Analysis of the codon use frequency of AMPK family genes from different species

In mammals, AMP-activated protein kinase (AMPK) is involved in the regulation of cellular energy homeostasis and, on the whole animal level, in regulating energy balance and food intake. In this paper, the relative synonymous codon use frequency of 40 AMPK family genes from seven mammal species (Bos taurus, Homo sapiens, Macaca mulatta, Mus musculus, Pan troglodytes, Rattus norvegicus, Sus scrofa) were analyzed using correspondence analysis and hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias in AMPK family genes, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Gene conversion limits divergence of mammalian TLR1 and TLR6

Background  

Toll-like receptors (TLR) recognize pathogen-associated molecular patterns and are important mediators of the innate immune system. TLR1 and TLR6 are paralogs and located in tandem on the same chromosome in mammals. They form heterodimers with TLR2 and bind lipopeptide components of gram-positive and gram-negative bacterial cell walls. To identify conserved stretches in TLR1 and TLR6, that may be important for their function, we compared their protein sequences in nine mammalian species(Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus, Rattus norvegicus; Erinaceus europaeus, Bos Taurus, Sus scrofa and Canis familiaris).     

Allozymic variation in four Indian species of genusMus: A comparative analysis

The present study focusses on allozyme variation in the commensal house mouseMus musculus, the pygmy field miceM. booduga andM. terricolor, and the spiny mouseM. platythrix. Genetic heterozygosity was estimated using a set of 24 polymorphic biochemical genetic markers. The extent of variability present inM. booduga, M. terricolor andM. platythrix has been compared with that in theM. musculus complex. Levels of allozyme variation at species level indicate thatM. musculus has the maximum heterogeneity, followed byM. booduga andM. terricolor, whileM. platythrix shows comparatively homogeneous genetic make-up. Gene frequency data have been used to trace phylogenetic relationships among these four species.     

Patterns of morphological evolution in the mandible of the house mouse Mus musculus (Rodentia: Muridae)

The worldwide distributed house mouse, Mus musculus, is subdivided into at least three lineages, Mus musculus musculus, Mus musculus domesticus, and Mus musculus castaneus. The subspecies occur parapatrically in a region considered to be the cradle of the species in Southern Asia (‘central region’), as well as in the rest of the world (‘peripheral region’). The morphological evolution of this species in a phylogeographical context is studied using a landmark‐based approach on mandible morphology of different populations of the three lineages. The morphological variation increases from central to peripheral regions at the population and subspecific levels, confirming a centrifugal sub‐speciation within this species. Furthermore, the outgroup comparison with sister species suggests that M. musculus musculus and populations of all subspecies inhabiting the Iranian plateau have retained a more ancestral mandible morphology, suggesting that this region may represent one of the relevant places of the origin of the species. Mus musculus castaneus, both from central and peripheral regions, is morphologically the most variable and divergent subspecies. Finally, the results obtained in the present study suggest that the independent evolution to commensalism in the three lineages is not accompanied by a convergence detectable on jaw morphology. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 635–647.     

Genetic analysis of protein variations in Mus musculus using two-dimensional electrophoresis

We have investigated the variation of proteins from crude homogenates of mouse kidneys in several strains of Mus musculus by means of two-dimensional electrophoresis. In this study, we have used the strains C57BL/6J, DBA/2J, CD-1, M. m. castaneus, and M. m. molossinus, as well as offspring from crosses among these strains. Out of the 100 loci screened, we have found nine loci showing interstrain differences. We have been able to identify three proteins as Id-1, Car-2, and Sep-1. The remaining variants are probably new loci in the mouse. Most of the variants (seven) can be mapped to a chromosome. We have found also that differences in the protein pattern as seen on two-dimensional gels are small among subspecies of Mus musculus.     

The uncharacterized gene 1700093K21Rik and flanking regions are correlated with reproductive isolation in the house mouse,Mus musculus

Reproductive barriers exist between the house mouse subspecies, Mus musculus musculus and M. m. domesticus, members of the Mus musculus species complex, primarily as a result of hybrid male infertility, and a hybrid zone exists where their ranges intersect in Europe. Using single nucleotide polymorphisms (SNPs) diagnostic for the two taxa, the extent of introgression across the genome was previously compared in these hybrid populations. Sixty-nine of 1316 autosomal SNPs exhibited reduced introgression in two hybrid zone transects suggesting maladaptive interactions among certain loci. One of these markers is within a region on chromosome 11 that, in other studies, has been associated with hybrid male sterility of these subspecies. We assessed sequence variation in a 20 Mb region on chromosome 11 flanking this marker, and observed its inclusion within a roughly 150 kb stretch of DNA showing elevated sequence differentiation between the two subspecies. Four genes are associated with this genomic subregion, with two entirely encompassed. One of the two genes, the uncharacterized 1700093K21Rik gene, displays distinguishing features consistent with a potential role in reproductive isolation between these subspecies. Along with its expression specifically within spermatogenic cells, we present various sequence analyses that demonstrate a high rate of molecular evolution of this gene, as well as identify a subspecies amino acid variant resulting in a structural difference. Taken together, the data suggest a role for this gene in reproductive isolation.     

Fructose bisphosphatase isozymes of the mouse. I. Inheritance

Electrophoretically detectable polymorphisms of fructose bisphosphatase (EC 3.1.3.11) have been found in the mouse. One polymorphism, found among inbred strains of Mus musculus and feral animals, affects the isozymes found in the muscle and in most other tissues examined but is not expressed in kidney, liver, or testis. These tissues have other electrophoretically distinct isozymes which are monomorphic in Mus musculus but are present as a different electromorph in the sympatric species Mus spretus. Breeding data have established that the genetic control of the muscle enzyme is expressed by an autosomal structural locus Fbp-1 which is distinct from that expressing the liver, kidney, and testis enzyme, Fbp-2. The organ-specific expression of the two loci suggests possible functional differences between the two products.This work was supported by the Medical Research Council.     

Evolutionary genetics of the suiformes as reconstructed using mtDNA sequencing

We have amplified and sequnced the entire mitochondrial DNA cytochromeb gene from four species of Suidae: babirusa, warthog, bearded pig, and some specimens belonging to different subspecies and populations of wild and domestic pigs (Sus scrofa). These sequences were aligned with additional mammalian sequences retrieved from the literature and were used to obtain phylogenetic trees of the Suiformes (Artiodactyla). Several species of Carnivora, Perissodactyla. Cetacea, and other Artiodactyla were used as outgroups. Molecular phylogenetic relationships among the Suiformes reflect their current taxonomy: Hippopotamidae, Tayassuidae, and Suidae are separated by deep genetic gaps, and the division of the Suidae into the subfamilies Babyrousinae., Phacochoerinae, and Suinae has strong genetic correlates. Cytochromeb sequences show differences among Asian and Western populations ofSus scrofa, agreeing with other genetic information (karyotypes blood groups, and protein variability). The two Italian subspecies of wild boar have unique mtDNA cytochromeb haplotypes. The evolutionary rates of cytochromeb sequences are different at transitions versus transversions as well as at first, second, and third positions of codons. Therefore, these classes of substitutions reached different levels of mutational saturation. Only transversions and the conservative first and second position substitutions are linearly related to genetic distances among the Suiformes. Therefore, divergence times were computed using unsaturated conserved nucleotide substitutions and calibrated using paleontological divergence times between some Artiodactyla. Transversions apparently evolve at remarkably regular rates in ungulate taxa which have accumulated less than 20% estimated sequence divergence, corresponding to about 40–45 million years of independent evolution. Molecular, information suggests that Hippopotamidae and Tayassuidae are not closely related (as stated by Pickford, 1986, 1989, 1993) and that the origin of babirusa and warthog (about 10–19 and 5–15 million years ago, respectively) is more recent than supported by current evolutionary reconstructions. The inferred origin of bearded pig is about 2.1 million years old, and genetic divergence among differentSus scrofa populations is probably a Pleistocene event. The addition of new sequences of Suiformes does not help in resolving the phylogenetic position ofHippopotamus amphibius, which shows weak but recurrent linkages with the cetacean evolutionary lineage.To whom correspondence should be addressed.     

Inferring the history of speciation in house mice from autosomal,X‐linked,Y‐linked and mitochondrial genes

Patterns of genetic differentiation among taxa at early stages of divergence provide an opportunity to make inferences about the history of speciation. Here, we conduct a survey of DNA‐sequence polymorphism and divergence at loci on the autosomes, X chromosome, Y chromosome and mitochondrial DNA in samples of Mus domesticus, M. musculus and M. castaneus. We analyzed our data under a divergence with gene flow model and estimate that the effective population size of M. castaneus is 200 000–400 000, of M. domesticus is 100 000–200 000 and of M. musculus is 60 000–120 000. These data also suggest that these species started to diverge approximately 500 000 years ago. Consistent with this recent divergence, we observed considerable variation in the genealogical patterns among loci. For some loci, all alleles within each species formed a monophyletic group, while at other loci, species were intermingled on the phylogeny of alleles. This intermingling probably reflects both incomplete lineage sorting and gene flow after divergence. Likelihood ratio tests rejected a strict allopatric model with no gene flow in comparisons between each pair of species. Gene flow was asymmetric: no gene flow was detected into M. domesticus, while significant gene flow was detected into both M. castaneus and M. musculus. Finally, most of the gene flow occurred at autosomal loci, resulting in a significantly higher ratio of fixed differences to polymorphisms at the X and Y chromosomes relative to autosomes in some comparisons, or just the X chromosome in others, emphasizing the important role of the sex chromosomes in general and the X chromosome in particular in speciation.     

Evaluating Purifying Selection in the Mitochondrial DNA of Various Mammalian Species

Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations.     

Data for estimating eaten prey masses from Eurasian lynx<Emphasis Type="Italic">Lynx Lynx</Emphasis> scats in Central and East Europe

To derive a model which allows estimating eaten prey masses from lynxLynx lynx Linnaeus, 1758 scats, we fed 3 roe deerCapreolus capreolus, 2 wild boarsSus scrofa, 1 fallow deerDama dama, 1 mouflonOvis ammon musimon, 1 European hareLepus europaeus and 1 daily diet of miceMus musculus to two adult lynx. The percentage of prey use decreased with an increase in the offered body mass of the prey individual. Conversion factors from dry matter scat mass to fresh matter mass of eaten prey (y) increased linearly as the eaten mass of the prey individual (x) rose:y = 15.06 + 1.330x,R ² = 0.643,F _1,7 = 12.6,p < 0.01. For estimating eaten prey masses from lynx scats we recommend to use (1) this equation as well as (2) prey type-specific conversion factors and (3) prey type-specific quotients of the eaten prey mass per scat.     

Ultrasonic Vocalizations of Male Mice Differ among Species and Females Show Assortative Preferences for Male Calls

Male house mice (Mus musculus) emit ultrasonic vocalizations (USVs) during courtship, which attract females, and we aimed to test whether females use these vocalizations for species or subspecies recognition of potential mates. We recorded courtship USVs of males from different Mus species, Mus musculus subspecies, and populations (F1 offspring of wild-caught Mus musculus musculus, Mus musculus domesticus (and F1 hybrid crosses), and Mus spicilegus), and we conducted playback experiments to measure female preferences for male USVs. Male vocalizations contained at least seven distinct syllable types, whose frequency of occurrence varied among species, subspecies, and populations. Detailed analyses of multiple common syllable types indicated that Mus musculus and Mus spicilegus could be discriminated based on spectral and temporal characteristics of their vocalizations, and populations of Mus musculus were also distinctive regardless of the classification model used. Females were able to discriminate USVs from different species, and showed assortative preferences for conspecific males. We found no evidence that females discriminate USVs of males from a different subspecies or separate populations of the same species, even though our spectral analyses identified acoustic features that differ between species, subspecies, and populations of the same species. Our results provide the first comparison of USVs between Mus species or between Mus musculus subspecies, and the first evidence that male USVs potentially facilitate species recognition.     

Evolutionary Lability of Context-Dependent Codon Bias in Bacteria

In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered. Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably between genomes. Received: 6 May 1999 / Accepted: 29 October 1999     

Linkage relationships of peptidase-7, Pep-7, in the mouse

An electrophoretically detectable variant of peptidase-7 in Mus musculus has been found and used to locate the structural gene, Pep-7, on chromosome 5. Gene order and recombination frequencies are estimated as Pep-7 3.5±2.0 Rw 8.8±2.2 go 20.0±4.6 bf.     

Ancient onset of geographical divergence,interpopulation genetic exchange,and natural selection on the Mc1r coat‐colour gene in the house mouse (Mus musculus)

We examined genetic variation in house mice from India and Pakistan, a predominant part of the predicted homeland of this species and also the territory of the subspecies Mus musculus castaneus (CAS), using a nuclear marker for seven tandemly arranged genes (Fanca–Spire2–Tcf25–Mc1r–Def8–Afg3l1–Dbndd1) and compared them with those previously determined for mice from other parts of Eurasia. Construction of a network with the concatenate sequences yielded three distinct clusters representing the three major subspecies groups: CAS, Mus musculus domesticus (DOM) and Mus musculus musculus (MUS). STRUCTURE analysis provided evidence for further subdivision of CAS into two main haplogroups within the Indian subcontinent. Single‐gene networks revealed not only gene‐specific architecture for subgrouping in CAS, but also allelic exchange among subspecies. These results suggest the earlier onset of allopatric divergence in the predicted homeland (the Middle East and Indian subcontinent) and subsequent intermittent admixing via gene flow across the CAS haplogroups and among the three subspecies groups. A comparison of the levels of nucleotide diversity among the gene regions revealed a less divergent state in the chromosome region containing Mc1r and its adjacent genes, indicative of a selective sweep, suggesting the involvement of natural selection in the Mc1r allelic variation. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 778–794.     

Allelic diversity at the Mhc-DQA locus in cotton rats (Sigmodon hispidus) and a comparison of DQA sequences within the family Muridae (Mammalia: Rodentia)

 The cotton rat (Sigmodon hispidus) is a common murid rodent of the southern United States, Mexico, and Central America. Using single-stranded conformation polymorphism analysis and DNA sequencing techniques, 11 DQA exon 2 alleles were detected among 180 S. hispidus from Caddo County, Oklahoma, USA. The alleles represent a single locus exhibiting a high level of polymorphism. Nucleotide and amino acid distance values among DQA alleles of S. hispidus were higher than those within Mus musculus and species of Rattus. Although the distribution of polymorphic amino acid residues among alleles of S. hispidus was similiar to that of Mus and Rattus, some residues of the α-helix region were more variable in S. hispidus. Comparisons of nonsynonymous and synonymous substitutions indicated a trend toward higher numbers of nonsynonymous substitutions; however, this difference was not significant statistically among S. hispidus alleles. To examine evolution of DQA alleleswithin Muridae, we performed a phylogenetic analysis that included DQA alleles from S. hispidus, Peromyscus leucopus, M. musculus, R. norvegicus, and six Australian species of Rattus. Results depicted monophyly for each genus, and this concordance between species and gene trees represents a lack of evidence for trans-species persistence of alleles among these genera. Received: 22 October 1998 / Revised: 17 March 1999     

Histamine: Its metabolism and localization in mammary gland

1. Mammary gland of mouse (Mus musculus), rat (Rattus rattus), guinea pig (Cavia porcellus), cow (Bos taurus) and pig (Sus scrofa) contains different but always high concentrations of histamine.2. Generally, the tissue histamine is localized in mast cells, although non-mast cell histamine immuno-reactivity is also present in mammary glands of the mouse, cow and pig. No histamine immunoreactive nerves could be detected.3. Mammary glands are able to synthesize and inactivate histamine; the activity of specific histidine decarboxylase and at least one of the catabolizing enzyme could be demonstrated.4. Histamine fulfils basic criteria for being involved in physiological function of mammary glands.     

Molecular identification of temperate Cricetidae and Muridae rodent species using fecal samples collected in a natural habitat

Molecular species identification from biological material collected at field sites has become an established ecological tool. However, extracting and amplifying DNA from degraded field samples, such as prey remains and feces that have been exposed to the elements, remains a challenge and costly. We collected 115 fecal samples of unknown small mammals, resembling fecal droppings of voles and mice (i.e., Cricetidae and Muridae), from a salt marsh in The Netherlands. We modified a previously published protocol into a relatively low-cost method with a PCR success of 95%. We demonstrate that species identification is possible for both Cricetidae and Muridae species using fecal samples of unknown age deposited in the field. For 90 samples, sequences of the variable control region in the mitochondrial genome were obtained and compared to published DNA sequences of small mammals occurring in north European salt marshes. A single sample, probably environmentally contaminated, appeared as Sus scrofa (n?=?1). We positively identified house mouse Mus musculus, being the positive control (n?=?1), and common vole Microtus arvalis (n?=?88). In 81 sequences of 251 nt without ambiguous bases, ten haplotypes were present. These haplotypes, representing the central lineage of the western subspecies M. arvalis arvalis, were separated by 20 mutations from published control region haplotypes of the western European lineages sampled in France. Unlike earlier studies of cytochrome b variation in coastal European populations, we did not find indications of recent purging of genetic variation in our study area.     

Genetic diversity of rodent species sold in South African pet shops

Murid rodents are considered globally important invasive species, yet they are still sold in the pet trade. Little is known about the genetic diversity of traded rodents, and many species are incorrectly identified in the pet trade. We used mitochondrial gene regions to assess the taxonomy and genetic diversity of 149 rodents sold in pet shops across eight South African provinces. We identified a total of 112 specimens as Mus musculus, while 31 were Rattus norvegicus, and six were identified as the southern African endemic, southern multimammate mouse Mastomys coucha. Phylogenetic analyses revealed that the three species were monophyletic. Mus musculus and R. norvegicus showed higher levels of genetic diversity, with 19 unique mtDNA haplotypes recovered for M. musculus and eight haplotypes for R. norvegicus. KwaZulu-Natal, Western Cape and Gauteng Provinces had the most unique haplotypes than other provinces. Our findings showed that non-native species are widely distributed in the South African pet trade industry, while M. coucha was not widely traded, although recorded in three provinces. This suggests that most provinces comply with the trade regulations on native species, but the threat of invasive rodents to South Africa's unique biodiversity is highlighted.     

Molecular Cloning, Mapping, and Polymorphism of the Porcine SCG2 gene

The secretogranin II (SCG2) gene is associated with the synthesis and secretion of follicle-stimulating hormone and luteinizing hormone. In the present study, we have determined the complete cDNA sequence of pig SCG2, which was submitted to GenBank with accession no. AY870646. Its complete open reading frame of 1,851 nucleotides encodes 616 amino acids. The predicted protein shares 80–87% identity with mouse, human, and bovine SCG2 proteins, and all four species share almost complete identity in the secretoneurin and EM66 domains. Pig SCG2 is a protein of 589 amino acids and 68,132 Da, preceded by a signal peptide of 27 residues. It contains nine pairs of dibasic residues, which are used as potential cleavage sites for generation of physiologically active peptides. Analysis of the SCG2 gene across the INRA-Minnesota porcine radiation hybrid panel indicates close linkage with microsatellite marker SW2608, located on Sus scrofa chromosome 15 (SSC15) q25, which harbors several QTL for ovulation rate and meat quality. Comparative sequencing and EST analysis revealed nine SNPs in porcine SCG2 cDNA, including seven SNPs in the coding region and two SNPs in the 3′ UTR. Four nonsynonymous SNPs (G622A, G1671T, C1718T, and A1790C) resulted in amino acid substitutions of Ala→Thr, Glu→Asp, Pro→Leu, and Asn→Thr, respectively.