Cloning of inversion breakpoints in the Anopheles gambiae complex traces a transposable element at the inversion junction

Anopheles arabiensis, one of the two most potent malaria vectors of the gambiae complex, is characterized by the presence of chromosomal paracentric inversions. Elucidation of the nature and the dynamics of these inversions is of paramount importance for the understanding of the population genetics and evolutionary biology of this mosquito and of the impact on malaria epidemiology. We report here the cloning of the breakpoints of the naturally occurring polymorphic inversion 2Rd′ of A. arabiensis. A cDNA clone that cytologically mapped on the proximal breakpoint was the starting material for the isolation of a cosmid clone that spanned the breakpoint. Analysis of the surrounding sequences demonstrated that adjacent to the distal breakpoint lies a repetitive element that exhibits distinct distribution in different A. arabiensis strains. Sequencing analysis of that area revealed elements characteristic of transposable element terminal repeats. We called this presumed transposable element Odysseus. The presence of Odysseus at the junction of the naturally occuring inversion 2Rd′ suggests that the inversion may be the result of the transposable element’s activity. Characteristics of Odysseus’ terminal region as well as its cytological distribution in different strains may indicate a relatively recent activity of Odysseus.

Resolving taxonomic uncertainty in vulnerable elasmobranchs : are the Madeira skate (Raja maderensis) and the thornback ray (Raja clavata) distinct species?

We are grateful to all those who helped with sample collection. This includes the MEDITS survey programme (IEO Mallorca) for Mediterranean samples. Portugal mainland samples were collected under the EU Data Collection Framework (DCF, PNAB). Azores specimens from the Department of Oceanography and Fisheries (DOP) of the University of the Azores (UAc) were collected under the project DEMERSAIS “Monitorização das espécies demersais dos Açores” financed by the Azorean government, and the project DEECON “Unravelling population connectivity for sustainable fisheries in the Deep Sea” project approved by the European Science Foundation (ESF) under the EUROCORES programme (proposal No 06-EuroDEEP-FP-008 & SFRH-EuroDEEP/0002/2007). This study was funded by the UK Natural Environment Research Council (NERC) Oceans 2025 Strategic Research Programme Theme 6 (Science for Sustainable Marine Resources). REB was supported by the Fisheries Society of the British Isles (FSBI), BSP was funded by the Fundação para a Ciência e a Tecnologia, SFRH/BPD/72351/2010 and JL was supported by The Alasdair Downes Marine Conservation Fund.

A trait-based approach for predicting species responses to environmental change from sparse data : how well might terrestrial mammals track climate change?

Funded by COST (European Cooperation in Science and Technology) CEH projects. Grant Numbers: NEC05264, NEC05100 Natural Environment Research Council UK. Grant Number: NE/J008001/1 © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

ALFRED: an allele frequency database for diverse populations and DNA polymorphisms—an update

ALFRED (the ALelle FREquency Database) is designed to store and disseminate frequencies of alleles at human polymorphic sites for multiple populations, primarily for the population genetics and molecular anthropology communities. Currently ALFRED has information on over 180 polymorphic sites for more than 70 populations. Since our initial release of the database we have focussed on increasing the quantity and quality of data, making reciprocal links between ALFRED and other related databases, and providing useful tools to make the data more comprehensible to the end user. ALFRED is accessible from the Kidd Lab home page (http://info.med.yale.edu/genetics/kkidd/) or from ALFRED directly (http://alfred.med.yale.edu/alfred/index.asp).

Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis.

Coccidioides immitis, cause of a recent epidemic of "Valley fever" in California, is typical of many eukaryotic microbes in that mating and meiosis have yet to be reported, but it is not clear whether sex is truly absent or just cryptic. To find out, we have undertaken a population genetic study using PCR amplification, screening for single-strand conformation polymorphisms, and direct DNA sequencing to find molecular markers with nucleotide-level resolution. Both population genetic and phylogenetic analyses indicate that C. immitis is almost completely recombining. To our knowledge, this study is the first to find molecular evidence for recombination in a fungus for which no sexual stage has yet been described. These results motivate a directed search for mating and meiosis and illustrate the utility of single-strand conformation polymorphism and sequencing with arbitrary primer pairs in molecular population genetics.

Inferring identify from DNA profile evidence.

The controversy over the interpretation of DNA profile evidence in forensic identification can be attributed in part to confusion over the mode(s) of statistical inference appropriate to this setting. Although there has been substantial discussion in the literature of, for example, the role of population genetics issues, few authors have made explicit the inferential framework which underpins their arguments. This lack of clarity has led both to unnecessary debates over ill-posed or inappropriate questions and to the neglect of some issues which can have important consequences. We argue that the mode of statistical inference which seems to underlie the arguments of some authors, based on a hypothesis testing framework, is not appropriate for forensic identification. We propose instead a logically coherent framework in which, for example, the roles both of the population genetics issues and of the nonscientific evidence in a case are incorporated. Our analysis highlights several widely held misconceptions in the DNA profiling debate. For example, the profile frequency is not directly relevant to forensic inference. Further, very small match probabilities may in some settings be consistent with acquittal. Although DNA evidence is typically very strong, our analysis of the coherent approach highlights situations which can arise in practice where alternative methods for assessing DNA evidence may be misleading.

Elysia timida (Risso, 1818) three decades of research

During the last 30 years, studies on Elysia timida (Risso, 1818) have addressed various aspects related to food sources, photosynthetic efficiency of kleptoplasts, population genetics, chemical ecology and reproductive biology, both in the Mediterranean Sea and in the Mar Menor coastal lagoon. E. timida shows a strong specific interaction with Acetabularia acetabulum, retaining functional chloroplasts for at least 45 days and obtaining extra energy in periods when food resources are scarce. It shows control of parapodia, avoiding pigment photodestruction under oversaturated light conditions. The chemical ecological relationships established between E. timida and its potential predator fish, Thalassoma pavo, have also been evaluated, and it has been found that that the extracts of the mollusc contain repellent and unpalatable polypropionate compounds. Population genetics has demonstrated the genetic divergence between populations showing high and significant values of FST and genetic distances, and at least six privative alleles that are not shared with Mediterranean populations have been detected in lagoon populations. This sacoglossan is a poecilogonic species, and its lagoon populations show a greater reproductive output than Mediterranean populations; they produce a greater number of egg masses and embyros per individual, and the capsules have a wider diameter.

Edinburgh, Scotland, United Kingdom, 1825 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: Plan of Edinburgh and its environs, from a survey by James Knox ; engd. by R. Scott. It was published by John Fairbairn 13, Waterloo Place, Manners & Miller, ... and John Anderson, Junr. in 1825. Scale [ca. 1:6,000]. The image inside the map neatline is georeferenced to the surface of the earth and fit to the 'British National Grid' coordinate system. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as roads, drainage, built-up areas and selected buildings, selected names of property owners, parks, ground cover, and more. Relief shown by hachures and spot heights. Includes population statistics from 1821 and note.This layer is part of a selection of digitally scanned and georeferenced historic maps from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of originators, ground condition dates, scales, and map purposes.

New York, N.Y. and vicinity, 1777 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: The country twenty five miles round New York, drawn by a gentleman from that city ; J. Barber, sculp., Holborn Hill. It was published by ... W. Hawkes (successor to T. Kitchin), No. 59, Holborn Hill, 1st January, 1777. Scale [ca. 1:220,000]. Covers the Metropolitan New York region. The image inside the map neatline is georeferenced to the surface of the earth and fit to the Universal Transverse Mercator (UTM) Zone 18N NAD83 projection. All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as roads, drainage, cities and towns, battle sites, fortifications, points of military interests, and more. Relief is shown pictorially. Shows radial distances from New York. Includes notes on military battles, "Chronological table of the most interesting occurrences since the commencement of hostilities in North America," distance table, and statistics of population and troops in lower margin. This layer is part of a selection of digitally scanned and georeferenced historic maps from The Harvard Map Collection as part of the Imaging the Urban Environment project. Maps selected for this project represent major urban areas and cities of the world, at various time periods. These maps typically portray both natural and manmade features at a large scale. The selection represents a range of regions, originators, ground condition dates, scales, and purposes.

La nécessité d'une multiplicité de concepts de gène en biologie

Le concept de gène est central en biologie. Certains ont avancé (Ruse (1971, 1976)) que la génétique classique pouvait être réduite à la génétique moléculaire. Dans le même ordre d'idée, Richard Dawkins, dans The Extended Phenotype, offre une double définition de son concept de gène qui présuppose qu'il soit possible d'opérer cette réduction. Nous comptons montrer que la génétique moléculaire et la génétique des populations ont chacune leurs problématiques propres en reconstituant l'histoire de la génétique depuis Darwin. Ensuite, nous expliciterons la position de Dawkins et soulignerons les contradictions auxquelles il parvient en raison de cette réduction infondée. À la suite de quoi, nous nous attarderons aux nouvelles découvertes moléculaires qui montrent qu'il n'est pas possible d'opérer la réduction d'un des concepts à l'autre. Nous terminerons en soulignant que la thèse génocentriste de Dawkins n'est pas mise en péril par l'abandon de la réduction, mais qu'il est nécessaire de tempérer ces prétentions. La conclusion globale de ce mémoire est qu'il est possible d'admettre le concept de Dawkins, mais pas la manière dont il l'utilise. Le concept est bon, il n'est tout simplement pas dans le bon cadre théorique.

La nécessité d'une multiplicité de concepts de gène en biologie

Le concept de gène est central en biologie. Certains ont avancé (Ruse (1971, 1976)) que la génétique classique pouvait être réduite à la génétique moléculaire. Dans le même ordre d'idée, Richard Dawkins, dans The Extended Phenotype, offre une double définition de son concept de gène qui présuppose qu'il soit possible d'opérer cette réduction. Nous comptons montrer que la génétique moléculaire et la génétique des populations ont chacune leurs problématiques propres en reconstituant l'histoire de la génétique depuis Darwin. Ensuite, nous expliciterons la position de Dawkins et soulignerons les contradictions auxquelles il parvient en raison de cette réduction infondée. À la suite de quoi, nous nous attarderons aux nouvelles découvertes moléculaires qui montrent qu'il n'est pas possible d'opérer la réduction d'un des concepts à l'autre. Nous terminerons en soulignant que la thèse génocentriste de Dawkins n'est pas mise en péril par l'abandon de la réduction, mais qu'il est nécessaire de tempérer ces prétentions. La conclusion globale de ce mémoire est qu'il est possible d'admettre le concept de Dawkins, mais pas la manière dont il l'utilise. Le concept est bon, il n'est tout simplement pas dans le bon cadre théorique.

Bayesian inferences on the recent island colonization history by the bird Zosterops lateralis lateralis

The founding of new populations by small numbers of colonists has been considered a potentially important mechanism promoting evolutionary change in island populations. Colonizing species, such as members of the avian species complex Zosterops lateralis, have been used to support this idea. A large amount of background information on recent colonization history is available for one Zosterops subspecies, Z. lateralis lateralis, providing the opportunity to reconstruct the population dynamics of its colonization sequence. We used a Bayesian approach to combine historical and demographic information available on Z. l. lateralis with genotypic data from six microsatellite loci, and a rejection algorithm to make simultaneous inferences on the demographic parameters describing the recent colonization history of this subspecies in four southwest Pacific islands. Demographic models assuming mutation–drift equilibrium or a large number of founders were better supported than models assuming founder events for three of four recently colonized island populations. Posterior distributions of demographic parameters supported (i) a large stable effective population size of several thousands individuals with point estimates around 4000–5000; (ii) a founder event of very low intensity with a large effective number of founders around 150–200 individuals for each island in three of four islands, suggesting the colonization of those islands by one flock of large size or several flocks of average size; and (iii) a founder event of higher intensity on Norfolk Island with an effective number of founders around 20 individuals, suggesting colonization by a single flock of moderate size. Our inferences on demographic parameters, especially those on the number of founders, were relatively insensitive to the precise choice of prior distributions for microsatellite mutation processes and demographic parameters, suggesting that our analysis provides a robust description of the recent colonization history of the subspecies.

Isolation and characterization of microsatellite loci from Helicoverpa armigera Hübner (Lepidoptera: Noctuidae)

Five microsatellite loci are presented for Helicoverpa armigera. These microsatellite loci were obtained through the construction of enriched libraries, overcoming previously reported difficulties with obtaining microsatellites from H. armigera and other Lepidoptera due to the low frequency of microsatellites in their genomes. The description of a further five microsatellite loci for H. armigera makes microsatellite based population genetics studies feasible.

Speciation of Antechinus stuartii and A. subtropicus (Marsupialia : Dasyuridae) in eastern Australia: molecular and morphological evidence

This paper evaluates the systematic status of the Antechinus populations of northern New South Wales and southern Queensland, using a combined morphological and molecular (allozymes and mitochondrial DNA) approach. Analysis of the d-loop section of the mitochondrial DNA control region revealed two highly supported clades within A. stuartii sensu lato that were sympatric in the Border Ranges of northern New South Wales. However, genetic distances between these clades were small ( approximately 3%), indicating that time of divergence was probably relatively recent. Allozyme electrophoresis also showed very small differences between clades/ species. Analyses of cranial and dental characters showed that the members of each of these clades differed morphologically and that the clades corresponded to A. stuartii and the recently described A. subtropicus. The combined results support the species status of A. stuartii and A. subtropicus, and suggest that speciation was likely a result of a recent vicariant event.