Admixture maps in R for Dummies

Before we get started, I’d like to point everyone to an excellent tutorial here by Kim Gilbert on making maps in R. I have been grappling with overlaying admixture plots, and migration routes on top of maps recently, and thought I’d put together a quick tutorial on that. What you will need:

  1. GPS coordinates
    Eg. gps.data
    ID,Lat,Lon
    1,33.72,-94.40
    2,34.1682185,-111.930907
    3,37.2718745,-119.2704153
    

  2. Admixture proportions – these are routinely printed out as the “Q” matrix by STRUCTURE, and in a file suffixed with a “Q” by ADMIXTURE. I added a column with sample sizes to this, to proportionately resize the admixture pies.
    Eg. admixprops.data
    K1,K2,Num
    0.836601,0.163399,12
    0.565904,0.434096,16
    0.508735,0.491265,18
    0.111114,0.888886,9
    

  3. maps() and plotrix() packages in R

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Is genetics a requirement for restoration?

Image from Luc Viatour (www.Lucnix.be)

The fields of conservation and genetics have relied heavily on one another for quite a while now (they even made an aptly named journal together!). Using genetic information is now an accepted, and even expected, step in recognizing and protecting species at risk. However, less attention has been paid to the role of genetic information during ecological restoration, the applied steps of manipulating ecosystems to a more historical or resilient state.

Thus, the aim of this paper is to review how genetics has been utilised in restoration ecology to the present and to identify ways in which genetics could be better utilised to inform restoration ecology in the future.

Mijangos et al. cite multiple cases in which the ecological assumptions made based on a species’ life history don’t match up with their genetic signature (example: some clonal species defy expectations by having a combinations of low seed dispersal and high population genetic diversity). These examples provide compelling support for a combination of genetics, ecology, and ecosystem services when making all restoration decisions.

Genetics can facilitate the evaluation of a restoration project by, for example, quantifying gene flow or demographic changes in the targeted populations. The role of genetics is not only limited to indirectly evaluating population dynamics or ecosystem processes however, as genetics can directly influence the success of restoration projects.

The authors provide a comprehensive review of how basic population genetic inference (effective population sizes, migration rates, connectivity, etc.) can benefit restoration goals. While this shouldn’t be surprising, providing a useful document for both molecular ecologists and restoration practitioners to look over and see the benefit of collaboration is a valuable contribution for the future of this young field.

Mijangos J.L., Pacioni C., Spencer P.B.S. & Craig M.D. (2014). Contribution of genetics to ecological restoration., Molecular Ecology, DOI: 10.1111/mec.12995

Posted in community ecology, conservation, Molecular Ecology, the journal, natural history, population genetics | Tagged , , | 1 Comment

Bugs fighting bugs: the evolution of the arthropod immune system.

Deer tick (Ixodes scapularis) photo courtesy of the Agricultural Research Service via Wikipedia

Since the beginning of time, animals have needed to protect themselves from invaders. They primarily do so via their innate immune system, in which trained killer cells attack foreign pathogens – ranging from microscopic bacteria to macroscopic worms. While we know a fair amount about the innate immune system of most vertebrates and some insects, we know comparatively little about the immune system of arthropods. Here is where the new preprint by William Palmer and Francis Jiggins comes in.

Using the recently acquired sequences of multiple arthropod genomes, the authors characterized the immune systems of some pretty icky arthropods: the Water Flea, the Coastal Centipede, Chinese Scorpion, the House Spider, the Deer Tick, and the Western Orchard Predatory Mite, and the Red Spider Mite. Interestingly, the authors found:

… both remarkable diversification of the immune response across the arthropods, and unexpected conservation and similarities to mammalian genes… These include a group of arthropod toll-like receptors that share structural similarity with vertebrate TLRs and cluster with them phylogenetically.

This is important because it suggest that some components of the innate immune system, such as TLRs – which recognize foreign microbes and activate immune cell responses, have deep roots in our evolutionary history. The authors state:

Our results confirm an ancient origin for the innate immune system, predating the split between protostomes and deuterostomes. We find striking examples of conservation between vertebrates and arthropods, despite these two groups having diverged before the Cambrian explosion some 543 million years ago.

W. Palmer & F. Jiggins “Comparative genomics reveals the origins and diversity of arthropod immune systems” BioRxiv. DOI: http://dx.doi.org/10.1101/010942

Posted in genomics, phylogenetics | 1 Comment

Different genetic paths lead to the same phenotypic destination

Male field crickets (Teleogryllus oceanicus) on the Hawaiian archipelago sing to attract mates using acoustic structures on their wings. While singing makes the ladies swoon, it also gives away the male cricket’s location, making it vulnerable to fatal attacks by a parasitoid fly (Ormia ochracea). In the last decade, male crickets that have lost the ability to sing have appeared, first on Kauai and then later on Oahu.

In their 2014 Current Biology paper, Pascoal et al. tested whether the presence of the silent, ‘flatwing’ phenotype on Oahu resulted from migration and introgression from the Kauai population or independent evolution of the trait on each island. Morphometric analyses showed Kauai and Oahu flatwing phenotypes were four times more different from one another than any two normal-winged phenotypes were from one another. Interestingly, this means different wing shapes achieve the same result- silence. Breeding crosses between normal and flatwing crickets showed flatwing is inherited as a Mendelian, sex-linked mutation on both islands. The shared mode of inheritance presents the possibility that a single mutation could produce the different flatwing phenotypes due to the different genetic backgrounds of the Kauai and Oahu crickets. The authors collected RADseq data and used a bulk segregant analysis (BSA) to identify single nucleotide polymorphisms (SNPs) in linkage disequilibrium with the flatwing phenotype in each population.

 If the observed population-level morphological differences are caused by expression of the same sequence variant in different genomic backgrounds after introgression, then the majority of linked SNPs should be shared between the two populations. In contrast, if the two wing-silencing phenotypes are caused by sequence variants that affect genetically distinct regions of the X chromosome, then the BSA should recover nonoverlapping sets of linked SNPs for each island.

And what did they find? The genome-wide scans showed a distinct set of SNPs were linked with flatwing in each island population, indicating different genomic architectures are responsible for the silent phenotypes in Hawaiian crickets. Essentially, this silent, flatwing trait has evolved independently on each island.

Divergent wing morphologies linked to different loci thus cause identical behavioral outcomes—silence—illustrating the power of selection to rapidly shape convergent adaptations from distinct genomic starting points.

Pascoal S, Cezard T, Eik-Nes A, et al. (2014) Rapid convergent evolution in wild crickets. Current Biology 24, 1369-1374.

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Happy as a clam, despite genetic uniformity

 

Corbicula fluminea. photo courtesy of Noel M. Burkhead - U.S. Geological Survey

Corbicula fluminea, photo courtesy of Noel M. Burkhead – U.S. Geological Survey

Introduced populations of non-native species are often associated with low genetic diversity, as measured by neutral genetic loci, and, thus, considered a paradox (but see Roman and Darling 2007). The study by Lise-Marie Pigneur and colleagues documents an extreme example of this putatively paradoxical phenomenon in the invasive clam genus Corbicula. The authors document four, undiversified genetic lineages in Europe and the Americas, whereas the native range, in the northwest Pacific, is characterized by higher levels of genetic diversity. Yet, the relationship between genetic diversity and invasion success is not as straight-forward as it might seem.

The apparent importance of the flexibility of reproductive mode to the success of low diversity invasions suggests that there is much to learn regarding how evolutionary history and life history characteristics affect the invasiveness of species. (Roman and Darling 2007)

The mixed mating system exhibited in the native range of these Corbicula clams may hold an enticing clue as to the success of the invasive lineages. The dioecious sexual lineages are strictly diploid, whereas the hermaphroditic asexual, or more specifically androgenetic (i.e., male parthenogenesis), lineages can be diploid, triploid or tetraploid. But, interestingly, the unreduced spermatozoon from one androgenetic lineage can fertilize an egg of another androgenetic lineage. The resultant progeny exhibit the nuclear genome from one and the mitochondrial genome from another lineage, a phenomenon termed egg parasitism or mitochondrial capture (e.g., Hedtke et al. 2008, Pigneur et al. 2012). Thus, despite reduced genetic diversity, androgenesis in Corbicula clams may combine clonality with the ability of rare genetic material exchange.

Associated with other life history traits of Corbicula lineages, it might have been a determinant mechanism that contributed to the invasiveness of undiversified populations of these clams. (Pigneur et al. 2014)

The role of life history traits coupled with labile reproductive systems in invasion success and invasive histories warrants further attention, especially in aquatic and marine environments.

J Roman and JA Darling (2007) Paradox lost: genetic diversity and the success of aquatic invasions. TREE 22: 454-464; http://dx.doi.org/10.1016/j.tree.2007.07.002

SM Hedtke, M Glaubrecht, DM Hills (2008) Rare gene capture in predominantly adrogenetic species. PNAS 108: 9520-9524; doi:10.1073/pnas.1106742108

L-M Pigneur, SM Hedtke, E Etoundi, K Van Doninck (2012) Androgenesis: a review through the study of the selfish shellfish Corbicula spp. Heredity 108: 581-591; doi:10.1038/hdy.2012.3

L-M Pigneur, E Etoundi, DC Aldridge, J Marescaux, N Yasuda and K Van Doninck (2014) Genetic uniformity and long-distance clonal dispersal in the invasive and androgenetic Corbicula clams.  Molecular Ecology 23: 5102-5116; doi: 10.1111/mec.12912

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Highlights from the 2014 Ecological Genomics Symposium

Ecological genomics is a rapidly growing field that aims to understand the genetic mechanisms responsible for the adaptive responses of organisms to their environment. I’m jumping into this area of research as a postdoc in the Kelly Lab at Louisiana State University and last weekend I attended the 12th annual Ecological Genomics Symposium hosted by the Ecological Genomics Institute at Kansas State University. The talks and posters presented at EGS covered a broad range of questions, critters, and data types- both phenotypic and genomic, but the common goal of many of the projects was to determine how genotype and environment influence the evolution of phenotypes. In this post I’ll highlight a small cross section of the exciting research I heard about at the meeting.

Dr. Zac Cheviron at the University of Illinois and Dr. Catherine Linnen at the University of Kentucky both study the (adorable) deer mouse Peromyscus maniculatus, but they focus on different adaptive traits that have evolved in this species. Deer mice have the broadest elevational distribution of any North American mammal, occurring from sea level to 4300 meters, and Zac studies how mouse populations have adapted to life at such extreme heights. His recent work has shown that under the hypoxic (i.e. low oxygen) conditions expected at high elevation, mice from the highlands outperform lowland mice by, generally speaking, using oxygen more efficiently. You can read about the very cool details of this work here and here.

The Deer mouse, Peromyscus maniculatus. Image courtesy of J. N. Stuart, Flickr

The Deer mouse, Peromyscus maniculatus. Photo courtesy of J. N. Stuart, Flickr

Deer mice found at lower elevation in the Nebraska Sand Hills have multiple traits, including light colored fur, that help them blend in with the light colored soil and avoid detection by avian predators. Catherine presented results from a recent Science paper showing that in light colored mice different phenotypic traits correspond to different mutations within a single gene called Agouti. This work is a great example of how single nucleotide polymorphisms (SNPs) can determine phenotype.

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The Ust’-Ishim Genome

Svante Paabo examines the 45000 year old Ust’-Ishim femur, Image courtesy: The Guardian

This year has been monumental in pulling together several interesting pieces in the human evolution out of Africa puzzle (Lazaridis et al., Ruiz-Linares et al., Skoglund et al., Huerta-Sanchez et al., Jeong et al., Pickrell et al., Raghavan et al., Sankararaman et al., etc.). In a study published last week, Fu et al. report the whole genome sequencing of a 45,000 year old modern human male from Ust’-Ishim in Western Siberia, which offers several conjectures to preceding studies. Genomic analyses reveal that this individual belonged to a population which (a) was more similar to modern day Eurasians than Africans in genetic diversity, (b) contained ~2.3 ± 0.3% of Neanderthal admixture, on similar scales as modern day Asians and Europeans, (c) contained longer IBD tracts of Neanderthal ancestry as expected (the Ust’-Ishim individual lived around the same time period as previously estimated Neanderthal admixture with modern humans out of Africa, around 50-60k ybp). Perhaps more importantly, this study also estimates autosomal mutation rates using a modified version of PSMC (Li and Durbin, 2011) to be around 0.43 x 10-9 per site per year which is on the lower end of previous studies which use pedigrees, and/or fossil records.

“…these rates are slower than those estimated using calibrations based on the fossil record and thus suggest older dates for the splits of modern human and archaic populations.

While the estimated autosomal mutation rate is perhaps more characteristic of modern humans that were subjected to the out of Africa bottleneck, this study has important implications for other studies that have continued to use larger mutation rates, including those cited above.

Fu, Qiaomei, et al. “Genome sequence of a 45,000-year-old modern human from western Siberia.” Nature 514.7523 (2014): 445-449. DOI: http://dx.doi.org/10.1038/nature13810

 

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The Tortoise Time Warp

Image Credit: Magnus Manske (Flickr)

Recent advances in genetic data analysis continue to provide the ability to reveal some amazingly detailed (and previously unattainable) information about species’ evolutionary history. In this recent study from Molecular Ecology, Dr. Ryan Garrick and colleagues use a variety of genetic data taken from Galápagos tortoises in combination with approximate Bayesian computation (ABC) analyses to document lineage fusion, a traditionally-neglected explanation for radiations in island species.

Yet the importance of fusion events in evolutionary radiations is likely underestimated because incipient lineages tend to fuse so rapidly that the underlying processes are seldom caught in the act, and so empirical evidence appears sparse (Fitzpatrick et al. 2009).

Galápagos giant tortoises provide a particularly interesting example by providing a valuable complement to the extensively documented radiations of Darwin’s finches. Now both enigmatic groups show evidence for reticulate evolutionary histories.

We suggest that, as for Darwin’s finches (Grant et al. 2005), hybridization among Galápagos giant tortoises has been a recurrent feature of their adaptive radiation.

Fitzpatrick B.M., D Kevin Kump, H Bradley Shaffer, Jeramiah J Smith & S Randal Voss (2009). Rapid fixation of non-native alleles revealed by genome-wide SNP analysis of hybrid tiger salamanders, BMC Evolutionary Biology, 9 (1) 176. DOI: http://dx.doi.org/10.1186/1471-2148-9-176

Garrick R.C., Michael A. Russello, Chaz Hyseni, Danielle L. Edwards, James P. Gibbs, Washington Tapia, Claudio Ciofi & Adalgisa Caccone (2014). Lineage fusion in Galápagos giant tortoises, Molecular Ecology, 23 (21) 5276-5290. DOI: http://dx.doi.org/10.1111/mec.12919

Grant P., B. Rosemary Grant, & K. Petren (2005). Hybridization in the Recent Past, The American Naturalist, 166 (1) 56-67. DOI: http://dx.doi.org/10.1086/430331

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New faces: Melissa DeBiasse

New contributor Melissa DeBiasse

New contributor Melissa DeBiasse

This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy

My name is Melissa DeBiasse and I am interested in the mechanisms that determine the distribution of genetic, phenotypic, and physiologic variation in marine invertebrates. My dissertation research in Mike Hellberg’s lab at Louisiana State University used multi-locus model-based methods to infer phylogeographic history and species boundaries in the Caribbean coral reef sponge Callyspongia. As a postdoc in Morgan Kelly’s lab at LSU, I am using experimental methods and transcriptomic data to understand the genomic basis of local adaptation in Tigriopus copepods. I am also interested in increasing the participation of underrepresented groups in STEM fields. When I’m not doing science, I love to run, sew, and enjoy the great food, music, and culture Louisiana has to offer.

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New faces: Noah Snyder-Mackler

New contributor Noah Snyder-Mackler.

New contributor Noah Snyder-Mackler.

This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy

Who are you? Is this an existential question? I guess my answer is that I’m Noah Snyder-Mackler – a researcher who studies non-human primate genetics and genomics at Duke University, but that’s not that deep, is it? A bit more: I received my BA in Psychology from the University of Pennsylvania in 2007 and my PhD from the same department and institution in 2012. My dissertation work focused on understanding social and genetic structure of the complex society of the gelada monkey.

Where are you? This one is definitely easier to answer than “Who am I?”. I’m currently a postdoc in Jenny Tung’s lab in the Department of Evolutionary Anthropology at Duke University.

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