Cryptic variation in an ecological indicator organism: mitochondrial and nuclear DNA sequence data confirm distinct lineages of Baetis harrisoni Barnard (Ephemeroptera: Baetidae) in southern Africa.
ABSTRACT: BACKGROUND:Baetis harrisoni Barnard is a mayfly frequently encountered in river studies across Africa, but the external morphological features used for identifying nymphs have been observed to vary subtly between different geographic locations. It has been associated with a wide range of ecological conditions, including pH extremes of pH 2.9-10.0 in polluted waters. We present a molecular study of the genetic variation within B. harrisoni across 21 rivers in its distribution range in southern Africa. RESULTS:Four gene regions were examined, two mitochondrial (cytochrome c oxidase subunit I [COI] and small subunit ribosomal 16S rDNA [16S]) and two nuclear (elongation factor 1 alpha [EF1?] and phosphoenolpyruvate carboxykinase [PEPCK]). Bayesian and parsimony approaches to phylogeny reconstruction resulted in five well-supported major lineages, which were confirmed using a general mixed Yule-coalescent (GMYC) model. Results from the EF1? gene were significantly incongruent with both mitochondrial and nuclear (PEPCK) results, possibly due to incomplete lineage sorting of the EF1? gene. Mean between-clade distance estimated using the COI and PEPCK data was found to be an order of magnitude greater than the within-clade distance and comparable to that previously reported for other recognised Baetis species. Analysis of the Isolation by Distance (IBD) between all samples showed a small but significant effect of IBD. Within each lineage the contribution of IBD was minimal. Tentative dating analyses using an uncorrelated log-normal relaxed clock and two published estimates of COI mutation rates suggest that diversification within the group occurred throughout the Pliocene and mid-Miocene (~2.4-11.5 mya). CONCLUSIONS:The distinct lineages of B. harrisoni correspond to categorical environmental variation, with two lineages comprising samples from streams that flow through acidic Table Mountain Sandstone and three lineages with samples from neutral-to-alkaline streams found within eastern South Africa, Malawi and Zambia. The results of this study suggest that B. harrisoni as it is currently recognised is not a single species with a wide geographic range and pH-tolerance, but may comprise up to five species under the phylogenetic species concept, each with limited pH-tolerances, and that the B. harrisoni species group is thus in need of taxonomic review.
Project description:Background:Free-tailed bats of the genus Otomops are poorly known, and most species are documented from a handful of widely scattered localities. Recently, two allopatric species of Otomops were recognized in continental Africa: Otomops martiensseni (Matschie, 1897) in southern, central and western Africa, and the new species O. harrisoni Ralph et al., 2015 in the northeast and in Yemen. Methods:We collected additional samples of Otomops in Kenya and Rwanda where the ranges of these taxa approach one another to clarify their geographic ranges and taxonomic status. Mitochondrial and nuclear intron sequences served to identify and delimit species; we also documented their echolocation call variation and ectoparasite complements. Results:Otomops martiensseni, the southern African species, was documented in northern Kenya in Marsabit National Park. O. harrisoni, the northeastern African-Arabian species, was documented in southern Kenya and in a cave in Musanze District, Rwanda. Moreover, individuals of both species were found together at the Musanze cave, establishing them in precise spatial and temporal sympatry. Analyses of mitochondrial and nuclear loci identify no evidence of admixture between these forms, although available samples limit the power of this analysis. Echolocation call differences are also apparent among the three localities we analyzed. Three orders of insects and two families of mites are newly reported as ectoparasites of O. harrisoni. Discussion:Our results corroborate species rank for O. harrisoni and establish a zone of potential geographic overlap with O. martiensseni spanning at least 800 km of latitude. The new records establish the species in sympatry in northern Rwanda and add an additional species to the bat faunas of both Kenya and Rwanda. Future studies are needed to understand Otomops roosting requirements and movements, thereby explaining the paucity of known colonies and yielding better estimates of their conservation status. The discovery of mixed roosting associations in Rwanda invites further investigation.
Project description:Background:The Mediterranean basin is known to be the cradle of many endemic species. Within mayflies (Insecta, Ephemeroptera), North African species belonging to the family Baetidae remain poorly known and, traditionally, affinities to European fauna were proposed. Recent studies, based on molecular reconstructions, showed closer relationships to Mediterranean islands fauna. New information:Baetidae were sampled from North-West Algerian wadis (Tafna basin) and involved in COI barcoding reconstructions. Seven species were identified. The subgenus Rhodobaetis is represented by Baetis atlanticus known previously from Macaronesian islands, Europe and Morocco and the Maghrebian endemic Baetis sinespinosus. Specimens, previously identified as Cloeon cf. dipterum, correspond to Cloeon peregrinator and, until now, only reported from Macaronesia. Besides the confirmation of endemicity of some species, such as Procloen stagnicola and B. sinespinosus, our molecular study showed quite original results for relationships between European, insular and Algerian species. Baetis maurus stood out as a North African endemic sister clade to an Iberian clade. Furthermore, we found clear interspecific distances between Algerian and European clades for A. cf. sinaica and B. cf. pavidus, suggesting the presence of cryptic species in Algeria. However, additional studies are needed, as, for the moment, no clear morphological characters were found to separate the different clades and support them as valid species.
Project description:The taxonomy and systematics of the genus <i>Baetis</i> Leach (Ephemeroptera: Baetidae) in Israel is clarified for the first time as part of an ongoing comprehensive survey of the Israeli mayfly fauna. Six clearly defined species are currently recognized in Israel, four of which are described here as new to science. The validity of all species is supported by a molecular analysis of the mitochondrial COI gene. A key for the identification of the Israeli species based on the nymphal stage is provided, as well as data on their distribution patterns and ecology. The local fauna represents four Palearctic species groups, three of which reach their limit of distribution range in Israel. <i>Baetis</i> species typically inhabit lotic, pristine habitats in northern Israel, with few exceptions for some species that can be found in the Dead Sea area or in ephemeral ponds.
Project description:The relationships between Cinara (Cupressobium) aphids inhabiting woody parts and leaves of conifers belonging to Cupressaceae have been studied using a mitochondrial gene (COI) and a nuclear gene (EF1-?). Based on the COI sequences, genetic distances between species ranged from 5.6 % between Cinara (C.) tujafilina (del Guercio) and Cinara (C.) juniperi (De Geer) to 10.5 % between C. (C.) tujafilina and Cinara (C.) mordvilkoi (Pašek). Genetic distances among EF1-? sequences were lower and showed from 0.1 % between C. cupressi and C. juniperi to 2.3 % between C. tujafilina and C. mordvilkoi. Molecular phylogenetic trees were constructed using the Bayesian inference (BI) phylogenetic analysis and maximum parsimony (MP) criterion. Phylogenetic trees obtained based on COI and EF1-? marker genes created two sister clades. Our results indicate that Cinara (Cupressobium) are a monophyletic group of aphids. Phylogenetic relationships amongst Cupressobium aphids do not result from the association with the host plant, but from the feeding site on the host plant or an ability to change the microhabitat on the plant. As closely related species inhabit similar microhabitats on different host plants, it suggests that the host switching is the main mode of speciation in this subgenus.
Project description:The fall armyworm (FAW) Spodoptera frugiperda (J. E. Smith) is a species native to the Americas. This polyphagous lepidopteran pest was first reported in Nigeria and the Democratic Republic of São Tomé and Principe in 2016, but its presence in eastern Africa has not been confirmed via molecular characterisation. In this study, FAW specimens from western and central Uganda were identified based on the partial mtDNA COI gene sequences, with mtDNA COI haplotypes matching those identified in Nigeria and São Tomé. In this study, we sequence an additional partial mtDNA Cyt b gene and also the partial mtDNA COIII gene in Ugandan FAW samples. We detected identical mitochondrial DNA haplotypes for both the mtDNA Cyt b and COI partial genes, while combining the mtDNA COI/Cyt b haplotypes and mtDNA COIII haplotypes enabled a new maternal lineage in the Ugandan corn-preferred FAW samples to be identified. Our results suggested that the African incursions of S. frugiperda involved at least three maternal lineages. Recent full genome, phylogenetic and microsatellite analyses provided evidence to support S. frugiperda as likely consisted of two sympatric sister species known as the corn-preferred and rice-preferred strains. In our Ugandan FAW populations, we identified the presence of mtDNA haplotypes representative of both sister species. It is not known if both FAW sister species were originally introduced together or separately, and whether they have since spread as a single population. Further analyses of additional specimens originally collected from São Tomé, Nigeria and throughout Africa would be required to clarify this issue. Importantly, our finding showed that the genetic diversity of the African corn-preferred FAW species is higher than previously reported. This potentially contributed to the success of FAW establishment in Africa. Furthermore, with the additional maternal lineages detected, there is likely an increase in paternal lineages, thereby increasing the diversity of the African FAW population. Knowledge of the FAW genetic diversity will be needed to assess the risks of introducing Bt-resistance traits and to understand the FAW incursion pathways into the Old World and its potential onward spread. The agricultural implications of the presence of two evolutionary divergent FAW lineages (the corn and the rice lineage) in the African continent are further considered and discussed.
Project description:A detailed description of the larvae of Baetis (Baetis) cypronyx <b>sp. n.</b>, a representative of the <i>Baetis alpinus</i> species-group within the mayfly family Baetidae, is provided, including a differential diagnosis with regard to closely related species of the group, especially <i>Baetis melanonyx</i> (Pictet, 1843) and <i>Baetis baroukianus</i> Thomas & Dia, 1984. The new species is mainly distinguished by mouthparts (i.e. the shape and setation of labrum, maxillary and labial palps, details of paraglossae and mandibular incisors), setation of legs and abdominal terga, and length of paracercus. All available data on the biology of this putative endemic species of Cyprus are summarized. Annotated distributional data of the 33 species of Baetidae so far recorded from the Mediterranean islands are given, including new records and also including first data from Malta.
Project description:The cotton aphid, Aphis gossypii, is one of the most biologically diverse species of aphids; a polyphagous species in a family where most are host specialists. It is economically important and belongs to a group of closely related species that has challenged aphid taxonomy. The research presented here seeks to clarify the taxonomic relationships and status of species within the Aphid gossypii group in the North American Midwest. Sequences of the mitochondrial cytochrome oxidase 1 (COI), nuclear elongation factor 1-? (EF1-?), and nuclear sodium channel para-type (SCP) genes were used to differentiate between Aphid gossypii and related species. Aphis monardae, previously synonymised with Aphid gossypii, is re-established as a valid species. Phylogenetic analyses support the close relationship of members of the Aphid gossypii group native to North America (Aphid forbesi, Aphid monardae, Aphid oestlundi, Aphid rubifolii, and Aphid rubicola), Europe (Aphid nasturtii, Aphid urticata and Aphid sedi), and Asia (Aphid agrimoniae, Aphid clerodendri, Aphid glycines, Aphid gossypii, Aphid hypericiphaga, Aphid ichigicola, Aphid ichigo, Aphid sanguisorbicola, Aphid sumire and Aphid taraxicicola). The North American species most closely related to Aphid gossypii are Aphid monardae and Aphid oestlundi. The cosmopolitan Aphid gossypii and Aphid sedi identified in the USA are genetically very similar using COI and EF1-? sequences, but the SCP gene shows greater genetic distance between them. We present a discussion of the biological and morphological differentiation of these species.
Project description:Parasites comprise a significant percentage of the biodiversity of the planet and are useful systems to test evolutionary and ecological hypotheses. In this study, we analyze the effect of host species identity and the immediate local species assemblage within mixed species colonies of nesting seabirds on patterns of genetic clustering within two species of multihost ectoparasitic lice. We use three genetic markers (one mitochondrial, COI, and two nuclear, EF1-? and wingless) and maximum likelihood phylogenetic trees to test whether (1) parasites show lineage sorting based on their host species; and (2) switching of lineages to the alternate host species depends on the immediate local species assemblage of individual hosts within a colony. Specifically, we examine the genetic structure of two louse species: Eidmanniella albescens, infecting both Nazca (Sula granti) and blue-footed boobies (Sula nebouxii), and Fregatiella aurifasciata, infecting both great (Fregata minor) and magnificent frigatebirds (Fregata magnificens). We found that host species identity was the only factor explaining the patterns of genetic structure in both parasites. In both cases, there is evident genetic differentiation depending on the host species. Thus, a revision of the taxonomy of these louse species is needed. One possible explanation of this pattern is extremely low louse migration rates between host species, perhaps influenced by fine-scale spatial separation of host species within mixed colonies, and low parasite infrapopulation numbers.
Project description:Introduction:Aquatic oligochaetes represent valuable indicators of the quality of sediments of watercourses and lakes, but their difficult identification based on morphological criteria compromises their more common use for eco-diagnostic analyses. This issue could be overcome by using DNA barcodes for species identification. A 10% threshold of cytochrome c oxidase (COI) divergence was proposed for differentiating between oligochaete species based on molecular and morphological data. A Swiss database of COI sequences of aquatic oligochaetes was initiated in 2012. The aim of this study is to complement the Swiss oligochaete database of COI sequences and to confirm the relevance of this threshold for species delimitation. Methods:We sequenced the COI sequence of 216 specimens collected in different regions of Switzerland and ITS2 region of some lineages whose delimitation with COI data was doubtful. Results:We distinguished 53 lineages, among which 34 were new for Switzerland and 17 sequenced for the first time. All the lineages were separated by more than 10% of COI variation, with the exception of some species within Nais and Uncinais. In these two genera, the threshold was lowered to 8% to be congruent with the morphological analysis. The total number of lineages reported so far for Switzerland is 75, including 59 morphospecies or unidentified species and 16 cryptic species. Discussion:Our study shows that the threshold of 10% of COI divergence is generally appropriate to distinguish aquatic oligochaete lineages, but that it must be adjusted for some species. The database reported here will be complemented in the future in parallel to the development of genetic oligochaete indices.
Project description:The invasive Asian tiger mosquito Aedes albopictus (Diptera: Culicidae) was first reported in central Africa in 2000, in Cameroon, with the indigenous mosquito species Ae. aegypti (Diptera: Culicidae). Today, this invasive species is present in almost all countries of the region, including the Central African Republic (CAR), where it was first recorded in 2009. As invasive species of mosquitoes can affect the distribution of native species, resulting in new patterns of vectors and concomitant risk for disease, we undertook a comparative study early and late in the wet season in the capital and the main cities of CAR to document infestation and the ecological preferences of the two species. In addition, we determined the probable geographical origin of invasive populations of Ae. albopictus with two mitochondrial DNA genes, COI and ND5. Analysis revealed that Ae. aegypti was more abundant earlier in the wet season and Ae. albopictus in the late wet season. Used tyres were the most heavily colonized productive larval habitats for both species in both seasons. The invasive species Ae. albopictus predominated over the resident species at all sites in which the two species were sympatric. Mitochondrial DNA analysis revealed broad low genetic diversity, confirming recent introduction of Ae. albopictus in CAR. Phylogeographical analysis based on COI polymorphism indicated that the Ae. albopictus haplotype in the CAR population segregated into two lineages, suggesting multiple sources of Ae. albopictus. These data may have important implications for vector control strategies in central Africa.