Belinda Appleton

Copy number variation and transposable elements feature in recent, ongoing adaptation at the Cyp6g1 locus.

The increased transcription of the Cyp6g1 gene of Drosophila melanogaster, and consequent resistance to insecticides such as DDT, is a widely cited example of adaptation mediated by cis-regulatory change. A fragment of an Accord transposable element inserted upstream of the Cyp6g1 gene is causally associated with resistance and has spread to high frequencies in populations around the world since the 1940s. Here we report the existence of a natural allelic series at this locus of D. melanogaster, involving copy number variation of Cyp6g1, and two additional transposable element insertions (a P and an HMS-Beagle). We provide evidence that this genetic variation underpins phenotypic variation, as the more derived the allele, the greater the level of DDT resistance. Tracking the spatial and temporal patterns of allele frequency changes indicates that the multiple steps of the allelic series are adaptive. Further, a DDT association study shows that the most resistant allele, Cyp6g1-[BP], is greatly enriched in the top 5% of the phenotypic distribution and accounts for ∼16% of the underlying phenotypic variation in resistance to DDT. In contrast, copy number variation for another candidate resistance gene, Cyp12d1, is not associated with resistance. Thus the Cyp6g1 locus is a major contributor to DDT resistance in field populations, and evolution at this locus features multiple adaptive steps occurring in rapid succession.

Mitochondrial DNA analysis of field populations of Helicoverpa armigera (Lepidoptera: Noctuidae) and of its relationship to H. zea

BackgroundHelicoverpa armigera and H. zea are amongst the most significant polyphagous pest lepidopteran species in the Old and New Worlds respectively. Separation of H. armigera and H. zea is difficult and is usually only achieved through morphological differences in the genitalia. They are capable of interbreeding to produce fertile offspring. The single species status of H. armigera has been doubted, due to its wide distribution and plant host range across the Old World. This study explores the global genetic diversity of H. armigera and its evolutionary relationship to H zea.ResultsWe obtained partial (511 bp) mitochondrial DNA (mtDNA) Cytochrome Oxidase-I (COI) sequences for 249 individuals of H. armigera sampled from Australia, Burkina Faso, Uganda, China, India and Pakistan which were associated with various host plants. Single nucleotide polymorphisms (SNPs) within the partial COI gene differentiated H. armigera populations into 33 mtDNA haplotypes. Shared haplotypes between continents, low F-statistic values and low nucleotide diversity between countries (0.0017 – 0.0038) suggests high mobility in this pest. Phylogenetic analysis of four major Helicoverpa pest species indicates that H. punctigera is basal to H. assulta, which is in turn basal to H. armigera and H. zea. Samples from North and South America suggest that H. zea is also a single species across its distribution. Our data reveal short genetic distances between H. armigera and H. zea which seem to have been established via a founder event from H. armigera stock at around 1.5 million years ago.ConclusionOur mitochondrial DNA sequence data supports the single species status of H. armigera across Africa, Asia and Australia. The evidence for inter-continental gene flow observed in this study is consistent with published evidence of the capacity of this species to migrate over long distances. The finding of high genetic similarity between Old World H. armigera and New World H. zea emphasises the need to consider work on both pests when building pest management strategies for either.

The Bassian Isthmus and the major ocean currents of southeast Australia influence the phylogeography and population structure of a southern Australian intertidal barnacle Catomerus polymerus (Darwin)

Southern Australia is currently divided into three marine biogeographical provinces based on faunal distributions and physical parameters. These regions indicate eastern and western distributions, with an overlap occurring in the Bass Strait in Victoria. However, studies indicate that the boundaries of these provinces vary depending on the species being examined, and in particular on the mode of development employed by that species, be they direct developers or planktonic larvae dispersers. Mitochondrial DNA sequence analysis of the surf barnacle Catomerus polymerus in southern Australia revealed an east–west phylogeographical split involving two highly divergent clades (cytochrome oxidase I 3.5 ± 0.76%, control region 6.7 ± 0.65%), with almost no geographical overlap. Spatial genetic structure was not detected within either clade, indicative of a relatively long‐lived planktonic larval phase. Five microsatellite loci indicated that C. polymerus populations exhibit relatively high levels of genetic divergence, and fall into four subregions: eastern Australia, central Victoria, western Victoria and Tasmania, and South Australia. FST values between eastern Australia (from the eastern mitochondrial DNA clade) and the remaining three subregions ranged from 0.038 to 0.159, with other analyses indicating isolation by distance between the subregions of western mitochondrial origin. We suggest that the east–west division is indicative of allopatric divergence resulting from the emergence of the Bassian land‐bridge during glacial maxima, preventing gene flow between these two lineages. Subsequently, contemporary ecological conditions, namely the East Australian, Leeuwin, and Zeehan currents and the geographical disjunctions at the Coorong and Ninety Mile Beach are most likely responsible for the four subregions indicated by the microsatellite data.

The use of molecular and morphological characters to resolve the taxonomic identity of cryptic species: the case of Miniopterus manavi (Chiroptera, Miniopteridae)

Based on recent molecular phylogenetic studies, the Old World bat family Miniopteridae, composed of species in the genus Miniopterus, has been shown to contain complex paraphyletic species, many of which are cryptic based on convergent morphological characters. Herein we resolve the phylogenetic relationships and taxonomy of the species complex M. manavi on Madagascar and in the Comoro Archipelago, where these animals occur in different bioclimatic zones. First using mitochondrial cytochrome‐b sequence data to define clades and then morphology to corroborate the molecular data, including comparisons to type specimens, we demonstrate that animals identified as this taxon are a minimum of three species: M. manavi sensu stricto occurs in at least the central portion of the Central Highlands; M. griveaudi has a broad distribution in lowland northern and central western Madagascar and the Comoros (Anjouan and Grande Comore), and M. aelleni sp. n. has been found in northern and western Madagascar and the Comoros (Anjouan). In each case, these three clades were genetically divergent and monophyletic and the taxa are diagnosable based on different external and craniodental characters. One aspect that helped to define the systematics of this group was isolation of DNA from one of the paratypes of M. manavi collected in 1896 and new topotypic material. Miniopterus manavi is most closely allied to a recently described species, M. petersoni. At several localities, M. griveaudi and M. aelleni have been found in strict sympatry, and together with M. manavi sensu stricto show considerable convergence in morphological characters, but are not immediate sister taxa. In defining and resolving the systematics of cryptic species, such as miniopterid bats, the process of defining clades with molecular tools, segregating the specimens accordingly, and identifying corroborative morphological characters has been notably efficient.

Specific Status of Populations on Madagascar Referred to Miniopterus fraterculus (Chiroptera: Vespertilionidae), with Description of a New Species

Abstract A new species of bat of the genus Miniopterus is described from Madagascar based on a series of specimens taken in the Central Highlands of the island. This new species previously was identified as M. fraterculus, which is widespread in portions of eastern and southern Africa. Comparisons between these 2 taxa were further complicated because M. fraterculus occurs in portions of its range in sympatry with a morphologically similar species, M. natalensis. Based on specimen material and associated tissue samples from near the type localities of M. natalensis and M. fraterculus, as well as access to some of the critical type specimens, morphological and genetic molecular analyses were used to determine that Malagasy specimens previously assigned to M. fraterculus represent a previously unrecognized species of Miniopterus endemic to the island. Given that the habitat used by Miniopterus sp. nov. is not necessarily associated with native forest, that it has a broad distribution across the Central Highlands, and that it has been found in synanthropic situations, this species is not considered a conservation concern.

Insights into the evolution of a cryptic radiation of bats: dispersal and ecological radiation of Malagasy Miniopterus (Chiroptera: Miniopteridae)

The past decade has seen a proliferation of new species of Miniopterus bats (family Miniopteridae) recognized from Madagascar and the neighboring Comoros archipelago. The interspecific relationships of these taxa, their colonization history, and the evolution of this presumed adaptive radiation have not been sufficiently explored. Using the mitochondrial cytochrome-b gene, we present a phylogeny of the Malagasy members of this widespread Old World genus, based on 218 sequences, of which 82 are new and 136 derived from previous studies. Phylogenetic analyses recovered 18 clades, which divide into five primary lineages: (1) M. griveaudi; (2) M. mahafaliensis, M. sororculus and X3; (3) M. majori, M. gleni and M. griffithsi; (4) M. brachytragos; M. aelleniA, and M. aelleniB; and (5) M. manavi and M. petersoni recovered as sister species, which were in turn linked to a group comprising M. egeri and five genetically distinct populations referred to herein as P3, P4, P5, P6 and P7. Beast analysis indicated that the initial divergence within the Malagasy Miniopterus radiation took place 4.5 Myr; most species diverged between 4 and 2.5 Myr, and a secondary period was between 1.25 and 1 Myr. DNA K2P-distances between recognized taxa ranged from 12.9% to 2.5% and intraspecific variation was less than 1.8%. Of the 18 identified clades, Latin binomials are only associated with 11, which indicates much greater differentiation than currently recognized for Malagasy Miniopterus. These data are placed in a context of the dispersal history of this genus on the island and patterns of ecological diversity.

Wings or winds: inferring bat migration in a stepping-stone archipelago

Eocene ocean currents and prevailing winds correlate with over‐water dispersals of terrestrial mammals from Africa to Madagascar. Since the Early Miocene (about 23 Ma), these currents flowed in the reverse direction, from the Indian Ocean towards Africa. The Comoro Islands are equidistant between Africa and Madagascar and support an endemic land vertebrate fauna that shares recent ancestry predominantly with Madagascar. We examined whether gene flow in two Miniopterus bat species endemic to the Comoros and Madagascar correlates with the direction of current winds, using uni‐ and bi‐parentally inherited markers with different evolutionary rates. Coalescence‐based analyses of mitochondrial matrilines support a Pleistocene (approximately 180 000 years ago) colonization event from Madagascar west to the Comoros (distance: 300 km) in the predicted direction. However, nuclear microsatellites show that more recent gene flow is restricted to a few individuals flying against the wind, from Grande Comore to Anjouan (distance: 80 km).

A molecular and morphological investigation of species boundaries and phylogenetic relationships in Australian free-tailed bats Mormopterus (Chiroptera : Molossidae)

Abstract. The taxonomic uncertainty surrounding several prominent genera of Australian microbat has been a long-standing impediment to research and conservation efforts on these groups. The free-tail bat genus Mormopterus is perhaps the most significant example, with a long history of acknowledged species-level confusion. This study uses a combined molecular and morphological approach to conduct a comprehensive assessment of species and subgeneric boundaries, between-species phylogenetic affinities and within-species phylogeographic structure in Australian members of Mormopterus. Phylogenetic analyses based on 759 base pairs of the NADH Dehydrogenase subunit 2 mitochondrial gene were concordant with species boundaries delineated using an expanded allozyme dataset and by phallic morphology, and also revealed strong phylogeographic structure within two species. The levels of divergence evident in the molecular and morphological analyses led us to recognise three subgenera within Australia: Micronomus, Setirostris subgen. nov. and Ozimops subgen. nov. Within Ozimops we recognise seven Australian species, three of which are new, and none are conspecific with Indo-Papuan species. The family Molossidae now comprises eleven species across three subgenera in Australia, making it the continent’s second most speciose family of bats.

The Use of Molecular Phylogenetic and Morphological Tools to Identify Cryptic and Paraphyletic Species: Examples from the Diminutive Long-fingered Bats (Chiroptera: Miniopteridae: Miniopterus) on Madagascar

Abstract Based on nearly complete (1125 bp) cytochrome-b sequence data and morphological characters, two new endemic species of Miniopterus are described from Madagascar that were previously identified as M. manavi. Using phylogenetic analysis, the basal nodes of major lineages in the Malagasy members of this genus are weakly supported, while, in most cases, the branches leading to each of the clades are well resolved. Miniopterus mahafaliensis, new species, occurs in the southwestern semidesert areas and M. brachytragos, new species, has a broad distribution across the northern half of the island, ranging across several different biomes. Phylogenetic inference indicates that these two new taxa are not closely related to M. manavi sensu stricto, with average genetic distances of 9.2% and 5.7% from this taxon, respectively. On the basis of this and previous revisions, the former M. manavi complex is now recognized to represent at least five taxa, which do not form a monophyletic group with respect to one another, and represent extraordinary examples of convergent evolution. Miniopterus brachytragos is closely related to the recently named M. aelleni, while M. mahafaliensis is not closely associated with any of these species. Molecular phylogenetic analysis was imperative to resolve the species limits of these taxa and morphology then provided the means to corroborate the recovered clades. There are localities on the island, specifically limestone karstic zones, where four species of the former M. manavi sensu lato complex occur in strict sympatry. These species often use the same day-roost caves and have similar external and craniodental measurements. This raises intriguing questions as to how these animals divide their worlds with regard to dietary regimes and foraging strategies, as well as their speciation history.

Antitropical distributions and species delimitation in a group of ophiocomid brittle stars (Echinodermata: Ophiuroidea: Ophiocomidae).

In this paper we examine the phylogeny and biogeography of the temperate genera of the Ophiocomidae (Echinodermata: Ophiuroidea) which have an interesting asymmetrical anti-tropical distribution, with two genera (Ophiocomina and Ophiopteris) previously considered to have a separate species in both the North and South hemispheres, and the third (Clarkcoma) diversifying in the southern Australian/New Zealand region. Our phylogeny, generated from one mitochondrial and two nuclear markers, revealed that Ophiopteris is sister to a mixed Ophiocomina/Clarkcoma clade. Ophiocomina was polyphyletic, with O. nigra and an undescribed species from the South Atlantic Ocean sister to a clade including Clarkcoma species and O. australis. The phylogeny also revealed a number of recently diverged lineages occurring within Clarkcoma, some of which are considered to be cryptic species due to the similarity in morphology combined with the apparent absence of interbreeding in a sympatric distribution, while the status of others is less certain. The phylogeny provides support for two transequatorial events in the group under study. A molecular clock analysis places both events in the middle to late Miocene. The analysis excludes a tectonic vicariance hypothesis for the antitropical distribution associated with the breakup of Pangaea and also excludes the hypothesis of more recent gene flow associated with Plio/Pleistocene glacial cycling.