Retention of low-fitness genotypes over six decades of admixture between native and introduced tiger salamanders

<p>Abstract</p> <p>Background</p> <p>Introductions of non-native tiger salamanders into the range of California tiger salamanders have provided a rare opportunity to study the early stages of secondary contact and hybridization. We produced first- and second-generation hybrid salamanders in the lab and measured viability among these early-generation hybrid crosses to determine the strength of the initial barrier to gene exchange. We also created contemporary-generation hybrids in the lab and evaluated the extent to which selection has affected fitness over approximately 20 generations of admixture. Additionally, we examined the inheritance of quantitative phenotypic variation to better understand how evolution has progressed since secondary contact.</p> <p>Results</p> <p>We found significant variation in the fitness of hybrids, with non-native backcrosses experiencing the highest survival and F2 hybrids the lowest. Contemporary-generation hybrids had similar survival to that of F2 families, contrary to our expectation that 20 generations of selection in the wild would eliminate unfit genotypes and increase survival. Hybrid survival clearly exhibited effects of epistasis, whereas size and growth showed mostly additive genetic variance, and time to metamorphosis showed substantial dominance.</p> <p>Conclusions</p> <p>Based on first- and second- generation cross types, our results suggest that the initial barrier to gene flow between these two species was relatively weak, and subsequent evolution has been generally slow. The persistence of low-viability recombinant hybrid genotypes in some contemporary populations illustrates that while hybridization can provide a potent source of genetic variation upon which natural selection can act, the sorting of fit from unfit gene combinations might be inefficient in highly admixed populations. Spatio-temporal fluctuation in selection or complex genetics has perhaps stalled adaptive evolution in this system despite selection for admixed genotypes within generations.</p

Shallow genetic divergence indicates a Congo–Nile riverine connection for the softshell turtle Trionyx triunguis

WOS: 000288389500022We sequenced 20 new, field-collected individuals for up to seven genes to explore the phylogeography and conservation genetics of the threatened Nile softshell turtle Trionyx triunguis, including the first known-locality specimen from sub-Saharan Africa. Samples from Cameroon (West Africa), the Mediterranean and Nile River differed by at most a single nucleotide per gene, indicating the potential for a recent connection between these currently disjunct populations via the Nile-Congo River systems. Recently reported mitochondrial diversity between Mediterranean and "sub-Saharan" samples of the Nile softshell indicate that significant divergence exists across the species' range, but that variation cannot be fully incorporated into our analysis since those samples lack specific locality data.Scientific and Technological Research Council of Turkey (TUBITAK)Turkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK); NSFNational Science Foundation (NSF) [DEB 0817042]; UC Davis Agricultural Experiment StationDwight Lawson collected the Cameroon turtle, and the San Diego Zoo provided a blood sample for our work, Permits were granted from the Republic of Turkey Ministry of Environment and Forestry. This work was supported by a grant from The Scientific and Technological Research Council of Turkey (TUBITAK), NSF grant DEB 0817042 and the UC Davis Agricultural Experiment Station. We thank Bob Thomson and members of the Shaffer lab for discussion. This study is a part of Muge Gidis's Ph.D. thesis

Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

<p>Abstract</p> <p>Background</p> <p>Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, and simulations have been used to examine this question. Most simulations have been based on few empirical loci, and suggest that well supported phylogenies can be determined with a very modest amount of data. Here we report the results of an empirical phylogenetic analysis of all 10 genera and 25 of 48 species of the new world pond turtles (family Emydidae) based on one mitochondrial (1070 base pairs) and seven nuclear loci (5961 base pairs), and a more biologically realistic simulation analysis incorporating variation among gene trees, aimed at determining how much more data might be necessary to recover weakly-supported nodes with strong support.</p> <p>Results</p> <p>Our mitochondrial-based phylogeny was well resolved, and congruent with some previous mitochondrial results. For example, all genera, and all species except <it>Pseudemys concinna</it>, <it>P. peninsularis</it>, and <it>Terrapene carolina </it>were monophyletic with strong support from at least one analytical method. The Emydinae was recovered as monophyletic, but the Deirochelyinae was not. Based on nuclear data, all genera were monophyletic with strong support except <it>Trachemys</it>, and all species except <it>Graptemys pseudogeographica</it>, <it>P. concinna</it>, <it>T. carolina</it>, and <it>T. coahuila </it>were monophyletic, generally with strong support. However, the branches subtending most genera were relatively short, and intergeneric relationships within subfamilies were mostly unsupported.</p> <p>Our simulations showed that relatively high bootstrap support values (i.e. ≥ 70) for all nodes were reached in all datasets, but an increase in data did not necessarily equate to an increase in support values. However, simulations based on a single empirical locus reached higher overall levels of support with less data than did the simulations that were based on all seven empirical nuclear loci, and symmetric tree distances were much lower for single versus multiple gene simulation analyses.</p> <p>Conclusion</p> <p>Our empirical results provide new insights into the phylogenetics of the Emydidae, but the short branches recovered deep in the tree also indicate the need for additional work on this clade to recover all intergeneric relationships with confidence and to delimit species for some problematic groups. Our simulation results suggest that moderate (in the few-to-tens of kb range) amounts of data are necessary to recover most emydid relationships with high support values. They also suggest that previous simulations that do not incorporate among-gene tree topological variance probably underestimate the amount of data needed to recover well supported phylogenies.</p

Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders

<p>Abstract</p> <p>Background</p> <p>Hybrid zones represent valuable opportunities to observe evolution in systems that are unusually dynamic and where the potential for the origin of novelty and rapid adaptation co-occur with the potential for dysfunction. Recently initiated hybrid zones are particularly exciting evolutionary experiments because ongoing natural selection on novel genetic combinations can be studied in ecological time. Moreover, when hybrid zones involve native and introduced species, complex genetic patterns present important challenges for conservation policy. To assess variation of admixture dynamics, we scored a large panel of markers in five wild hybrid populations formed when Barred Tiger Salamanders were introduced into the range of California Tiger Salamanders.</p> <p>Results</p> <p>At three of 64 markers, introduced alleles have largely displaced native alleles within the hybrid populations. Another marker (<it>GNAT1</it>) showed consistent heterozygote deficits in the wild, and this marker was associated with embryonic mortality in laboratory F2's. Other deviations from equilibrium expectations were idiosyncratic among breeding ponds, consistent with highly stochastic demographic effects.</p> <p>Conclusion</p> <p>While most markers retain native and introduced alleles in expected proportions, strong selection appears to be eliminating native alleles at a smaller set of loci. Such rapid fixation of alleles is detectable only in recently formed hybrid zones, though it might be representative of dynamics that frequently occur in nature. These results underscore the variable and mosaic nature of hybrid genomes and illustrate the potency of recombination and selection in promoting variable, and often unpredictable genetic outcomes. Introgression of a few, strongly selected introduced alleles should not necessarily affect the conservation status of California Tiger Salamanders, but suggests that genetically pure populations of this endangered species will be difficult to maintain.</p

Rotational master equation for cold laser-driven molecules

The equations of motion for the molecular rotation are derived for vibrationally cold dimers that are polarized by off-resonant laser light. It is shown that, by eliminating electronic and vibrational degrees of freedom, a quantum master equation for the reduced rotational density operator can be obtained. The coherent rotational dynamics is caused by stimulated Raman transitions, whereas spontaneous Raman transitions lead to decoherence in the motion of the quantized angular momentum. As an example the molecular dynamics for the optical Kerr effect is chosen, revealing decoherence and heating of the molecular rotation.Comment: 11 pages, 5 figures, to appear in Phys. Rev.

Rapid progress on the vertebrate tree of life

<p>Abstract</p> <p>Background</p> <p>Among the greatest challenges for biology in the 21st century is inference of the tree of life. Interest in, and progress toward, this goal has increased dramatically with the growing availability of molecular sequence data. However, we have very little sense, for any major clade, of how much progress has been made in resolving a full tree of life and the scope of work that remains. A series of challenges stand in the way of completing this task but, at the most basic level, progress is limited by data: a limited fraction of the world's biodiversity has been incorporated into a phylogenetic analysis. More troubling is our poor understanding of what fraction of the tree of life is understood and how quickly research is adding to this knowledge. Here we measure the rate of progress on the tree of life for one clade of particular research interest, the vertebrates.</p> <p>Results</p> <p>Using an automated phylogenetic approach, we analyse all available molecular data for a large sample of vertebrate diversity, comprising nearly 12,000 species and 210,000 sequences. Our results indicate that progress has been rapid, increasing polynomially during the age of molecular systematics. It is also skewed, with birds and mammals receiving the most attention and marine organisms accumulating far fewer data and a slower rate of increase in phylogenetic resolution than terrestrial taxa. We analyse the contributors to this phylogenetic progress and make recommendations for future work.</p> <p>Conclusions</p> <p>Our analyses suggest that a large majority of the vertebrate tree of life will: (1) be resolved within the next few decades; (2) identify specific data collection strategies that may help to spur future progress; and (3) identify branches of the vertebrate tree of life in need of increased research effort.</p

Direct quality prediction in resistance spot welding process: Sensitivity, specificity and predictive accuracy comparative analysis

In this work, several of the most popular and state-of-the-art classification methods are compared as pattern recognition tools for classification of resistance spot welding joints. Instead of using the result of a non-destructive testing technique as input variables, classifiers are trained directly with the relevant welding parameters, i.e. welding current, welding time and the type of electrode (electrode material and treatment). The algorithms are compared in terms of accuracy and area under the receiver operating characteristic (ROC) curve metrics, using nested cross-validation. Results show that although there is not a dominant classifier for every specificity/sensitivity requirement, support vector machines using radial kernel, boosting and random forest techniques obtain the best performance overallSpanish MICINN Project CSD2010-00034 (SimulPast CONSOLIDER-INGENIO 2010) and by the Junta de Castilla y León GREX251-200