearctic region probably because: (i) they were blocked by the Black Sea and the Caucasus, (ii) the long term presence of fieldmice populations in the Balkans prevented their expansion. These are genetically differentiated from the European and Russian ones and could be described as a particular subspecies. This result emphasises the importance of Turkey and the Near and Middle East regions as a refuge for Palearctic mammals.


Subject(s)
Demography , Muridae/genetics , Phylogeny , Analysis of Variance , Animals , Base Sequence , Cluster Analysis , DNA Primers , DNA, Mitochondrial/genetics , Europe , Genetic Variation , Geography , Haplotypes/genetics , Middle East , Models, Genetic , Molecular Sequence Data , Sequence Analysis, DNA
17.
Isotopes Environ Health Stud ; 39(3): 197-210, 2003 Sep.
Article in English | MEDLINE | ID: mdl-14521281

ABSTRACT

The paleodiet and paleoenvironmental context of two extinct species from Tenerife island, one giant rat Canariomys bravoi and one giant lizard Gallotia goliath, have been investigated using carbon and nitrogen isotopic compositions of fossil bone collagen. Preliminary to this study, a calibration of the isotopic variations of bone collagen from modern Rat Rattus rattus, Rabbit Oryctolagus cuniculus and Lizard Gallotia galotti relative to environmental conditions on Tenerife Islands has been attempted. No clear relationship could be found between collagen delta13C and delta15N values and aridity; the only relevant factors seem to be seashore proximity for rat, and the relative amount of C3 and CAM plants. It seems that anthropic activities have interfered with the expected relationships between collagen isotopic compositions and environmental conditions. Most fossil specimens yielded well preserved collagen. The isotopic composition of giant rat and giant lizard collagen suggest a purely C3 environment, possibly more humid than today on Tenerife. Large ranges of nitrogen isotopic compositions, especially within giant rats, may be due to local environmental conditions. Further work is needed in order to provide more valuable paleobiological information in order to better understand the role of environmental factors in the evolution and extinction of insular endemic species on Tenerife.


Subject(s)
Biological Evolution , Collagen/chemistry , Environment , Lizards , Muridae , Animals , Carbon Isotopes/analysis , Climate , Nitrogen Isotopes/analysis , Paleontology , Rats , Spain
18.
Mol Ecol ; 12(3): 685-97, 2003 Mar.
Article in English | MEDLINE | ID: mdl-12675824

ABSTRACT

We sequenced 965 base pairs of the mitochondrial DNA cytochrome b from 102 woodmice (Apodemus sylvaticus) collected from 40 European localities. The aims of the study were to answer the following questions. (i) Did the Mediterranean peninsulas play a role as refuge for woodmice? (ii) Is genetic variability of A. sylvaticus higher in the Mediterranean region compared with northern Europe? (iii) Are the patterns of the postglacial colonization of Europe by woodmice similar to those presently recognized for other European species? The results provide a clear picture of the impact of the Quaternary glaciations on the genetic and geographical structure of the woodmouse. Our analyses indicate a higher genetic variability of woodmice in the Mediterranean peninsulas compared to northern Europe, suggesting a role of the former as refuge regions for this small mammal. An original pattern of postglacial colonization is proposed where the Iberian and southern France refuge populations colonized almost all European regions. The Sicilian population appears to be very differentiated and highly variable. This emphasizes the importance of this island as a 'hot spot' for the intraspecific genetic diversity of the woodmouse. Finally, woodmice in North Africa originated from southwestern Europe, most probably as a result of a recent anthropogenic introduction.


Subject(s)
DNA, Mitochondrial/genetics , Muridae/genetics , Phylogeny , Animals , Base Sequence , Cytochrome b Group/chemistry , Cytochrome b Group/genetics , DNA, Mitochondrial/chemistry , Europe , Evolution, Molecular , Genetic Variation , Genetics, Population , Haplotypes , Molecular Sequence Data , Sequence Analysis, DNA
19.
Mol Phylogenet Evol ; 23(2): 123-36, 2002 May.
Article in English | MEDLINE | ID: mdl-12069545

ABSTRACT

Phylogenetic relationships among 17 extant species of Murinae, with special reference to the genus Apodemus, were investigated using sequence data from the nuclear protein-coding gene IRBP (15 species) and the two mitochondrial genes cytochrome b and 12S rRNA (17 species). The analysis of the three genes does not resolve the relationships between Mus, Apodemus, and Rattus but separates Micromys from these three genera. The analysis of the two mitochondrial regions supported an association between Apodemus and Tokudaia and indicated that these two genera are more closely related to Mus than to Rattus or Micromys. Within Apodemus, the mitochondrial data sets indicated that 8 of the 9 species analyzed can be sorted into two main groups: an Apodemus group, with A. agrarius, semotus, and peninsulae, and a Sylvaemus group, with uralensis, flavicollis, alpicola, sylvaticus, and hermonensis. The position of Apodemus mystacinus is ambiguous and might be either included in Sylvaemus or considered a distinct subgenus, Karstomys, more closely related to Sylvaemus than to Apodemus. Estimation of the divergence time for these taxa suggests a separation between 7 and 8 My ago for the three groups (mystacinus and the two subgenera Apodemus and Sylvaemus). Within each subgenus, divergence times are between 5.4 and 6 My for Apodemus and between 2.2 and 3.5 My for Sylvaemus and mystacinus.


Subject(s)
Cytochrome b Group/genetics , Eye Proteins , Muridae/genetics , Phylogeny , RNA, Ribosomal/genetics , Retinol-Binding Proteins/genetics , Animals , Cell Nucleus/genetics , DNA/chemistry , DNA/genetics , DNA, Mitochondrial/genetics , Genetic Variation , Molecular Sequence Data , Muridae/classification , Rats , Sequence Analysis, DNA , Time Factors
20.
Mol Biol Evol ; 18(11): 2017-31, 2001 Nov.
Article in English | MEDLINE | ID: mdl-11606698

ABSTRACT

Phylogenetic relationships between 32 species of rodents representing 14 subfamilies of Muridae and four subfamilies of Dipodidae were studied using sequences of the nuclear protein-coding genes Lecithin Cholesterol Acyl Transferase (LCAT) and von Willebrand Factor (vWF). An examination of some evolutionary properties of each data matrix indicates that the two genes are rather complementary, with lower rates of nonsynonymous substitutions for LCAT. Both markers exhibit a wide range of GC3 percentages (55%-89%), with several taxa above 70% GC3 for vWF, which indicates that those exonic regions might belong to the richest class of isochores. The primary sequence data apparently harbor few saturations, except for transitions on third codon positions for vWF, as indicated by comparisons of observed and expected pairwise values of substitutions. Phylogenetic trees based on 1,962 nucleotidic sites from the two genes indicate that the 14 Muridae subfamilies are organized into five major lineages. An early isolation leads to the clade uniting the fossorial Spalacinae and semifossorial Rhizomyinae with a strong robustness. The second lineage includes a series of African taxa representing nesomyines, dendromurines, cricetomyines, and the sole living member of mystromyines. The third one comprises only the mouselike hamster CALOMYSCUS: The fourth clade represents the cricetines, myospalacines, sigmodontines, and arvicolines, whereas the fifth one comprises four "traditional" subfamilies (Gerbillinae, Murinae, Otomyinae, and Acomyinae). Within these groups, we confirm the monophyly of almost all studied subfamilies, namely, Spalacinae, Rhizomyinae, Nesomyinae, Cricetomyinae, Arvicolinae, Sigmodontinae, Cricetinae, Gerbillinae, Acomyinae, and Murinae. Finally, we present evidence that the sister group of Acomyinae is Gerbillinae, and we confirm a nested position of Myospalacinae within Cricetinae and Otomyinae within Murinae. From a biogeographical point of view, the five main lineages spread and radiated from Asia with different degrees of success: the first three groups are now represented by a limited number of species and genera localized in some regions, whereas the last two groups radiated in a large variety of species and genera dispersed all over the world.


Subject(s)
Evolution, Molecular , Muridae/genetics , Animals , Base Composition , Exons/genetics , GC Rich Sequence/genetics , Genetic Variation , Likelihood Functions , Molecular Sequence Data , Phosphatidylcholine-Sterol O-Acyltransferase/genetics , Phylogeny , Species Specificity , von Willebrand Factor/genetics
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