JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
Contrasting patterns of polymorphism and selection in bacterial-sensing toll-like receptor 4 in two house mouse subspecies.
Ecol Evol
PUBLISHED: 06-20-2014
Show Abstract
Hide Abstract
Detailed investigation of variation in genes involved in pathogen recognition is crucial for understanding co-evolutionary processes between parasites and their hosts. Triggering immediate innate response to invading microbes, Toll-like receptors (TLRs) belong presently among the best-studied receptors of vertebrate immunity. TLRs exhibit remarkable interspecific variation and also intraspecific polymorphism is well documented. In humans and laboratory mice, several studies have recently shown that single amino acid substitution may significantly alter receptor function. Unfortunately, data concerning polymorphism in free-living species are still surprisingly scarce. In this study, we analyzed the polymorphism of Toll-like receptor 4 (Tlr4) over the Palearctic range of house mouse (Mus musculus). Our results reveal contrasting evolutionary patterns between the two recently (0.5 million years ago) diverged house mouse subspecies: M. m. domesticus (Mmd) and M. m. musculus (Mmm). Comparison with cytochrome b indicates strong directional selection in Mmd Tlr4. Throughout the whole Mmd western Palaearctic region, a single variant of the ligand-binding region is spread, encoded mainly by one dominant haplotype (71% of Mmd). In contrast, Tlr4 in Mmm is much more polymorphic with several haplotypes at intermediate frequencies. Moreover, we also found clear signals of recombination between two principal haplogroups in Mmm, and we identified eight sites under positive selection in our dataset. Our results suggest that observed differences in Tlr4 diversity may be attributed to contrasting parasite-mediated selection acting in the two subspecies.
Related JoVE Video
Protein evolution of Toll-like receptors 4, 5 and 7 within Galloanserae birds.
Genet. Sel. Evol.
PUBLISHED: 06-11-2014
Show Abstract
Hide Abstract
Toll-like receptors (TLR) are essential activators of the innate part of the vertebrate immune system. In this study, we analysed the interspecific variability of three TLR (bacterial-sensing TLR4 and TLR5 and viral-sensing TLR7) within the Galloanserae bird clade, investigated their phylogeny, assessed their structural conservation and estimated site-specific selection pressures.
Related JoVE Video
First evidence of independent pseudogenization of toll-like receptor 5 in passerine birds.
Dev. Comp. Immunol.
PUBLISHED: 01-17-2014
Show Abstract
Hide Abstract
Toll-like receptor 5 (TLR5) is a Pattern-recognition receptor responsible for microbial flagellin detection in vertebrates and, hence, recognition of potentially pathogenic bacteria. Herein, we report emergence of TLR5 pseudogene in several phylogenetic lineages of passerine birds (Aves: Passeriformes). Out of 47 species examined in this study 18 possessed a TLR5 pseudogene. Phylogenetic analysis together with the type of mutation responsible for pseudogenization indicate that TLR5 pseudogene emerged at least seven times independently in passerines. Lack of any functional copy of the gene has been verified based on TLR5 mRNA blood expression in four species representing the four main passerine lineages possessing the TLR5 pseudogene. Our results suggest that the non-functional TLR5 variant is fixed in those lineages or, at least, that individuals homozygote in the TLR5 pseudogene are frequent in the investigated species. Further research is needed to assess the impact of the TLR5 loss on immunological performance in birds.
Related JoVE Video
Contrasted evolutionary histories of two Toll-like receptors (Tlr4 and Tlr7) in wild rodents (MURINAE).
BMC Evol. Biol.
PUBLISHED: 07-11-2013
Show Abstract
Hide Abstract
In vertebrates, it has been repeatedly demonstrated that genes encoding proteins involved in pathogen-recognition by adaptive immunity (e.g. MHC) are subject to intensive diversifying selection. On the other hand, the role and the type of selection processes shaping the evolution of innate-immunity genes are currently far less clear. In this study we analysed the natural variation and the evolutionary processes acting on two genes involved in the innate-immunity recognition of Microbe-Associated Molecular Patterns (MAMPs).
Related JoVE Video
Parentage analysis of Ansells mole-rat family groups indicates a high reproductive skew despite relatively relaxed ecological constraints on dispersal.
Mol. Ecol.
PUBLISHED: 03-14-2013
Show Abstract
Hide Abstract
To better understand evolutionary pathways leading to eusociality, interspecific comparisons are needed, which would use a common axis, such as that of reproductive skew, to array species. African mole-rats (Bathyergidae, Rodentia) provide an outstanding model of social evolution because of a wide range of social organizations within a single family; however, their reproductive skew is difficult to estimate, due to their cryptic lifestyle. A maximum skew could theoretically be reached in groups where reproduction is monopolized by a stable breeding pair, but the value could be decreased by breeding-male and breeding-female turnover, shared reproduction and extra-group mating. The frequency of such events should be higher in species or populations inhabiting mesic environments with relaxed ecological constraints on dispersal. To test this prediction, we studied patterns of parentage and relatedness within 16 groups of Ansells mole-rat (Fukomys anselli) in mesic miombo woodland. Contrary to expectation, there was no shared reproduction (more than one breeder of a particular sex) within the studied groups, and proportion of immigrants and offspring not assigned to current breeding males was low. The within-group parentage and relatedness patterns observed resemble arid populations of eusocial Fukomys damarensis, rather than a mesic population of social Cryptomys hottentotus. As a possible explanation, we propose that the extent ecological conditions affect reproductive skew may be markedly affected by life history and natural history traits of the particular species and genera.
Related JoVE Video
Strong population genetic structuring in an annual fish, Nothobranchius furzeri, suggests multiple savannah refugia in southern Mozambique.
BMC Evol. Biol.
PUBLISHED: 03-04-2013
Show Abstract
Hide Abstract
Intraspecific genetic variation of African fauna has been significantly affected by pronounced climatic fluctuations in Plio-Pleistocene, but, with the exception of large mammals, very limited empirical data on diversity of natural populations are available for savanna-dwelling animals. Nothobranchius furzeri is an annual fish from south-eastern Africa, inhabiting discrete temporary savannah pools outside main river alluvia. Their dispersal is limited and population processes affecting its genetic structure are likely a combination of those affecting terrestrial and aquatic taxa. N. furzeri is a model taxon in ageing research and several populations of known geographical origin are used in laboratory studies. Here, we analysed the genetic structure, diversity, historical demography and temporal patterns of divergence in natural populations of N. furzeri across its entire distribution range.
Related JoVE Video
Multilocus phylogeography of the European ground squirrel: cryptic interglacial refugia of continental climate in Europe.
Mol. Ecol.
PUBLISHED: 01-17-2013
Show Abstract
Hide Abstract
The theory of classical and cryptic Pleistocene refugia is based mainly on historical changes in temperature, and the refugia are usually defined within a latitudinal gradient. However, the gradient of oceanic-continental climate (i.e. longitudinal) was also significantly variable during glacial cycles with important biotic consequences. Range-wide phylogeography of the European ground squirrel (EGS) was used to interpret the evolutionary and palaeogeographical history of the species in Europe and to shed light on its glacial-interglacial dynamic. The EGS is a steppe-inhabiting species and the westernmost member of the genus in the Palaearctic region. We have analysed 915 specimens throughout the present natural range by employing mitochondrial DNA sequences (cytochrome b gene) and 12 nuclear microsatellite markers. The reconstructed phylogeography divides the species into two main geographical groups, with deep substructuring within both groups. Bulgaria is the centre of the ancestral area, and it also has the highest genetic diversity within the species. The northernmost group of the EGS survived in the southern part of Pannonia throughout several glacial-interglacial cycles. Animals from this population probably repeatedly colonized areas further to the north and west during the glacial periods, while in the interglacial periods, the EGS distribution contracted back to this Pannonian refugium. The EGS thus represents a species with a glacial expansion/interglacial contraction palaeogeographical dynamics, and the Pannonian and southeastern Balkanian steppes are supported as cryptic refugia of continental climate during Pleistocene interglacials.
Related JoVE Video
MHC class IIB exon 2 polymorphism in the Grey partridge (Perdix perdix) is shaped by selection, recombination and gene conversion.
PLoS ONE
PUBLISHED: 01-01-2013
Show Abstract
Hide Abstract
Among bird species, the most studied major histocompatibility complex (MHC) is the chicken MHC. Although the number of studies on MHC in free-ranging species is increasing, the knowledge on MHC variation in species closely related to chicken is required to understand the peculiarities of bird MHC evolution. Here we describe the variation of MHC class IIB (MHCIIB) exon 2 in a population of the Grey partridge (Perdix perdix), a species of high conservation concern throughout Europe and an emerging galliform model in studies of sexual selection. We found 12 alleles in 108 individuals, but in comparison to other birds surprisingly many sites show signatures of historical positive selection. Individuals displayed between two to four alleles both on genomic and complementary DNA, suggesting the presence of two functional MHCIIB loci. Recombination and gene conversion appear to be involved in generating MHCIIB diversity in the Grey partridge; two recombination breakpoints and several gene conversion events were detected. In phylogenetic analysis of galliform MHCIIB, the Grey partridge alleles do not cluster together, but are scattered through the tree instead. Thus, our results indicate that the Grey partridge MHCIIB is comparable to most other galliforms in terms of copy number and population polymorphism.
Related JoVE Video
Evaluation of two approaches to genotyping major histocompatibility complex class I in a passerine-CE-SSCP and 454 pyrosequencing.
Mol Ecol Resour
PUBLISHED: 10-24-2011
Show Abstract
Hide Abstract
Genes of the highly dynamic major histocompatibility complex (MHC) are directly linked to individual fitness and are of high interest in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high levels of polymorphism in the MHC region, making genotyping of MHC a challenging task. Here, we compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) analysis and 454 GS FLX Titanium pyrosequencing. According to our findings, the number of MHC variants (called alleles for simplicity) detected by CE-SSCP is significantly lower than detected by 454. To resolve discrepancies between the two methods, we cloned and Sanger sequenced a MHC class I amplicon for an individual with high number of alleles. We found a perfect congruence between cloning/Sanger sequencing results and 454. Thus, in case of multi-locus amplification, CE-SSCP considerably underestimates individual MHC diversity. However, numbers of alleles detected by both methods are significantly correlated, although the correlation is weak (r = 0.32). Thus, in systems with highly duplicated MHC, 454 provides more reliable information on individual diversity than CE-SSCP.
Related JoVE Video
Tula virus in populations of small terrestrial mammals in a rural landscape.
Vector Borne Zoonotic Dis.
PUBLISHED: 04-28-2010
Show Abstract
Hide Abstract
Over 5 years (2000-2004), populations of small mammals from a rural landscape in southern Moravia (Czech Republic) were investigated for the presence of Tula virus (TULV) antigen using the ELISA set Hantagnost. In total, 1566 individuals from 10 species were examined. The prevalence in the common vole (Microtus arvalis Pallas 1778), the main reservoir of TULV, was 10% (n = 871). The prevalence of TULV antigen increases with its population numbers. The highest number of TULV antigen-positive common voles was found in set-aside plots and winter crops, such as rape and winter wheat. All these habitats are important for common vole overwintering. Older and heavier individuals were more often hantavirus antigen positive. From the other small mammal species, 186 pygmy field mice (Apodemus uralensis Pallas, 1811) were examined, of which 3 were positive, which represents the first hantavirus antigen positive record for this species, and of 195 wood mice (Apodemus sylvaticus Linnaeus, 1758) only 1 was positive. The remaining five rodent species (Apodemus flavicollis Melchior, 1834, Mus musculus Linnaeus, 1758, Micromys minutus Pallas, 1771, Myodes glareolus Schreber, 1780, Microtus subterraneus de Sélys-Longchamps, 1836) and two Soricomorpha (Sorex araneus Linnaeus, 1758, Sorex minutus Linnaeus, 1766) were hantavirus antigen negative.
Related JoVE Video
Mate choice for nonadditive genetic benefits correlate with MHC dissimilarity in the rose bitterling (Rhodeus ocellatus).
Evolution
PUBLISHED: 02-09-2010
Show Abstract
Hide Abstract
Good genes models of mate choice predict additive genetic benefits of choice whereas the compatibility hypothesis predicts nonadditive fitness benefits. Here the Chinese rose bitterling, Rhodeus ocellatus, a freshwater fish with a resource-based mating system, was used to separate additive and nonadditive genetic benefits of female mate choice. A sequential blocked mating design was used to test female mate preferences, and a cross-classified breeding design coupled with in vitro fertilizations for fitness benefits of mate choice. In addition, the offspring produced by the pairing of preferred and nonpreferred males were reared to maturity and their fitness traits were compared. Finally, the MHC DAB1 gene was typed and male MHC genotypes were correlated with female mate choice. Females showed significant mate preferences but preferences were not congruent among females. There was a significant interaction of male and female genotype on offspring survival, rate of development, growth rate, and body size. No significant male additive effects on offspring fitness were observed. Female mate preferences corresponded with male genetic compatibility, which correlated with MHC dissimilarity. It is proposed that in the rose bitterling genetic compatibility is the mechanism by which females obtain a fitness benefit through mate choice and that male MHC dissimilarity, likely mediated by odor cues, indicates genetic compatibility.
Related JoVE Video
Breeding resource distribution affects selection gradients on male phenotypic traits: experimental study on lifetime reproductive success in the bitterling fish (Rhodeus amarus).
Evolution
PUBLISHED: 02-14-2009
Show Abstract
Hide Abstract
The spatial distribution of breeding resources can have pronounced demographic and evolutionary consequences. We used 20 experimental groups of the bitterling (Rhodeus amarus), an annual fish with a promiscuous, resource-based mating system, and extended breeding season to investigate how the spatial distribution (clumped or regular) of bitterling oviposition sites (live freshwater mussels) affected offspring production, variation in reproductive success, and directional selection on phenotypic traits over their entire reproductive lifetime. We did not detect any effect of resource distribution on offspring production or variation in reproductive success among individual fish, although variation between replicates was higher with a clumped distribution. This finding is discussed with regard to the incidence of alternative mating behaviors (sneaking) within the limitations imposed by our experimental design. Breeding resource distribution had a significant effect on selection on male phenotypic traits. Stronger directional selection on traits associated with intrasexual competition for fertilizations, gonad mass (an indicator of sperm competition), and the extent of red, carotenoid-based pigment in the iris (an index of dominance status), was detected with a clumped resource distribution. With a regular resource distribution, a stronger positive selection on male body size was detected. We discuss the implications of our results for natural populations.
Related JoVE Video
Absence of spermatozoal CD46 protein expression and associated rapid acrosome reaction rate in striped field mice (Apodemus agrarius).
Reprod. Biol. Endocrinol.
PUBLISHED: 01-25-2009
Show Abstract
Hide Abstract
In rodents, the cell surface complement regulatory protein CD46 is expressed solely on the spermatozoal acrosome membrane. Ablation of the CD46 gene is associated with a faster acrosome reaction. Sperm from Apodemus flavicollis (yellow-necked field mice), A. microps (pygmy field mice) and A. sylvaticus (European wood mice) fail to express CD46 protein and exhibit a more rapid acrosome reaction rate than Mus (house mice) or BALB/c mice. A. agrarius (striped field mice) belong to a different Apodemus subgenus and have pronounced promiscuity and large relative testis size. The aim of this study was to determine whether A. agrarius sperm fail to express CD46 protein and, if so, whether A. agrarius have a faster acrosome reaction than Mus.
Related JoVE Video
Invasion genetics of the introduced black rat (Rattus rattus) in Senegal, West Africa.
Mol. Ecol.
Show Abstract
Hide Abstract
An understanding of the evolutionary history and dynamics of invasive species is required for the construction of predictive models of future spread and the design of biological management measures. The black rat (Rattus rattus) is a major vertebrate invader with a worldwide distribution. Despite the severe ecological, economic and health impacts of this species, its evolutionary history has been little studied. We carried out extensive specimen sampling in Senegal, West Africa, and used microsatellite markers to describe the pattern and processes of invasion in this large continental area. The genetic data obtained were combined with historical knowledge concerning the presence of this species in Senegal. Data were analysed by a combination of Bayesian clustering and approximate Bayesian computation methods. The invasion pathways closely paralleled the history of human trade routes in Senegal. In several places, we detected the occurrence of multiple introductions from genetically different sources. Long-distance migration between towns and villages was also observed. Our findings suggest that genetic bottlenecks and admixture have played a major role in shaping the genetics of invasive black rats. These two processes may generate genetic novelty and favour rapid evolution along the invasion pathways.
Related JoVE Video
High diversity of RNA viruses in rodents, Ethiopia.
Emerging Infect. Dis.
Show Abstract
Hide Abstract
We investigated synanthropic small mammals in the Ethiopian Highlands as potential reservoirs for human pathogens and found that 2 rodent species, the Ethiopian white-footed mouse and Awash multimammate mouse, are carriers of novel Mobala virus strains. The white-footed mouse also carries a novel hantavirus, the second Murinae-associated hantavirus found in Africa.
Related JoVE Video
High prevalence and species diversity of Helicobacter spp. detected in wild house mice.
Appl. Environ. Microbiol.
Show Abstract
Hide Abstract
PCR diagnostics detected 100% prevalence of Helicobacter in 425 wild house mice (Mus musculus) from across central Europe. Of seven species identified, the five most frequent were Helicobacter rodentium (78%), H. typhlonius (53%), H. hepaticus (41%), H. bilis (30%), and H. muridarum (1%). Double infections were more common (42%) than single (30%) and triple (21%) infections. Wild house mice could be considered potential reservoirs of Helicobacter strains for both humans and other vertebrates.
Related JoVE Video
Development and characterization of multiplex panels of microsatellite markers for Syphacia obvelata, a parasite of the house mouse (Mus musculus), using a high throughput DNA sequencing approach.
Mol. Biochem. Parasitol.
Show Abstract
Hide Abstract
Syphacia obvelata is a common gastro-intestinal parasitic nematode of the house mouse (Mus musculus), a prime model rodent species. Investigations of the genetic structure, variability of parasite populations and other biological aspects of this host-parasite system are limited due to the lack of genetic resources for S. obvelata. To fill this gap, we developed a set of microsatellite markers for S. obvelata, using a 454 pyrosequencing approach. We designed three multiplex panels allowing genotyping of 10 polymorphic loci and scrutinized them on 42 samples from two different regions inhabited by two different house mouse subspecies (Mus musculus musculus and M. m. domesticus). The numbers of alleles ranged from 2 to 6 with mean observed heterozygosities 0.1476 and 0.2095 for domesticus and musculus worms, respectively. The described markers will facilitate further studies on population biology and co-evolution of this host-parasite system.
Related JoVE Video
Female rose bitterling prefer MHC-dissimilar males: experimental evidence.
PLoS ONE
Show Abstract
Hide Abstract
The role of genetic benefits in female mate choice remains a controversial aspect of sexual selection theory. In contrast to "good allele" models of sexual selection, "compatible allele" models of mate choice predict that females prefer mates with alleles complementary to their own rather than conferring additive effects. While correlative results suggest complementary genetic effects to be plausible, direct experimental evidence is scarce. A previous study on the Chinese rose bitterling (Rhodeus ocellatus) demonstrated a positive correlation between female mate choice, offspring growth and survival, and the functional dissimilarity between the Major Histocompatibility Complex (MHC) alleles of males and females. Here we directly tested whether females used cues associated with MHC genes to select genetically compatible males in an experimental framework. By sequentially pairing females with MHC similar and dissimilar males, based on a priori known MHC profiles, we showed that females discriminated between similar and dissimilar males and deposited significantly more eggs with MHC dissimilar males. Notably, the degree of dissimilarity was an important factor for female decision to mate, possibly indicating a potential threshold value of dissimilarity for decision making, or of an indirect effect of the MHC.
Related JoVE Video
Rodent damage to natural and replanted mountain forest regeneration.
ScientificWorldJournal
Show Abstract
Hide Abstract
Impact of small rodents on mountain forest regeneration was studied in National Nature Reserve in the Beskydy Mountains (Czech Republic). A considerable amount of bark damage was found on young trees (20%) in spring after the peak abundance of field voles (Microtus agrestis) in combination with long winter with heavy snowfall. In contrast, little damage to young trees was noted under high densities of bank voles (Myodes glareolus) with a lower snow cover the following winter. The bark of deciduous trees was more attractive to voles (22% damaged) than conifers (8%). Young trees growing in open and grassy localities suffered more damage from voles than those under canopy of forest stands (?² = 44.04, P < 0.001). Natural regeneration in Nature Reserve was less damaged compared to planted trees (?² = 55.89, P < 0.001). The main factors influencing the impact of rodent species on tree regeneration were open, grassy habitat conditions, higher abundance of vole species, tree species preferences- and snow-cover condition. Under these conditions, the impact of rodents on forest regeneration can be predicted. Foresters should prefer natural regeneration to the artificial plantings.
Related JoVE Video

What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.