Genomics: the “four-headed beast” of Big Data

Big Data in the cloud. Photo from internap.com

Big Data in the cloud. Photo from internap.com

When I bought my first laptop in 2005, it came with a free 64MB flash drive*, which I thought was pretty awesome. Given the rate at which genomic data generation has increased in the past decade, the storage capacity of that flash drive is laughable today. In their new PLOS Biology paper, Stephens et al. talk about genomics as a Big Data science, compare it to other Big Data domains (Astronomy, YouTube, and Twitter, specifically), and project where genomics is headed in the next decade in terms of data acquisition, storage, distribution, and analysis. Continue reading

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The Butterfly Effect

This might just take the prize for the ‘spiciest’ story in molecular co-evolution for 2015, yet. While a lot of the press coverage sounds like caterpillar thanksgiving, the science behind this study stands for the almost incredible power of molecular phylogenetics in unveiling the adaptive evolution of traits.

Edger et al. (2015) in a recent study report the coincident evolutionary arms-race of Brassicales (angiosperms that include mustard, horseradish, cabbage, broccoli, etc.), and their predatory butterflies in the family Pieridae. Using whole transcriptome sequences of Brassicales, and nuclear gene phylogneis for Pieridae, Edger et al. (2015) perform phylogenetic analyses across 1155 genes, calibrated using fossil estimates to date/delineate genome duplication, and diversification events in glucosinolate(purportedly evolved toxic plant defenses against predatory Pierid caterpillars, but rendering the characteristic sharp tastes to edible Brassicales) pathways.

Fossil calibrated phylogenetic reconstructions of Brassicales, and Pieridae showing co-evolutionary diversification (of glucosinolates) in Brassicales, and detoxification in Pieridae. Image courtesy: Fig. 1 of Edger et al. (2015).

Key findings of this study include:

  1. the appearance of glucosinolates after a whole genome duplication event in Brassicales (~78 Mya),
  2. the ability of Brassicales to synthesize glucosinolates from substrates was ancestral,
  3. the escalation of glucosinolate diversity in Brassicales was a result of an arms-race against butterflies due to retention and neofunctionalization of genes after single gene, and whole genome duplications, and
  4. subsequent evolution of adaptation to toxicity of glucosinolates in different Pieridae coincides with diversification events in Brassicales and vice versa.
  Consistent with the hypothesis that retention of duplicates after WGD is driven by selective benefits, previous analyses indicates a high metabolic cost of glucosinolate production, a result incompatible with the retention of glucosinolate duplicate being neutral.

Reference:

Edger, Patrick P., et al. “The butterfly plant arms-race escalated by gene and genome duplications.” Proceedings of the National Academy of Sciences(2015): 201503926.

Posted in adaptation, evolution, genomics, natural history, population genetics, selection, speciation, transcriptomics | Tagged , , , , | 1 Comment

Can hybridization save a species, genes, or both?

Climate change is real, species are going to move around, and it will definitely cause some problems.

Even if you aren’t a conservation biologist, the above common knowledge has likely permeated into your scientific life at some level. What conservation biologists plan to do about it likely has not.

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Mixed modeling of methylation measures (increase your power by 60%)

Do you want to increase your power to detect differentially methylated CpG sites by 60%*? Yes?! Then do I have the pre-print for you. Continue reading

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marmap

A couple years ago, Benoit Simon-Bouhet ended up sharing an office with Eric Pante, then a post-doc fellow in his former lab. The two quickly realized they were in a lab in which few people had the expertise or taste for coding. Thus, on a daily basis, they were both approached by colleagues and students to take a look at their data analysis and graphics. Meanwhile, they had their own not-so-easy tasks of creating publication-quality maps for themselves as well as their colleagues. They both had bits and pieces of R scripts scattered around their hard drives to (i) import bathymetric data previously downloaded locally from public databases, (ii) reshape these data in a form suitable for plotting in R and (iii) plot the bathymetry together with other data such as sampling sites or other locations of interest. The process was tedious, convoluted (especially for the manually download online bathymetric data) and required a good knowledge of the R scripting langage. In order to ease this process, the two embarked on creating marmap (short for marine maps) …

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Dōmo arigatō

Along with my collaborators, Erik Sotka, Courtney Murren, Allan Strand and our battery of students, we have embarked on an intense summer field season. Erik and I are leading the effort of sampling populations of the introduced red seaweed Gracilaria vermiculophylla. It is native to the northwest Pacific, but has been introduced to every continental margin in the Northern Hemisphere in the last few decades.

To date, studies on marine invasions focus principally on demographic and ecological processes, and the importance of evolutionary processes has been rarely tested. Moreover, there are surprisingly few studies that compare native and non-native populations in their biology or ecology. Our current project integrates population genetics, field surveys and common-garden laboratory experiments to address the role of rapid evolutionary adaptation in invasion success.

The weed that launched a massive collaborative project tracings its evolution during invasion

The weed that launched a massive collaborative project tracings its evolution during invasion

For my part, I knew my summer would be filled with a month long sojourn in Japan, with short trips every 10 – 15 days around North America bookended by a month long trip to sample European coastlines with a return to my old haunts in northwestern France.

Alas, Erik’s first leg in Japan (see some photos here) resulted in a mountain (or maybe seamount, see my next post on the R package marmap!) of live algae for culturing and phenotyping! Life became decidedly hurried!

Our students: Paige Bippus (CofC undergrad, Class of '16, middle right), Lauren Lees (CofC undergrad, Class of '17, middle left), Sarah Shainker (CofC undergrad, Class of '16, bottom middle) and Ben Flanagan (CofC GPMB grad student, Class of '17)

Our students: Paige Bippus (CofC undergrad, Class of ’16, middle right), Lauren Lees (CofC undergrad, Class of ’17, middle left), Sarah Shainker (CofC undergrad, Class of ’16, bottom middle) and Ben Flanagan (CofC GPMB grad student, Class of ’17)

No pre-emptive posts were penned … just shepherding our fantastic students into the ins and outs of red algal culturing, while keeping up morale with the endless playlists of Songza (80’s Prom being a particular favorite due to the aptly timed “Turning Japanese” while processing Japanese populations of G. vermiculophylla).

I had spoken with Jeremy about posting field work stories as well as highlighting the research of interest to TME readers from the marine labs we’d be visiting throughout the summer. Yet, once again, time did not allow for live posts while in country … so over the next few weeks, I’ll be posting some field anecdotes as well as a description of the different places we had the opportunity and good fortune to visit.

We are celebrating our Independence Day in the US this weekend, so I’ll leave all of you with a few pictures for the long holiday weekend! As well as a massive thank you to all of our hosts in Japan who made this a hugely successful as well as a once in a lifetime trip!

Kelp drying in Muroran, Hokkaido, Japan

Kelp drying in Muroran, Hokkaido, Japan

The tale of an urchin and an anemone

The tale of an urchin and an anemone

Erik Sotka, Rob Hadfield (my partner in crime and in the field in Japan!) and me at one field site in Akkeshi, Hokkaido, Japan

Erik Sotka, Rob Hadfield (my partner in crime in life and in the field in Japan!) and me at one field site in Akkeshi, Hokkaido, Japan

Benten-jinja Shrine in Akkeshi-ko

Benten-jinja Shrine in Akkeshi-ko

Marimo from Akan-ko

Marimo from Akan-ko

Fushimi Inari-taisha in Kyoto

Fushimi Inari-taisha in Kyoto

Kimono

Kimono

Dinner with one of our hosts, Dr. Masahiro Nakaoka in Kimitsu

Dinner with one of our hosts, Dr. Masahiro Nakaoka, in Kimitsu

Dōmo arigatō!

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Societal constructs, and Genetic diversity

While we grapple with numerous discoveries of variation in genomic diversity in humans, interest has subsequently risen in understanding their causes/results. Two recent papers describe experiments to determine (a) the effects of marital rules (who gets to marry whom) on genomic diversity (Guillot et al. 2015), and (b) the correlations between effectively random-mating, and inbreeding human populations and various health-related quantitative traits (Joshi et al. 2015).

Sums of Runs of Homozygosity (SROH) shown as a function of cohorts of human populations. Figure courtesy: Fig. 1 from Joshi et al. (2015) http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature14618_F1.html

Sums of Runs of Homozygosity (SROH) shown as a function of cohorts of human populations. Figure courtesy: Fig. 1 from Joshi et al. (2015) http://www.nature.com/nature/journal/vaop/ncurrent/fig_tab/nature14618_F1.html

Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity, Guillot et al. Molecular Biology and Evolution, 2015.

Marital rules – societal constructs on who marries whom are predominant in several human populations. Biologically, one would hypothesize that these rules also influence genetic diversity of the population, and thus the fitness of offspring. Guillot et al. (2015) attempt via simulations, and analyses of SNP diversity in an Indonesian population to quantify relaxed, or strict adherence to these rules, particularly the MBD rule (or Mother’s Brother’s Daughter) wherein men are required to marry their mother’s brother’s daughter. Key findings of the study include (a) strict MBD marital rules lead to a reduction in genomic diversity under simulations, (b) non-adherence of strict MBD rules in the Rindi community in Eastern Indonesia, an island population in which marital rules have been extensively studied.

Certainly, reduced genetic diversity under a strict interpretation of the APA marriage rules suggests that there was little biological incentive for communities to enforce marriage rules strongly, at least for long periods of time.

Directional dominance on stature and cognition in diverse human populations, Joshi PK et al. Nature, 2015.

While the detrimental effects of inbreeding (and marital rules like in Guillot et al. above) have been extensively studied in Mendelian traits in humans, most fitness traits are complex, and polygenic. Joshi et al. (2015) as part of the ROH (Runs of Homozygosity) consortium investigate 16 quantitative traits that have fitness consequences in humans and their correlations with homozygosity. Analyses of SNP arrays for ROH in more than 300,000 individuals revealed (a) differences in ROH lengths, and demography (with African populations containing the least homozygosity, and isolated populations, including Amish, and Hutterites containing the most homozygosity), (b) an average reduction of 1.2 cm in height, and 137 ml in forced expiratory volumes in offspring of first cousins, (c) 0.3 standard deviations reduction in general cognitive ability, and 10 months’ reduction in educational attainment in offspring of first cousins, and (d) no significant effect in 12 other fitness related traits (particularly to do with cardio-metabolism).

We have demonstrated the existence of directional dominance on four complex traits (stature, lung function, cognitive ability and educational attainment), while showing any effect on another 12 health-related traits is at least almost an order of magnitude smaller, non-linear or non-existent.

References:

Joshi, Peter K., et al. “Directional dominance on stature and cognition in diverse human populations.” Nature (2015) DOI:10.1038/nature14618

Guillot, Elsa G., et al. “Relaxed observance of traditional marriage rules allows social connectivity without loss of genetic diversity.” Molecular biology and evolution (2015). DOI: 10.1093/molbev/msv102

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Understanding amphibian disease inside out

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A Common Frog (Rana temporaria) – Photo by Bernie Kohl

In the spring of 2010, I was doing amphibian surveys among a few wetlands in Eastern Kentucky that were known for their excellent diversity. As I sauntered up to a familiar study site, I was greeted with an amphibian massacre. Hundreds of dead tadpoles floated on the surface of the wetland, creating a raft of amphibian biomass unlike anything I’d ever seen.

I was stunned. What happened? Continue reading

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Gene expression analysis- are we doing it wrong?

In the last few weeks, three new preprints have come out suggesting that like Jack Butler dropping his kids off at school in the movie Mr. Mom, when it comes to differential gene expression analyses, we’re doing it wrong. Continue reading

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The Kennewick, and the Oase I

Last week was glorious for ancient DNA enthusiasts – here are some quick blurbs on findings from genomic analyses of the Kennewick man, and the Oase I individual.

Facial reconstructions of the Oase I individual (L), and the Kennewick man (R). Image courtesies: The Smithsonian Magazine  (http://thumbs.media.smithsonianmag.com//filer/51/9f/519fea8a-a215-48fe-ba09-fae09a0bb3e3/kennewick-hero.jpg__800x600_q85_crop.jpg), Dons Maps (http://donsmaps.com/romaniancaveskull.html)

Facial reconstructions of the Oase I individual (L), and the Kennewick man (R). Image courtesies: The Smithsonian Magazine (http://thumbs.media.smithsonianmag.com//filer/51/9f/519fea8a-a215-48fe-ba09-fae09a0bb3e3/kennewick-hero.jpg__800x600_q85_crop.jpg), Dons Maps (http://donsmaps.com/romaniancaveskull.html)

The ancestry and affiliations of Kennewick Man, Rasmussen et al. (2015) Nature DOI: 10.1038/nature14625

There has been much ado over the ancestry of the Kennewick Man – carbon-dating studies have dated his remains to ~8,500 ybp, morphological studies maintain distinction from Native American (Pacific Northwestern) ancestry, and teams of scientists and tribes battle on over the impending fate of the remains. Rasmussen et al. (2015) in an interesting turn of events, analyze genomic ancestry of the Kennewick man, and find clear evidence of Native American ancestry using both a PCA, and f3-statistics. Important findings of this study include: (a) rejection of Ainu/Polynesian ancestry of the Kennewick man, as suggested by morphological studies, (b) similarity in admixture proportions to Native American, particularly among claimant tribes, and (c) direct or derivative ancestry of current Native Americans from the Kennewick man. While this answers some questions about the ancestry of the Kennewick man, it also brings forth unaddressed details of ancestral admixture, and migration in Holocene Americas.

Identifying which modern Native American groups are most closely related to Kennewick Man is not possible at this time, since our comparative DNA database of modern people is limited, particularly for Native American groups in the United States.

An early modern human from Romania with a recent Neanderthal ancestor, Fu et al. (2015) Nature DOI: 10.1038/nature14558

Meanwhile, in a much more distant past, the Kennewick man’s ancestors were still diversifying out of Africa, admixing with Neanderthals around 37,000-86,000 ybp, with little knowledge of the process of admixture, or understanding of Neanderthal extinction. Fu et al. (2015) analyze ancient genomic DNA from the Oase I individual, one of the oldest modern human remains yet discovered to report 6.0% -9.4%  Neanderthal ancestry. In comparison with the Ust’-Ishim, Kostenki, and modern Chinese and European individuals, the Oase I individual contains 2-4 fold higher Neanderthal alleles. Analysis of IBD segment lengths (i.e. identical segments, unbroken by recombination) also indicates that the Neanderthal admixture occurred within 4-6 generations ancestral to the Oase I individual.

However, the absence of a clear relationship of the Oase 1 individual to later modern humans in Europe suggests that he may have been a member of an initial early modern human population that interbred with Neanderthals but did not contribute much to later European populations

References:

Rasmussen, Morten, et al. “The ancestry and affiliations of Kennewick Man.”Nature (2015). DOI: 10.1038/nature14625

Fu, Qiaomei, et al. “An early modern human from Romania with a recent Neanderthal ancestor.” Nature (2015). DOI: 10.1038/nature14558

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