Peter Ralph
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Articles by Peter Ralph
Many biofuels haven't panned out. Could algae make the clean diesel and aviation fuel Australia needs?
Credit: Pixabay/CC0 Public Domain Diesel is critical to Australia. Any supply disruption has immediate and widespread consequences, given Australia imports almost 80% of its liquid fuels. As the energy shocks of the Iran war ripple out, Australia's leaders have scrambled to shore up supplies of fuel—especially diesel and aviation fuel. Disruptions to fuel supplies have happened before, such as in 2008 and 2022. This disruption won't be the last. What should policymakers do?
Many biofuels haven’t panned out. Could algae make the clean diesel and aviation fuel Australia needs? Original
Diesel is critical to Australia. Any supply disruption has immediate and widespread consequences, given Australia imports almost 80% of its liquid fuels. As the energy shocks of the Iran war ripple out, Australia’s leaders have scrambled to shore up supplies of fuel – especially diesel and aviation fuel. Disruptions to fuel supplies have happened before, such as in 2008 and 2022. This disruption won’t be the last. What should policymakers do?
Likelihoods for a general class of ARGs under the SMC
Abstract Ancestral recombination graphs (ARGs) are the focus of much ongoing research interest. Recent progress in inference has made ARG-based approaches feasible across of range of applications, and many new methods using inferred ARGs as input have appeared. This progress on the long-standing problem of ARG inference has proceeded in two distinct directions. First, the Bayesian inference of ARGs under the Sequentially Markov Coalescent (SMC), is now practical for tens-to-hundreds of samples.
Sweeps in space: leveraging geographic data to identify beneficial alleles in Anopheles gambiae
Abstract As organisms adapt to environmental changes, natural selection modifies the frequency of non-neutral alleles. For beneficial mutations, the outcome of this process may be a selective sweep, in which an allele rapidly increases in frequency and perhaps reaches fixation within a population. Selective sweeps have well-studied effects on patterns of local genetic variation in panmictic populations, but much less is known about the dynamics of sweeps in continuous space.
A forest is more than its trees: haplotypes and inferred ARGs
Abstract Foreshadowing haplotype-based methods of the genomics era, it is an old observation that the ``junction'' between two distinct haplotypes produced by recombination is inherited as a Mendelian marker. In this paper, we describe how this recombination-mediated information can in many cases be recovered from inference based solely on polymorphic markers.
Estimation of spatial demographic maps from polymorphism data using a neural network
1 INTRODUCTION To study, conserve and manage populations, we must characterize where individuals live and how they move. For instance, differences in habitat suitability cause local geographic regions to support higher or lower numbers of individuals. Similarly, landscape features such as mountain ranges restrict dispersal to or from different areas.
Estimation of spatial demographic maps from polymorphism data using a neural network
Abstract A fundamental goal in population genetics is to understand how variation is arrayed over natural landscapes. From first principles we know that common features such as heterogeneous population densities and source sink dynamics of dispersal should shape genetic variation over space, however there are few tools currently available that can deal with these ubiquitous complexities.
Genetic architecture, spatial heterogeneity, and the coevolutionary arms race between newts and snakes
Abstract Coevolution between two species can lead to exaggerated phenotypes that vary in a correlated manner across space. However, the conditions under which we expect such spatially varying coevolutionary patterns in polygenic traits are not well-understood. We investigate the coevolutionary dynamics between two species undergoing reciprocal adaptation across space and time, using simulations inspired by the Taricha newt - Thamnophis garter snake system.
link-ancestors: Fast simulation of local ancestry with tree sequence software
Abstract It is challenging to simulate realistic tracts of genetic ancestry on a scale suitable for simulation based inference. We present an algorithm that enables this information to be extracted efficiently from tree sequences produced by simulations run with msprime and SLiM. Competing Interest Statement The authors have declared no competing interest.
Shared evolutionary processes shape landscapes of genomic variation in the great apes
Abstract For at least the past five decades population genetics, as a field, has worked to describe the precise balance of forces that shape patterns of variation in genomes. The problem is challenging because modelling the interactions between evolutionary processes is difficult, and different processes can impact genetic variation in similar ways.
Evidence for admixture and rapid evolution during glacial climate change in an alpine specialist
Abstract The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success in surviving highly heterogeneous environments.
Large effects and the infinitesimal model
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Evaluating evidence for co-geography in the Anopheles Plasmodium host-parasite system
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Save the planet with green industries using algae
Loading metrics Open Access Perspective ? This is an uncorrected proof. We can use photosynthesis to capture carbon and make industries greener. Algae-driven carbon capture and manufacturing offer the potential for reducing CO2 emissions while also producing commodities such as bioplastics. Citation: Ralph PJ, Pernice M (2023) Save the planet with green industries using algae. PLoS Biol 21(3): e3002061.
Shared evolutionary processes shape landscapes of genomic variation in the great apes
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slendr: a framework for spatio-temporal population genomic simulations on geographic landscapes
Abstract One of the goals of population genetics is to understand how evolutionary forces shape patterns of genetic variation over time. However, because populations evolve across both time and space, most evolutionary processes also have an important spatial component, acting through phenomena such as isolation by distance, local mate choice, or uneven distribution of resources.
Archivings -Rainbow and Werrap Tennis Clubs
Rainbow-Jeparit Argus Archivings -Rainbow and Werrap Tennis Clubs Oct 26 2021 Updated 6 hours ago 1 min read By Peter Ralph, Sec RAHS BACK in 1913 a pennant competition between Rainbow and Werrap Tennis Clubs was keenly contested, and today we have parts of a November 1 “Argus” column on one such encounter “played on the beautifully situated courts of the latter on Wednesday last, which resulted in a decisive victory for Rainbow.” And thanks to our access to the collection of Kath Robinson,...
Red Gum saw mill
This scene was photographed in the early 1900s of the hardwood redgum sawmilling operation conducted by the Chaplin brothers at Lake Hindmarsh for some years. Photo: CONTRIBUTED. Rainbow-Jeparit Argus Archivings: Red Gum saw mill Oct 21 2021 Updated 2 hours ago 1 min read By Peter Ralph, Sec. RAHS For those familiar with the wonderful historical mural painted on
The Wimmera's historic horse troughs
Rainbow-Jeparit Argus Archivings: The Wimmera’s historic horse troughs Oct 13 2021 Updated 6 hours ago 2 min read By Peter Ralph, Sec. RAHS WE often reminisce about people, places and events from the past, and every so often acknowledge the tireless work done by teams of bullocks and horses in those earlier days of settlement. Tales of loyal dogs often feature too.
Efficiently Summarizing Relationships in Large Samples: A General Duality Between Statistics of Genealogies and Genomes
Abstract As a genetic mutation is passed down across generations, it distinguishes those genomes that have inherited it from those that have not, providing a glimpse of the genealogical tree relating the genomes to each other at that site. Statistical summaries of genetic variation therefore also describe the underlying genealogies.
Space is the Place: Effects of Continuous Spatial Structure on Analysis of Population Genetic Data
Abstract Real geography is continuous, but standard models in population genetics are based on discrete, well-mixed populations. As a result, many methods of analyzing genetic data assume that samples are a random draw from a well-mixed population, but are applied to clustered samples from populations that are structured clinally over space.
Archivings
News Archivings Apr 29 2020 ByPeter Ralph, Secretary RAHS Firstly this week we return to our items on the 1919 Spanish ‘flu where a n
More protein and good for the planet: 9 reasons we should be eating microalgae
by Martina Doblin, Donna Sutherland and Peter Ralph, The Conversation Credit: CSIRO As the climate warms, the land we use for growing energy-intensive crops such as wheat and corn is becoming less productive. We need to find ways to feed the earth's growing population that isn't so burdensome on the environment. One potential solution is to cultivate microalgae—microscopic aquatic organisms that are packed with nutrients.
More protein and good for the planet: 9 reasons we should be eating microalgae
As the climate warms, the land we use for growing energy-intensive crops such as wheat and corn is becoming less productive. We need to find ways to feed the earth’s growing population that isn’t so burdensome on the environment. One potential solution is to cultivate microalgae - microscopic aquatic organisms that are packed with nutrients. Microalgae are single-celled organisms that look like tiny pills and taste a bit like grass.
Sexually Antagonistic Selection on Genetic Variation is Rare in Humans
New Results doi: https://doi.org/10.1101/2020.03.26.009670 Abstract Sex and sexual differentiation are ubiquitous across the tree of life. Because females and males often have substantially different functional requirements, we would expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci.
Levels of Diatom Minor Sterols Respond to Changes in Temperature and Salinity
Open AccessArticle by Ana Cristina Jaramillo-Madrid *, Justin Ashworth and Peter J. Ralph Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia * Author to whom correspondence should be addressed.
Predicting Geographic Location From Genetic Variation with Deep Neural Networks
Abstract Most organisms are more closely related to nearby than distant members of their species, creating spatial autocorrelations in genetic data. This allows us to predict the location of origin of a genetic sample by comparing it to a set of samples of known geographic origin. Here we describe a deep learning method, which we call Locator, to accomplish this task faster and more accurately than existing approaches.
Are populations like a circuit? The relationship between isolation by distance and isolation by resistance
AbstractA number of methods commonly used in landscape genetics use an analogy to electrical resistance on a network to describe and fit barriers to movement across the landscape using genetic distance data. These are motivated by a mathematical equivalence between electrical resistance between two nodes of a network and the "commute time", which is the mean time for a random walk on that network to leave one node, visit the other, and return.
Local PCA shows how the effect of population structure differs along the genome
AbstractPopulation structure leads to systematic patterns in measures of mean relatedness between individuals in large genomic datasets, which are often discovered and visualized using dimension reduction techniques such as principal component analysis (PCA). Mean relatedness is an average of the relationships across locus-specific genealogical trees, which can be strongly affected on intermediate genomic scales by linked selection and other factors.
Inferring Continuous and Discrete Population Genetic Structure Across Space
AbstractA classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations.
Inferring Continuous and Discrete Population Genetic Structure Across Space
The Genetics Society of America (GSA), founded in 1931, is the professional membership organization for scientific researchers and educators in the field of genetics. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level. Online ISSN: 1943-2631
Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise
AbstractIn this paper, we study the general problem of extracting information from spatially explicit genomic data to inform inference of ecologically and geographically realistic population models. We describe methods and apply them to simulations motivated by the demography of the Mojave desert tortoise (Gopherus agassizii).
The tempo of linked selection: emergence of a heterogeneous genomic landscape during a recent radiation of monkeyflowers
The tempo of linked selection: emergence of a heterogeneous genomic landscape during a recent radiation of monkeyflowers Sean Stankowski, Madeline A Chase, Allison M Fuiten, Peter L Ralph, Matthew A Streisfeld bioRxiv 342352; doi: https://doi.org/10.1101/342352
System drift and speciation
AbstractEven if a species' phenotype remains unchanged over evolutionary time, the underlying mechanism may have changed, as distinct molecular pathways can realize identical phenotypes. Here we use quantitative genetics and linear system theory to study how a gene network underlying a conserved phenotype evolves, as the genetic drift of small mutational changes to these molecular pathways cause a population to explore the set of mechanisms with identical phenotypes.
Desert Tortoises in the Genomic Age: Population Genetics and the Landscape
Desert Tortoises in the Genomic Age: Population Genetics and the Landscape H. Bradley Shaffer, Evan McCartney-Melstad, Peter L. Ralph, Gideon Bradburd, Erik Lundgren, Jannet Vu, Bridgette Hagerty, Fran Sandmeier, Chava Weitzman, C. Richard Tracy bioRxiv 195743; doi: https://doi.org/10.1101/195743
Inferring Continuous and Discrete Population Genetic Structure Across Space
AbstractA classic problem in population genetics is the characterization of discrete population structure in the presence of continuous patterns of genetic differentiation. Especially when sampling is discontinuous, the use of clustering or assignment methods may incorrectly ascribe differentiation due to continuous processes (e.g., geographic isolation by distance) to discrete processes, such as geographic, ecological, or reproductive barriers between populations.
Local PCA shows how the effect of population structure differs along the genome
AbstractPopulation structure leads to systematic patterns in measures of mean relatedness between individuals in large genomic datasets, which are often discovered and visualized using dimension reduction techniques such as principal component analysis (PCA).
A Spatial Framework for Understanding Population Structure and Admixture
There are many different methods to learn how population structure and demographic processes have left their mark on patterns of genetic variation within and between populations. Model-based approaches focus on developing a detailed view of the migrational history of a small number of populations, often assuming one or a small number of large, randomly mating populations (i.e. little or no geographic structure).
The Geography of Recent Genetic Ancestry across Europe
Loading metrics Open Access Peer-reviewed Research Article Citation: Ralph P, Coop G (2013) The Geography of Recent Genetic Ancestry across Europe. PLoS Biol 11(5): e1001555. https://doi.org/10.1371/journal.pbio.1001555 Academic Editor: Chris Tyler-Smith, The Wellcome Trust Sanger Institute, United Kingdom Received: July 16, 2012; Accepted: March 27, 2013; Published: May 7, 2013 Copyright: © 2013 Ralph, Coop.
Parallel Adaptation: One or Many Waves of Advance of an Advantageous Allele?
Models for detecting the effect of adaptation on population genomic diversity are often predicated on a single newly arisen mutation sweeping rapidly to fixation. However, a population can also adapt to a new environment by multiple mutations of similar phenotypic effect that arise in parallel, at the same locus or different loci.
Convergent Evolution During Local Adaptation to Patchy Landscapes
Species often encounter, and adapt to, many patches of similar environmental conditions across their range. Such adaptation can occur through convergent evolution if different alleles arise in different patches, or through the spread of shared alleles by migration acting to synchronize adaptation across the species.
The Spatial Mixing of Genomes in Secondary Contact Zones
Recent genomic studies have highlighted the important role of admixture in shaping genome-wide patterns of diversity. Past admixture leaves a population genomic signature of linkage disequilibrium (LD), reflecting the mixing of parental chromosomes by segregation and recombination. These patterns of LD can be used to infer the timing of admixture, but the results of inference can depend strongly on the assumed demographic model.
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