Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. Average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalistAstatotilapia-likeancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.One Sentence Summary: The genomes of 73 cichlid fish species from Lake Malawi uncover evolutionary processes underlying a large adaptive evolutionary radiation.

GENETIC DIVERGENCE AND GEOGRAPHIC DISTRIBUTION OF FROGS IN GENUS FEJERVARYA FROM INDONESIA INFERRED FROM MITOCHONDRIAL 16S rRNA GENE ANALYSIS

The Indonesian archipelago is an ideal setting for the study of speciation and biogeography. This archipelago is divided into three island groups based on zoogeography: Sundaland, Wallaceaand the Australian region. In this paper we used frogs in genus Fejervarya (Bolkay) to study biogeography and examine patterns of gene flow across proposed zoogeographic boundaries. Severalmolecular studies on Fejervarya species from Indonesia have been carried out, but comparative studies among members of the genus Fejervarya have yet to be performed. In order to elucidate genetic divergence and geographic distribution of these frogs, we conducted a molecular analysis of the mitochondrial 16S rRNA gene using 179 frogs from five Fejervarya species. In total we collected from 32 localities in Sumatra, Kalimantan (Indonesian part of Borneo), Java, Bali, Sulawesi and Lesser Sunda Islands in Indonesia. Molecular phylogenetic analysis recovered 35 haplotypes and showed that frogs in the genus Fejervarya were divided into two well-supported clades. The first group were of three species, F. limnocharis, F. iskandari and F. cf. verruculosa and the other group clade consisted of Fejervarya cancrivora and Fejervarya sp. (Sulawesi-type). The average sequence divergence among these four species ranged from 1.09 to 16.03% (mean = 11.29±2.83%). The present results clearly show that there are five Fejervarya species in the Indonesian archipelago. Fejervarya limnocharis and F. cancrivora are widely distributed and sympatric in Sumatra, Borneo and Java. Fejervarya iskandari is not endemic to Java and also occurs in the Lesser Sundas. Fejervarya cf. verruculosa and Fejervarya sp. (Sulawesi-type) are endemic to Lesser Sunda and Sulawesi Island, respectively. Key words: Fejervarya, genetic divergence, geographic distribution, 16S rRNA gene

Nesting biology and DNA barcode analysis of Ceratina dupla and C. mikmaqi, and comparisons with C. calcarata (Hymenoptera: Apidae: Xylocopinae)

Using DNA barcode analysis, nest collections, and pan-trapping we compared molecular differences, nesting behaviour, and phenology of three of the four species of Ceratina Latreille present in the Niagara Region of southern Ontario, Canada: C. dupla Say, C. calcarata Robertson, and C. mikmaqi Rehan and Sheffield. Ceratina dupla and C. mikmaqi were separated by five fixed nucleotide differences and an average sequence divergence of 1.86%. In our population, C. mikmaqi and C. calcarata were common and C. dupla was rare. Ceratina dupla nested earlier than C. mikmaqi and C. calcarata, and sometimes produced a second brood in late July – early August. Each species constructed linear nests in the pith of dead twigs, C. mikmaqi and C. dupla usually in Fuller's teasel (Dipsacus fullonum L.; Dipsacaceae) and C. calcarata usually in raspberry (Rubus L.; Rosaceae). Genetically distinct, each species occupies a slightly different niche in the Niagara bee assemblage.

A Population Genetics-Based and Phylogenetic Approach to Understanding the Evolution of Virulence in the Genus Listeria

ABSTRACT The genus Listeria includes (i) the opportunistic pathogens L. monocytogenes and L. ivanovii, (ii) the saprotrophs L. innocua, L. marthii, and L. welshimeri, and (iii) L. seeligeri, an apparent saprotroph that nevertheless typically contains the prfA virulence gene cluster. A novel 10-loci multilocus sequence typing scheme was developed and used to characterize 67 isolates representing six Listeria spp. (excluding L. grayi) in order to (i) provide an improved understanding of the phylogeny and evolution of the genus Listeria and (ii) use Listeria as a model to study the evolution of pathogenicity in opportunistic environmental pathogens. Phylogenetic analyses identified six well-supported Listeria species that group into two main subdivisions, with each subdivision containing strains with and without the prfA virulence gene cluster. Stochastic character mapping and phylogenetic analysis of hly, a gene in the prfA cluster, suggest that the common ancestor of the genus Listeria contained the prfA virulence gene cluster and that this cluster was lost at least five times during the evolution of Listeria, yielding multiple distinct saprotrophic clades. L. welshimeri, which appears to represent the most ancient clade that arose from an ancestor with a prfA cluster deletion, shows a considerably lower average sequence divergence than other Listeria species, suggesting a population bottleneck and a putatively different ecology than other saprotrophic Listeria species. Overall, our data suggest that, for some pathogens, loss of virulence genes may represent a selective advantage, possibly by facilitating adaptation to a specific ecological niche.

Hepatitis B virus genotype G epidemiology and co-infection with genotype A in Canada

Hepatitis B virus (HBV) genotype G (HBV/G) is an unusual variant, and little is known about its epidemiology and natural history, particularly the requirement for a co-infecting HBV genotype and their relationship during infection. This study investigated the quasispecies nature of co-infecting genotypes in 39 samples collected over a 6 year period from 13 HBV/G-infected patients. HBV/G infections were found to occur predominantly in males (92 %) and were primarily associated with male homosexual sex (67 %). All patients were infected with HBV/G and HBV/A, or a recombinant HBV/A/G strain. Co-infecting genotypic prevalence was often observed to fluctuate over time, with periods of HBV/G monoinfection in some patients. The average sequence divergence among Canadian HBV/G strains was 1.57±0.62 %. Thus, all HBV/G infections in Canada occur in the context of co-infection or recombination with HBV/A, and strains display increased sequence divergence compared with all known HBV/G sequences described to date.

Three evolutionarily significant units for conservation in the iguanid genus Brachylophus

We examined phylogenetic relationships within the genus Brachylophus, which comprises two endangered iguana species endemic to the South Pacific islands of Fiji and Tonga. Genetic variation among Fijian Crested Iguanas B. vitiensis and Fijian and Tongan Banded Iguanas B. fasciatus was analysed using mitochondrial DNA (mtDNA) cytochrome b (cyt b) characterized from 35 individuals from island populations. Three distinct clades of Brachylophus were identified. The most divergent clade comprised B. fasciatus from Tonga, which supports the recognition of Tongan iguanas as a separate species. Molecular clock estimates suggested that the average sequence divergence (6.4%) between Tongan and Fijian B. fasciatus clades equated to 7 - 15.8 MY of separation, confirming that extant Brachylophus species have a long history of evolution in situ in the Fijian and Tongan archipelago. Phylogenetic analyses also revealed that Fijian B. fasciatus and B. vitiensis iguana populations were not reciprocally monophyletic. One clade comprised two mtDNA haplotypes from the Fijian islands of Monu, Monuriki, Devuilau, Waya and Yadua Taba. The other clade comprised B. fasciatus haplotypes from Kadavu and Gau, which was divergent from both the aforementioned Fijian clade (dA = 3.5%), and the Tongan clade (dA = 6.4%). In addition to mtDNA data, variation was assessed at microsatellite loci, and significant differentiation between iguana populations was detected. Based on both mtDNA and microsatellite analysis, the conservation priorities for these endangered lizards must be reassessed to protect iguanas as three distinct evolutionarily significant units.

Evolution of duplicated growth hormone genes in autotetraploid salmonid fishes

A defining character of the piscine family Salmonidae is autotetraploidy resulting from a genome-doubling event some 25–100 million years ago. Initially, duplicated genes may have undergone concerted evolution and tetrasomic inheritance. Homeologous chromosomes eventually diverged and the resulting reduction in recombination and gene conversion between paralogous genes allowed the re-establishment of disomic inheritance. Among extant salmonine fishes (e.g. salmon, trout, char) the growth hormone (GH) gene is generally represented by two functional paralogs, GH1 and GH2. Sequence analyses of salmonid GH genes from species of subfamilies Coregoninae (whitefish, ciscos) and Salmoninae were used to examine the evolutionary history of the duplicated GH genes. Two divergent GH gene paralogs were also identified in Coregoninae, but they were not assignable to the GH1 and GH2 categories. The average sequence divergence between the coregonine GH genes was more than twofold lower than the corresponding divergence between the salmonine GH1 and GH2. Phylogenetic analysis of the coregonine GH paralogs did not resolve their relationship to the salmonine paralogs. These findings suggest that disomic inheritance of two GH genes was established by different mechanisms in these two subfamilies.Key words: salmon, phylogeny, growth hormone, disomy, tetraploidy.

Homology of Escherichia coli R773 arsA, arsB, and arsC Genes in Arsenic-Resistant Bacteria Isolated from Raw Sewage and Arsenic-Enriched Creek Waters

ABSTRACT The occurrence and diversity of the Escherichia coli R773 ars operon were investigated among arsenic-resistant enteric and nonenteric bacteria isolated from raw sewage and arsenic-enriched creek waters. Selected isolates from each creek location were screened for ars genes by colony hybridization and PCR. The occurrence of arsA, arsB, and arsC determined by low-stringency colony hybridization (31 to 53% estimated mismatch) was 81, 87, and 86%, respectively, for 84 bacteria isolated on arsenate- and arsenite-amended media from three locations. At moderate stringency (21 to 36% estimated mismatch), the occurrence decreased to 42, 56, and 63% for arsA, arsB, and arsC, respectively. PCR results showed that the ars operon is conserved in some enteric bacteria isolated from creek waters and raw sewage. The occurrence of the arsBC genotype was about 50% in raw sewage enteric bacteria, while arsA was detected in only 9.4% of the isolates (n = 32). The arsABC and arsBC genotypes occurred more frequently in enteric bacteria isolated from creek samples: 71.4 and 85.7% (n = 7), respectively. Average sequence divergence within arsB for six creek enteric bacteria was 20% compared to that of the E. coli R773 ars operon. Only 1 of 11 pseudomonads screened by PCR was positive for arsB. The results from this study suggest that significant divergence has occurred in the ars operon among As-resistant E. coli strains and in Pseudomonas spp.

Restriction Analysis of Mitochondrial DNA from the Yellow-footed Rock-wallaby, Petrogale xanthopus: Implications for Management

The extent of mitochondrial DNA divergence between populations of the vulnerable yellow-footed rock- wallaby, Petrogale xanthopus, was assessed by restriction analysis. Of the 15 restriction endonucleases, five were informative, with a single unique haplotype identified in P. x. celeris from Queensland (Qld) (n = 8) and a further two unique haplotypes in three sampled populations of P. x. xanthopus from New South Wales (NSW) (n = 1) and South Australia (SA) (n = 9). The two subspecies of P. xanthopus were found to be genetically distinct (average sequence divergence = 0·72%). As this divergence is greater than that found between some Petrogale species, it is recommended that populations of P. x. xanthopus and P. x. celeris be managed independently both in captivity and the wild. The NSW population of P. x. xanthopus appears genetically similar to those in SA, although these data are limited.

Mitochondrial DNA variation and the evolution of Robertsonian chromosomal races of house mice, Mus domesticus.

The house mouse, Mus domesticus, includes many distinct Robertsonian (Rb) chromosomal races with diploid numbers from 2n = 22 to 2n = 38. Although these races are highly differentiated karyotypically, they are otherwise indistinguishable from standard karyotype (i.e., 2n = 40) mice, and consequently their evolutionary histories are not well understood. We have examined mitochondrial DNA (mtDNA) sequence variation from the control region and the ND3 gene region among 56 M. domesticus from Western Europe, including 15 Rb populations and 13 standard karyotype populations, and two individuals of the sister species, Mus musculus. mtDNA exhibited an average sequence divergence of 0.84% within M. domesticus and 3.4% between M. domesticus and M. musculus. The transition/transversion bias for the regions sequenced is 5.7:1, and the overall rate of sequence evolution is approximately 10% divergence per million years. The amount of mtDNA variation was as great among different Rb races as among different populations of standard karyotype mice, suggesting that different Rb races do not derive from a single recent maternal lineage. Phylogenetic analysis of the mtDNA sequences resulted in a parsimony tree which contained six major clades. Each of these clades contained both Rb and standard karyotype mice, consistent with the hypothesis that Rb races have arisen independently multiple times. Discordance between phylogeny and geography was attributable to ancestral polymorphism as a consequence of the recent colonization of Western Europe by mice. Two major mtDNA lineages were geographically localized and contained both Rb and standard karyotype mice. The age of these lineages suggests that mice have moved into Europe only within the last 10,000 years and that Rb populations in different geographic regions arose during this time.