sedaDNA sleuths: embracing your inner Sherlock

Posted on 6 Mar, 2015 by Stacy Krueger-Hadfield

Awhile back fellow TME contributor Rob Denton posted about a recent review on environmental DNA by Pedersen et al. (2015).
Environmental DNA (eDNA) is obtained from samples such as sediments, ice or water and can provide scientific sleuths with tantalizing clues about past and present biodiversity.

© BBC

© BBC


Smith et al. (2015) used sealed sediment cores to combine evidence from microgeomorphology, microfossils and sedimentary ancient DNA (sedaDNA) to reconstruct the biotic changes that occurred during the occupation of the present day Isle of Wight during the Mesolithic to Neolithic transition in which a hunter-gather economy was replaced by agriculture.
Sequence data is traditionally reliant upon discrete sources of material that has come from an individual plant or animal. But, individual plants and animals also leave behind extracellular DNA in the environment.
By using ancient DNA, Smith et al. (2015) detected DNA sequences associated with wheat as well as the proportion of these sequences in the plant profile increased as the soil samples were extracted from sedimentary layers closer to the present day.
As highlighted by Larson (2015), the methodology and results from studies like these are intriguing for arm-chair time traveling, but go beyond that in potentially challenging the chronology of historical events and tracing the dispersal of plants and animals.
References
 Larson G (2015) How wheat came to Britain. Science 347 (6225): 945-946
Pedersen MW (2015). Ancient and modern environmental DNA, Philosophical Transactions of the Royal Society B: Biological Sciences, 370 (1660) 20130383
Smith O et al. (2015) Sedimentary DNA from a submerged site reveals wheat in the British Isles 8000 years ago. Science 347 (6225): 998-1001

Posted in bioinformatics, domestication, genomics, natural history, next generation sequencing, Paleogenomics | Tagged , , , | 1 Comment

dN(eutralist) > dS(electionist)? Part 2

Posted on 5 Mar, 2015 by Arun Sethuraman

Last week’s post dealt with the debate over differences in the efficacy of purifying selection across human genomes. This week, we’ll look at the differences in de novo mutation rates across populations. The human de novo mutation rate has gone through a lot of recalibrations over the last few years (2.5 x 10-8 mutations per nucleotide per generation – Nachman and Crowell (2000) to 1.2 x 10-8 mutations per nucleotide per generation – Scally and Durbin (2012), Campbell et al. (2012), etc.), with plenty of variation with types of loci, male versus female germlines, and mutation types.
The de novo mutation rate is influenced by environmental changes resulting in DNA damage. The extent to which these de novo mutations arise, and are maintained in a population are also intertwined with (a) the population’s demography, and (b) the selection regimes at these mutated, and linked loci. A comprehensive study of de novo mutations (compared to the ancestral population) that are fixed (also called ‘private alleles’) in a population, but are still segregating in a third population should thus reveal the local dynamics of novel mutations.

harris

Overrepresentation of TCC->TTC within Europe, Figure 1 from Harris (2015) – http://dx.doi.org/10.1073/pnas.1418652112


Harris (2015) in a recent study of the variation in the frequencies of de novo mutations across the Phase 1 of the 1000 Genome Project data reports elevated mutation rates of a certain class (TCC->TTC) of non-synonymous substitutions in Europeans, when compared to Asians and Africans, which have often been linked to UV related damage. Noticeably, this also coincides with the evolution of lighter skin in Europeans after diversification outside of Africa, although no direct correlates (or positive selection for this class of mutations) between the two phenomena have been established or studied. In general, her results indicate (1) elevated C->T transitions in all Europeans, particularly in a class of TCC->TTC, (2) this ‘change’ in mutation rate occurred in the common ancestor of all Europeans, after divergence out of Africa, but prior to diversification inside Europe, around 25,000-60,000 ybp, (3) the non-bioinformatic (i.e. not due to erroneous detection methods) cause of this observation, and (4) a bias in transcription-coupled repair mechanism in “correcting” this class of mutations in European populations.
Some interesting questions arise as a consequence of these results, which feed well into our continuing debate about the dynamics of novel mutations.

  • Seeing that the (1) elevated levels of TCC->TTC mutations in Europeans occurred as a result of some environmental change (here excessive UV damage), (2) there is a bias in the transcription-coupled repair mechanism in correcting these mutations in Europeans, and (3) that these mutations are fixed in the population, one would surmise that this is a definitive consequence of the demography on European populations?
  • The observation that there isn’t any difference in the efficacy of purifying selection across Europeans, and Asians (as reported by Do et al. (2015)), is conditional on the same mutation rate across Europeans and Asians, which as Harris reports, isn’t true across all classes of loci. So perhaps demography (say a population bottleneck, or expansion) did play a role in the efficacy of purifying selection after all?

Feel free to add your comments!
References:
Harris, K. Evidence for recent, population-specific evolution of the human mutation rate, Proceedings of the National Academy of Sciences, DOI:http://dx.doi.org/10.1073/pnas.1418652112

Posted in evolution, mutation, theory | Tagged , , , | Leave a comment

Toying with eigenvectors

Posted on 4 Mar, 2015 by Rob Denton

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There are few things I enjoy more than when someone takes the time to clearly communicate a complex idea. The whole “you don’t know it until you teach it” phenomenon gives me the utmost respect for those who put effort into bridging the gap to us non-experts. Oftentimes, the clearest way to communicate something complex is visually, and I want to share a cool example with you:
Eigenvectors and eigenvalues: explained visually by Victor Powell and Lewis Lehe
We use eigenvector-based linear algebra for a multitude of analyses in molecular ecology, from the types of clustering analyses offered by adegenet (PCA, CCA, DPCA, YMCA?, ASPCA?) to the estimation of phylogenetic signal. If you stared as hopelessly as I did at the chalk board during undergraduate math courses, learning what the heck an eigenvalue is could have been an uphill battle. If only I would have had these arrows to move around!
Bonus: you can also check out modules on Principal Components and Markov Chains! I know you can’t resist a good Markov Chain.

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Behavioral individuality reveals genetic control of phenotypic variability

Posted on 3 Mar, 2015 by Noah Snyder-Mackler

High-throughput measure of drosophila "handedness" ; from Buchanan et al (2014), doi:10.1101/008565;

High-throughput measure of drosophila “handedness”. From Buchanan et al (2014), doi:10.1101/008565


Studies of animal personality (or, “behavioral syndromes”, if you choose your words carefully) are so hot right now. One of the assumptions of such studies is that natural selection has somehow favored this behavioral variability/plasticity (and not just differences in means across genotypes). To date, however, no studies have shown a genetic basis underlying such intragenotypic phenotypic variability. Well, no studies until now…
Continue reading →

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Sometimes selection gives you more bang for your buck

Posted on 2 Mar, 2015 by Melissa DeBiasse

Sydney rock oysters on the half shell. Photo from Time Out Sydney www.au.timeout.com

Sydney rock oysters on the half shell. Photo from Time Out Sydney www.au.timeout.com


Most species experience many environmental stressors simultaneously which means the direction and magnitude of evolutionary responses will depend on trade-offs between traits whose relationship may prevent them from being simultaneously optimized. Multiple sources of stress may act in opposing ways, for example an increase in salinity tolerance may come at the expense of thermal tolerance, or selection for a particular trait may results in other beneficial changes (adaptive or non-adaptive) in other traits.
Parker et al. (2011) found that Sydney rock oyster larvae selectively bred for fast growth and disease resistance (desirable traits for an economically important, aquaculture species) were more resilient against ocean acidification (OA, i.e. high pCO2 / low pH) than wild type oysters.

[T]he negative impact of exposure to elevated pCO2 on larval shell growth, development and overall survival was significantly lower in S. glomerata bred for disease resistance and fast growth when compared to non-selected ‘wild type’ oysters. Most significantly, it was demonstrated that exposing adults from the S. glomerata selective breeding lines to elevated pCO2 during reproductive conditioning further increased the CO2 tolerance of their larvae.

In a recent Molecular Ecology paper, Thompson et al. used proteomics to test for molecular differences between adult wild type and selectively bred Sydney rock oysters exposed to experimental high pCO2 conditions. They found that the proteomes of the adult oysters changed substantially under OA conditions and that responses varied between the selectively bred and wild type populations. Under high pCO2, the wild type population had an increase in expression of proteins involved in an inducible stress response. However, the selectively bred oysters downregulated these genes and performed poorly under OA.

We argue that this reflects a tradeoff, whereby an adaptive capacity for enhanced mitochondrial energy production in the selectively bred population may help to protect larvae from the effects of elevated CO2, whilst being deleterious to adult oysters.

References:

Parker, L. M., Ross, P. M., Raftos, D., Thompson, E., & O’Connor, W. A. (2011). The proteomic response of larvae of the Sydney rock oyster, Saccostrea glomerata to elevated pCO2. Australian Zoologist, 35(4), 1011-1023. DOI: 10.7882/AZ.2011.056

 
Thompson, E. L., O’Connor, W., Parker, L., Ross, P., & Raftos, D. A. (2015). Differential proteomic responses of selectively bred and wild Sydney rock oyster populations exposed to elevated CO2. Molecular Ecology. DOI: 10.1111/mec.13111

Posted in adaptation, evolution, proteomics | Leave a comment

Just like an elephant and a manatee …

Posted on 27 Feb, 2015 by Stacy Krueger-Hadfield

© evolgen at scienceblogs.com

© evolgen at scienceblogs.com


There is a positive correlation between the time since two lineages have diverged and the strength of the reproductive barriers between them.
Rothfels et al. (2015) have described a natural hybridization event between two fern genera that diverged from one another approximately 60 million years ago. This is an incredibly deep hybridization event,

roughly akin to an elephant hybridizing with a manatee or a human with a lemur.

In animals and flowering plants, reproductive barriers evolve quickly, such that species are incompatible after several millions of years. Yet, a fern found in the French Pyrenees was morphologically intermediate between two genera that were even placed in different families (Rothfels et al. 2012, 2015).
The fern, now called xCystocarpium roskamianum is infertile, but grows

vigorously via rhizome growth and does well in cultivation.

This new study

provides a new upper limit for the length of time it may take before reproductive barriers are complete, in this case, a cumulative total of approximately 120 million years of independent evolution (60 million years for each parent lineage).

This is the deepest natural hybridization event yet documented in plants or animals. In other words, both pre-zygotic and post-zygotic barriers have remained incomplete for a really long time!
Ferns have free-living haploid and diploid stages, both of which are multicellular. They may have

greater developmental robustness to variations of dosage and gene-gene interactions. … Particularly useful would be a series of laboratory crosses of ferns and other nonflowering plants to investigate the strength of viability isolation across a range of evolutionary depths in these groups.

What is really interesting is that the pattern of slower evolution of reproductive isolation in groups that are characterized by abiotic gamete dispersal (e.g., wind or water) implicates the operation of selection at levels other than the individual.

One reason we live in a world with more than 250,000 species of flowering plants but only around 10,000 fern species (and approximately 1,000 gymnosperms, 1,200 lycophytes, 12,000 mosses, 9,000 liverworts, and 100 hornworts) may just be that populations of non-flowering lineages take longer to achieve complete genetic separation from one another because the have fewer mechanisms to prevent the sperm of one species from encountering the egg of another.

References
Rothfels et al. (2012) A revised family-level classification for eupolypod II ferns (Polypodiidae: Polypodiales). Taxon 61:515–533.
Rothfels et al. (2015) Natural Hybridization between Genera That Diverged from Each Other Approximately 60 Million Years Ago. Am Nat 185: 433-442.

Posted in Coevolution, evolution, natural history, speciation | Tagged , , , | Leave a comment

dN(eutralist) > dS(electionist)? Part 1

Posted on 26 Feb, 2015 by Arun Sethuraman

In a new series of posts, I will now proffer neutralist and selectionist reviews of recent publications. I point readers to an excellent review of the debate by Masatoshi Nei (2005). Besides being a fun exercise in PoV’s, I hope that these posts will prompt some healthy discussions on the state-of-the-science.
First blood – efficacy of purifying selection, prompted by publications I reported on from this post, and another recent publication by Do et al. (2015). I will leave the debate over ‘efficiency’ versus ‘efficacy’ of selection for another day (eg, see this thread).
What is purifying selection?
Simply put, the purging of deleterious (harmful) allelic variants from a population is termed purifying selection. It is also termed negative selection (to signify the sign of the selection coefficient at such alleles).
How is the efficacy of purifying selection measured?
The efficacy of purifying selection depends on at least two major contributors – the selection coefficient (s) of the mutant allele (a measure of its fitness and viability in the population), and the effective population size (Ne – a measure of the amount of drift in the population). A large portion of the neutralist-selectionist debate focused on the contributions of these two factors to molecular evolution as against mutation itself. Consequently, alleles under purifying selection would be expected to have greater levels of synonymous polymorphisms, than non-synonymous polymorphisms (dS > dN), and be maintained in populations (particularly in genes involved in reproductive fitness). Studies that have examined the differences in polymorphisms across modern humans in Africa and Europeans have determined (a) smaller Ne in human populations outside of Africa (bottlenecks), and subsequently (b) lower efficacy of purifying selection in removing weakly deleterious mutant non-synonymous substitutions.
What did Do et al. (2015) do?
They define a statistic called Rx|y which is a ratio of the number of derived mutations that are seen in one genome X, and not in genome Y, to the vice versa. This measures the relative number of mutations accumulated (given that mutation rate is the same across X and Y), compared to an outgroup (here Pan troglodytes), and should be an indicator of the efficacy of purifying selection. If selection has been equally effective, Rx|y should be = 1. Looking across a variety of datasets (exomes, and whole genomes) from West Africans versus Europeans (and through simulations), Do et al. find that Rx|y is “indistinguishable” from 1.

Thus, our data provide no evidence that purging of weakly deleterious mutations has been less effective in Europeans than in West Africans

Supporting the nearly neutral theory, since most of the genome is comprised of alleles segregating neutrally (or nearly neutrally, meaning under very weak balancing selection), the fate of a new mutant allele (and the rate at which selection affects the Rx|y statistic) is determined by drift on two different classes of alleles – non-synonymous and synonymous sites during the course of, and after a population bottleneck (which also supports previous observations of dS > dN in Europeans versus West Africans).

Simulations showing variation of the R statistic versus selection coefficients in modern humans. Figure 2 from Do et al. (2015) - courtesy: http://www.nature.com/ng/journal/v47/n2/full/ng.3186.html?WT.ec_id=NG-201502

Simulations showing variation of the R statistic versus selection coefficients in modern humans. Figure 2 from Do et al. (2015) – courtesy: http://www.nature.com/ng/journal/v47/n2/full/ng.3186.html?WT.ec_id=NG-201502


Analyses of deep sequenced genomes of a Denisovan and Neandertal to estimate the same Rx|y statistic, compared to modern humans showed (a) smaller population sizes in both archaic populations, (b) correspondingly lower levels of genetic diversity in both, but (c) faster accumulation of deleterious mutations in Denisovans than in Neandertals since their divergence, apparently contradicting the observation in modern humans (bottlenecked ancestral populations undergoing an overall depletion of non-synonymous sites, which are affected to a greater degree by purifying selection).
From a selectionist PoV, this implies that a good demographic model (which parametrizes the length of bottlenecks, and a joint distribution of selection and dominance coefficients) is required before denouncing differences in genomic load between populations.
Interested in this debate? Leave your comments below!
References:
Do, Ron, et al. “No evidence that selection has been less effective at removing deleterious mutations in Europeans than in Africans.” Nature genetics (2015). http://dx.doi.org/10.1038/ng.3186
Nei, Masatoshi. “Selectionism and neutralism in molecular evolution.” Molecular biology and evolution 22.12 (2005): 2318-2342. http://dx.doi.org/10.1093/molbev/msi242
Dobzhansky, Theodosius. Genetics of the evolutionary process. Vol. 139. New York: Columbia University Press, 1970.

Posted in evolution, genomics, mutation, population genetics, theory | Tagged , , | 15 Comments

The conservation genomics gap

Posted on 25 Feb, 2015 by Rob Denton

Bakerloo_line_-_Waterloo_-_Mind_the_gap
Is genomic data a boon or a hurdle for conservation? Aaron Shafer and Jochen Wolf take a strong stance on the issue in a newly-published review in Trends in Ecology and Evolution: genomic data could be really useful for conservation, but not until more effort is put into bridging the basic-applied research gap.

Under the premise that assisting conservation of the world’s biota is its ultimate purpose, the emerging field of conservation genomics must openly and pragmatically discuss its potential contribution toward this goal. While there are prominent examples where genetic approaches have made inroads influencing conservation efforts (e.g., Florida panther augmentation [8,9]) and wildlife enforcement (i.e., detecting illegal harvesting [10]), it is not immediately clear that the conservation community and society more broadly have embraced genomics as a useful tool for conservation.

At its core, genomic data provides a drastic increase in the number of potentially informative markers for some of the most fundamental and important components of conservation genetics, such as the estimation of demographic parameters and describing the viability of small populations. On top of that, the promise of identifying adaptive loci offers a huge benefit in prioritizing the conservation of unique populations. But as the authors point out, the interpretations of these analyses are often difficult and the availability of user-friendly analysis pipelines is expectedly lagging behind. And since other novel aspects of genomic data (eDNA and transcriptomics, for example) are still mainly in exploratory phases, where does that leave the actual benefit of genomics to those with conservation questions?

Here, we propose that conservation practitioners are
best served by focusing on broad-scale population genetic patterns that might be relevant to conservation issues of interest. From a practical viewpoint, the difference between three and five migrants per generation is not important, but three versus 500 is.

Shafer et al. describe a conservation genomics gap that is preventing the application of genomic data to conservation problems. And as the technologies associate with sequencing leave the Sanger sequencers of the world to rot, those who aren’t prepared to make the jump may be left behind.

The Conservation Genomics Gap: Figure 1 from Shafer et al. (2015)

The Conservation Genomics Gap: Figure 1 from Shafer et al. (2015)

…advances in genomic methods might contribute to an increasing gap between research and application without a concerted effort on the part of both scientists and conservation practitioners to build effective bridges. Broadly speaking, these gaps can be described in terms of the knowledge, tools (i.e., standardized methods and user-friendly analytical pipelines), finances, and communications needed to link fundamental research with applied science.

The real debate here is one of funding for basic and applied research and the call for “real-world” application of genomics.

However, there is a more systemic problem with the
current state of conservation genomics, in that there is little incentive for academic researchers – whom in many ways lead the conceptual debate and the development of genomic tools vital to application – to engage fully in applied conservation. Applied conservation genomics research is generally not reinforced in current funding schemes and some academic research is branded as conservation (perhaps only as a selling feature for publication), even when it has little real-world conservation value.

Strong words hopefully beget strong discussion and solutions for this problem.
Shafer A.B.A., Paulo C. Alves, Linnea Bergström, Michael W. Bruford, Ioana Brännström, Guy Colling, Love Dalén, Luc De Meester, Robert Ekblom et al.  (2015) Genomics and the challenging translation into conservation practice, Trends in Ecology & Evolution, 30 (2) 78-87. DOI: http://dx.doi.org/10.1016/j.tree.2014.11.009

Posted in conservation, genomics | Tagged | 6 Comments

Bigger on the inside

Posted on 24 Feb, 2015 by Jeremy Yoder
The "universal library" of Interstellar. (Image via.)
The “universal library” of Interstellar. (Image via.)

The Molecular Ecologist receives a small commission for purchases made on Bookshop.org via links from this post.

Evolutionary biology is, fundamentally, the study of how populations of living things change over time. Different creatures live different lives, and at any given point in time they seem to do so relatively well, which poses a question: how do you get from one reasonably well-adapted form to another? At first glance, some of the transformations we see in the fossil record and reconstruct from genetic relationships are incredible. Even over millions of years, can there really be an adaptive path from something that looked like a hyaena to a modern blue whale? From a Tyrannosaurus to a mockingbird? From a lily to a Joshua tree?

Consider some trait related to a critter’s fitness, like the thickness of a bird’s beak. If a small beak is good for collecting small seeds, and a bigger beak is good for cracking big seeds, and there aren’t many seeds of intermediate size in the local environment, maybe the relationship between beak size (the trait) and fitness (the ability to efficiently turn seeds into more birds) looks something like this:

(jby)
(jby)
Continue reading →
Posted in adaptation, book review, evolution, genomics | Tagged , | Leave a comment

This is your brain on Human accelerated regulatory enhancer (HARE5)

Posted on 24 Feb, 2015 by Noah Snyder-Mackler

Pinky and the Brain


Four decades have passed since King and Wilson published their seminal paper “Evolution at Two Levels in Humans and Chimpanzees“. In it, they proposed that the large behavioral and morphological differences between us and our closest relatives, chimpanzees, could not be accounted for by the minimal molecular differences between us at the level of proteins; rather that these behavioral and morphological differences were more likely to be due to changes in mechanisms that regulate the expression of genes.
We’ve come a
long way since then. Continue reading →

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