Browsing by Author "Patton, John C."
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- Africanization in the United States: Replacement of Feral European Honeybees (Apis mellifera L.) by an African Hybrid SwarmPublication . Pinto, M. Alice; Rubink, William L.; Patton, John C.; Coulson, Robert N.; Johnston, J. SpencerThe expansion of Africanized honeybees from South America to the southwestern United States in 50 years is considered one of the most spectacular biological invasions yet documented. In the American tropics, it has been shown that during their expansion Africanized honeybees have low levels of introgressed alleles from resident European populations. In the United States, it has been speculated, but not shown, that Africanized honeybees would hybridize extensively with European honeybees. Here we report a continuous 11-year study investigating temporal changes in the genetic structure of a feral population from the southern United States undergoing Africanization. Our microsatellite data showed that (1) the process of Africanization involved both maternal and paternal bidirectional gene flow between European and Africanized honeybees and (2) the panmitic European population was replaced by panmitic mixtures of A. m. scutellata and European genes within 5 years after Africanization. The post-Africanization gene pool (1998–2001) was composed of a diverse array of recombinant classes with a substantial European genetic contribution (mean 25–37%). Therefore, the resulting feral honeybee population of south Texas was best viewed as a hybrid swarm.
- Candidate loci for selection in Iberian honey bees: a genome-wide scan using SNP genotypingPublication . Pinto, M. Alice; Chávez-Galarza, Julio; Muñoz, Irene; De la Rúa, Pilar; Azevedo, João; Patton, John C.; Johnston, J. SpencerOver the last 20 years Iberian honey bees (IHB) have been scrutinized with a variety of genetic markers including morphology, allozymes, mtDNA, and microsatellites. The complex patterns and processes revealed have yet to be fully understood. While mtDNA is useful to reveal the maternal component, biparental markers capture genome-wide effects (admixture, expansions, and contractions) and locus-specific effects (selection). Accordingly, we expect to dissect out, through genome-wide scans, neutral and selection effects. In this study, the Illumina GoldenGate Assay was used to genotype SNPs across the complete genome of IHBs. The SNP data set was analyzed for evidence of selection using a frequentist, FDIST, and a Bayesian method, BayeScan. Additionally, a spatial analysis method (MatSAM) was used to test for associations between SNPs and climatic variables. With these approaches we detected 8 loci with a strong signal of directional selection. The genome positions and putative gene functions, given in the HB genomic resources, suggest that these putatively selected loci are strong candidates for selection. The spatial representation of these same loci reveals a clinal pattern of variation, further supporting selection. Our approach allows for a rigorous consideration of selection as the underlying cause of observed patterns of diversity and contrast with previous studies where evocation of selection was merely speculative.
- Detection of loci under selection in Apis mellifera iberiensis as compared with two frequentist methodsPublication . Chávez-Galarza, Julio; Henriques, Dora; Johnston, J. Spencer; Azevedo, João; Muñoz, Irene; De la Rúa, Pilar; Patton, John C.; Costa, Filipe Oliveira; Pinto, M. AliceGenome scans with many genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under selection. The recent advent of high-throughput Single Nucleotide Polymorphism (SNP) genotyping technologies have opened new perspective of research and these markers are commonly observed in functional genes making them ideal markers to study adaptive molecular variation. This approach has become commonly employed in ecological and population genetics studies to detect outlier loci that are putatively under selection. Herein, we show a preliminary exploration of a gnome scan to detect signatures of selection on the Iberian honey bee genome The objective of this study was to determine loci under selection of A m. iberiensis by using SNPs. Over 711 individuals were sampled in the lberian Peninsula across three Latitudinal transects and then genotyped for 1536 SNPs using the Golden Gate Assay of Illumina. Loci under selection were identified by two frequentist methods: Fdist, implemented in LOSITAN, and BAYESCAN. There were identified 22 loci under selection by BAYESCAN and 12 Loci by LOSITAN, being 10 Loci detected by both methods. The SNPs under selection were located in linkage group I1 4, 6, 7, 8, 9, 10, 11 , 12, 13 and 15 from honey bee genome and may be related to genes with diverse functions as hormonal, nervous, development, cell signaling and some unknown.
- Estrutura populacional e variabilidade genética da abelha ibérica (Apis mellifera iberiensis) revelada por marcadores do adn mitocondrial e nuclear: implicações na actividade apícolaPublication . Pinto, M. Alice; Chávez-Galarza, Julio; Henriques, Dora; Rufino, José; Azevedo, João; Muñoz, Irene; De la Rúa, Pilar; Patton, John C.; Johnston, J. SpencerA conservação da diversidade genética das populações locais de abelhas é fundamental à sustentabilidade da atividade apícola. Primeiro, porque a diversidade genética é a matéria-prima sobre a qual a seleção (natural ou artificial) atua, permitindo a adaptaçãoo das abelhas às cada vez mais rápidas alteracões ambientais (poluição, pesticidas, novos patogénios e parasitas) e às exigências de uma atividade apícola cada vez mais competitiva. Segundo, porque a perda de diversidade genética pode conduzir à consanguinidade e à redução do valor adaptativo das colónias podendo-se traduzir em perdas de produtividade, maior número de machos diploides e menor resistência aos parasitas e patogénios, entre outros efeitos. A compreensão dos padrões espaciais de diversidade genética, e dos processos históricos e contemporâneos que têm moldado essa diversidade ao longo dos tempos, é crucial para uma melhor gestão e conservação da abelha ibérica (Apis mellifera iberiensis). Apesar dos inúmeros estudos conduzidos na Península lbérica nas últimas décadas, os padrões e processos de diversidade genética são ainda mal compreendidos. De facto, a grande variedade de marcadores genéticos (morfolugia, alozimas, ADN mitocondrial, microsatélites) que tem sido utilizada tem revelado padrões incongruentes de diversidade fazendo da abelha ibérica a mais complexa subespécie na ampla área de distribuição geográfica da espécie Apis mellifera. Nesta comunicação serão apresentados os resultados de um estudo que proporcionará a caracterização mais completa da abelha ibérica jamais realizada através de uma amostragem de elevada resolução quer a nível geográfico quer a nível do seu genoma. Para tal utilizaram-se simultaneamente marcadores mitocondriais (região intergénica tRNAleu-cox2) e nucleares neutrais testados (311 SNPs), e avancadas ferramentas analíticas numa coleção de 711 colónias amostradas ao longo de três transeptos ibéricos (costa Atlântica, região central e costa Mediterrânica). Os resultados deste estudo confirmam a elevada complexidade e forte estruturação da abelha ibérica refletida (i) no cline com orientação sudoeste-nordeste formado pelas linhagens evolutivas Africana (A) e da Europa Ocidental (M) e (ii) no acentuado contraste da composição genética das populações do Mediterrâneo e do Atlântico. Em oposição a outros trabalhos genéticos, neste estudo o padrão recuperado pelos SNPs é congruente com a variação materna. Por último, este estudo mostra que o grau de introgressão da linhagem C na abelha ibérica é negligenciável, contrastando fortemente com a outra subespécie da linhagem M, Apis mellifera mellifera. As eventuais implicacões destes resultados na atividade apicola serão discutidas numa perspetiva de preservação da integridade genética da abelha ibérica.
- Evidence of African honey bees mitotypes in the southern United States prior to Africanization as revealed by mtDNA sequence dataPublication . Pinto, M. Alice; Sheppard, Walter S.; Johnston, J. Spencer; Rubink, William L.; Coulson, Robert N.; Patton, John C.The standard protocol for assessing honey bees with a mitotype derived from an African origin is the amplification of a segment of cytochrome b and subsequent digestion of the amplified fragment with the restriction enzyme Bgl II. A previous survey of 451pre-Africanization honey bees from the southern U. S. revealed three bees with restriction pattern consistent with an African mitotype. To confirm these bees truly represented mitotypes of African origin we developed a new primer pair for amplification of cytochrome b, which utilizes internal sequencing primers to allow high quality direct sequence products. Using this system we amplified a mtDNA fragment of ~1,200 base-pairs (bp), taht included most of cytochrome b, serine (UCA) tRNA, and a small portion (s) of the ND-1 gene (s). Honey bees from ten morphometrically identified Apis mellifera subspecies (42 honey bee workers, each representing a different colony) from Old World and three honey bee workers (each representing a different colony) from the southern United States exhibiting an African phenotype as revealed by BglII restriction enzyme analysis were sequenced. The analysis showed that two of the three honey bees were of eastern European ancestry. These bees had lost the BglII cut site by a first position (C->A) transversion mutation. The third honey bee was found to have a sequence of African clade bees. This defining substitution for the African clade was found to be a third position (T->C) transiton mutation.
- Evolutionary history of the Iberian honey bee (Apis mellifera iberiensis): a genome-wide approachPublication . Pinto, M. Alice; Johnston, J. Spencer; Azevedo, João; Muñoz, Irene; Chávez-Galarza, Julio; Castro, João Paulo; De la Rúa, Pilar; Patton, John C.The Iberian Peninsula has been recognized as a hot spot of diversity and endemisms for numerous plant and animal species, and the honeybee is no exception. Honeybees occur naturally in Europe, Africa and the Middle East. In this vast range of habitats, adaptation to the diverse ecological conditions has led to evolution of over 29 subspecies, which have been grouped into five lineages. The Iberian Peninsula harbours two of such lineages (A and M) and the greatest genetic diversity and complexity across Europe. Unraveling the evolutionary forces underlying such complex patterns of diversity has been a major goal of numerous studies and an increasingly important undertaking given the escalating threats to the honeybee populations (e.g. diseases, parasites, pesticides, colony collapse disorder, genetic pollution). Herein we will present an ongoing research project which is using cutting edge molecular and analytical tools to disentangle the evolutionary forces shaping the Iberian honeybee diversity. The genome scan approach used in this study will enable dissection of genome-wide (expansions, contractions, admixture) from genome-specific forces (selection). Furthermore, the honeybee genomic resources will enable exploration of the molecular basis of adaptation. We anticipate that this study will provide unprecedented insights into the history and adaptive divergence of honeybees and the findings can be applied for designing conservation programs of locally adapted ecotypes.
- Evolutionary history of the Iberian honey bee (Apis mellifera iberiensis): a genome-wide approachPublication . Pinto, M. Alice; Johnston, J. Spencer; Azevedo, João; Muñoz, Irene; Chávez-Galarza, Julio; Castro, João Paulo; De la Rúa, Pilar; Patton, John C.The Iberian Peninsula has been recognized as a hot spot of diversity and endemisms for numerous plant and animal species, and the honeybee is no exception. Honey bees occur naturally in Europe, Africa and the Middle East. In this vast range of habitats, adaptation to the diverse ecological conditions has led to evolution of over 29 subspecies, which have been grouped into five lineages. The Iberian Peninsula harbours two of such lineages (A and M) and the greatest genetic diversity and complexity across Europe. Unraveling the evolutionary forces underlying such complex patterns of diversity has been a major goal of numerous studies and an increasingly important undertaking given the escalating threats to the honey bee populations (e.g. diseases, parasites, pesticides, colony collapse disorder, genetic pollution). Herein we will present an ongoing research project which is using cutting edge molecular and analytical tools to disentangle the evolutionary forces shaping the Iberian honey bee diversity. The genome scan approach that will be used in this study will enable dissection of genome-wide (expansions, contractions, admixture) from genome-specific forces (selection). Furthermore, the honey bee genomic resources will enable exploration of the molecular basis of adaptation. We anticipate that this study will provide unprecedented insights into the history and adaptive divergence of honey bees and the findings can be applied for designing conservation programs to protect locally adapted ecotypes.
- Honey bees (Hymenoptera: Apidae) of african origin exist in non-africanized areas of the Southern United States: evidence from mitochondrial DNAPublication . Pinto, M. Alice; Sheppard, Walter S.; Johnston, J. Spencer; Rubink, William L.; Coulson, Robert N.; Schiff, Nathan M.; Kandemir, Irfan; Patton, John C.Descendents of Apis mellifera scutellata Lepeletier (Hymenoptera: Apidae) (the Africanized honey bee) arrived in the United States in 1990. Whether this was the Þrst introduction is uncertain. A survey of feral honey bees from non-Africanized areas of the southern United States revealed three colonies (from Georgia, Texas, and New Mexico) with a diagnostic African mitochondrial DNA cytochrome b/BglII fragment pattern. To assess maternal origin of these colonies, we developed a primer pair for ampliÞcation of a cytochrome b fragment and sequenced using internal sequencing primers. Samples of the three reported honey bee colonies plus another 42 representing the 10 subspecies known to have been introduced in the United States were sequenced. Of the three colonies, the colonies from Texas and New Mexico matched subspecies of European maternal ancestry, whereas the colony from Georgia was of African ancestry. Contrary to expectations, the mitotype of the latter colony was more similar to that exhibited by sub-Saharan A. m. scutellata than to the mitotypes common in north African A. m. intermissa Maa or Portuguese and Spanish A. m. iberiensis Engel. This Þnding was consistent with anecdotal evidence that A. m. scutellata has been sporadically introduced into the United States before the arrival of the Africanized honey bee from South America.
- Identification of africanized honey bee (Hymenoptera: apidae) mitochondrial DNA: validation of a rapid polymerase chain reaction-based assayPublication . Pinto, M. Alice; Johnston, J. Spencer; Rubink, William L.; Coulson, Robert N.; Patton, John C.; Sheppard, Walter S.Polymerase chain reaction (PCR)-ampliÞed mitochondrialDNA(mtDNA)assays have been used in studies of the Africanization process in neotropical feral and managed honey bee populations. The approach has been adopted, in conjunction with morphometric analysis, to identify Africanized bees for regulatory purposes in the United States such as in California. In this study, 211 Old World colonies, representing all known introduced subspecies in the United States, and 451 colonies from non-Africanized areas of the southern United States were screened to validate a rapid PCR-based assay for identiÞcation of Africanized honey bee mtDNA. This PCR-based assay requires a single enzyme digestion (BglII) of a single PCR-ampliÞed segment of the cytochrome b gene. The BglII polymorphism discriminates the mitochondrial haplotype (mitotype) of Apis mellifera scutellata L. (ancestor of Africanized bees) from that of A. m. mellifera, A. m. caucasia, A. m. ligustica, A. m. carnica, A. m. lamarcki, A. m. cypria, A. m. syriaca, and some A. m. iberiensis, but not from that of A. m. intermissa and some A. m. iberiensis. Nonetheless, given the very low frequency ( 1%) of African non-A. m. scutellata mitotype present before arrival of Africanized bees in the United States, cytochrome b/BglII assay can be used to identify maternally Africanized bees with a high degree of reliability.
- Is there Apis mellifera ligustica and A. m. carnica introgression in A. m. iberiensis?Publication . Chávez-Galarza, Julio; Johnston, J. Spencer; Azevedo, João; Muñoz, Irene; De la Rúa, Pilar; Patton, John C.; Costa, Filipe Oliveira; Pinto, M. AliceSeveral studies have grouped the A. mellifera subspecies into five lineages (A, M, C, O and Y). Honey bees occurring in the Iberian Peninsula are considered a particular subspecies, named Apis mellifera iberiensis, originated by natural hybridization among lineages A (African) and M (western European). This study seeks to identify the level of introgression of lineage C honey bees (A. m. ligustica and A.m. carnica) in Iberian honey bees potentially caused by introduction of foreign queens by carrying out a genome wide analysis using SNPs. Over 748 individuals belonging to 23 populations sampled across three Iberian transects were genotyped for 1536 SNPs. Honey bees of lineage C A. m. ligustica and A. m. carnica were used as reference populations. The level of introgression was assessed by using Bayesian clustering methods. Our results indicate that introgression of A. m. ligustica and A.m. carnica is not noticeable in all A. m. iberiensis populations.
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