Population genetics of Ceratitis capitata in South Africa: implications for dispersal and pest management

Global invasion history with climate-related allele frequency shifts in the invasive Mediterranean fruit fly (Diptera, Tephritidae: Ceratitis capitata)

The Mediterranean fruit fly (Ceratitis capitata) is a globally invasive species and an economically significant pest of fruit crops. Understanding the evolutionary history and local climatic adaptation of this species is crucial for developing effective pest management strategies. We conducted a comprehensive investigation using whole genome sequencing to explore (i) the invasion history of C. capitata with an emphasis on historical admixture and (ii) local climatic adaptation across African, European, Central, and South American populations of C. capitata. Our results suggest a stepwise colonization of C. capitata in Europe and Latin America in which Mediterranean and Central American populations share an ancestral lineage. Conversely, South American invasion history is more complex, and our results partly suggest an old secondary invasion into South America from Europe or a colonization of South America directly from Africa, followed by admixture with an European lineage. Throughout its invasive range, C. capitata is challenged with diverse climatic regimes. A genome wide association study identified a relationship between allele frequency changes and specific bioclimatic variables. Notably, we observed a significant allele frequency shift related to adaptation to cold stress (BIO6), highlighting the species' ability to rapidly adapt to seasonal variations in colder climates.

Latitudinal variation in survival and immature development of Ceratitis capitata populations reared in two key overwintering hosts

Ceratitis capitata, a major agricultural pest, is currently expanding its geographic distribution to northern, temperate areas of Europe. Its seasonal biology and invasion success depend on temperature, humidity and host availability. In coastal warmer Mediterranean regions and cooler temperature areas, bitter oranges and apples serve as overwintering hosts during the larval stage. We assessed the overwintering capacity of C. capitata populations obtained from different areas of the northern hemisphere by studying the survival and development rates of immature stages in both fruits under laboratory conditions. Eggs from each population were artificially inserted in the flesh of the two hosts and kept at 15, 20, or 25 °C until pupation and adult emergence. Climatic analysis of the area of the population origin showed combined effects of latitude, host and macroclimatic variables on immature survival and development rates. Egg to adult survival rates and developmental duration were longer in apples than in bitter oranges. For populations originated from southern-warmer areas, egg to adult developmental duration was prolonged and adult emergence reduced at 15 °C compared to those populations obtained from northern regions. Our findings reveal varying plastic responses of medfly populations to different overwintering hosts and temperatures highlighting the differential overwintering potential as larvae within fruits. This study contributes towards better understanding the medfly invasion dynamics in temperate areas of Northern Europe and other parts of the globe with similar climates.

Divergent east-west lineages in an Australian fruit fly, (Bactrocera jarvisi), associated with the Carpentaria Basin divide

Bactrocera jarvisi is an endemic Australian fruit fly species (Diptera: Tephritidae). It occurs commonly across tropical and subtropical coastal Australia, from far-northern Western Australia, across the 'Top End' of the Northern Territory, and then down the Queensland east coast. Across this range, its distribution crosses several well documented biogeographic barriers. In order to better understand factors leading to the divergence of Australian fruit fly lineages, we carried out a population genetic study of B. jarvisi from across its range using genome-wide SNP analysis, utilising adult specimens gained from trapping and fruit rearing. Populations from the Northern Territory (NT) and Western Australia were genetically similar to each other, but divergent from the genetically uniform east-coast (= Queensland, QLD) population. Phylogenetic analysis demonstrated that the NT population derived from the QLD population. We infer a role for the Carpentaria Basin as a biogeographic barrier restricting east-west gene flow. The QLD populations were largely panmictic and recognised east-coast biogeographic barriers play no part in north-south population structuring. While the NT and QLD populations were genetically distinct, there was evidence for the historically recent translocation of flies from each region to the other. Flies reared from different host fruits collected in the same location showed no genetic divergence. While a role for the Carpentaria Basin as a barrier to gene flow for Australian fruit flies agrees with existing work on the related B. tryoni, the reason(s) for population panmixia for B. jarvisi (and B. tryoni) over the entire Queensland east coast, a linear north-south distance of >2000km, remains unknown.

Genetics reveals shifts in reproductive behaviour of the invasive bird parasite Philornis downsi collected from Darwin’s finch nests

Due to novel or dynamic fluctuations in environmental conditions and resources, host and parasite relationships can be subject to diverse selection pressures that may lead to significant changes during and after invasion of a parasite. Genomic analyses are useful for elucidating evolutionary processes in invasive parasites following their arrival to a new area and host. Philornis downsi (Diptera: Muscidae), the avian vampire fly, was introduced to the Galápagos Islands circa 1964 and has since spread across the archipelago, feeding on the blood of developing nestlings of endemic land birds. Since its discovery, there have been significant changes to the dynamics of P. downsi and its novel hosts, such as shifting mortality rates and changing oviposition behaviour, however no temporal genetic studies have been conducted. We collected P. downsi from nests and traps from a single island population over a 14-year period, and genotyped flies at 469 single nucleotide polymorphisms (SNPs) using restriction-site associated DNA sequencing (RADSeq). Despite significant genetic differentiation (FST) between years, there was no evidence for genetic clustering within or across four sampling years between 2006 and 2020, suggesting a lack of population isolation. Sibship reconstructions from P. downsi collected from 10 Darwin’s finch nests sampled in 2020 showed evidence for shifts in reproductive behaviour compared to a similar genetic analysis conducted in 2004–2006. Compared with this previous study, females mated with fewer males, individual females oviposited fewer offspring per nest, but more unique females oviposited per nest. These findings are important to consider within reproductive control techniques, and have fitness implications for both parasite evolution and host fitness.

Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition

Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the Tephritidae family, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographic history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1,907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographic regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonised environments.

Fine Scale Microevolutionary and Demographic Processes Shaping a Wild Metapopulation Dynamics of the South American Fruit Fly Anastrepha fraterculus

Anastrepha fraterculus (Wiedmann) is an important American pest species. Knowledge of its population dynamics is of particular interest for ecology, evolutionary biology, and management programs. In the present study, phenotypic, genotypic, and spatial data were combined, within the frame of landscape genetics, to uncover the spatial population genetic structure (SGS) and demographic processes of an Argentinian local population from the Yungas ecoregion. Eight simple sequence repeats (SSR) loci and six morphometric traits were analysed considering the hierarchical levels: tree/fruit/individual. Genetic variability estimates were high (H_E = 0.72, R_A = 4.39). Multivariate analyses of phenotypic data showed that in average 52.81% of variance is explained by the tree level, followed by between individuals 28.37%. Spatial analysis of morphological traits revealed a negative autocorrelation in all cases. SGS analysis and isolation by distance based on SSR showed no significant autocorrelation for molecular coancestry. The comparison between phenotypic (P_ST) and molecular (F_ST) differentiation identified positive selection in different fruits for all traits. Bayesian analysis revealed a cryptic structure within the population, with three clusters spatially separated. The results of this study showed a metapopulation dynamics. The genetic background of the components of this metapopulation is expected to change through time due to seasonality, repopulation activities, and high gene flow, with an estimated dispersal ability of at least 10 km. Effective population size (Ne) of the metapopulation was estimated in around 800 flies, and within subpopulations (clusters) Ne was associated with the levels of genetic drift experienced by the founding lineages.

Analysis of Genetic Diversity of Banana Weevils (Cosmopolites sordidus) (Coleoptera: Curculionidae) Using Transcriptome-Derived Simple Sequence Repeat Markers

The banana weevil, Cosmopolites sordidus (Germar) (Coleoptera: Curculionidae) is an economically important insect pest of bananas. It causes up to 100% yield losses and substantial lifespan reduction in bananas. Advances in genomics, proteomics, and sequencing technologies have provided powerful pathways to genotyping disastrous pests such as C. sordidus. However, such technologies are often not available to the majority of rural subtropical African banana growers and pest control managers. This study was therefore motivated by the need to create cheap and easily accessible C. sordidus genotyping methods that could be deployed by banana pest control managers to the benefit of C. sordidus control programs in the tropics where such advanced technologies are not readily accessible. We used an in-house C. sordidus transcriptome from the an-ongoing study from which we mined an array of simple sequence repeat (SSR) markers. Of these, six highly polymorphic transcriptome-derived SSR markers were used to successfully genotype within and among banana weevil population genetic diversity of 12 C. sordidus populations collected from four banana-growing agro-ecological zones (AEZs) in Uganda. The developed transcriptome-derived SSR markers can be used by researchers in population genetics for characterization of the C. sordidus and identification of new genes that are linked to traits of particular interest. The significant genetic diversity revealed in C. sordidus provides pertinent information for integrated pest management strategies.

Looking at the big picture: worldwide population structure and range expansion of the cosmopolitan pest Ceratitis capitata (Diptera, Tephritidae)

The Mediterranean fruit fly, Ceratitis capitata (Weidemann), is considered one of the most significant tephritid pest species worldwide and is an exotic species in most of its range. Here, we investigated polymorphism at 14 microsatellite loci for a total of 126 populations of C. capitata from six geographical regions, applying network theory and cluster analyses. Analyses revealed nine distinct modules for the Central American region and one in each of the remaining five regions. Bayesian cluster analysis revealed that the highest level of genetic partitioning corresponds with the presence of 3 well-defined genetic clusters. Our results confirm the African origin for Mediterranean populations based on genetic diversity and suggest a direct invasion of C. capitata from the Mediterranean to Central-America. South American populations show links with Central-America, but also exhibit indications of direct admixture with the European cluster. Additionally, the network analysis proposes a South American origin for the Madeiran and Hawaiian flies. Cluster analysis corroborates the hypothesis of a Mediterranean origin for Australian samples. Our work provides novel insights regarding the migration history of Medfly worldwide.

Ecological phylogeography and coalescent models suggest a linear population expansion of Anastrepha fraterculus (Diptera: Tephritidae) in southern South America

This work is a first approach to an integrated view of the genetics, ecology and dispersion patterns of Anastrepha fraterculus in southern South America. We studied the association of genetic variation with geographical patterns and environmental variables to provide insight into the crucial factors that drive the structure and dynamics of fly populations. Data from a 417 bp mitochondrial COII gene fragment from seven Argentinian populations and one South Brazilian population (from five ecoregions grouped in three biomes) were used to identify population clusters using a model-based Bayesian phylogeographical and ecological clustering approach. The sequences were also analysed under a coalescent model to evaluate historical demographic changes. We identified 19 different haplotypes and two clusters differing in all the environmental covariables. The assumption of neutral evolution and constant population size was rejected, and the population growth parameters suggested a linear population expansion starting 2500 years before present. The most likely ancestral location is Posadas, from where A. fraterculus would have expanded southwards and westwards in Argentina. This result is consistent with Holocene changes and anthropic factors related to the expansion of the Tupí–Guaraní culture, 3000–1500 years before present.

Genetic structure and symbiotic profile of worldwide natural populations of the Mediterranean fruit fly, Ceratitis capitata

BACKGROUND

The Mediterranean fruit fly, Ceratitis capitata, is a cosmopolitan agricultural pest of worldwide economic importance and a model for the development of the Sterile Insect Technique (SIT) for fruit flies of the Tephritidae family (Diptera). SIT relies on the effective mating of laboratory-reared strains and natural populations, and therefore requires an efficient mass-rearing system that will allow for the production of high-quality males. Adaptation of wild flies to an artificial laboratory environment can be accompanied by negative effects on several life history traits through changes in their genetic diversity and symbiotic communities. Such changes may lead to reduced biological quality and mating competitiveness in respect to the wild populations. Profiling wild populations can help understand, and maybe reverse, deleterious effects accompanying laboratory domestication thus providing insects that can efficiently and effectively support SIT application.

RESULTS

In the present study, we analyzed both the genetic structure and gut symbiotic communities of natural medfly populations of worldwide distribution, including Europe, Africa, Australia, and the Americas. The genetic structure of 408 individuals from 15 distinct populations was analyzed with a set of commonly used microsatellite markers. The symbiotic communities of a subset of 265 individuals from 11 populations were analyzed using the 16S rRNA gene-based amplicon sequencing of single individuals (adults). Genetic differentiation was detected among geographically distant populations while adults originated from neighboring areas were genetically closer. Alpha and beta diversity of bacterial communities pointed to an overall reduced symbiotic diversity and the influence of the geographic location on the bacterial profile.

CONCLUSIONS

Our analysis revealed differences both in the genetic profile and the structure of gut symbiotic communities of medfly natural populations. The genetic analysis expanded our knowledge to populations not analyzed before and our results were in accordance with the existing scenarios regarding this species expansion and colonization pathways. At the same time, the bacterial communities from different natural medfly populations have been characterized, thus broadening our knowledge on the microbiota of the species across its range. Genetic and symbiotic differences between natural and laboratory populations must be considered when designing AW-IPM approaches with a SIT component, since they may impact mating compatibility and mating competitiveness of the laboratory-reared males. In parallel, enrichment from wild populations and/or symbiotic supplementation could increase rearing productivity, biological quality, and mating competitiveness of SIT-important laboratory strains.

Genetic diversity of Calliphora vicina (Diptera: Calliphoridae) in the Iberian Peninsula based on cox1, 16S and ITS2 sequences

The study of Diptera at the scene of a crime can provide essential information for the interpretation of evidence. Phylogeographic reconstruction could help differentiate haplotypes of a dipteran species in a geographical area, clarifying, for example, the details of a possible relocation of a corpse. In addition, inferring the ancestral areas of distribution helps to understand the current status of the species and its biogeographic history. One of the most important species in forensic entomology is Calliphora vicina Rovineau-Desvoidy, 1830 (Diptera: Calliphoridae). The aim of this work is to increase our knowledge of this species in the Iberian Peninsula using 464 specimens from Spain and Portugal. These samples were identified using morphological keys and by molecular methods using fragments of the cox1, 16S and ITS2 genes. The phylogeographic history of these populations was inferred from haplotype networks and the reconstruction of ancestral areas of distribution. The molecular results corroborated the morphological identifications of the samples. Phylogeographic networks showed no geographical structure, as haplotypes are shared among almost all populations. reconstruct ancestral state in phylogenies analyses showed a high rate of movement among populations, possibly related to human activity. These results suggest that this species had a very rapid and recent spatial and demographic expansion throughout the Iberian Peninsula.

Spatial genetic structure in the rock hyrax (Procavia capensis) across the Namaqualand and western Fynbos areas of South Africa — a mitochondrial and microsatellite perspective

The interplay between biotic and abiotic environments is increasingly recognized as a major determinant of spatial genetic patterns. Among spatial genetic studies, saxicolous or rock-dwelling species remain underrepresented in spite of their strict dependence on landscape structure. Here we investigated patterns and processes operating at different spatial (fine and regional scales) and time scales (using mitochondrial and microsatellite markers) in the rock hyrax (Procavia capensis (Pallas, 1766)). Our focus was on the western seaboard of South Africa and included two recognized biodiversity hotspots (Cape Floristic Region and Succulent Karoo). At fine spatial scale, significant genetic structure was present between four rocky outcrops in an isolated population, likely driven by the social system of this species. At a broader spatial scale, ecological dependence on rocky habitat and population-level processes, in conjunction with landscape structure, appeared to be the main drivers of genetic diversity and structure. Large areas devoid of suitable rocky habitat (e.g., the Knersvlakte, Sandveld, and Cape Flats, South Africa) represent barriers to gene flow in the species, although genetic clusters closely follow climatic, geological, and phytogeographic regions, possibly indicating ecological specialization or adaptation as contributing factors enforcing isolation. Taken together, our study highlights the need to consider both intrinsic and extrinsic factors when investigating spatial genetic structures within species.

Worldwide Phylogeography of Ceratitis capitata (Diptera: Tephritidae) Using Mitochondrial DNA

The Mediterranean fruit fly, Ceratitis capitata (Weidemann), is one of the most economically important tephritid species worldwide. It has spread across six geographic regions as a result of successful invasions and continues to cause substantial losses to agricultural communities. Our study examined 1,864 flies originating from 150 localities, using mitochondrial DNA sequencing methods. We tested for population structure and revealed the genetic diversity for 1,592 specimens gathered from 144 wild fly collections from 46 countries representing the entire geographic range for this species. We also include in this study 272 Sterile Insect Technique (SIT) specimens from four SIT facilities. We recovered 202 haplotypes from the current sampling and updated previously published work to reveal a total of 231 haplotypes for this pest. These data show population structure at and below the regional level for these collections, shedding light on the current demographics for this species. We observed four common haplotypes, seen among 62% of the samples sequenced that have worldwide distribution. Three haplotypes were seen in SIT flies, with one seen as the predominant haplotype. Our work showed that two of the haplotypes were private to SIT flies, not present among wild fly collections. However, a third haplotype common among wild fly collections was also seen in one SIT facility but at a low frequency based on the current sampling. We provide guidance on the interpretation of these methods for the source estimation of current and future infestations.

Population genetic structure of Bemisia tabaci MED (Hemiptera: Aleyrodidae) in Korea

The sweet potato whitefly, Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) is a major agricultural pest that causes economic damages worldwide. In particular, B. tabaci MED (Mediterranean) has resulted in serious economic losses in tomato production of Korea. In this study, 1,145 B. tabaci MED females from 35 tomato greenhouses in different geographic regions were collected from 2016 to 2018 (17 populations in 2016, 13 in 2017, and five in 2018) and analyzed to investigate their population genetic structures using eight microsatellite markers. The average number of alleles per population (NA) ranged from 2.000 to 5.875, the expected heterozygosity (HE) ranged from 0.218 to 0.600, the observed heterozygosity (HO) ranged from 0.061 to 0.580, and the fixation index inbreeding coefficient (FIS) ranged from -0.391 to 0.872 over the three years of the study. Some significant correlation (p < 0.05) was present between genetic differentiations (FST) and geographical distance, and a comparatively high proportion of variation was found among the B. tabaci MED populations. The B. tabaci MED populations were divided into two well-differentiated genetic clusters within different geographic regions. Interestingly, its genetic structures converged into one genetic cluster during just one year. The reasons for this genetic change were speculated to arise from different fitness, insecticide resistance, and insect movement by human activities.

Phylogeography Approach of Diloboderus abderus (Coleoptera: Melolonthidae) in the Southern Cone of America

Diloboderus abderus (Sturm, 1826) (Coleoptera: Melolonthidae) is a serious soil pest of corn, wheat, oat, and natural and cultivated pastures in Argentina, Paraguay, Uruguay, and southern Brazil. Despite its economic importance, the genetic diversity and population structure of D. abderus remain unknown. We sequenced a fragment of the mitochondrial gene cytochrome oxidase I region (COI), of six populations of D. abderus from the Southern Cone of America. The mtDNA marker revealed a high haplotype diversity, high pairwise F_ST values, and significant genetic variations among populations. No correlation was found between genetic and geographical distances, yet the most common haplotype (Dab01) was present in four out of the six populations. Analysis of molecular variance showed that most of the variation was within populations of D. abderus. Tajima's D and Fu's F_S tests indicated no evidence that D. abderus populations are under recent expansion. Our results indicate that genetic-based traits will likely remain localized or spread slowly, and management strategies need to be undertaken on a small scale.

Phenotypic plasticity in clutch size regulation among populations of a potential invasive fruit fly from environments that vary in host heterogeneity and isolation

Phenotypic plasticity is thought to evolve in response to environmental unpredictability and can shield genotypes from selection. However, selection can also act on plastic traits. Egg-laying behaviour, including clutch size regulation, is a plastic behavioural trait among tephritid fruit flies. We compared plasticity in clutch size regulation among females of Anastrepha ludens populations stemming from environments that differed in the degree of predictability in egg-laying opportunities. Clutch size regulation in response to hosts of different sizes was compared among flies from (a) a wild, highly isolated population, (b) a wild population that switches seasonally from a small wild host fruit that varies greatly in abundance to an abundant large-sized commercial host, and (c) a laboratory population. Flies from all three populations adjusted clutch number and size according to host size. However, flies from the heterogeneous wild environment were more plastic in adjusting clutch size than flies from agricultural settings that also laid fewer eggs; yet both populations were more plastic in adjusting clutch size in line with host size when compared with laboratory females. When wild and orchard females encountered the largest host, clutch size was extremely variable and egg regulation did not follow the same trend. Heterogeneity in host availability in space and time appears to be as important as seasonal variation in host size in maintaining plastic clutch size regulation behaviour. In stable environments, there was a clear reduction in the plasticity of these traits.

Tracking the Origins of Fly Invasions; Using Mitochondrial Haplotype Diversity to Identify Potential Source Populations in Two Genetically Intertwined Fruit Fly Species (Bactrocera carambolae and Bactrocera dorsalis [Diptera: Tephritidae])

Bactrocera carambolae Drew and Hancock and Bactrocera dorsalis (Hendel) (Diptera: Tephritidae) are important pests of many fruits. These flies have been spread across the world through global travel and trade, and new areas are at risk of invasion. Whenever new invasive populations are discovered, quick and accurate identification is needed to mitigate the damage they can cause. Determining invasive pathways can prevent further spread of pests as well as subsequent reinvasions through the same pathway. Molecular markers can be used for both species identification and pathway analysis. We analyzed 1,601 individuals from 19 populations using 765 base pairs of the mitochondrial cytochrome oxidase I (COI) gene to infer the haplotype diversity and population structure within these flies from across their native and invasive ranges. We analyzed these samples by either grouping by species or geographic populations due to the genetic similarity in the mitochondrial genome. We found no genetic structure between B. dorsalis and B. carambolae and our findings suggest recent and most likely ongoing, genetic exchange between these two species in the wild. Hyper-diverse mitochondrial genetic diversity in the native range suggests large population sizes and relatively high mutation rates. Only 52% of the haplotypes found in the trap captures from California are shared with haplotypes from flies found in our global survey, indicating significant genetic diversity in the native range that is missing from our samples. However, these results provide a foundation for the accurate determination of the provenance of invasive populations around the world.

Population genetics and migration pathways of the Mediterranean fruit fly Ceratitis capitata inferred with coalescent methods

Background

Invasive species are a growing threat to food biosecurity and cause significant economic losses in agricultural systems. Despite their damaging effect, they are attractive models for the study of evolution and adaptation in newly colonised environments. The Mediterranean fruit fly, Ceratitis capitata, as a member of the family Tephritidae, is one of the most studied invasive species feeding on many fruit crops in the tropics and subtropics worldwide. This study aims to determine the global macrogeographic population structure of Ceratitis capitata and reconstruct its potential migration routes.

Method

A partial mitochondrial cytochrome oxidase I gene from >400 individual medflies and 14 populations from four continents was sequenced and subjected to Bayesian demographic modelling.

Results

The Afrotropical populations (Kenya, South Africa and Ghana) harbour the majority of haplotypes detected, which also are highly divergent, in accordance with the presumed ancestral range of medflies in Sub-Saharan Africa. All other populations in the presumed non-native areas were dominated by a single haplotype also present in South Africa, in addition to a few, closely related haplotypes unique to a single local population or regional set, but missing from Africa. Bayesian coalescence methods revealed recent migration pathways from Africa to all continents, in addition to limited bidirectional migration among many local and intercontinental routes.

Conclusion

The detailed investigation of the recent migration history highlights the interconnectedness of affected crop production regions worldwide and pinpoints the routes and potential source areas requiring more specific quarantine measures.

Geographic variation and plasticity in climate stress resistance among southern African populations of Ceratitis capitata (Wiedemann) (Diptera: Tephritidae)

Traits of thermal sensitivity or performance are typically the focus of species distribution modelling. Among-population trait variation, trait plasticity, population connectedness and the possible climatic covariation thereof are seldom accounted for. Here, we examine multiple climate stress resistance traits, and the plasticity thereof, for a globally invasive agricultural pest insect, the Mediterranean fruit fly, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae). We also accounted for body size and population genetic connectivity among distinct populations from diverse bioclimatic regions across southern Africa. Desiccation resistance, starvation resistance, and critical thermal minimum (CT_min) and maximum (CT_max) of C. capitata varied between populations. For thermal tolerance traits, patterns of flexibility in response to thermal acclimation were suggestive of beneficial acclimation, but this was not the case for desiccation or starvation resistance. Population differences in measured traits were larger than those associated with acclimation, even though gene flow was high. Desiccation resistance was weakly but positively affected by growing degree-days. There was also a weak positive relationship between CT_min and temperature seasonality, but CT_max was weakly but negatively affected by the same bioclimatic variable. Our results suggest that the invasive potential of C. capitata may be supported by adaptation of tolerance traits to local bioclimatic conditions.

Population structure and patterns of geographic differentiation of Bactrocera oleae (Diptera: Tephritidae) in Eastern Mediterranean Basin

The olive fly (Bactrocera oleae) is the most destructive pest of olives in most commercial olive-growing regions worldwide. Significant economic damage to olive production is caused by the larvae of this fly, which feed on the pulp of Olea fruits. Studying the genetic structure of insect pest populations is essential for the success of pest management strategies. Our primary goal in the present study was to examine the population structures of olive flies collected over a wide geographic area from Turkey, a representative of eastern Mediterranean region, using two mitochondrial DNA sequences as genetic markers. The data revealed a high level of genetic variability in olive fly populations and a moderate level of genetic differentiation between Mediterranean and Aegean populations in Turkey. We also merged the sequences obtained in the present study with previously published sequences from across the world into the data matrix. Strong population substructure and a significant correlation between genetic and geographic distances were detected in northern Mediterranean basin populations of B. oleae, indicating the possibility of a westward expansion of the species in the continent. In addition, our results revealed a very close genetic relationship between the Aegean and Iranian populations, which suggests that B. oleae was introduced to Iran from western parts of Turkey. However, additional markers and analytical approaches are required to determine the exact colonization route of olive fly.

Population genetics of an alien whitefly in China: implications for its dispersal and invasion success

Invasive genotypes may be associated with their ability to access the invasion habitat. The whitefly, Bemisia tabaci Q, has been an important agricultural pest in China since 2008. In order to identify the invasion routes and to provide insight into its invasion success in China, we analyzed the composition, distribution, and genetic diversity of mitochondrial haplotypes of B. tabaci Q. Samples were obtained from 23 provincial level administrative units in 2011, and analyses conducted based on the mtCOI. Our results revealed five haplotypes (abbreviated as Q1H1-Q1H5) were present in the Q1 subclade based on 773-bp mtCOI fragment analysis. The diversity of haplotypes indicated the B. tabaci Q populations were derived from multiple invasion sources originating from the western Mediterranean region. Among the haplotypes, Q1H1 was dominant, followed by Q1H2. The whitefly populations were generally characterized by low levels of genetic diversity based on the 773-bp mtCOI fragment. Similar results were obtained when the 657-bp fragment was analyzed using the procedure in a previous report. Potential mechanisms contributing to the dominance of the Q1H1 in China are also discussed. These results will be helpful in revealing the mechanisms that enabled the successful invasion of B. tabaci Q into the country.

Screening mitochondrial DNA sequence variation as an alternative method for tracking established and outbreak populations of Queensland fruit fly at the species southern range limit

Understanding the relationship between incursions of insect pests and established populations is critical to implementing effective control. Studies of genetic variation can provide powerful tools to examine potential invasion pathways and longevity of individual pest outbreaks. The major fruit fly pest in eastern Australia, Queensland fruit fly Bactrocera tryoni (Froggatt), has been subject to significant long‐term quarantine and population reduction control measures in the major horticulture production areas of southeastern Australia, at the species southern range limit. Previous studies have employed microsatellite markers to estimate gene flow between populations across this region. In this study, we used an independent genetic marker, mitochondrial DNA (mtDNA) sequences, to screen genetic variation in established and adjacent outbreak populations in southeastern Australia. During the study period, favorable environmental conditions resulted in multiple outbreaks, which appeared genetically distinctive and relatively geographically localized, implying minimal dispersal between simultaneous outbreaks. Populations in established regions were found to occur over much larger areas. Screening mtDNA (female) lineages proved to be an effective alternative genetic tool to assist in understanding fruit fly population dynamics and provide another possible molecular method that could now be employed for better understanding of the ecology and evolution of this and other pest species.

De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae)

The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.

Genetic diversity and population structure of Anastrepha striata (Diptera: Tephritidae) in three natural regions of southwestern Colombia using mitochondrial sequences

Anastrepha striata is widely distributed across the Americas and is a pest of economically important crops, especially crops of the Myrtaceae family. Insect population structures can be influenced by the presence of physical barriers or characteristics associated with habitat differences. This study evaluated the effect of the Western Andes on the population structure of A. striata. Individuals were collected from Psidium guajava fruits from three natural regions of southwestern Colombia (Pacific Coast, mountainous region and the inter-Andean valley of the Cauca River). Based on a 1318 bp concatenated of the genes Cytochrome Oxidase subunit I (COI) and NADH dehydrogenase subunit 6 (ND6), 14 haplotypes with few changes among them (between 1 and 3) were found. There was only one dominant haplotype in all three regions. No genetic structure associated with the three eco-geographical regions of the study was found. Moreover, the Western Andes are not an effective barrier for the genetic isolation of the populations from the Pacific Coast compared with the inter-Andean valley populations. This genetic homogeneity could be partially due to anthropogenic intervention, which acts as a dispersal agent of infested fruits. Another hypothesis to explain the lack of structure would be the relatively recent arrival of A. striata to the region, as indicated by an analysis of the demographic history, which reveals a process of population expansion. This study represents the first attempt to understand the population genetics of A. striata in Colombia and could contribute to the integral management of this pest.

Mediterranean fruit fly on Mimusops zeyheri indigenous to South Africa: a threat to the horticulture industry

BACKGROUND

Claims abound that the Transvaal red milkwood, Mimusops zeyheri, indigenous to areas with tropical and subtropical commercial fruit trees and fruiting vegetables in South Africa, is relatively pest free owing to its copious concentrations of latex in the above-ground organs. On account of observed fruit fly damage symptoms, a study was conducted to determine whether M. zeyheri was a host to the notorious quarantined Mediterranean fruit fly (Ceratitis capitata).

RESULTS

Fruit samples were kept for 16-21 days in plastic pots containing moist steam-pasteurised growing medium with tops covered with a mesh sheath capable of retaining emerging flies. Microscopic diagnosis of the trapped flies suggested that the morphological characteristics were congruent with those of C. capitata, which was confirmed through cytochrome c oxidase I (COI) gene sequence alignment with a 100% bootstrap value and 99% confidence probability when compared with those from the National Centre for Biotechnology Information database.

CONCLUSION

This study demonstrated that M. zeyheri is a host of C. capitata. Therefore, C. capitata from infestation reservoirs of M. zeyheri fruit trees could be a major threat to the tropical and subtropical fruit industries in South Africa owing to the fruit-bearing nature of the new host. © 2015 Society of Chemical Industry.

Investigating population differentiation in a major African agricultural pest: evidence from geometric morphometrics and connectivity suggests high invasion potential

The distribution, spatial pattern and population dynamics of a species can be influenced by differences in the environment across its range. Spatial variation in climatic conditions can cause local populations to undergo disruptive selection and ultimately result in local adaptation. However, local adaptation can be constrained by gene flow and may favour resident individuals over migrants-both are factors critical to the assessment of invasion potential. The Natal fruit fly (Ceratitis rosa) is a major agricultural pest in Africa with a history of island invasions, although its range is largely restricted to south east Africa. Across Africa, C. rosa is genetically structured into two clusters (R1 and R2), with these clusters occurring sympatrically in the north of South Africa. The spatial distribution of these genotypic clusters remains unexamined despite their importance for understanding the pest's invasion potential. Here, C. rosa, sampled from 22 South African locations, were genotyped at 11 polymorphic microsatellite loci and assessed morphologically using geometric morphometric wing shape analyses to investigate patterns of population structure and determine connectedness of pest-occupied sites. Our results show little to no intraspecific (population) differentiation, high population connectivity, high effective population sizes and only one morphological type (R2) within South Africa. The absence of the R1 morphotype at sites where it was previously found may be a consequence of differences in thermal niches of the two morphotypes. Overall, our results suggest high invasion potential of this species, that area-wide pest management should be undertaken on a country-wide scale, and that border control is critical to preventing further invasions.

Exceptionally High Levels of Genetic Diversity in Wheat Curl Mite (Acari: Eriophyidae) Populations from Turkey

Recent research on the wheat curl mite species complex has revealed extensive genetic diversity that has distinguished several genetic lineages infesting bread wheat (Triticum aestivum L.) and other cereals worldwide. Turkey is the historical region of wheat and barley (Hordeum vulgare L.) domestication and diversification. The close relationship between these grasses and the wheat curl mite provoked the question of the genetic diversity of the wheat curl mite in this region. The scope of the study was to investigate genetic differentiation within the wheat curl mite species complex on grasses in Turkey. Twenty-one wheat curl mite populations from 16 grass species from nine genera (Agropyron sp., Aegilops sp., Bromus sp., Elymus sp., Eremopyrum sp., Hordeum sp., Poa sp., Secale sp., and Triticum sp.) were sampled in eastern and southeastern Turkey for genetic analyses. Two molecular markers were amplified: the cytochrome oxidase subunit I coding region of mtDNA (COI) and the D2 region of 28S rDNA. Phylogenetic analyses revealed high genetic variation of the wheat curl mite in Turkey, primarily on Bromus and Hordeum spp., and exceptionally high diversity of populations associated with bread wheat. Three wheat-infesting wheat curl mite lineages known to occur on other continents of the world, including North and South America, Australia and Europe, were found in Turkey, and at least two new genetic lineages were discovered. These regions of Turkey exhibit rich wheat curl mite diversity on native grass species. The possible implications for further studies on the wheat curl mite are discussed.

Local and regional scale genetic variation in the Cape dune mole-rat, Bathyergus suillus

The distribution of genetic variation is determined through the interaction of life history, morphology and habitat specificity of a species in conjunction with landscape structure. While numerous studies have investigated this interplay of factors in species inhabiting aquatic, riverine, terrestrial, arboreal and saxicolous systems, the fossorial system has remained largely unexplored. In this study we attempt to elucidate the impacts of a subterranean lifestyle coupled with a heterogeneous landscape on genetic partitioning by using a subterranean mammal species, the Cape dune mole-rat (Bathyergus suillus), as our model. Bathyergus suillus is one of a few mammal species endemic to the Cape Floristic Region (CFR) of the Western Cape of South Africa. Its distribution is fragmented by rivers and mountains; both geographic phenomena that may act as geographical barriers to gene-flow. Using two mitochondrial fragments (cytochrome b and control region) as well as nine microsatellite loci, we determined the phylogeographic structure and gene-flow patterns at two different spatial scales (local and regional). Furthermore, we investigated genetic differentiation between populations and applied Bayesian clustering and assignment approaches to our data. Nearly every population formed a genetically unique entity with significant genetic structure evident across geographic barriers such as rivers (Berg, Verlorenvlei, Breede and Gourits Rivers), mountains (Piketberg and Hottentots Holland Mountains) and with geographic distance at both spatial scales. Surprisingly, B. suillus was found to be paraphyletic with respect to its sister species, B. janetta-a result largely overlooked by previous studies on these taxa. A systematic revision of the genus Bathyergus is therefore necessary. This study provides a valuable insight into how the biology, life-history and habitat specificity of animals inhabiting a fossorial system may act in concert with the structure of the surrounding landscape to influence genetic distinctiveness and ultimately speciation.

Effects of within-generation thermal history on the flight performance of Ceratitis capitata: colder is better

The influence of thermal history on temperature-dependent flight performance was investigated in an invasive agricultural pest insect, Ceratitis capitata (Diptera: Tephritidae). Flies were exposed to one of four developmental acclimation temperatures (Tacc: 15, 20, 25, 30°C) during their pupal stage and tested at these temperatures (Ttest) as adults using a full-factorial study design. Major factors influencing flight performance included sex, body mass, Ttest and the interaction between Ttest and Tacc. Successful flight performance increased with increasing Ttest across all acclimation groups (from 10% at 15°C to 77% at 30°C). Although Tacc did not affect flight performance independently, it did have a significant interaction effect with Ttest. Multiple comparisons showed that flies which had been acclimated to 15°C and 20°C performed better than those acclimated to 25°C and 30°C when tested at cold temperatures, but warm-acclimated flies did not outperform cold-acclimated flies at warmer temperatures. This provides partial support for the 'colder is better' hypothesis. To explain these results, several flight-related traits were examined to determine whether Tacc influenced flight performance as a consequence of changes in body or wing morphology, whole-animal metabolic rate or cytochrome c oxidase enzyme activity. Although significant effects of Tacc could be detected in several of the traits examined, with an emphasis on sex-related differences, increased flight performance could not be explained solely on the basis of changes in any of these traits. Overall, these results are important for understanding dispersal physiology despite the fact that the mechanisms of acclimation-related changes in flight performance remain unresolved.

Niche overlap of congeneric invaders supports a single-species hypothesis and provides insight into future invasion risk: implications for global management of the Bactrocera dorsalis complex

Background

The invasive fruit fly, Bactrocera invadens, has expanded its range rapidly over the past 10 years. Here we aimed to determine if the recent range expansion of Bactrocera invadens into southern Africa can be better understood through niche exploration tools, ecological niche models (ENMs), and through incorporating information about Bactrocera dorsalis s.s., a putative conspecific species from Asia. We test for niche overlap of environmental variables between Bactrocera invadens and Bactrocera dorsalis s.s. as well as two other putative conspecific species, Bactrocera philippinensis and B. papayae. We examine overlap and similarity in the geographical expression of each species’ realised niche through reciprocal distribution models between Africa and Asia. We explore different geographical backgrounds, environmental variables and model complexity with multiple and single Bactrocera species hypotheses in an attempt to predict the recent range expansion of B. invadens into northern parts of South Africa.

Principal Findings

Bactrocera invadens has a high degree of niche overlap with B. dorsalis s.s. (and B. philippinensis and B. papayae). Ecological niche models built for Bactrocera dorsalis s.s. have high transferability to describe the range of B. invadens, and B. invadens is able to project to the core range of B. dorsalis s.s. The ENMs of both Bactrocera dorsalis and B. dorsalis combined with B. philipenesis and B. papayae have significantly higher predictive ability to capture the distribution points in South Africa than for B. invadens alone.

Conclusions/Significance

Consistent with other studies proposing these Bactrocera species as conspecific, niche similarity and overlap between these species is high. Considering these other Bactrocera dorsalis complex species simultaneously better describes the range expansion and invasion potential of B. invadens in South Africa. We suggest that these species should be considered the same–at least functionally–and global quarantine and management strategies applied equally to these Bactrocera species.

Population distribution and synchronized dynamics in a metapopulation model in two geographic scales

In this paper, a metapopulation model composed of patches distributed in two spatial scales is proposed in order to study the stability of synchronous dynamics. Clusters of patches connected by short-range dispersal are assumed to be formed. Long distance dispersal is responsible to link patches that are in different clusters. During each time step, we assume that there are three processes involved in the population dynamics: (a) the local dynamics, which consists of reproduction and survival; (b) short-range dispersal of individuals between the patches of each cluster; and (c) the movement between the clusters. First we present an analytic criterion for regional synchronization, where the clusters evolve with the same dynamics. We then discuss the possibility of a full synchronism, where all patches in the network follow the same time evolution. The existence of such a state is not always ensured, even considering that all patches have the same local dynamics. It depends on how the individuals are distributed among the local patches that compose a cluster after long-range dispersal takes place in the regional scale. An analytic criterion for the stability of synchronized trajectories in this case is obtained.

High genetic diversity and structured populations of the oriental fruit moth in its range of origin

The oriental fruit moth Grapholita ( = Cydia) molesta is a key fruit pest globally. Despite its economic importance, little is known about its population genetics in its putative native range that includes China. We used five polymorphic microsatellite loci and two mitochondrial gene sequences to characterize the population genetic diversity and genetic structure of G. molesta from nine sublocations in three regions of a major fruit growing area of China. Larval samples were collected throughout the season from peach, and in late season, after host switch by the moth to pome fruit, also from apple and pear. We found high numbers of microsatellite alleles and mitochondrial DNA haplotypes in all regions, together with a high number of private alleles and of haplotypes at all sublocations, providing strong evidence that the sampled area belongs to the origin of this species. Samples collected from peach at all sublocations were geographically structured, and a significant albeit weak pattern of isolation-by-distance was found among populations, likely reflecting the low flight capacity of this moth. Interestingly, populations sampled from apple and pear in the late season showed a structure differing from that of populations sampled from peach throughout the season, indicating a selective host switch of a certain part of the population only. The recently detected various olfactory genotypes in G. molesta may underly this selective host switch. These genetic data yield, for the first time, an understanding of population dynamics of G. molesta in its native range, and of a selective host switch from peach to pome fruit, which may have a broad applicability to other global fruit production areas for designing suitable pest management strategies.

Migration and dispersal may drive to high genetic variation and significant genetic mixing: the case of two agriculturally important, continental hoverflies (Episyrphus balteatus and Sphaerophoria scripta)

Population structure of pests and beneficial species is an important issue when designing management strategies to optimize ecosystem services. In this study, we investigated for the first time the population structure at a continental scale of two migratory species of hoverflies providing both pest regulation and pollination services [Episyrphus balteatus and Sphaerophoria scripta (Diptera: Syrphidae)]. To achieve this objective, we used two sets of 12 species-specific microsatellite markers on a large-scale sampling from all over Europe. Our findings showed a high level of genetic mixing resulting in a lack of genetic differentiation at a continental scale and a great genetic diversity in the two species. All the pairwise FST values between European localities were less 0.05 in the two species. These low values reflect a large-scale genetic mixing probably caused by the existence of frequent migratory movements in the two species. Mantel tests revealed isolation-by-distance pattern on the East-West axis, but not on the North-South axis. This isolation-by-distance pattern confirms the existence of North-South migratory movements in both directions and suggests an important step by step dispersal. Population features shown by this study are common in invasive species and pests, but are not often observed in beneficial species. They reflect great colonization abilities and a high adaptive potential when dealing with a changing environment. Our results highlight the two studied species as particularly interesting beneficial insects for pollination and pest predation in the current context of global change.