Search

Using a combination of different methods to investigate the suitability of a fragment of the cytochrome c oxidase I gene (COI), we succeeded in partially resolving phylogenetic relationships in Delphacidae from the level of species to subfamily. Spectral analysis applied to the relatively noisy COI data proved to be especially useful. It clearly showed when phylogenetic signals were not completely randomized and it was very helpful for identifying problem areas in the dataset. Relationships among the four sampled subfamilies were completely resolved. In contrast to the tree based on morphological characters, we found evidence that Asiraca and Ugyops are sister groups (supporting monophyly of Asiracinae) and that Stenocraninae are the sister group of Kelisiinae. Contradictory signals were observed within Delphacini, but there are characters that support a close relationship between Conomelus and Megamelus. Other than this, the COI data gave support for the monophyly of Kelisiinae, Delphacinae, Chloriona and Javesella. Although third codon positions may appear to be saturated within the 'modern' Delphacidae (Delphacini), they still contain important phylogenetic signals at the deepest taxonomic level. The easiest explanation for this is the difference in amino acid usage between Asiracinae and non-Asiracinae. Overall, this fragment of the COI gene seems to be useful for a rather wide taxonomic range in Delphacidae, except maybe for resolving generic relationships in the large tribe Delphacini.

The Common Hamster (Cricetus cricetus L.) has suffered from changes in agricultural practices. In some Western European countries the populations have become so small and scattered that they are threatened with extinction. We studied the genetic diversity of mitochondrial and major histoincompatibility complex (MHC) loci in the few animals left in the South of the Netherlands and in three animals from the Alsace region in France, and compared it to the diversity in Dutch animals in the past (samples taken from stuffed animals in museum collections dating back to the period 1924-1956) and in a large present-day population from Czech Republic. For the mitochondrial cytochrome b gene, SNP mapping demonstrated a total of nine alleles among 14 Czech samples, of which one (possibly two) was present in the Dutch museum samples, and only one in the current Dutch animals. For the MHC genes, DQA exon 2 and 3 showed no variation, while 14 different alleles were found at DRB exon 2. The Czech population contained 13 different alleles in 15 animals sampled, and most animals were heterozygous (Ho = 0.80, He = 0.91). Therefore, the solitary living Hamster maintains, in nature, a large diversity at this MHC locus. The Dutch museum samples contained eight different alleles in 20 samples, and they were slightly less heterozygous (Ho = 0.60, He = 0.75). All but one of these alleles were also found in the Czech samples. In contrast, the present Dutch and French animals (a total of 16 samples) contained only one of these alleles, and all animals were genetically identical and homozygous. We conclude that the remaining animals have lost all diversity at this MHC locus. This is probably the result of a severe bottleneck, which may have been quite severe, reducing diversity in many loci. In addition, the remaining Dutch animals are partly derived from one family. These animals are now part of a breeding program. Options for restocking the genetic diversity are discussed

Enforcing the ban on meat-and-bone meal in feed for farmed animals, and especially ruminants, is considered an important measure to prevent the spread of bovine spongiform encephalopathy. The authors describe current analytical methods for the detection and identification of animal tissues in feed. In addition, recently approved requirements, such as the ban of intra-species recycling (practice of feeding an animal species with proteins derived from the bodies, or parts of bodies, of the same species) are described. In principle, four different approaches are currently applied, i.e. microscopic analysis, polymerase chain reaction, immunoassay analysis and near infrared spectroscopy or microscopy. The principal performance characteristics of these methods are presented and compared, and their specific advantages and disadvantages described. Special emphasis is also placed on the impact of rendering conditions, particularly high temperatures and on the use of molecular biology techniques.

Background The aim of this study was to develop a nucleotide geometrical model of the circular mitochondrial DNA (mt-DNA) structure using Geant4-DNA toolkit to predict the radiation-induced damages such as single-strand breaks (SSB), double-strand breaks (DSB), and some other physical parameters. Methods Our model covers the organization of a circular human mt genetic system. The current model includes all 16,659 base pairs of human mt-DNA. This new mt-DNA model has been preliminarily tested in this work by determining SSB and DSB DNA damage yields and site-hit probabilities due to the impact of proton particles. The accuracy of the geometry was determined by three-dimensional visualization in various ring element numbers. The hit locations were determined with respect to a reference coordinate system, and the corresponding base pairs were stored in the ROOT output file. Results The coordinate determination according to the algorithm was consistent with the expected results. The output results contain the information about the energy transfers in the backbone region of the DNA double helix. The output file was analyzed by root analyzing tools. Estimation of SSBs and DSBs yielded similar results with the increment of incident particle linear energy transfer. In addition, these values seem to be consistent with the corresponding experimental determinations. Conclusions This model can be used in numerical simulations of mt-DNA radiation interactions to perform realistic evaluations of DNA-free radical reactions. This work will be extended to supercoiled conformation in the near future.

The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.

Little is known about the Australian snubfin (Orcaella heinsohni) and Indo-Pacific humpback (Sousa chinensis) dolphins (‘snubfin’ and ‘humpback dolphins’, hereafter) of north-western Australia. While both species are listed as ‘near threatened’ by the IUCN, data deficiencies are impeding rigorous assessment of their conservation status across Australia. Understanding the genetic structure of populations, including levels of gene flow among populations, is important for the assessment of conservation status and the effective management of a species. Using nuclear and mitochondrial DNA markers, we assessed population genetic diversity and differentiation between snubfin dolphins from Cygnet (n = 32) and Roebuck Bays (n = 25), and humpback dolphins from the Dampier Archipelago (n = 19) and the North West Cape (n = 18). All sampling locations were separated by geographic distances >200 km. For each species, we found significant genetic differentiation between sampling locations based on 12 (for snubfin dolphins) and 13 (for humpback dolphins) microsatellite loci (F ST = 0.05–0.09; P

Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat availability and anthropogenic exploitation. We therefore analysed samples from over 1500 individuals collected from 22 colonies spanning the Western and Eastern Atlantic and the Baltic Sea regions, represented by 350 bp of the mitochondrial hypervariable region and up to nine microsatellites. Strong population structure was observed at both types of marker, and highly asymmetrical patterns of gene flow were also inferred, with the Orkney Islands being identified as a source of emigrants to other areas in the Eastern Atlantic. The Baltic and Eastern Atlantic regions were estimated to have diverged a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Sea. Approximate Bayesian computation also identified genetic signals consistent with postglacial population expansion across much of the species range, suggesting that grey seals are highly responsive to changes in habitat availability.

Two anchovy forms identified from their external morphology and designated as 'Silver' and 'Blue' anchovies were captured in Mersin Bay (Eastern Mediterranean Sea). Silver anchovy seemed to inhabit shallower waters (9-77 m) than Blue anchovy (majority at depths of 69-111 m). Significant differences in body shape, which was analyzed through geometric morphometrics, and in otolith shape, examined using Fourier analysis, separated the two forms. Length polymorphisms at two intron and 9 microsatellite loci showed strong genetic differences between the two forms. Mersin-Bay Blue anchovy were genetically related to Engraulis encrasicolus from the Western Mediterranean Sea. Mersin-Bay Silver anchovy possessed an original genetic composition that distinguished them from both E. encrasicolus and Engraulis albidus at the two intron loci, while presenting affinities to E. albidus based on microsatellite markers. Mersin-Bay Silver anchovy were assigned to the latter species, of which they are considered as a geographically isolated population. This is the first record of E. albidus in the Levantine basin and confirmation of its presence in the Eastern Mediterranean Sea. These results have implications for the management of anchovy populations and their habitats. (C) 2014 Elsevier B.V. All rights reserved. TUBITAK (The Scientific and Technological Research Council of Turkey)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [1080566, 1076066, 107T154, 106G005]; TUBITAK National Post-Doctoral Research Scholarship ProgramTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK); SeaDataNet-EU [026212]; UPGRADE BlackSeaScene-EU [226592] We are grateful to Dr. Yaisel J. Borrell for sharing microsatellite genotype data, to Dr. Dominique Ponton (IRD), Drs. Fusun Ozer and Dr. Devrim Tezcan (IMS-METU) for their help and advice, to Serdar Sakinan and other scientists who obtained and identified the anchovy samples, to Cihan Ayanoglu (METU) for running the Minitab programme, and to Allison Kideys (IMS-METU) for copy-editing the manuscript. This work was financed by the TUBITAK (The Scientific and Technological Research Council of Turkey) projects: Small Pelagic Fishes (1080566), TARAL (1076066), TBAG (107T154) and KAMAG TURKHAYGEN-I (106G005). A.K. was supported by TUBITAK National Post-Doctoral Research Scholarship Program, SeaDataNet-EU FP6 (026212) and UPGRADE BlackSeaScene-EU FP7 (226592) projects.

BACKGROUND: Simulated nucleotide or amino acid sequences are frequently used to assess the performance of phylogenetic reconstruction methods. BEAST, a Bayesian statistical framework that focuses on reconstructing time-calibrated molecular evolutionary processes, supports a wide array of evolutionary models, but lacked matching machinery for simulation of character evolution along phylogenies. RESULTS: We present a flexible Monte Carlo simulation tool, called πBUSS, that employs the BEAGLE high performance library for phylogenetic computations to rapidly generate large sequence alignments under complex evolutionary models. πBUSS sports a user-friendly graphical user interface (GUI) that allows combining a rich array of models across an arbitrary number of partitions. A command-line interface mirrors the options available through the GUI and facilitates scripting in large-scale simulation studies. πBUSS may serve as an easy-to-use, standard sequence simulation tool, but the available models and data types are particularly useful to assess the performance of complex BEAST inferences. The connection with BEAST is further strengthened through the use of a common extensible markup language (XML), allowing to specify also more advanced evolutionary models. To support simulation under the latter, as well as to support simulation and analysis in a single run, we also add the πBUSS core simulation routine to the list of BEAST XML parsers. CONCLUSIONS: πBUSS offers a unique combination of flexibility and ease-of-use for sequence simulation under realistic evolutionary scenarios. Through different interfaces, πBUSS supports simulation studies ranging from modest endeavors for illustrative purposes to complex and large-scale assessments of evolutionary inference procedures. Applications are not restricted to the BEAST framework, or even time-measured evolutionary histories, and πBUSS can be connected to various other programs using standard input and output format. 13 pages, 2 figures, 1 table ispartof: BMC bioinformatics vol:15 issue:1 pages:133- ispartof: location:England status: published

An increasing number of molecular studies are indicating that, in a wide variety of species, genes directly related to fertilization evolve at extraordinarily high rates. We try to gain insight into the dynamics of this rapid evolution and its underlying mechanisms by means of a simple theoretical model. In the model, sexual selection and sympatric speciation act together in order to drive rapid divergence of gamete recognition proteins. In this process, intraspecific competition for fertilizations enlarges male gamete protein variation by means of evolutionary branching, which initiates sympatric speciation. In addition, avoidance of competition for fertilizations between the incipient species drives the rapid evolution of gamete recognition proteins. This mechanism can account for both strong stabilizing selection on gamete recognition proteins within species and rapid divergence between species. Moreover, it can explain the empirical finding that the rate of divergence of fertilization genes is not constant, but highest between closely related species.

Ultrastructural morphology (transmission electron microscopy) and localisation of cisplatin-induced platinum (Pt)-DNA adducts (immunoelectron microscopy) were analysed in the human small cell lung cancer cell line GLC(4) and its 40-fold in vitro acquired cisplatin-resistant subline GLC(4)-CDDP, which is characterised by among other things, a decreased DNA platination. Immunolabelling of Pt-DNA adducts was performed with the polyclonal antibody GPt,known to detect the main Pt-containing intrastrand and interstrand DNA adducts, Morphological analysis of GLC(4) and GLC(4)-CDDP at the ultrastructural level showed cells with a high nucleus/cytoplasm ratio with the majority of nuclei containing one or more nucleoli. GLC(4)-CDDP showed, in contrast to GLC(4), an extensive Golgi apparatus and an increased number of mitochondria DNA platination was detectable in both GLC(4) and GLC(4)-CDDP. Immunoelectron microscopy showed Pt-DNA adducts primarily in the nucleus, preferentially at loci with high-density chromatin (e.g. heterochromatin, pars granulosa around nucleoli, condensed DNA in proliferating and apoptotic cells), and in mitochondria. The level of detectable Pt-DNA adducts was cell cycle status-dependent. In both cell lines, Pt-DNA adduct levels increased from non-dividing interphase cells to dividing cells and were highest in cells undergoing apoptosis. Overall localisation of Pt-DNA adducts was comparable in GLC(4) and GLC(4)-CDDP cells. (C) 2001 Elsevier Science Inc. All rights reserved.

Clinal patterns of autosomal genetic diversity within Europe have been interpreted in previous studies in terms of a Neolithic demic diffusion model for the spread of agriculture; in contrast, studies using mtDNA have traced many founding lineages to the Paleolithic and have not shown strongly clinal variation. We have used 11 human Y-chromosomal biallelic polymorphisms, defining 10 haplogroups, to analyze a sample of 3,616 Y chromosomes belonging to 47 European and circum-European populations. Patterns of geographic differentiation are highly nonrandom, and, when they are assessed using spatial autocorrelation analysis, they show significant clines for five of six haplogroups analyzed. Clines for two haplogroups, representing 45% of the chromosomes, are continentwide and consistent with the demic diffusion hypothesis. Clines for three other haplogroups each have different foci and are more regionally restricted and are likely to reflect distinct population movements, including one from north of the Black Sea. Principal-components analysis suggests that populations are related primarily on the basis of geography, rather than on the basis of linguistic affinity. This is confirmed in Mantel tests, which show a strong and highly significant partial correlation between genetics and geography but a low, nonsignificant partial correlation between genetics and language. Genetic-barrier analysis also indicates the primacy of geography in the shaping of patterns of variation. These patterns retain a strong signal of expansion from the Near East but also suggest that the demographic history of Europe has been complex and influenced by other major population movements, as well as by linguistic and geographic heterogeneities and the effects of drift. Z.H.R. was supported by a BBSRC Studentship, T.Z. by a Wellcome Trust Bioarchaeology Studentship, M.E.H. by an MRC Studentship, F.R.S. by the Leverhulme Trust, and L.P. by Ph.D. grant PRAXIS XXI/BD/13632/97 from Fundacao para a Ciencia e a Tecnologia. D.C.R. is a Glaxo Wellcome Research Fellow. C.T.-S. is supported by the CRC, and M.A.J. is a Wellcome Trust Senior Fellow in Basic Biomedical Science, supported by grant 057559. Iberian sample collection was partially funded by multidisciplinary project grant PR182/96 6745 from Complutense University.

Patterns of substitution in chloroplast encoded trnL_F regions were compared between species of Actaea (Ranunculales), Digitalis (Scrophulariales), Drosera (Caryophyllales), Panicoideae (Poales), the small chromosome species clade of Pelargonium (Geraniales), each representing a different order of flowering plants, and Huperzia (Lycopodiales). In total, the study included 265 taxa, each with900-bp sequences, totaling 0.24 Mb. Both pairwise and phylogeny-based comparisons were used to assess nucleotide substitution patterns. In all six groups, we found that transition/transversion ratios, as estimated by maximum likelihood on most-parsimonious trees, ranged between 0.8 and 1.0 for ingroups. These values occurred both at low sequence divergences, where substitutional saturation, i.e., multiple substitutions having occurred at the same (homologous) nucleotide position, was not expected, and at higher levels of divergence. This suggests that the angiosperm trnL-F regions evolve in a pattern different from that generally observed for nuclear and animal mtDNA (transitional/transversion ratioor = 2). Transition/transversion ratios in the intron and the spacer region differed in all alignments compared, yet base compositions between the regions were highly similar in all six groups. A-T and G-C transversions were significantly less frequent than the other four substitution types. This correlates with results from studies on fidelity mechanisms in DNA replication that predict A-T and G-C transversions to be least likely to occur. It therefore strengthens confidence in the link between mutation bias at the polymerase level and the actual fixation of substitutions as recorded on evolutionary trees, and concomitantly, in the neutrality of nucleotide substitutions as phylogenetic markers.

Three randomly amplified polymorphic DNA (RAPD) markers, OPA-12420, OPB-061200 and OPA-01700, species specific to the root-knot nematode species Meloidogyne arenaria, M. incognita and M. javanica respectively, were identified. After sequencing these RAPD-PCR products, longer primers of 18 to 23 nucleotides were designed to complement the terminal DNA sequences of the DNA fragments. This resulted in three pairs of species specific primers that were used to amplify the sequence characterised amplified regions (SCARs). The developed sets of SCAR primers were successfully used in straightforward, fast and reliable PCR assays to identify M. incognita, M. javanica and M. arenaria. The length variant SCAR markers can be amplified from DNA from egg masses, second stage juveniles and females. This species identification technique is therefore independent of the nematode's life cycle stage. Moreover the SCAR-PCR assay was successfully applied using DNA extracts from infested plant material. The method has potential to be optimised for routine practical diagnostic tests facilitating the control of these economically important pest organisms. Identification de Meloigyne incognita, M. javanica et M. arenaria au moyen de l'amplification de régions de séquences caractéristiques (SCAR) par une technique PCR - Trois marqueurs d'ADN polymorphique amplifiée au hasard (RAPD) OPA-12420, OPB-O61200 et OPA-OI700, respectivement spécifiques des espèces de nématodes Meloidogyne arenaria, M. incognita et M. javanica, ont été identifiés. Après le séquençage de ces produits RAPD-PCR, les amorces les plus longues de 18 à 23 nucléotides ont été choisies pour compléter les séquences terminales d'ADN des fragments d'ADN. Cela a conduit à trois paires d'amorces spécifiques de l'espèce, utilisées pour amplifier les régions des séquences caractéristiques (SCAR). Les lots d'amorces SCAR mis au point ont été utilisés avec succès lors d'essais directs, rapides et surs pour identifier M. incognita, M. javanica et M. arenia. Les marqueurs peuvent être amplifiés à partir de l'ADN des masses d'oeufs, des juvéniles de deuxième stade ou des femelles. Cette technique d'identification spécifique est donc indépendante des différents états de développement du nématode. De plus la technique SCAR-PCR a été appliquée avec succès à l'ADN extrait du matériel végétal infesté. Cette méthode présente des potentialités d'amélioration permettant d'envisager des tests pratiques d'identification de routine, facilitant ainsi le contrôle de ces parasites économiquement importants.

We developed a simple and reliable method to identify carnivore scats to species using PCR and RFLP of a portion of the mtDNA cytochrome b gene, which works for seven of the most common carnivores in western North America. We identified a short (196 bp) polymorphic region of cytochrome b which would be easily amplifiable even from degraded DNA, developed a primer set, and isolated a set of three restriction enzymes (HpaII, DdeI, HpyCH4V) that would identify the seven target species. In order to test whether this protocol would effectively identify scats obtained in the field we collected 243 carnivore scats from 12 sites in the San Francisco Bay area. Eighty five percent (206) of our samples successfully amplified and were subsequently identified to species using our RFLP protocol. We selected 108 of these samples to sequence; our species identifications based on sequencing were identical to those obtained using our PCR-RFLP method. Our PCR-RFLP method is a simple and efficient means to identify carnivore scats to species, eliminating the need for sequencing, which is costly and requires more laboratory equipment. The technique can also be modified depending on the species present at a particular site. It allows for rapid and noninvasive assessment of multiple carnivore taxa and is particularly useful for surveying populations across many sites.

Recent cytogenetic analysis of a series of human renal oncocytomas revealed the presence of a recurring chromosomal translocation (5;11)(q35;q13) as sole anomaly in a subset of the tumors. The molecular characterization of this translocation was initiated using two primary t(5;11)-positive renal oncocytomas and a panel of somatic cell hybrids derived from one of these tumors, in conjunction with fluorescence in situ hybridization (FISH) and Southern blot analysis. The breakpoint in chromosome band 11q13 could be located within a genomic interval of at maximum 400 Kb immediately centromeric to the BCL1 locus. (C) Elsevier Science Inc., 1997.

Multiple sources of evidence show that the skuas (Aves: Stercorariidae) are a monophyletic group, closely related to gulls (Laridae). On morphological and behavioural evidence the Stercorariidae are divided into two widely divergent genera, Catharacta and Stercorarius, consistent with observed levels of nuclear and mitochondrial gene divergence. Catharacta skuas are large-bodied and with one exception breed in the Southern Hemisphere. Stercorarius skuas (otherwise known as jaegers) are smaller bodied and breed exclusively in the Northern Hemisphere. Evidence from both mitochondrial and nuclear genomes and from ectoparasitic lice (Insecta: Phthiraptera) shows that the Pomarine skua, S. pomarinus, which has been recognized as being somewhat intermediate in certain morphological and behavioural characteristics, is much more closely related to species in the genus Catharacta, especially to the Northern Hemisphere-breeding Great skua, C. skua, than it is to the other two Stercorarius skuas, the Arctic skua, S. parasiticus and the Longtailed skua, S. longicaudus. Three possible explanations that might account for this discordant aspect of skua phylogeny are explored. These involve (i) the segregation of ancestral polymorphism, (ii) convergent evolution of morphology and behaviour or (iii) inter-generic hybridization. The available evidence from both nuclear and mitochondrial genomes does not exclude any of these hypotheses. Thus, resolution of this enigma of skua phylogeny awaits further work.

Genetic markers, defined as variable regions of DNA, can be utilized for distinguishing individuals or populations. As long as markers are independent, it is easy to combine the information they provide. For nonrecombinant sequences like mtDNA, choosing the right set of markers for forensic applications can be difficult and requires careful consideration. In particular, one wants to maximize the utility of the markers. Until now, this has mainly been done by hand. We propose an algorithm that finds the most informative subset of a set of markers. The algorithm uses a depth first search combined with a branch-and-bound approach. Since the worst case complexity is exponential, we also propose some data-reduction techniques and a heuristic. We implemented the algorithm and applied it to two forensic caseworks using mitochondrial DNA, which resulted in marker sets with significantly improved haplotypic diversity compared to previous suggestions. Additionally, we evaluated the quality of the estimation with an artificial dataset of mtDNA. The heuristic is shown to provide extensive speedup at little cost in accuracy. AuthorCount: 4;Funding Agencies:Foundation of German Business (Stiftung der Deutschen Wirtschaft, SDW);Knuth and Alice Wallenberg Foundation

Rapid development of broad regional and international DNA barcode libraries have brought new insights into the species diversity of many areas and groups. Many new species, even within well-investigated species groups, have been discovered based initially on differences in DNA barcodes. We barcoded 437 collection specimens belonging to 40 pre-identified Palearctic species of the Elachista bifasciella group of moths (Lepidoptera, Elachistidae). Although the study group has been a subject of several careful morphological taxonomic examinations, an unexpectedly high number of previously undetected putative species is revealed, resulting in a 34% rise in species number in the study area. The validity of putative new species was subsequently supported with diagnostic morphological traits. We show that DNA barcodes provide a powerful method of detecting potential new species even in taxonomic groups and geographic areas that have previously been under considerable morphological taxonomic scrutiny.

Despite no obvious barrier to gene flow, historical environmental processes and ecological specializations can lead to genetic differentiation in highly mobile animals. Ecotypes emerged in several large mammal species as a result of niche specializations and/or social organization. In the North-West Atlantic, two distinct bottlenose dolphin (Tursiops truncatus) ecotypes (i.e. ‘coastal’ and ‘pelagic’) have been identified. Here, we investigated the genetic population structure of North-East Atlantic (NEA) bottlenose dolphins on a large scale through the analysis of 381 biopsy-sampled or stranded animals using 25 microsatellites and a 682-bp portion of the mitochondrial control region. We shed light on the likely origin of stranded animals using a carcass drift prediction model. We showed, for the first time, that coastal and pelagic bottlenose dolphins were highly differentiated in the NEA. Finer-scale population structure was found within the two groups. We suggest that distinct founding events followed by parallel adaptation may have occurred independently from a large Atlantic pelagic population in the two sides of the basin. Divergence could be maintained by philopatry possibly as a result of foraging specializations and social organization. As coastal environments are under increasing anthropogenic pressures, small and isolated populations might be at risk and require appropriate conservation policies to preserve their habitats. While genetics can be a powerful first step to delineate ecotypes in protected and difficult to access taxa, ecotype distinction should be further documented through diet studies and the examination of cranial skull features associated with feeding.

There are three described subspecies of fin whales (Balaenoptera physalus): B. p. physalus Linnaeus, 1758 in the Northern Hemisphere, B. p. quoyi Fischer, 1829 in the Southern Hemisphere, and a recently described pygmy form, B. p. patachonica Burmeister, 1865. The discrete distribution in the North Pacific and North Atlantic raises the question of whether a single Northern Hemisphere subspecies is valid. We assess phylogenetic patterns using similar to 16 K base pairs of the complete mitogenome for 154 fin whales from the North Pacific, North Atlantic - including the Mediterranean Sea - and Southern Hemisphere. A Bayesian tree of the resulting 136 haplotypes revealed several well-supported clades representing each ocean basin, with no haplotypes shared among ocean basins. The North Atlantic haplotypes (n = 12) form a sister clade to those from the Southern Hemisphere (n = 42). The estimated time to most recent common ancestor (TMRCA) for this Atlantic/Southern Hemisphere clade and 81 of the 97 samples from the North Pacific was approximately 2 Ma. 14 of the remaining North Pacific samples formed a well-supported clade within the Southern Hemisphere. The TMRCA for this node suggests that at least one female from the Southern Hemisphere immigrated to the North Pacific approximately 0.37 Ma. These results provide strong evidence that North Pacific and North Atlantic fin whales should not be considered the same subspecies, and suggest the need for revision of the global taxonomy of the species.

International audience; Captive-bred mallards Anas platyrhynchos have been released for hunting purposes at a very large scale in Europe since the mid-1970s. In spite of a potential genetic impact, the actual contribution of restocked mallards to the genome of the target population has received little attention. The genetic structure of modern wild mallards in the Camargue, Southern France, was assessed from two samples: one originating from shot birds in hunting bags and one from presumed wild ducks captured alive in a hunting-free reserve. Reference samples originated from five mallard farms, as well as from museum samples collected before the mid-1970s (i.e. before massive mallard releases started). Our results revealed that the genetic signature of wild wintering mallards has not changed significantly because museum and presumed wild samples from the Camargue hunting-free nature reserve were genetically similar, and clearly differentiated from the farm mallards. This suggests that mallard releases in the Camargue or elsewhere in France, although massive, have not actually translated into complete admixture of wild and captive genomes, most likely due to low survival of released birds once in the wild. Nevertheless, although genetic introgression of the wild population by captive-bred was contained, we found significant rates of hybridization between wild and captive-bred mallards in modern samples. This result suggests that long-term releases of captive-bred mallards, if carried on at such large scale, could compromise irreversibly the genetic structure and composition of European mallards. This work contributes to fill in the gap on the monitoring of the genetic consequences of large-scale game releases for exploitation.

Oceanic islands have been a test ground for evolutionary theory, but here, we focus on the possibilities for evolutionary study created by offshore islands. These can be colonized through various means and by a wide range of species, including those with low dispersal capabilities. We use morphology, modern and ancient sequences of cytochrome b (cytb) and microsatellite genotypes to examine colonization history and evolutionary change associated with occupation of the Orkney archipelago by the common vole (Microtus arvalis), a species found in continental Europe but not in Britain. Among possible colonization scenarios, our results are most consistent with human introduction at least 5100 bp (confirmed by radiocarbon dating). We used approximate Bayesian computation of population history to infer the coast of Belgium as the possible source and estimated the evolutionary timescale using a Bayesian coalescent approach. We showed substantial morphological divergence of the island populations, including a size increase presumably driven by selection and reduced microsatellite variation likely reflecting founder events and genetic drift. More surprisingly, our results suggest that a recent and widespread cytb replacement event in the continental source area purged cytb variation there, whereas the ancestral diversity is largely retained in the colonized islands as a genetic ‘ark’. The replacement event in the continental M. arvalis was probably triggered by anthropogenic causes (land‐use change). Our studies illustrate that small offshore islands can act as field laboratories for studying various evolutionary processes over relatively short timescales, informing about the mainland source area as well as the island.

International audience; We describe Halmaheramys bokimekot Fabre, Pages, Musser, Fitriana, Semiadi & Helgengen.etsp.nov., a new genus and species of murine rodent from the North Moluccas, and study its phylogenetic placement using both molecular and morphological data. We generated a densely sampled mitochondrial and nuclear DNA data set that included most genera of Indo-Pacific Murinae, and used probabilistic methodologies to infer their phylogenetic relationships. To reconstruct their biogeographical history, we first dated the topology and then used a Lagrange analysis to infer ancestral geographic areas. Finally, we combined the ancestral area reconstructions with temporal information to compare patterns of murine colonization among Indo-Pacific archipelagos. We provide a new and comprehensive molecular phylogenetic reconstruction for Indo-Pacific Murinae, with a focus on the Rattus division. Using previous results and those presented in this study, we define a new Indo-Pacific group within the Rattus division, composed of Bullimus, Bunomys, Paruromys, Halmaheramys, Sundamys, and Taeromys. Our phylogenetic reconstructions revealed a relatively recent diversification from the Middle Miocene to Plio-Pleistocene associated with several major dispersal events. We identified two independent Indo-Pacific dispersal events from both western and eastern Indo-Pacific archipelagos to the isolated island of Halmahera, which led to the speciations of H.bokimekotgen.etsp.nov. and Rattus morotaiensis Kellogg, 1945. We propose that a Middle Miocene collision between the Halmahera and Sangihe arcs may have been responsible for the arrival of the ancestor of Halmaheramys to eastern Wallacea. Halmaheramys bokimekotgen. et sp.nov. is described in detail, and its systematics and biogeography are documented and illustrated.(c) 2013 The Linnean Society of London

International audience; Seven root-knot nematodes (RKN), including Meloidogyne exigua, M. incognita, M. paranaensis, M. enterolobii, M. arabicida, M. izalcoensis and M. arenaria are major pathogens of coffee crop in the Americas. Species-specific primers for their identification have been developed for five of them and constitute a fast and reliable method of identification. Here we report a PCR-based assay for specific detection of M. arabicida and M. izalcoensis. Random Amplified Polymorphic DNA fragments specific for these two species were converted into sequence characterized amplified region (SCAR) markers. PCR amplification using the SCAR primers produced a specific fragment of 300 bp and 670 bp for M. arabicida and M. izalcoensis, respectively, which were absent in other coffee-associated Meloidogyne spp. tested. SCAR primers also allowed successful amplification of DNA from single second-stage juveniles (J2), males and females. In addition, these primers were able to unambiguously detect the target species in nematode suspensions extracted from soil and roots samples, in different isolates of the same species or when used in multiplex PCR reactions containing mixtures of species. These results demonstrated the effectiveness of these SCAR markers and their multiplex use with those previously developed for M. exigua, M. incognita, M. paranaensis, M. enterolobii and M. arenaria constitute an essential detection tool. This diagnostic kit will contribute for specific J2 identification of the major RKN infecting coffee from field samples in the Americas.

A recently developed method for estimating the variability of nucleotide sites in a sequence alignment [Van de Peer, Y., Van der Auwera, G, and,De Wachter, R. (1996) J. Mel. Evol. 42, 201-210] was applied to bacterial 16S, 5S and 23S rRNAs, In this method, the variability of each nucleotide site is defined as its evolutionary rate relative to the average evolutionary rate of all the nucleotide sites of the molecule. Spectra of evolutionary rates were calculated for each rRNA and show the fastest evolving sites substituting at rates more than 1000 times that of the slowest ones. Variability maps are presented for each rRNA, consisting of secondary structure models where the variability of each nucleotide site is indicated by means of a colored dot. The maps can be interpreted in terms of higher order structure, function and evolution of the molecules and facilitate the selection of areas suitable for the design of PCR primers and hybridization probes. Variability measurement is also important for the precise estimation of evolutionary distances and the inference of phylogenetic trees.

İslam, Gündüz (Balikesir Author), The western house mouse (Mus musculus domesticus) is standardly characterised by a karyotype of 40 acrocentric chromosomes. However, within the West European and North African parts of its range there are numerous local races defined by reduced chromosome numbers and metacentric chromosomes (review: NACHMAN and SEARLE 1995). The presence of metacentric chromosomes reflects the fusion of pairs of acrocentric chromosomes at their centromeres (Robertsonian fusions), any metacentrics so formed may evolve into other metacentrics by whole-arm reciprocal translocations (WARTs: HAUFFE and PIALEK 1997). Races with metacentrics may be characterised by a diploid number as low as 22 chromosomes (CAPANNA el al. 1976).

One of the most common problems in fisheries is the definition of management units. Albacore Thunnus alalunga is an important species for commercial fisheries. Its population struc- ture is still partially unknown; however, on the basis of fisheries data, tagging experiments, and morpho-ecological studies, 6 management units are currently accepted for this species. The main objective of this study was to define genetic entities within T. alalunga and to discuss the appro- priateness of current management units. For this purpose, 13 microsatellite loci were applied to 551 albacore samples collected worldwide, and the population genetic structure was assessed. The most relevant differences between management and genetic units were that (1) Atlantic and Indian Ocean samples are genetically indistinguishable, and (2) possible differentiation exists within the Pacific Ocean and also within the Mediterranean Sea. Thus, this study provides genetic information to clarify albacore population delimitation, which is a key factor to reach the demanded sustainable management of this resource.

Two stocks of bluefin tuna (Thunnus thynnus) inhabit the north Atlantic; the western and eastern stocks spawn in the Gulf of Mexico and the Mediterranean Sea respectively. Trans-Atlantic movements occur outside spawning time whereas natal homing maintains stock structure. Commercial fisheries may exploit a mixed assemblage of both stocks. The incorporation of mixing rates into stock assessment is precluded by uncertainties surrounding stock discrimination. Otolith shape descriptors were used to characterise western and eastern stocks of Atlantic bluefin tuna in the present study and to estimate stock composition in catches of unknown origin. Otolith shape varied with length and between locations and years. Within a restricted size range (200–297-cm fork length (FL)) the two stocks were distinguished with an accuracy of 83%. Bayesian stock mixture analysis indicated that samples from the east Atlantic and Mediterranean were predominantly of eastern origin. The proportion assigned to the eastern stock showed slight spatial variation; however, overlapping 95% credible intervals indicated no significant difference (200–297cm FL: central Atlantic, 73–100%; Straits of Gibraltar, 73–100%; Morocco, 50–99%; Portugal 64–100%). Otolith shape could be used in combination with other population markers to improve the accuracy of mixing rate estimates for Atlantic bluefin tuna.

Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-27T11:28:16Z No. of bitstreams: 0Bitstream added on 2014-05-27T14:32:16Z : No. of bitstreams: 1 2-s2.0-84873867256.pdf: 796974 bytes, checksum: 64f172274307a2abd3e5977743eb1671 (MD5) Made available in DSpace on 2014-05-27T11:28:16Z (GMT). No. of bitstreams: 0 Previous issue date: 2013-01-30 Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. FST calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection. © 2013 Petersen et al. University of Minnesota College of Veterinary Medicine, St Paul, MN Texas AandM University College of Veterinary Medicine and Biomedical Science, College Station, TX Swedish University of Agricultural Sciences Department of Animal Breeding and Genetics, Uppsala University of Kentucky Department of Veterinary Science, Lexington, KY University of California Davis School of Veterinary Medicine, Davis, CA Equine Analysis, Midway, KY University Estadual Paulista Department of Veterinary Clinical Science, Botucatu-SP University College Dublin School of Veterinary Medicine, Dublin University of Azores Institute for Biotechnology and Bioengineering Biotechnology Centre of Azores, Angra do Heroísmo University of Veterinary Medicine Hannover Institute for Animal Breeding and Genetics, Hannover University of Perugia Faculty of Veterinary Medicine, Perugia Animal Health Trust, Lanwades Park, Newmarket, Suffolk French National Institute for Agricultural Research-Animal Genetics and Integrative Biology Unit, Jouy en Josas University of Sydney Veterinary Science, New South Wales Nihon Bioresource College, Koga, Ibaraki University of Helsinki Faculty of Veterinary Medicine, Helsinki University College Dublin College of Agriculture, Food Science and Veterinary Medicine, Belfield, Dublin University of Bern Institute of Genetics, Bern Institute of Cancer Research Breakthrough Breast Cancer Research Centre, London Royal Veterinary College Comparative Neuromuscular Diseases Laboratory, London Swiss National Stud Farm Agroscope Liebefeld-Posieux Research Station, Avenches Norwegian School of Veterinary Science Department of Basic Sciences and Aquatic Medicine, Oslo Animal DNA Diagnostics Ltd, Cambridge Laboratory of Racing Chemistry Department of Molecular Genetics, Utsunomiya, Tochigi

Understanding phylogenetic relationships within species complexes of disease vectors is crucial for identifying genomic changes associated with the evolution of epidemiologically important traits. However, the high degree of genetic similarity among sibling species confounds the ability to determine phylogenetic relationships using molecular markers. The goal of this study was to infer the ancestral–descendant relationships among malaria vectors and nonvectors of the Anopheles gambiae species complex by analyzing breakpoints of fixed chromosomal inversions in ingroup and several outgroup species. We identified genes at breakpoints of fixed overlapping chromosomal inversions 2Ro and 2Rp of An. merus using fluorescence in situ hybridization, a whole-genome mate-paired sequencing, and clone sequencing. We also mapped breakpoints of a chromosomal inversion 2La (common to An. merus, An. gambiae, and An. arabiensis) in outgroup species using a bioinformatics approach. We demonstrated that the ‘‘standard’’ 2R+p arrangement and ‘‘inverted’’ 2Ro and 2La arrangements are present in outgroup species Anopheles stephensi, Aedes aegypti, and Culex quinquefasciatus. The data indicate that the ancestral species of the An. gambiae complex had the 2Ro, 2R+p, and 2La chromosomal arrangements. The ‘‘inverted’’ 2Ro arrangement uniquely characterizes a malaria vector An. merus as the basal species in the complex. The rooted chromosomal phylogeny implies that An. merus acquired the 2Rp inversion and that its sister species An. gambiae acquired the 2R+o inversion from the ancestral species. The karyotype of nonvectors An. quadriannulatus A and B was derived from the karyotype of the major malaria vector An. gambiae. We conclude that the ability to effectively transmit human malaria had originated repeatedly in the complex. Our findings also suggest that saltwater tolerance originated first in An. merus and then independently in An. melas. The new chromosomal phylogeny will facilitate identifying the association of evolutionary genomic changes with epidemiologically important phenotypes. This work was supported by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, www.niaid.nih.gov, grants 1R21AI081023 and 1R21AI094289 to IVS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Published version

Long-distance migrant waders breeding in the Arctic often have globally structured populations, largely because they were isolated in glacial or interstadial refugia or were restricted to fragmented coastal wetlands in winter. Conversely, inland species using continentally distributed wetlands appear to be less structured (more often panmictic), presumably because they are less likely to have been isolated by multiple refugia or by current events. We analyzed genetic variation in a widely distributed inland species, the ruff (Philomachus pugnax), sampled from seven Eurasian breeding localities, and from migration routes and wintering areas in Europe and Africa. One mitochondrial marker (N = 118) and eight nuclear microsatellites (N = 170) showed: (1) high genetic variation; (2) large genetic distances among mitochondrial (private) haplotypes within breeding populations; (3) the absence of a signature of isolation-by-distance; and (4) a distribution of private microsatellite alleles indicating dispersal between Scandinavia and Siberia but not between western and eastern Siberia. These results were consistent with a large refugial population during the Last Glacial Maximum, and postglacial long range expansions spreading ancestral polymorphisms, and not with a stepping-stone model of gene flow. The divergence between breeding populations in Europe and Siberia was dated to approximately 12 000 years ago. Although genetic population structure is presently statistically non-existent, support for evolving population structure came from analyses of geographical variation in two relevant phenotypic traits: wing length and the timing of migration. Analysis of 6077 individuals sampled on migration in 2002-08 revealed that, in each year, shorter-winged birds migrated through significantly later than longer-winged birds. The late-passing birds were associated with more westerly breeding localities. In conclusion, the lack of genetic structuring in ruffs (and other inland species we examined) contrasts with strong structuring in many coastal species. This suggests that the ability to use more widely available inland habitat influences the evolution of genetic structure and the maintenance of genetic variation in waders. (C) 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106, 641656.

Adaptation to different ecological environments can promote speciation. Although numerous examples of such ecological speciation now exist, the genomic basis of the process, and the role of gene flow in it, remains less understood. This is, at least in part, because systems that are well characterized in terms of their ecology often lack genomic resources. In this study, we characterize the transcriptome of Timema cristinae stick insects, a system that has been researched intensively in terms of ecological speciation, but for which genomic resources have not been previously developed. Specifically, we obtained >1 million 454 sequencing reads that assembled into 84 937 contigs representing approximately 18 282 unique genes and tens of thousands of potential molecular markers. Second, as an illustration of their utility, we used these genomic resources to assess multilocus genetic divergence within both an ecotype pair and a species pair of Timema stick insects. The results suggest variable levels of genetic divergence and gene flow among taxon pairs and genes and illustrate a first step towards future genomic work in Timema.

Although benthic marine algae are essential components of marine coastal systems that have been influenced profoundly by past and present climate change, our knowledge of seaweed phylogeography is limited. The brown alga Ishige okamurae Yendo occurs in the northwest Pacific, where it occupies a characteristic belt in the exposed intertidal zone. To understand the patterns of genetic diversity and the evolutionary history of this species, we analyzed mitochondrial cox3 from 14 populations (221 individuals) throughout its range. The 17 haplotypes found in this study formed five distinct clades, indicating significant genetic structure. The high differentiation and number of unique (private) haplotypes may result from the recolonization of the species from glacial refugia. Three putative refugia, each with high genetic diversity, were identified: southern Korea (including Jeju Island), northern Taiwan, and central Pacific Japan. Recolonization of I. okamurae was probably determined by ocean currents and changes in sea level during the last glacial period.

International audience; The spruce coneworm, Dioryctria abietella Denis & Schiffermu " ller ( Lepidoptera: Pyralidae), is a major pest in spruce seed orchards in Europe. Initial work on its pheromone ecology reported significant attraction of males to ( 9Z, 11E)- tetradecadienyl acetate ( 9Z, 11E- 14: OAc), but this compound appeared to be a very weak attractant in field trials. In this study, we show that a second female- produced compound, the polyunsaturated long- chain hydrocarbon ( 3Z, 6Z, 9Z, 12Z, 15Z)- pentacosapentaene ( C25 pentaene), is a strong synergist to 9Z, 11E- 14: OAc, and that both compounds are needed for significant attraction of males. In field- trapping experiments, the highest catches were obtained with high amounts of pentaene added to the acetate ( acetate: pentaene ratio from 1 : 10 to 1 : 30) and the highest doses ( 1- 3 mg per rubber septum dispenser) were the most attractive. Two potential behavioural synergists, ( Z)- 9- tetradecenyl acetate and ( 9Z, 12E)- tetradecadienyl acetate, turned out to be behavioural antagonists and both reduced trap catch of D. abietella in a dose- dependent way when added individually to the binary blend. The recent discovery of the C25 pentaene as a pheromone component of D. abietella, as well as of three North American congeners, suggests that the use of a mixture of so- called type I and type II pheromone compounds is a widespread motif of sexual communication within the genus. The identification of a highly attractive sex pheromone will help in developing efficient strategies for monitoring and control of D. abietella populations in European spruce seed orchards.

Document Type : Book Chapter; Plants possess compartmentalized genomes that are distributed in the nucleus and in two organelles: the mitochondria (mt) and plastids (pt). The crucial functions of these organelles require interaction between products encoded by the organelle genome and the nucleus. Hence, coadaptation contributes to the evolution of plant genomes, leading to a cooperative coevolution between interacting gene products that are encoded in different compartments. In addition, the different modes of inheritance between the Mendelian nuclear genes and uniparental organelles create a genomic conflict that also contributes to shape the evolution of some mt and nuclear genes: those involved in cytonuclear male sterilities. Pentatricopeptide repeat proteins have been involved in the evolution of the mt-nuclear conflict, but are also suspected to participate in the cooperative coadaptation between the nuclear compartment and organelle genomes. Several lines of evidence indicate that organelle genetic variations contribute to plant adaptation to their environment. So far, very few studies have identified potentially adaptive organelle variants. Nevertheless, it is very likely that cytonuclear coadaptation interferes with cytoplasmic adaptation to the environment. Both phenomena must therefore be considered in future work aiming at a better understanding of the evolution of organelle genes and adaptive component.

Correspondence: Stephane Derocles, Fax: +33 2 23 48 51 70; E-mail: stephane.derocles@agrocampus-ouest.fr; International audience; Reliable identification of Aphidiinae species (Braconidae) is a prerequisite for conducting studies on aphidparasitoid interactions at the community level. However, morphological identification of Aphidiinae species remains problematic even for specialists and is almost impossible with larval stages. Here, we compared the efficiency of two molecular markers [mitochondrial cytochrome c oxydase I (COI) and nuclear long wavelength rhodopsin (LWRh)] that could be used to accurately identify about 50 species of Aphidiinae that commonly occur in aphidparasitoid networks in northwestern Europe. We first identified species on a morphological basis and then assessed the consistency of genetic and morphological data. Probably because of mitochondrial introgression, Aphidius ervi and A.microlophii were indistinguishable on the basis of their COI sequences, whereas LWRh sequences discriminated these species. Conversely, because of its lower variability, LWRh failed to discriminate two pairs of species (Aphidius aquilus, Aphidius salicis, Lysiphlebus confusus and Lysiphlebus fabarum). Our study showed that no unique locus but a combination of two genes should be used to accurately identify members of Aphidiinae.

Recently diverged species are challenging for identification, yet they are frequently of special interest scientifically as well as from a regulatory perspective. DNA barcoding has proven instrumental in species identification, especially in insects and vertebrates, but for the identification of recently diverged species it has been reported to be problematic in some cases. Problems are mostly due to incomplete lineage sorting or simply lack of a 'barcode gap' and probably related to large effective population size and/or low mutation rate. Our objective was to compare six methods in their ability to correctly identify recently diverged species with DNA barcodes: neighbor joining and parsimony (both tree-based), nearest neighbor and BLAST (similarity-based), and the diagnostic methods DNA-BAR, and BLOG. We analyzed simulated data assuming three different effective population sizes as well as three selected empirical data sets from published studies. Results show, as expected, that success rates are significantly lower for recently diverged species (∼75%) than for older species (∼97%) (P

Asymmetrical gene flow, which has frequently been documented in naturally occurring hybrid zones, can result from various genetic and demographic factors. Understanding these factors is important for determining the ecological conditions that permitted hybridization and the evolutionary potential inherent in hybrids. Here, we characterized morphological, nuclear, and chloroplast variation in a putative hybrid zone between Schiedea menziesii and S. salicaria, endemic Hawaiian species with contrasting breeding systems. Schiedea menziesii is hermaphroditic with moderate selfing; S. salicaria is gynodioecious and wind-pollinated, with partially selfing hermaphrodites and largely outcrossed females. We tested three hypotheses: 1) putative hybrids were derived from natural crosses between S. menziesii and S. salicaria, 2) gene flow via pollen is unidirectional from S. salicaria to S. menziesii and 3) in the hybrid zone, traits associated with wind pollination would be favored as a result of pollen-swamping by S. salicaria. Schiedea menziesii and S. salicaria have distinct morphologies and chloroplast genomes but are less differentiated at the nuclear loci. Hybrids are most similar to S. menziesii at chloroplast loci, exhibit nuclear allele frequencies in common with both parental species, and resemble S. salicaria in pollen production and pollen size, traits important to wind pollination. Additionally, unlike S. menziesii, the hybrid zone contains many females, suggesting that the nuclear gene responsible for male sterility in S. salicaria has been transferred to hybrid plants. Continued selection of nuclear genes in the hybrid zone may result in a population that resembles S. salicaria, but retains chloroplast lineage(s) of S. menziesii.

To access the final version, follow the next link. http://www.springerlink.com/content/t1809472211lk67q/, Aim Geographical (allopatric) speciation is a dynamic process whose footprints in the living world are a continuum of stages of increasing divergence. Geographical speciation can also contribute to the evolution of marine taxa. This study looked for two of these evolutionary stages (i.e. structured populations and sibling species) in the diversification patterns of two Atlantic skates (Raja, suborder Rajoidea) which exhibited high morphological and ecological conservativism, (undefined)

As a consequence of colonisation from different glacial refugia, many northern European taxa are split into distinct western and eastern lineages. However, as for the nine-spined stickleback (Pungitius pungitius), the exact location of the contact zone between lineages often remains poorly known. We assessed the genetic differentiation and diversity in the nine-spined stickleback within Europe using 1037 base pairs of cytochrome b sequence for 320 individuals from 57 locations, including pond, lake, river, and coastal habitats. Our main aims were (i) to locate the contact zone between the previously recognized western and eastern lineages, (ii) investigate latitudinal patterns in genetic diversity, (iii) compare genetic diversity among different habitat types, and (iv) date the known split between eastern and western lineages. The data revealed the split between eastern and western to be located across the Danish Straits and roughly following the Norway/Sweden border to the North. Reference sites from Canada form their own clades, and one of the Canadian sites was found to have a haplotype common to the Eastern European lineage, possibly representing an ancestral polymorphism. The split between the two European clades was dated to approximately 1.48 million years ago (Mya), and between Canada and Europe to approximately 1.62 Mya. After controlling for habitat effects, nucleotide (but not haplotype) diversity across populations decreased with increasing latitude. Coastal populations showed significantly higher haplotype diversity (but not nucleotide diversity) than pond populations, but there were no detectable differences in haplotype diversity among different freshwater habitat types (viz. river, lake and pond populations), or between coastal and lake/river populations. Sequences were found to cluster according to their geographic proximity, rather than by habitat type, and all habitat types were found within each major clade, implying that colonisation and adaptation between the coastal and freshwater environments in different regions must have occurred in parallel.

In many marine fish species, genetic population structure is typically weak because populations are large, evolutionarily young and have a high potential for gene flow. We tested whether genetic markers influenced by natural selection are more efficient than the presumed neutral genetic markers to detect population structure in Atlantic herring (Clupea harengus), a migratory pelagic species with large effective population sizes. We compared the spatial and temporal patterns of divergence and statistical power of three traditional genetic marker types, microsatellites, allozymes and mitochondrial DNA, with one microsatellite locus, Cpa112, previously shown to be influenced by divergent selection associated with salinity, and one locus located in the major histocompatibility complex class IIA (MHC-IIA) gene, using the same individuals across analyses. Samples were collected in 2002 and 2003 at two locations in the North Sea, one location in the Skagerrak and one location in the low-saline Baltic Sea. Levels of divergence for putatively neutral markers were generally low, with the exception of single outlier locus/sample combinations; microsatellites were the most statistically powerful markers under neutral expectations. We found no evidence of selection acting on the MHC locus. Cpa112, however, was highly divergent in the Baltic samples. Simulations addressing the statistical power for detecting population divergence showed that when using Cpa112 alone, compared with using eight presumed neutral microsatellite loci, sample sizes could be reduced by up to a tenth while still retaining high statistical power. Our results show that the loci influenced by selection can serve as powerful markers for detecting population structure in high gene-flow marine fish species. Heredity (2011) 106, 270-280; doi:10.1038/hdy.2010.71; published online 16 June 2010

DNA sequencing has revolutionized yeast taxonomy. Although initially rDNA sequences proved to be universal and convenient for assigning phylogenetic relationships, it was eventually supplanted by multigene analysis, which provided more discriminating and robust results. This led to a new classification of the major yeast clades, which is still used as a reference today. More recently, the availability of a large number of complete genome sequences has given a new perspective on the molecular taxonomy of yeasts by providing a high number of genes to compare. It also highlighted an unexpected aspect of yeast genome evolution: the existence of interspecific hybrids outside of the industrial Saccharomyces clade. Together with the loss of heterozygosity in interspecific hybrids and a reduced sexuality leading to clonal propagation, this observation obliges us to reexamine the present concept of species. In parallel, the ongoing challenge is to find a universal molecular marker, to improve fast authentication and, if possible, phylogeny of yeasts. The future of yeast taxonomy will involve the sequencing of more genomes, thorough analysis of populations to obtain a good representation of the biodiversity and integration of these data into dedicated databases. (C) 2011 Academie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Recent findings suggest a convergence of time scales between ecological and evolutionary processes which is usually explained in terms of rapid micro evolution resulting in evolution on ecological time scales. A similar convergence, however, can also emerge when slow ecological processes take place on evolutionary time scales. A good example of such a slow ecological process is the colonization of remote aquatic habitats by passively dispersed zooplankton. Using variation at the protein coding mitochondrial COI gene, we investigated the balance between mutation and migration as drivers of genetic diversity in two Branchipodopsis fairy shrimp species (Crustacea, Anostraca) endemic to remote temporary rock pool clusters at the summit of isolated mountaintops in central South Africa. We showed that both species colonized the region almost simultaneously c. 0.8 My ago, but exhibit contrasting patterns of regional genetic diversity and demographic history. The haplotype network of the common B. cf. wolfi showed clear evidence of 11 long distance dispersal events (up to 140 km) with five haplotypes that are shared among distant inselbergs, as well as some more spatially isolated derivates. Similar patterns were not observed for B. drakensbergensis presumably since this rarer species experienced a genetic bottleneck. We conclude that the observed genetic patterns reflect rare historic colonization events rather than frequent ongoing gene flow. Moreover, the high regional haplotype diversity combined with a high degree of haplotype endemicity indicates that evolutionary- (mutation) and ecological (migration) processes in this system operate on similar time scales. ispartof: PLoS One vol:6 issue:11 ispartof: location:United States status: published

The hermaphroditic Mangrove Killifish, Kryptolebias marmoratus, is the world's only vertebrate that routinely self-fertilizes. As such, highly inbred and presumably isogenic "clonal" lineages of this androdioecious species have long been maintained in several laboratories and used in a wide variety of experiments that require genetically uniform vertebrate specimens. Here we conduct a genetic inventory of essentially all laboratory stocks of the Mangrove Killifish held worldwide. At 32 microsatellite loci, these stocks proved to show extensive interline differentiation as well as some intraline variation, much of which can be attributed to post-origin de novo mutations and/or to the segregation of polymorphisms from wild progenitors. Our genetic findings also document that many of the surveyed laboratory strains are not what they have been labeled, apparently due to the rather frequent mishandling or unintended mixing of various laboratory stocks over the years. Our genetic inventory should help to clarify much of this confusion about the clonal identities and genetic relationships of laboratory lines, and thereby help to rejuvenate interest in K. marmoratus as a reliable vertebrate model for experimental research that requires or can capitalize upon "clonal" replicate specimens. © 2010 Tatarenkov et al.