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Characterization and 454 pyrosequencing of Major
Histocompatibility Complex class I genes in the
great tit reveal complexity in a passerine system
Background:
The critical role of Major Histocompatibility Complex (Mhc) genes in disease resistance andtheir highly polymorphic nature make them exceptional candidates for studies investigatinggenetic effects on survival, mate choice and conservation. Species that harbor many Mhc lociand high allelic diversity are particularly intriguing as they are potentially under strongselection and studies of such species provide valuable information as to the mechanismsmaintaining Mhc diversity. However comprehensive genotyping of complex multilocussystems has been a major challenge to date with the result that little is known about theconsequences of this complexity in terms of fitness effects and disease resistance.
Results:
In this study, we genotyped the Mhc class I exon 3 of the great tit (Parus major) from twonest-box breeding populations near Oxford, UK that have been monitored for decades.Characterization of Mhc class I exon 3 was adopted and bidirectional sequencing was carriedusing the 454 sequencing platform. Full analysis of sequences through a stepwise variantvalidation procedure allowed reliable typing of more than 800 great tits based on 214,357reads; from duplicates we estimated the repeatability of typing as 0.94. A total of 862 alleleswere detected, and the presence of at least 16 functional loci was shown - the highest numbercharacterized in a wild bird species. Finally, the functional alleles were grouped into 17supertypes based on their antigen binding affinities.
Conclusions:
We found extreme complexity at the Mhc class I of the great tit both in terms of allelicdiversity and gene number. The presence of many functional loci was shown, together with apseudogene family and putatively non-functional alleles; there was clear evidence thatfunctional alleles were under strong balancing selection. This study is the first step towardsan in-depth analysis of this gene complex in this species, which will help understanding howparasite-mediated and sexual selection shape and maintain host genetic variation in nature.We believe that study systems like ours can make important contributions to the field ofevolutionary biology and emphasize the necessity of integrating long-term field-based studieswith detailed genetic analysis to unravel complex evolutionary processes.
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Phylogeography and dispersal in the velvet gecko
(Oedura lesueurii), and potential implications for
conservation of an endangered snake
(Hoplocephalus bungaroides)
Background:
To conserve critically endangered predators, we also need to conserve the prey species uponwhich they depend. Velvet geckos (Oedura lesueurii) are a primary prey for the endangeredbroad-headed snake (Hoplocephalus bungaroides), which is restricted to sandstone habitatsin southeastern Australia. We sequenced the ND2 gene from 179 velvet geckos, to clarify thelizards' phylogeographic history and landscape genetics. We also analysed 260 records froma longterm (3-year) capture-mark-recapture program at three sites, to evaluate dispersal ratesof geckos as a function of locality, sex and body size.
Results:
The genetic analyses revealed three ancient lineages in the north, south and centre of thespecies' current range. Estimates of gene flow suggest low dispersal rates, constrained by theavailability of contiguous rocky habitat. Mark-recapture records confirm that these lizards arehighly sedentary, with most animals moving < 30 m from their original capture site even overmulti-year periods.
Conclusion:
The low vagility of these lizards suggests that they will be slow to colonise vacant habitatpatches; and hence, efforts to restore degraded habitats for broad-headed snakes may need toinclude translocation of lizards.
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Molecular evolution of pentatricopeptide repeat
genes reveals truncation in species lacking an editing
target and structural domains under distinct
selective pressures
Background:
Pentatricopeptide repeat (PPR) proteins are required for numerous RNA processing events inplant organelles including C-to-U editing, splicing, stabilization, and cleavage. Fifteen PPRproteins are known to be required for RNA editing at 21 sites in Arabidopsis chloroplasts,and belong to the PLS class of PPR proteins. In this study, we investigate the co-evolution offour PPR genes (CRR4, CRR21, CLB19, and OTP82) and their six editing targets inBrassicaceae species. PPR genes are composed of approximately 10 to 20 tandem repeats andeach repeat has two alpha-helical regions, helix A and helix B, that are separated by short coilregions. Each repeat and structural feature was examined to determine the selective pressureson these regions.
Results:
All of the PPR genes examined are under strong negative selection. Multiple independentlosses of editing site targets are observed for both CRR21 and OTP82. In several specieslacking the known editing target for CRR21, PPR genes are truncated near the 17th PPRrepeat. The coding sequences of the truncated CRR21 genes are maintained under strongnegative selection; however, the 3' UTR sequences beyond the truncation site havesubstantially diverged. Phylogenetic analyses of four PPR genes show that sequencescorresponding to helix A are highly compared to helix B sequences. Differential evolutionaryselection of helix A versus helix B is observed in both plant and mammalian PPR genes.
Conclusion:
PPR genes and their cognate editing sites are mutually constrained in evolution. Editing sitesare frequently lost by replacement of an edited C with a genomic T. After the loss of anediting site, the PPR genes are observed with three outcomes: first, few changes are detectedin some cases; second, the PPR gene is present as a pseudogene; and third, the PPR gene ispresent but truncated in the C-terminal region. The retention of truncated forms of CRR21that are maintained under strong negative selection even in the absence of an editing sitetarget suggests that unrecognized function(s) might exist for this PPR protein. PPR genesequences that encode helix A are under strong selection, and could be involved in RNAsubstrate recognition.
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A genome-wide study of recombination rate
variation in Bartonella henselae
Background:
Rates of recombination vary by three orders of magnitude in bacteria but the reasons for thisvariation is unclear. We performed a genome-wide study of recombination rate variationamong genes in the intracellular bacterium Bartonella henselae, which has among the lowestestimated ratio of recombination relative to mutation in prokaryotes.
Results:
The 1.9 Mb genomes of B. henselae strains IC11, UGA10 and Houston-1 genomes showedonly minor gene content variation. Nucleotide sequence divergence levels were less than 1%and the relative rate of recombination to mutation was estimated to 1.1 for the genomeoverall. Four to eight segments per genome presented significantly enhanced divergences, themost pronounced of which were the virB and trw gene clusters for type IV secretion systemsthat play essential roles in the infection process. Consistently, multiple recombination eventswere identified inside these gene clusters. High recombination frequencies were alsoobserved for a gene putatively involved in iron metabolism. A phylogenetic study of thisgene in 80 strains of Bartonella quintana, B. henselae and B. grahamii indicated differentpopulation structures for each species and revealed horizontal gene transfers acrossBartonella species with different host preferences.
Conclusions:
Our analysis has shown little novel gene acquisition in B. henselae, indicative of a closedpan-genome, but higher recombination frequencies within the population than previouslyestimated. We propose that the dramatically increased fixation rate for recombination eventsat gene clusters for type IV secretion systems is driven by selection for sequence variability.
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Phylogenomics of the benzoxazinoid biosynthetic
pathway of Poaceae: gene duplications and origin of
the Bx cluster
Background:
The benzoxazinoids 2,4-dihydroxy-1,4-benzoxazin-3-one (DIBOA) and 2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOA), are key defense compounds present in majoragricultural crops such as maize and wheat. Their biosynthesis involves nine enzymesthought to form a linear pathway leading to the storage of DI(M)BOA as glucosideconjugates. Seven of the genes (Bx1-Bx6 and Bx8) form a cluster at the tip of the short arm ofmaize chromosome 4 that includes four P450 genes (Bx2-5) belonging to the same CYP71Csubfamily. The origin of this cluster is unknown.
Results:
We show that the pathway appeared following several duplications of the TSA gene (alpha-subunit of tryptophan synthase) and of a Bx2-like ancestral CYP71C gene and the recruitmentof Bx8 before the radiation of Poaceae. The origins of Bx6 and Bx7 remain unclear. Wedemonstrate that the Bx2-like CYP71C ancestor was not committed to the benzoxazinoidpathway and that after duplications the Bx2-Bx5 genes were under positive selection on a fewsites and underwent functional divergence, leading to the current specific biochemicalproperties of the enzymes. The absence of synteny between available Poaceae genomesinvolving the Bx gene regions is in contrast with the conserved synteny in the TSA generegion.
Conclusions:
These results demonstrate that rearrangements following duplications of an IGL/TSA geneand of a CYP71C gene probably resulted in the clustering of the new copies (Bx1 and Bx2) atthe tip of a chromosome in an ancestor of grasses. Clustering favored cosegregation and tip chromosomal location favored gene rearrangements that allowed the further recruitment ofgenes to the pathway. These events, a founding event and elongation events, may have beenthe key to the subsequent evolution of the benzoxazinoid biosynthetic cluster.
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Immune genes undergo more adaptive evolution
than non-immune system genes in Daphnia pulex
Background:
Understanding which parts of the genome have been most influenced by adaptive evolutionremains an unsolved puzzle. Some evidence suggests that selection has the greatest impact onregions of the genome that interact with other evolving genomes, including loci that areinvolved in host-parasite co-evolutionary processes. In this study, we used a populationgenetic approach to test this hypothesis by comparing DNA sequences of 30 putative immunesystem genes in the crustacean Daphnia pulex with 24 non-immune system genes.
Results:
In support of the hypothesis, results from a multilocus extension of the McDonald-Kreitman(MK) test indicate that immune system genes as a class have experienced more adaptiveevolution than non-immune system genes. However, not all immune system genes showevidence of adaptive evolution. Additionally, we apply single locus MK tests and calculatepopulation genetic parameters at all loci in order to characterize the mode of selection(directional versus balancing) in the genes that show the greatest deviation from neutralevolution.
Conclusions:
Our data are consistent with the hypothesis that immune system genes undergo more adaptiveevolution than non-immune system genes, possibly as a result of host-parasite arms races.The results of these analyses highlight several candidate loci undergoing adaptive evolutionthat could be targeted in future studies.
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Genomic characterization of the European sea bass
Dicentrarchus labrax reveals the presence of a novel
uncoupling protein (UCP) gene family member in
the teleost fish lineage
Background:
Uncoupling proteins (UCP) are evolutionary conserved mitochondrial carriers that controlenergy metabolism and therefore play important roles in several physiological processes suchas thermogenesis, regulation of reactive oxygen species (ROS), growth control, lipidmetabolism and regulation of insulin secretion. Despite their importance in variousphysiological processes, their molecular function remains controversial. The evolution andphylogenetic distribution may assist to identify their general biological function andstructure-function relationships. The exact number of uncoupling protein genes in the fishgenome and their evolution is unresolved.
Results:
Here we report the first characterisation of UCP gene family members in sea bass,Dicentrarchus labrax, and then retrace the evolution of the protein family in vertebrates. FourUCP genes that are shared by five other fish species were identified in sea bass genome.Phylogenetic reconstitution among vertebrate species and synteny analysis revealed thatUCP1, UCP2 and UCP3 evolved from duplication events that occurred in the commonancestor of vertebrates, whereas the novel fourth UCP originated specifically in the teleostlineage. Functional divergence analysis among teleost species revealed specific amino acidpositions that have been subjected to altered functional constraints after duplications.
Conclusions:
This work provides the first unambiguous evidence for the presence of a fourth UCP gene inteleost fish genome and brings new insights into the evolutionary history of the gene family.Our results suggest functional divergence among paralogues which might result from longtermand differential selective pressures, and therefore, provide the indication that UCP genesmay have diverse physiological functions in teleost fishes. Further experimental analysis ofthe critical amino acids identified here may provide valuable information on the physiologicalfunctions of UCP genes.
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Selection for altruism through random drift in variable
size populations
Background:
Altruistic behavior is defined as helping others at a cost to oneself and a lowered fitness. Thelower fitness implies that altruists should be selected against, which is in contradiction withtheir widespread presence is nature. Present models of selection for altruism (kin ormultilevel) show that altruistic behaviors can have 'hidden' advantages if the 'common good'produced by altruists is restricted to some related or unrelated groups. These models aremostly deterministic, or assume a frequency dependent fitness.
Results:
Evolutionary dynamics is a competition between deterministic selection pressure andstochastic events due to random sampling from one generation to the next. We show here thatan altruistic allele extending the carrying capacity of the habitat can win by increasing therandom drift of "selfish" alleles. In other terms, the fixation probability of altruistic genes canbe higher than those of a selfish ones, even though altruists have a smaller fitness. Moreoverwhen populations are geographically structured, the altruists advantage can be highlyamplified and the fixation probability of selfish genes can tend toward zero. The aboveresults are obtained both by numerical and analytical calculations. Analytical results areobtained in the limit of large populations.
Conclusions:
The theory we present does not involve kin or multilevel selection, but is based on theexistence of random drift in variable size populations. The model is a generalization of theoriginal Fisher-Wright and Moran models where the carrying capacity depends on thenumber of altruists.
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The phylogenetics of Anguillicolidae (Nematoda: Anguillicolidea), swimbladder parasites of eels
Background:
Anguillicolidae Yamaguti, 1935 is a family of parasitic nematode infecting fresh-water eels of the genus Anguilla, comprising five species in the genera Anguillicola and Anguillicoloides. Anguillicoloides crassus is of particular importance, as it has recently spread from its endemic range in the Eastern Pacific to Europe and North America, where it poses a significant threat to new, naive hosts such as the economic important eel species Anguilla anguilla and Anguilla rostrata. The Anguillicolidae are therefore all potentially invasive taxa, but the relationships of the described species remain unclear. Anguillicolidae is part of Spirurina, a diverse clade made up of only animal parasites, but placement of the family within Spirurina is based on limited data.
Results:
We generated an extensive DNA sequence dataset from three loci (the 5' one-third of the nuclear small subunit ribosomal RNA, the D2-D3 region of the nuclear large subunit ribosomal RNA and the 5' half of the mitochondrial cytochrome c oxidase I gene) for the five species of Anguillicolidae and used this to investigate specific and generic boundaries within the family, and the relationship of Anguillicolidae to other spirurine nematodes. Neither nuclear nor mitochondrial sequences supported monophyly of Anguillicoloides. Genetic diversity within the African species Anguillicoloides papernai was suggestive of cryptic taxa, as was the finding of distinct lineages of Anguillicoloides novaezelandiae in New Zealand and Tasmania. Phylogenetic analysis of the Spirurina grouped the Anguillicolidae together with members of the Gnathostomatidae and Seuratidae.
Conclusions:
The Anguillicolidae is part of a complex radiation of parasitic nematodes of vertebrates with wide host diversity (chondrichthyes, teleosts, squamates and mammals), most closely related to other marine vertebrate parasites that also have complex life cycles. Molecular analyses do not support the recent division of Anguillicolidae into two genera. The described species may hide cryptic taxa, identified here by DNA taxonomy, and this DNA barcoding approach may assist in tracking species invasions. The propensity for host switching, and thus the potential for invasive behaviour, is found in A. crassus, A. novaezelandiae and A. papernai, and thus may be common to the group.
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Perforin evolved from a gene duplication of MPEG1,
followed by a complex pattern of gene gain and loss
within Euteleostomi
Background:
The pore-forming protein perforin is central to the granule-exocytosis pathway used bycytotoxic lymphocytes to kill abnormal cells. Although this mechanism of killing isconserved in bony vertebrates, cytotoxic cells are present in other chordates andinvertebrates, and their cytotoxic mechanism has not been elucidated. In order to understandthe evolution of this pathway, here we characterize the origins and evolution of perforin.
Results:
We identified orthologs and homologs of human perforin in all but one species analysed fromEuteleostomi, and present evidence for an earlier ortholog in Gnathostomata but not in moreprimitive chordates. In placental mammals perforin is a single copy gene, but there aremultiple perforin genes in all lineages predating marsupials, except birds. Our comparisons ofthese many-to-one homologs of human perforin show that they mainly arose from lineagespecificgene duplications in multiple taxa, suggesting acquisition of new roles or differentmodes of regulation. We also present evidence that perforin arose from duplication of theancient MPEG1 gene, and that it shares a common ancestor with the functionally relatedcomplement proteins.
Conclusions:
The evolution of perforin in vertebrates involved a complex pattern of gene, as well as intron,gain and loss. The primordial perforin gene arose at least 500 million years ago, at around thetime that the major histocompatibility complex-T cell receptor antigen recognition systemwas established. As it is absent from primitive chordates and invertebrates, cytotoxic cellsfrom these lineages must possess a different effector molecule or cytotoxic mechanism.
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