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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New faces: Stacy Krueger-Hadfield

New contributor Stacy A. Krueger-Hadfield

New contributor Stacy A. Krueger-Hadfield

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? Stacy A. Krueger-Hadfield.

Where are you? Currently, a post-doctoral fellow at the College of Charleston, based at the Grice Marine Laboratory.

What do you study? I am an evolutionary ecologist. Though I have dabbled with some animal models, I mainly use marine algae (both macro- and micro-) to address questions pertaining to population connectivity in marine environments, life history evolution and the impacts of global climate change on marine populations. Currently, I am a co-PI on NSF-funded research investigating the invasive history of the red seaweed Gracilaria vermiculophylla in which we are using a combination of genotype and phenotype to explore the impacts of the invasion along both North American and European coastlines. For more information, see my website and the research page (www.quooddy.com).

What do you do when you’re not studying it? I enjoy traveling, reading, writing (in all forms) and taking pictures.

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WTF (What’s The Function?)

Schoolhouse Rock!

Schoolhouse Rock!

Jay Shendure’s editorial, “Life after genetics”, points out that we, as geneticists, should shift our focus from variant-finding (e.g., GWAS) to understanding the functional implications of disease-associated variants:

“We are in a period of rich discovery in human genetics and genomics. The ascertainment of genetic variation, previously the rate-limiting step for genetic analysis, has been revolutionized by new technologies for high-density genotyping, exome sequencing and genome sequencing.
Amid this success, it is important to remember that genetics is a means to one or several ends (such as a biological understanding of disease mechanisms, or identifying the basis of disease in a specific patient) rather than an end in itself. The ultimate impact of our field will depend not only on whether we can get the genetics right, but also on whether or not subsequent goals are achieved.”

The editorial is aimed at human geneticists, but the message rings true for all who study genetics – molecular ecologists included. Finding a genotype-phenotype association is just the first step. We should strive for a more in depth and comprehensive understanding.

Shendure’s editorial highlights some potential ways to bridge the gap between genotype and function. One possible route is the using the rapidly developing in vitro genome editing techniques, such as CRISPR/Cas9.

One could easily extend this editorial to include other genomic-phenotype associations, including epigenetic modifications. Great, so you’ve found an association. What’s the function?

Jay Shendure. 2014. Life after genetics. Genome Medicine. doi:10.1186/s13073-014-0086-2.

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New faces: Rob Denton

New contributor Rob Denton

New contributor Rob Denton

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? I’m a 4th year PhD candidate in the Department of Evolution, Ecology, and Organismal Biology at Ohio State University.

Where are you? Columbus, Ohio, USA

What do you study? North America is home to one of the weirdest amphibians in the world, a group of all-female salamanders that mainly reproduce clonally but occasionally “steal” sperm from males of other species. This method of reproduction is unique among vertebrates and has been around for quite a long time (~6 million years), but it is difficult to explain how this all-female lineage stays in balance with the sexual salamanders that they take advantage of by having their cake (not making males) and eating it too (still getting new genetic diversity). I study some of factors that may drive the coexistence between sexual salamander species and this all-female lineage.

What do you do when you’re not studying it? Academically, I’m also interested in the science of teaching and learning, especially how inquiry and technology affect students’ learning. Non-academically, I’m a husband, father, homebrewer, and hockey fan. I’m lucky enough that my job takes me to do a lot of things that I enjoy outside of work anyway, like traveling to interesting places and finding wildlife.

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