Breakdown in the Process of Incipient Speciation in Anopheles gambiae.

Genetics. 2013 Jan 18;

Authors: Nwakanma DC, Neafsey DE, Jawara M, Adiamoh M, Lund E, Rodrigues A, Loua KM, Konate L, Sy N, Dia I, Awolola TS, Muskavitch MA, Conway DJ

Abstract
Understanding genetic causes and effects of speciation in sympatric populations of sexually-reproducing eukaryotes is challenging, controversial, and of practical importance for controlling rapidly evolving pests and pathogens. The major African malaria vector mosquito Anopheles gambiae sensu stricto (s.s.) is considered to contain two incipient species with strong reproductive isolation, hybrids between the M and S molecular forms being very rare. Following recent observations of higher proportions of hybrid forms at a few sites in West Africa, we conducted new surveys of 12 sites in four contiguous countries (The Gambia, Senegal, Guinea Bissau, and Republic of Guinea). Identification and genotyping of 3499 An. gambiae s.s. revealed high frequencies of M/S hybrid forms at each site, ranging from 5% to 42%, and a large spectrum of inbreeding coefficient values from 0.11 to 0.76, spanning most of the range expected between the alternative extremes of panmixia and assortative mating. Year-round sampling over two years at one of the sites in The Gambia showed that M/S hybrid forms had similar relative frequencies throughout periods of marked seasonal variation in mosquito breeding and abundance. Genome-wide scans with an Affymetrix high-density single nucleotide polymorphism (SNP) microarray enabled replicate comparisons of pools of different molecular forms, in three separate populations. These showed strong differentiation between M and S forms only in the pericentromeric region of the X chromosome that contains the molecular form-specific marker locus, with only a few other loci showing minor differences. In the X chromosome, the M/S hybrid forms were more differentiated from M than S forms, supporting a hypothesis of asymmetric introgression and backcrossing, which will substantially affect spread of resistance to insecticides, and alleles influencing malaria parasite infectivity.

PMID: 23335339 [PubMed - as supplied by publisher]

Megabase-scale Inversion Polymorphism in the Wild Ancestor of Maize.

Genetics. 2012 Apr 27;

Authors: Fang Z, Pyhäjärvi T, Weber AL, Dawe RK, Glaubitz JC, Sánchez González JD, Ross-Ibarra C, Doebley J, Morrell PL, Ross-Ibarra J

Abstract
Chromosomal inversions are thought to play a special role in local adaptation, through dramatic suppression of recombination, which favors the maintenance of locally adapted alleles. However, relatively few inversions have been characterized in population genomic data. Based on single nucleotide polymorphism (SNP) genotyping across a large panel of Zea mays, we have identified a ~50 Mb region on the short arm of chromosome 1 where patterns of polymorphism are highly consistent with a polymorphic paracentric inversion that captures more than 700 genes. Comparison to other taxa in Zea and Tripsacum suggests that the derived, inverted state is present only in the wild Zea mays subspecies parviglumis and mexicana, and is completely absent in domesticated maize. Patterns of polymorphism suggest that the inversion is ancient, and geographically widespread in parviglumis. Cytological screens find little evidence for inversion loops, suggesting that inversion heterozygotes may suffer few cross-over induced fitness consequences. The inversion polymorphism shows evidence of adaptive evolution, including a strong altitudinal cline, a statistical association with environmental variables and phenotypic traits, and a skewed haplotype frequency spectrum for inverted alleles.

PMID: 22542971 [PubMed - as supplied by publisher]

Combining sperm typing and linkage disequilibrium analyses reveals differences in selective pressures or recombination rates across human populations.

Genetics. 2007 Feb;175(2):795-804

Authors: Clark VJ, Ptak SE, Tiemann I, Qian Y, Coop G, Stone AC, Przeworski M, Arnheim N, Di Rienzo A

A previous polymorphism survey of the type 2 diabetes gene CAPN10 identified a segment showing an excess of polymorphism levels in all population samples, coinciding with localized breakdown of linkage disequilibrium (LD) in a sample of Hausa from Cameroon, but not in non-African samples. This raised the possibility that a recombination hotspot is present in all populations and we had insufficient power to detect it in the non-African data. To test this possibility, we estimated the crossover rate by sperm typing in five non-African men; these estimates were consistent with the LD decay in the non-African, but not in the Hausa data. Moreover, resequencing the orthologous region in a sample of Western chimpanzees did not show either an excess of polymorphism level or rapid LD decay, suggesting that the processes underlying the patterns observed in humans operated only on the human lineage. These results suggest that a hotspot of recombination has recently arisen in humans and has reached higher frequency in the Hausa than in non-Africans, or that there is no elevation in crossover rate in any human population, and the observed variation results from long-standing balancing selection.

PMID: 17151245 [PubMed - indexed for MEDLINE]

Estimating the contribution of mutation, recombination and gene conversion in the generation of haplotypic diversity.

Genetics. 2006 Jul;173(3):1705-23

Authors: Morrell PL, Toleno DM, Lundy KE, Clegg MT

Recombination occurs through both homologous crossing over and homologous gene conversion during meiosis. The contribution of recombination relative to mutation is expected to be dramatically reduced in inbreeding organisms. We report coalescent-based estimates of the recombination parameter (rho) relative to estimates of the mutation parameter (theta) for 18 genes from the highly self-fertilizing grass, wild barley, Hordeum vulgare ssp. spontaneum. Estimates of rho/theta are much greater than expected, with a mean rho/theta approximately 1.5, similar to estimates from outcrossing species. We also estimate rho with and without the contribution of gene conversion. Genotyping errors can mimic the effect of gene conversion, upwardly biasing estimates of the role of conversion. Thus we report a novel method for identifying genotyping errors in nucleotide sequence data sets. We show that there is evidence for gene conversion in many large nucleotide sequence data sets including our data that have been purged of all detectable sequencing errors and in data sets from Drosophila melanogaster, D. simulans, and Zea mays. In total, 13 of 27 loci show evidence of gene conversion. For these loci, gene conversion is estimated to contribute an average of twice as much as crossing over to total recombination.

PMID: 16624913 [PubMed - indexed for MEDLINE]