101 research outputs found
Temperature-driven global sea-level variability in the Common Era
No full textWe assess the relationship between temperature and global sea-level (GSL) variability over the Common Era through a statistical metaanalysis of proxy relative sea-level reconstructions and tide-gauge data. GSL rose at 0.1 ± 0.1 mm/y (2σ) over 0–700 CE. A GSL fall of 0.2 ± 0.2 mm/y over 1000–1400 CE is associated with ∼0.2 °C global mean cooling. A significant GSL acceleration began in the 19th century and yielded a 20th century rise that is extremely likely (probability P≥0.95) faster than during any of the previous 27 centuries. A semiempirical model calibrated against the GSL reconstruction indicates that, in the absence of anthropogenic climate change, it is extremely likely (P=0.95) that 20th century GSL would have risen by less than 51% of the observed 13.8±1.5 cm. The new semiempirical model largely reconciles previous differences between semiempirical 21st century GSL projections and the process model-based projections summarized in the Intergovernmental Panel on Climate Change’s Fifth Assessment Report.This article is available Open Access at the Link to published version: http://dx.doi.org/10.1016/j.emospa.2016.02.006Also available as related resources: Supporting Information (PDF), Dataset S1 (PDF), Dataset S2 (Excel), Dataset S3 (Excel).Peer reviewe
Characterization of the AMP-activated protein kinase kinase from rat liver and identification of threonine 172 as the major site at which it phosphorylates AMP-activated protein kinase
No full textWe have developed a sensitive assay for the AMP-activated protein kinase kinase, the upstream component in the AMP-activated protein kinase cascade. Phosphorylation and activation of the downstream kinase by the upstream kinase absolutely requires AMP and is antagonized by high (millimolar) concentrations of ATP. We have purified the upstream kinase > 1000-fold from rat liver; a variety of evidence indicates that the catalytic subunit may be a polypeptide of 58 kDa. The physical properties of the downstream and upstream kinases, e.g. catalytic subunit masses (63 versus 58 kDa) and native molecular masses (190 versus 195 kDa), are very similar. However, unlike the downstream kinase, the upstream kinase is not inactivated by protein phosphatases. The upstream kinase phosphorylates the downstream kinase at a single major site on the a subunit, i.e. threonine 172, which lies in the 'activation segment' between the DFG and APE motifs. This site aligns with activating phosphorylation sites on many other protein kinases, including Thr on calmodulin-dependent protein kinase I. As well as suggesting a mechanism of activation of AMP-activated protein kinase, this finding is consistent with our recent report that the AMP-activated protein kinase kinase can slowly phosphorylate and activate calmodulin-dependent protein kinase I, at least in vitro (Hawley, S. A., Selbert, M. A., Goldstein, E.G., Edelman, A. M., Carling, D., and Hardie, D. G. (1995) J. Biol. Chem. 270, 27186-27191)
BUNTING HYBRID ZONE
No full textUsing cline fitting and divergence population genetics, we tested a prediction of Haldane\u27s rule: autosomal alleles should introgress more than z-linked alleles or mitochondrial haplotypes across the Passerina amoena/Passerina cyanea (Aves: Cardinalidae) hybrid zone. We screened 222 individuals collected along a transect in the Great Plains of North America that spans the contact zone for mitochondrial (two genes), autosomal (four loci) and z-linked (two loci) markers. Maximum-likelihood cline widths estimated from the mitochondrial (223 km) and z-linked (309 km) datasets were significantly narrower on average than the autosomal cline widths (466 km). We also found that mean coalescent-based estimates of introgression were larger for the autosomal loci (0.63 genes/generation, scaled to the mutation rate μ) than for both the mitochondrial (0.27) and z-linked loci (0.59). These patterns are consistent with Haldane\u27s rule, but the among-locus variation also suggests many independently segregating loci are required to investigate introgression patterns across the genome. These results provide the first comprehensive comparison of mitochondrial, sex-linked, and autosomal loci across an avian hybrid zone and add to the body of evidence suggesting that sex chromosomes play an important role in the formation and maintenance of reproductive isolation between closely related species. © 2008 The Author(s)
Mating On The Margins: The Impacts of Social Network Structure and Climate On Gene Flow In A Hybrid Zone Between California (Callipepla Californica) and Gambel’s Quail (Callipepla Gambelii)
No full textHybridization between genetically distinct lineages can shape important population processes such as local adaptation, genetic divergence, population persistence, and range expansion. Studies of hybrid zones – areas of contact and interbreeding between divergent populations – have played a key role in revealing ecological, genetic, and behavioral factors that promote or inhibit genetic exchange. Behavior can strongly influence rates and patterns of hybridization between animal taxa as individuals must identify, attract, and compete for mates prior to reproduction. Yet, few studies have examined reproductive behaviors in natural hybrid zones within the fine-scale social structure in which they naturally occur. Climate can also dictate where species overlap in sympatry, and determine the fitness of hybrid offspring. I had two primary goals: 1) to examine how traits structure social behavior and hybridization within sympatric populations, and 2) to test the effects of climate on population genetic structure at larger spatial and temporal scales. I conducted research across a hybrid zone between the California (Callipepla californica) and Gambel’s (Callipepla gambelii) quail in the deserts and mountains of Southern Califonia. I used novel social network analyses on behavioral data collected from RFID tags to test how phenotype and genotype influence social behavior and reproduction in a hybrid quail population. I found that mating opportunities were strongly influenced by assortment of birds based upon phenotype, but that behavioral reproductive isolation was weak within sympatry. Hybridization between species was influenced by behavioral assortment based upon a complex mix of traits, avoidance of interbreeding with kin, and temporal shifts in social structure of breeding populations over time. I compared contemporary genomic data with historic estimates of admixture to test how the position of the hybrid zone has changed over an abnormally hot and dry two-decade period. Recent changes in climatic conditions strongly predicted an observed downhill movement of the hybrid zone, and this movement may be facilitated by adaptive introgression. My research presents novel analytical approaches and contributes towards goals of quantifying the relative contributions of different reproductive barriers within hybrid zones.</p
Evolutionary history and hybridization in Passerina buntings
No full textUnderstanding the genetic basis of speciation is of fundamental importance to evolutionary biology and hybrid zones offer unique natural laboratories in which to investigate the ecological and evolutionary processes important in creating and maintaining biological diversity. By comparing introgression patterns of different loci, researchers can begin to identify genetic regions that contribute to reproductive isolation between hybridizing taxa. In taxa, like birds, with heterogametic females, Haldane’s rule predicts that mtDNA and z-linked loci will introgress less than autosomal loci. I tested this prediction using the hybrid zone between Passerina cyanea (Indigo Bunting) and Passerina amoena (Lazuli Bunting), two species that hybridize where their breeding ranges overlap in the Great Plains of North America. Although a recent mtDNA-based phylogenetic hypothesis of the genus Passerina suggested these two species are not sister taxa, I found, using DNA sequence data from ten nuclear loci, that they are more closely related to each other than either is to P. caerulea (the mtDNA sister to P. ameona). Both cline-based and coalescent-based analyses of mtDNA (two genes), z-linked (two loci), and autosomal (four) loci indicated a reduction in introgression of both mtDNA and z-linked loci, relative to autosomal loci. These patterns, consistent with the predictions of Haldane’s rule, suggested the sex-chromosomes may play a large role in reproductive isolation between P. cyanea and P. amoena. Using DNA sequence data from an additional eight z-linked loci, I explored patterns of differential introgression of ten z-linked loci. Introgression of one z-linked locus, VLDLR9, was significantly less than introgression of the other nine loci, pointing to a candidate region for reproductive isolation between P. cyanea and P. amoena. Interestingly, VLDLR9 is an intron of the very-low density lipoprotein receptor, which plays an active role in egg laying. Additionally, in a particular strain of chickens, a point mutation in the VLDLR gene produces females that do not lay eggs. While my data are insufficient to adequately address the role VLDLR may play in maintaining reproductive isolation between P. cyanea and P. amoena, the hypothesis that female buntings may have trouble laying eggs warrants further investigation
Mating On The Margins: The Impacts of Social Network Structure and Climate On Gene Flow In A Hybrid Zone Between California (Callipepla Californica) and Gambel’s Quail (Callipepla Gambelii)
No full textHybridization between genetically distinct lineages can shape important population processes such as local adaptation, genetic divergence, population persistence, and range expansion. Studies of hybrid zones – areas of contact and interbreeding between divergent populations – have played a key role in revealing ecological, genetic, and behavioral factors that promote or inhibit genetic exchange. Behavior can strongly influence rates and patterns of hybridization between animal taxa as individuals must identify, attract, and compete for mates prior to reproduction. Yet, few studies have examined reproductive behaviors in natural hybrid zones within the fine-scale social structure in which they naturally occur. Climate can also dictate where species overlap in sympatry, and determine the fitness of hybrid offspring. I had two primary goals: 1) to examine how traits structure social behavior and hybridization within sympatric populations, and 2) to test the effects of climate on population genetic structure at larger spatial and temporal scales. I conducted research across a hybrid zone between the California (Callipepla californica) and Gambel’s (Callipepla gambelii) quail in the deserts and mountains of Southern Califonia. I used novel social network analyses on behavioral data collected from RFID tags to test how phenotype and genotype influence social behavior and reproduction in a hybrid quail population. I found that mating opportunities were strongly influenced by assortment of birds based upon phenotype, but that behavioral reproductive isolation was weak within sympatry. Hybridization between species was influenced by behavioral assortment based upon a complex mix of traits, avoidance of interbreeding with kin, and temporal shifts in social structure of breeding populations over time. I compared contemporary genomic data with historic estimates of admixture to test how the position of the hybrid zone has changed over an abnormally hot and dry two-decade period. Recent changes in climatic conditions strongly predicted an observed downhill movement of the hybrid zone, and this movement may be facilitated by adaptive introgression. My research presents novel analytical approaches and contributes towards goals of quantifying the relative contributions of different reproductive barriers within hybrid zones.</p
Gene sampling strategies for multi-locus population estimates of genetic diversity (theta).
No full textTheoretical work suggests that data from multiple nuclear loci provide better estimates of population genetic parameters than do single loci, but just how many loci are needed and how much sequence is required from each has been little explored.To investigate how much data is required to estimate the population genetic parameter theta (4N(e)mu) accurately under ideal circumstances, we simulated datasets of DNA sequences under three values of theta per site (0.1, 0.01, 0.001), varying in both the total number of base pairs sequenced per individual and the number of equal-length loci. From these datasets we estimated theta using the maximum likelihood coalescent framework implemented in the computer program Migrate. Our results corroborated the theoretical expectation that increasing the number of loci impacted the accuracy of the estimate more than increasing the sequence length at single loci. However, when the value of theta was low (0.001), the per-locus sequence length was also important for estimating theta accurately, something that has not been emphasized in previous work.Accurate estimation of theta required data from at least 25 independently evolving loci. Beyond this, there was little added benefit in terms of decreasing the squared coefficient of variation of the coalescent estimates relative to the extra effort required to sample more loci
Figure 1
No full text<p>Influence of increasing the number of loci sampled per individual on the coalescent estimates of θ (0.1, 0.01, 0.001): (A) improvement in accuracy (mean<sup>2</sup>/variance), loci sampled are 1 kb in length; (B) improvement in squared coefficient of variation ((standard deviation/mean)<sup>2</sup>), loci sampled are 1 kb in length; (C) accuracy, loci sampled are 5 kb in length, θ = 0.001 (see text); (D) squared coefficient of variation, loci are 5 kb in length (see text).</p
buntings: introgression patterns of sex-linked loci identify a candidate gene region for reproductive isolation
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