Permanent genetic resources added to molecular ecology resources database 1 August 2010 – 30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis · Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Disrupted fine-scale population processes in fragmented landscapes despite large-scale genetic connectivity for a widespread and common cooperative breeder : the superb fairy-wren (Malurus cyaneus)

Understanding how habitat fragmentation affects population processes (e.g. dispersal) at different spatial scales is of critical importance to conservation. We assessed the effects of habitat fragmentation on dispersal and regional and fine-scale population structure in a currently widespread and common cooperatively breeding bird species found across south-eastern Australia, the superb fairy-wren Malurus cyaneus. Despite its relative abundance and classification as an urban tolerant species, the superb fairy-wren has declined disproportionately from low tree-cover agricultural landscapes across the Box-Ironbark region of north-central Victoria, Australia. Loss of genetic connectivity and disruption to its complex social system may be associated with the decline of this species from apparently suitable habitat in landscapes with low levels of tree cover. To assess whether reduced structural connectivity has had negative consequences for genetic connectivity in the superb fairy-wren, we used a landscape-scale approach to compare patterns of genetic diversity and gene flow at large (landscape/regional) and fine (site-level) spatial scales. In addition, using genetic distances, for each sex, we tested landscape models of decreased dispersal through treeless areas (isolation-by-resistance) while controlling for the effect of isolation-by-distance. Landscape models indicated that larger-scale gene flow across the Box-Ironbark region was constrained by distance rather than by lack of structural connectivity. Nonetheless, a pattern of isolation-by-resistance for males (the less-dispersive sex) and lower genetic diversity and higher genetic similarity within sites in low-cover fragmented landscapes indicated disruption to fine-scale gene flow mechanisms and/or mating systems. Although loss of structural connectivity did not appear to impede gene flow at larger spatial scales, fragmentation appeared to affect fine-scale population processes (e.g. local gene flow mechanisms and/or mating systems) adversely and may contribute to the decline of superb fairy-wrens in fragmented landscapes in the Box-Ironbark region. © 2012 British Ecological Society.

Unravelling migratory connectivity in marine turtles using multiple methods

1. Comprehensive knowledge of the fundamental spatial ecology of marine species is critical to allow the identification of key habitats and the likely sources of anthropogenic threats, thus informing effective conservation strategies. 2. Research on migratory marine vertebrates has lagged behind many similar terrestrial animal groups, but studies using electronic tagging systems and molecular techniques offer great insights. 3. Marine turtles have complex life history patterns, spanning wide spatio-temporal scales. As a result of this multidimensional complexity, and despite extensive effort, there are no populations for which a truly holistic understanding of the spatial aspects of the life history has been attained. There is a particular lack of information regarding the distribution and habitats utilized during the first few years of life. 4. We used satellite tracking technology to track individual turtles following nesting at the green turtle Chelonia mydas nesting colony at Poilão Island, Guinea Bissau; the largest breeding aggregation in the eastern Atlantic. 5. We further contextualize these data with pan-Atlantic molecular data and oceanographic current modelling to gain insights into likely dispersal patterns of hatchlings and small pelagic juveniles. 6. All adult turtles remained in the waters of West Africa, with strong connectivity demonstrated with Banc D’Arguin, Mauritania. 7. Despite shortcomings in current molecular markers, we demonstrate evidence for profound sub-structuring of marine turtle stocks across the Atlantic; with a high likelihood based on oceanographic modelling that most turtles from Guinea-Bissau are found in the eastern Atlantic. 8. Synthesis and applications. There is an increased need for a better understanding of spatial distribution of marine vertebrates demonstrating life histories with spatio-temporal complexity. We propose the synergistic use of the technologies and modelling used here as a working framework for the future rapid elucidation of the range and likely key habitats used by the different life stages from such species.

Expected shannon entropy and shannon differentiation between subpopulations for neutral genes under the finite island model

Shannon entropy H and related measures are increasingly used in molecular ecology and population genetics because (1) unlike measures based on heterozygosity or allele number, these measures weigh alleles in proportion to their population fraction, thus capturing a previously-ignored aspect of allele frequency distributions that may be important in many applications; (2) these measures connect directly to the rich predictive mathematics of information theory; (3) Shannon entropy is completely additive and has an explicitly hierarchical nature; and (4) Shannon entropy-based differentiation measures obey strong monotonicity properties that heterozygosity-based measures lack. We derive simple new expressions for the expected values of the Shannon entropy of the equilibrium allele distribution at a neutral locus in a single isolated population under two models of mutation: the infinite allele model and the stepwise mutation model. Surprisingly, this complex stochastic system for each model has an entropy expressable as a simple combination of well-known mathematical functions. Moreover, entropy- and heterozygosity-based measures for each model are linked by simple relationships that are shown by simulations to be approximately valid even far from equilibrium. We also identify a bridge between the two models of mutation. We apply our approach to subdivided populations which follow the finite island model, obtaining the Shannon entropy of the equilibrium allele distributions of the subpopulations and of the total population. We also derive the expected mutual information and normalized mutual information ("Shannon differentiation") between subpopulations at equilibrium, and identify the model parameters that determine them. We apply our measures to data from the common starling (Sturnus vulgaris) in Australia. Our measures provide a test for neutrality that is robust to violations of equilibrium assumptions, as verified on real world data from starlings.

Colour polymorphism is likely to be disadvantageous to some populations and species due to genetic architecture and morph interactions

Polymorphism describes two or more distinct, genetically determined, phenotypes that co-occur in the same population, where the rarest morph is maintained at a frequency above the mutation rate (Ford 1945; Huxley 1955). In a recent opinion piece, we explored a new idea regarding the role of genetic architectures and morph interactions in colour polymorphisms and how this can negatively affect population performance (Bolton et al. 2015). In this issue of Molecular Ecology, Forsman (2016) thoroughly discusses the current evidence for polymorphisms enhancing population performance and critiques the validity of the definitions of polymorphism we use in our original paper. We respond by clarifying that the negative consequences of polymorphisms that we discussed are likely to be most pertinent in species that have a particular set of characteristics, such as strong sexual or social interactions between morphs and discrete genetic architectures. Although it was not our intention to redefine polymorphism, we do believe that there should be further discussion about refining or characterizing balanced polymorphisms with respect to the degree of morph sympatry, discreteness of traits and their underlying genetic architecture, and the types of selection that drive and maintain the variation. The latter describes whether polymorphism is primarily maintained by external factors such as predation pressure or internal factors such as interactions with members of the same species. The contribution of Forsman (2016) is useful to this discussion, and we hope that our exchange of opinions will inspire new empirical and theoretical ideas on the origin and maintenance of colour polymorphisms.

Molecular sex-typing in shorebirds: a review of an essential method for research in evolution, ecology and conservation

Knowing the correct sex of individuals is essential both for research in evolutionary ecology and for practical conservation. Recent molecular advances have produced cheap, quick and reliable methods for sexing birds including chicks, juveniles, immatures and adults. Shorebird researchers have not yet fully utilised these advances. Here we provide an overview of work in this area to date with two objectives: (i) to review the major applications of molecular sexing and findings of shorebird research so far, and (ii) to provide an essential guide on how to carry out molecular sexing using current methods whilst avoiding methodological pitfalls. We encourage shorebird researchers to make better use of molecular sex-typing techniques in studies of conservation, migration, foraging ecology and breeding behaviour.

Molecular systematic studies of freshwater prawns of the genus Macrobrachium

Freshwater prawns in the genus Macrobrachium are found throughout the tropical and subtropical regions of the world, however, evolutionary relationships are poorly understood. Using molecular techniques taxonomic uncertainty is resolved and the evolution and distribution of this enigmatic genus across a range of taxonomic and geographic levels is examined.

Molecular systematic studies of freshwater crayfish of the the genus Cherax

This study investigated the molecular systematics and zoogeography of freshwater crayfish species (yabbies) of the genus Cherax throughout Australia. Using DNA sequencing of up to five gene regions and phylogenetic methods of analyses, this study provided new insights into the taxonomy and evolution of this important group of Australian freshwater invertebrates.

Molecular genetic studies of the yabby, Cherax destructor Clark

A study of genetic variation in the yabby (Cherax destructor) was undertaken using a number of different molecular techniques. The results have significantly improved our understanding of the genetic structure, evolution and taxonomy of this important freshwater species. The findings also contribute to the sustainable exploitation of yabbies for aquaculture.

Molecular genetic variation in Galaxias maculatus (Osteichthys: Galaxiidae)

The "common jollytail", Galaxias maculatus, is a freshwater minnow-like fish that is distributed across the Southern Hemisphere and occurs abundantly in inland waterways of south-eastern Australia. Molecular genetic data were collected from samples of this species throughout western Victoria to evaluate hypotheses concerning the taxonomy and evolution of this ecologically important fish.

The biology and ecology of the ocean sunfish Mola mola : a review of current knowledge and future research perspectives

Relatively little is known about the biology and ecology of the world’s largest (heaviest) bony fish, the ocean sunfish Mola mola, despite its worldwide occurrence in temperate and tropical seas. Studies are now emerging that require many common perceptions about sunfish behaviour and ecology to be re-examined. Indeed, the long-held view that ocean sunfish are an inactive, passively drifting species seems to be entirely misplaced. Technological advances in marine telemetry are revealing distinct behavioural patterns and protracted seasonal movements. Extensive forays by ocean sunfish into the deep ocean have been documented and broad-scale surveys, together with molecular and laboratory based techniques, are addressing the connectivity and trophic role of these animals. These emerging molecular and movement studies suggest that local distinct populations may be prone to depletion through bycatch in commercial fisheries. Rising interest in ocean sunfish, highlighted by the increase in recent publications, warrants a thorough review of the biology and ecology of this species. Here we review the taxonomy, morphology, geography, diet, locomotion, vision, movements, foraging ecology, reproduction and species interactions of M. mola. We present a summary of current conservation issues and suggest methods for addressing fundamental gaps in our knowledge.

Ecology of urban malaria vectors in Niamey, Republic of Niger

BACKGROUND: Urbanization in African cities has major impact on malaria risk. Niamey, the capital of the Republic of Niger, is situated in the West African Sahel zone. The short rainy season and human activities linked with the Niger River influence mosquito abundance. This study aimed at deciphering the factors of distribution of urban malaria vectors in Niamey.

METHODS: The distribution of mosquito aquatic stages was investigated monthly from December 2002 to November 2003, at up to 84 breeding sites, throughout Niamey. An exploratory analysis of association between mosquito abundance and environmental factors was performed by a Principal Component Analysis and confirmed by Kruskall-Wallis non-parametric test. To assess the relative importance of significant factors, models were built for Anopheles and Culicinae. In a second capture session, adult mosquitoes were collected weekly with pyrethrum sprays and CDC light-traps from June 2008 to June 2009 in two differentiated urban areas chosen after the study's first step. Members of the Anopheles gambiae complex were genotyped and Anopheles females were tested for the presence of Plasmodium falciparum circumsporozoite antigens using ELISA.

RESULTS: In 2003, 29 % of 8420 mosquitoes collected as aquatic stages were Anopheles. They were significantly more likely to be found upstream, relatively close to the river and highly productive in ponds. These factors remained significant in regression and generalized linear models. The Culicinae were found significantly more likely close to the river, and in the main temporary affluent stream. In 2009, Anopheles specimens, including Anopheles gambiae s.l. (95 %), but also Anopheles funestus (0.6 %) accounted for 18 % of the adult mosquito fauna, with a large difference between the two sampled zones. Three members of the An. gambiae complex were found: Anopheles arabiensis, Anopheles coluzzii, and An. gambiae. Nineteen (1.3 %) out of 1467 females tested for P. falciparum antigen were found positive.

CONCLUSION: The study provides valuable update knowledge on malaria vector ecology and distribution in Niamey. The identification of spatial and environmental risk factors could pave the way to larval source management strategy and allow malaria vector control to focus on key zones for the benefit of the community.