Francesco Nardi

An extensive field survey combined with a phylogenetic analysis reveals rapid and widespread invasion of two alien whiteflies in China.

Background To understand the processes of invasions by alien insects is a pre-requisite for improving management. The whitefly Bemisia tabaci is a cryptic species complex that contains some of the most invasive pests worldwide. However, extensive field data to show the geographic distribution of the members of this species complex as well as the invasion by some of its members are scarce. Methodology/Principal Findings We used field surveys and published data to assess the current diversity and distribution of B. tabaci cryptic species in China and relate the indigenous members to other Asian and Australian members of the complex. The survey covered the 16 provinces where indigenous B. tabaci occur and extends this with published data for the whole of China. We used molecular markers to identify cryptic species. The evolutionary relationships between the different Asian B. tabaci were reconstructed using Bayesian methods. We show that whereas in the past the exotic invader Middle East-Asia Minor 1 was predominant across China, another newer invader Mediterranean is now the dominant species in the Yangtze River Valley and eastern coastal areas, and Middle East-Asia Minor 1 is now predominant only in the south and south eastern coastal areas. Based on mtCO1 we identified four new cryptic species, and in total we have recorded 13 indigenous and two invasive species from China. Diversity was highest in the southern and southeastern provinces and declined to north and west. Only the two invasive species were found in the northern part of the country where they occur primarily in protected cropping. By 2009, indigenous species were mainly found in remote mountainous areas and were mostly absent from extensive agricultural areas. Conclusions/Significance Invasions by some members of the whitefly B. tabaci species complex can be rapid and widespread, and indigenous species closely related to the invaders are replaced.

Population structure and colonization history of the olive fly, Bactrocera oleae (Diptera, Tephritidae).

The olive fly, Bactrocera oleae, is the major pest of olives in most commercial olive‐growing regions worldwide. The species is abundant in the Mediterranean basin and has been introduced recently into California and Mexico, creating problems for quarantine protection and international trade. Here, we use nuclear microsatellite markers and mitochondrial sequences to examine the history of olive fly range expansion and colonization. Sampled populations span the current distribution of the olive fly worldwide, including South and Central Africa, Pakistan, Mediterranean Europe and Middle East, California, and Mexico. The Pakistani populations appear to be genetically well differentiated from the remaining populations, though rooting the origins of the species is problematic. Genetic similarity and assignment tests cluster the remaining populations into two genetic groups — Africa and a group including the Mediterranean basin and the American region. That Africa, and not the Mediterranean, is the origin of flies infesting cultivated olive is supported by the significantly greater genetic diversity at microsatellite loci in Africa relative to the Mediterranean area. The results also indicate that the recent invasion of olive flies in the American region most likely originated from the Mediterranean area.

Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea

BackgroundThe phylogeny of Arthropoda is still a matter of harsh debate among systematists, and significant disagreement exists between morphological and molecular studies. In particular, while the taxon joining hexapods and crustaceans (the Pancrustacea) is now widely accepted among zoologists, the relationships among its basal lineages, and particularly the supposed reciprocal paraphyly of Crustacea and Hexapoda, continues to represent a challenge. Several genes, as well as different molecular markers, have been used to tackle this problem in molecular phylogenetic studies, with the mitochondrial DNA being one of the molecules of choice. In this study, we have assembled the largest data set available so far for Pancrustacea, consisting of 100 complete (or almost complete) sequences of mitochondrial genomes. After removal of unalignable sequence regions and highly rearranged genomes, we used nucleotide and inferred amino acid sequences of the 13 protein coding genes to reconstruct the phylogenetic relationships among major lineages of Pancrustacea. The analysis was performed with Bayesian inference, and for the amino acid sequences a new, Pancrustacea-specific, matrix of amino acid replacement was developed and used in this study.ResultsTwo largely congruent trees were obtained from the analysis of nucleotide and amino acid datasets. In particular, the best tree obtained based on the new matrix of amino acid replacement (MtPan) was preferred over those obtained using previously available matrices (MtArt and MtRev) because of its higher likelihood score. The most remarkable result is the reciprocal paraphyly of Hexapoda and Crustacea, with some lineages of crustaceans (namely the Malacostraca, Cephalocarida and, possibly, the Branchiopoda) being more closely related to the Insecta s.s. (Ectognatha) than two orders of basal hexapods, Collembola and Diplura. Our results confirm that the mitochondrial genome, unlike analyses based on morphological data or nuclear genes, consistently supports the non monophyly of Hexapoda.ConclusionThe finding of the reciprocal paraphyly of Hexapoda and Crustacea suggests an evolutionary scenario in which the acquisition of the hexapod condition may have occurred several times independently in lineages descending from different crustacean-like ancestors, possibly as a consequence of the process of terrestrialization. If this hypothesis was confirmed, we should therefore re-think our interpretation of the evolution of the Arthropoda, where terrestrialization may have led to the acquisition of similar anatomical features by convergence. At the same time, the disagreement between reconstructions based on morphological, nuclear and mitochondrial data sets seems to remain, despite the use of larger data sets and more powerful analytical methods.

The mitochondrial genome of the olive fly Bactrocera oleae: two haplotypes from distant geographical locations

The complete sequence of the olive fly (Bactrocera oleae) mitochondrial genome has been determined. Two independent haplotypes, from flies of distant geographical origin (Italy and Portugal) were completely sequenced. The molecule is 15 815 bp long, and shows the gene content and organization typical of insects, namely thirteen protein coding genes (PCGs) encoding proteins involved in oxidative phosphorylation, two rRNAs, twenty‐two tRNAs and a long (949 bp) noncoding region. The genomes of the two fly specimens share the same arrangement, differing by a mere thirty‐one point mutations. The differences are mostly transitions (26) and synonymous substitutions in PCGs (21). The two new sequences are compared with others already present in the database.

Domestication of olive fly through a multi-regional host shift to cultivated olives: Comparative dating using complete mitochondrial genomes

The evolutionary history of the olive fly, Bactrocera oleae, was reconstructed in a phylogenetic and coalescent framework using full mitochondrial genome data from 21 individuals covering the entire worldwide distribution of the species. Special attention was given to reconstructing the timing of the processes under study. The early subdivision of the olive fly reflects the Quaternary differentiation between Olea europea subsp. europea in the Mediterranean area and the two lineages of Olea europea subsp. cuspidata in Africa and Asia, pointing to an early and close association between the olive fly and its host. The geographic structure and timing of olive fly differentiation in the Mediterranean indicates a clear connection with the post-glacial recolonization of wild olives in the area, and is irreconcilable with the early historical process of domestication and spread of the cultivated olive from its Levantine origin. Therefore, we suggest an early co-history of the olive fly with its wild host during the Quaternary and post-glacial periods and a multi-regional shift of olive flies to cultivated olives as these cultivars gradually replaced wild olives in historical times.

Deep phylogeographic divisions and long‐term persistence of forest invertebrates (Hexapoda: Collembola) in the North‐Western Mediterranean basin

The North‐Western Mediterranean basin is well known for its high number of relictual endemic taxa, and has been indicated as one of the world’s major biodiversity hotspots at the species level. A possible contributing factor may be long‐term persistence of populations and their prolonged stability. This study was designed to investigate the phylogeographic structure of three common species of the genus Lepidocyrtus (Hexapoda: Collembola), soil‐dwelling arthropods characterized by limited dispersal capabilities and generally associated with forest habitats. We observed a remarkable geographic structure, with numerous deeply divergent genetic lineages occupying islands as well as mainland sites with no apparent gene flow among most sites, even across distances of only tens of kilometres. The reconstructed time frame for the evolution of these lineages suggests divergence between 5 and 15 Ma. This indicates a remarkably ancient origin and long‐term persistence of individual lineages over a fine geographic scale despite the occurrence of abrupt sea level and climatic fluctuations in the area. This further suggests that currently recognized morphological species might be a serious underestimation of the true springtail biodiversity within this region.

High divergence across the whole mitochondrial genome in the "pan-Antarctic" springtail Friesea grisea: Evidence for cryptic species?

Collembola are one of the few hexapod groups adapted to live in the harsh environmental conditions of Antarctic terrestrial ecosystems. Diversity is limited to a few species that can be very abundant in coastal deglaciated sites. A remarkable lack of overlap in Collembola species composition is evident between Western and Eastern Antarctica, and Friesea grisea is currently the only species whose distribution is thought to span these two main regions of the continent. However, our analysis of the complete sequences of the mitochondrial genomes from specimens obtained from each of the two regions showed unexpected genetic divergence, well above the average levels observed between populations belonging to the same species, and so indicating that these are actually separate species, despite their lack of distinguishing morphology. Detailed analysis of the two genomes showed the presence of a non-coding region observed between trnS(uga) and nad1. Other features of these mitochondrial genomes, such as base compositional bias, secondary structure features of tRNAs and the presence of regulatory elements in the control region, are described and discussed from an evolutionary standpoint.

The complete mitochondrial genome of the Antarctic springtail Cryptopygus antarcticus (Hexapoda: Collembola)

BackgroundMitogenomics data, i.e. complete mitochondrial genome sequences, are popular molecular markers used for phylogenetic, phylogeographic and ecological studies in different animal lineages. Their comparative analysis has been used to shed light on the evolutionary history of given taxa and on the molecular processes that regulate the evolution of the mitochondrial genome. A considerable literature is available in the fields of invertebrate biochemical and ecophysiological adaptation to extreme environmental conditions, exemplified by those of the Antarctic. Nevertheless, limited molecular data are available from terrestrial Antarctic species, and this study represents the first attempt towards the description of a mitochondrial genome from one of the most widespread and common collembolan species of Antarctica.ResultsIn this study we describe the mitochondrial genome of the Antarctic collembolan Cryptopygus antarcticus Willem, 1901. The genome contains the standard set of 37 genes usually present in animal mtDNAs and a large non-coding fragment putatively corresponding to the region (A+T-rich) responsible for the control of replication and transcription. All genes are arranged in the gene order typical of Pancrustacea. Three additional short non-coding regions are present at gene junctions. Two of these are located in positions of abrupt shift of the coding polarity of genes oriented on opposite strands suggesting a role in the attenuation of the polycistronic mRNA transcription(s). In addition, remnants of an additional copy of trnL(uag) are present between trnS(uga) and nad1. Nucleotide composition is biased towards a high A% and T% (A+T = 70.9%), as typically found in hexapod mtDNAs. There is also a significant strand asymmetry, with the J-strand being more abundant in A and C. Within the A+T-rich region, some short sequence fragments appear to be similar (in position and primary sequence) to those involved in the origin of the N-strand replication of the Drosophila mtDNA.ConclusionThe mitochondrial genome of C. antarcticus shares several features with other pancrustacean genomes, although the presence of unusual non-coding regions is also suggestive of molecular rearrangements that probably occurred before the differentiation of major collembolan families. Closer examination of gene boundaries also confirms previous observations on the presence of unusual start and stop codons, and suggests a role for tRNA secondary structures as potential cleavage signals involved in the maturation of the primary transcript. Sequences potentially involved in the regulation of replication/transcription are present both in the A+T-rich region and in other areas of the genome. Their position is similar to that observed in a limited number of insect species, suggesting unique replication/transcription mechanisms for basal and derived hexapod lineages. This initial description and characterization of the mitochondrial genome of C. antarcticus will constitute the essential foundation prerequisite for investigations of the evolutionary history of one of the most speciose collembolan genera present in Antarctica and other localities of the Southern Hemisphere.

Molecular phylogeny of the apterygotan insects based on nuclear and mitochondrial genes

Summary Basal hexapodan orders (Apterygota) are traditionally divided in two well defined taxonomic groups, Entognatha and Ectognatha. Entognathy (the enclosed mouthparts condition) is considered the most distinctive character joining the Ellipura (Protura+ Collembola) with the order Diplura, whereas the presence of exposed mouthparts (ectognathy) is the feature shared by Microcoryphia and Zygentoma with the pterygote insects. In spite of the growing interest for the evolutionary history of the Apterygota, there is no complete agreement among the general phylogenetic hypotheses based on the study of morphological characters. In this study we analyzed the DNA sequence of segments of the nuclear Elongation Factor-1α(EF-1α) and of the mitochondrial 12S rRNA genes, and used different methods of phylogenetic reconstruction. The 12S gene seems to be more suited than the EF-1α to resolve some of the most outstanding systematic disputes, whereas the lack of resolution at the deeper nodes does not allow to assess the phylogenetic relationships within Microcoryphia and between ectognathan orders. We have obtained a fairly high support for the monophyly of the orders Diplura and Zygentoma. In the 12S analysis, the Ellipura and the Entognatha form monophyletic assemblages. In addition, the study of the distribution of introns in the EF-1α suggests a relationship between Collembola and Diplura.

The Oriental Fruit Fly, Bactrocera dorsalis, in China: Origin and Gradual Inland Range Expansion Associated with Population Growth

The oriental fruit fly, Bactrocera dorsalis, expanded throughout mainland China in the last century to become one of the most serious pests in the area, yet information on this process are fragmentary. Three mitochondrial genes (nad1, cytb and nad5) were used to infer the genetic diversity, population structure and demographic history of the oriental fruit fly from its entire distribution range in China. High levels of genetic diversity, as well as a significant correspondence between genetic and geographic distances, suggest that the invasion process might have been gradual, with no associated genetic bottlenecks. Three population groups could be identified, nevertheless the overall genetic structure was weak. The effective number of migrants between populations, estimated using the coalescent method, suggested asymmetric gene flow from the costal region of Guangdong to most inland regions. The demographic analysis indicates the oriental fruit fly underwent a recent population expansion in the Central China. We suggest the species originated in the costal region facing the South China Sea and gradually expanded to colonize mainland China, expanding here to high population numbers.