Phylogeography, genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences: A systematic review and meta-analysis

Objective To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country. Methods We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran. Results T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612–0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F

Phylogeography, genetic variability and structure of Acanthamoeba metapopulations in Iran inferred by 18S ribosomal RNA sequences: A systematic review and meta-analysis

OBJECTIVE@#To verify phylogeography and genetic structure of Acanthamoeba populations among the Iranian clinical isolates and natural/artificial environments distributed in various regions of the country.@*METHODS@#We searched electronic databases including Medline, PubMed, Science Direct, Scopus and Google Scholar from 2005 to 2016. To explore the genetic variability of Acanthamoeba sp, 205 sequences were retrieved from keratitis patients, immunosuppressed cases and environmental sources as of various geographies of Iran.@*RESULTS@#T4 genotype was the predominant strain in Iran, and the rare genotypes belonged to T2, T3, T5 (Acanthamoeba lenticulata), T6, T9, T11, T13 and T15 (Acanthamoeba jacobsi). A total of 47 unique haplotypes of T4 were identified. A parsimonious network of the sequence haplotypes demonstrated star-like feature containing haplogroups IR6 (34.1%) and IR7 (31.2%) as the most common haplotypes. In accordance with the analysis of molecular variance, the high value of haplotype diversity (0.612-0.848) of Acanthamoeba T4 represented genetic variability within populations. Neutrality indices of the 18S ribosomal RNA demonstrated negative values in all populations which represented a considerable divergence from neutrality. The majority of genetic diversity belonged to the infected contact lens and dust samples in immunodeficiency and ophthalmology wards, which indicated potential routes for exposure to a pathogenic Acanthamoeba sp. in at-risk individuals. A pairwise fixation index (F) was from low to high values (0.02433-0.41892). The statistically F points out that T4 is genetically differentiated between north-west, north-south and central-south metapopulations, but not differentiated between west-central, west-south, central-south, and north-central isolates.@*CONCLUSIONS@#An occurrence of IR6 and IR7 displays that possibly a gene flow of Acanthamoeba T4 occurred after the founder effect or bottleneck experience through ecological changes or host mobility. This is the first systematic review and meta-analysis providing new approaches into gene migration and transmission patterns of Acanthamoeba sp, and targeting at the high-risk individuals/sources among the various regions of Iran.

Birds of a central São Paulo woodlot: 1. Censuses 1982-2000

Some 263 birds were recorded near and in a 230-ha patch of semideciduous forest in cane fields of central São Paulo, Brazil. Subtracting 67 open-area species, 22 of marshes or creeks, 10 vagrants and 12 recorded later, 152 forest and border species were recorded in 1982-86, much like what was observed in a similar woodlot near Campinas. Both woodlots lost species gradually over the years. Some birds avoided hard cane-field edges, preferring soft bushy edges. Of open-area species, 22 seemed to have disappeared by 1997 due to earlier high El Niño rains or rare permanently open habitats in the sugar cane; 17 new species were mostly nocturnal ones not noted earlier, or occasional visitors. Forest and borders lost 31 species, gaining five of dry regions and one winter visitor. Several migrants from the south appeared only in wet years before recent greenhouse effects, some resident birds were hunted, and canopy hummingbirds were perhaps still present. Dry-forest travel-prone or "metapopulational" species moved their centers of distribution, partly concealing loss of moist-forest diversity.

Foram listadas 263 aves próximo e dentro de uma mata semidecídua de 230 ha em meio a plantações de cana-de-açúcar, na região central do Estado de São Paulo, Brasil. Subtraindo-se 67 espécies de áreas abertas, 22 de riachos, 10 vagantes e 12 observadas mais tarde, cerca de 152 espécies de mata e de borda foram observadas entre 1982-86, semelhantemente às observadas em uma mata próxima a Campinas. Ambas as matas perderam espécies gradualmente. Algumas aves evitaram as margens "duras" dos canaviais, preferindo as margens "macias" arbustivas. Das espécies de área aberta, parece que 22 desapareceram até 1997, em razão das abundantes chuvas anteriores causadas por El Niño, ou pela raridade de habitats permanentemente abertos nos canaviais; 17 espécies "novas" eram principalmente noturnas que não haviam sido checadas anteriormente, ou visitantes ocasionais. A mata e as bordas perderam 37 espécies, ganhando 5 de regiões secas e 1 visitante de inverno. Vários migrantes do sul apareceram somente em anos chuvosos antes do recente efeito estufa; algumas aves residentes foram caçadas, e os beija-flores das copas talvez estivessem presentes ainda. As espécies de zonas secas, prones à movimentação ou "metapopulacionais", movem os centros de distribuição, camuflando parcialmente a perda de diversidade da mata úmida.