Monthly Archives: September 2012

Our paper: An age-of-allele test of neutrality for transposable element insertions not at equilibrium

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[This author post is by Justin Blumenstiel and Casey Bergman on An age-of-allele test of neutrality for transposable element insertions not at equilibrium, available from the arXiv here]

Studies over the past several decades in Drosophila melanogaster have demonstrated that TE insertion alleles in natural populations tend to segregate at low frequency, particularly in regions of the genome that have a high recombination rate where natural selection is most effective. These results have largely supported a model where natural selection acts to remove deleterious TE insertions from the genome.  The prevailing model of why TE insertions are deleterious is that they lead to chromosomal aberrations that occur when dispersed, non-allelic repeated sequences crossover with one another. This model is known as the ectopic recombination model and it has an important feature. Since each new insertion has the potential to recombine with all the other copies in the genome, fitness will go down faster and faster with each new copy. This yields a stable equilibrium in TE copy number.

But, are TEs at equilibrium in natural populations? Genome sequencing studies have shown that the rate of TE proliferation can vary widely over time and any given TE family may demonstrate non-equilibrium “boom and bust” behavior. How do we reconcile studies that assume equilibrium with the fact that we know TE dynamics are not at equilibrium? To deal with this problem, I began developing this model out of a class project with John Wakeley while I was a graduate student over a decade ago. This model arose of some work I published in 200­2 with Hartl and Lozovsky on the age structure of non-LTR elements in D. melanogaster. I wrote this model up for my Ph.D. thesis and presented a preliminary version in a paper with Neafsey and Hartl in 2004, but it sat on the back burner until I reviewed a paper by Bergman and Bensasson in 2007 that showed many TE families in D. melanogaster have recently inserted in the genome and may not be at equilibrium.

Shortly after their paper came out I contacted Casey with the model from my thesis and we decided to push this idea forward as a collaboration, which has taken several a few years to come to fruition (both being busy with other projects and starting our labs). Things started to really move ahead when Miaomiao He in Casey’s lab generated a crucial data set that could be specifically applied to the model – strain-specific presence/absence data for a very large number of TE insertions ascertained from the D. melanogaster genome sequence.  After a few more years with it on simmer, working out several kinks in the mean time (e.g. incorporating host  demography, trying many different methods for estimating the posterior distribution of TE ages), Casey and I finally wrapped it up just as Haldane’s Sieve is starting to hit its stride. I expect that all my papers in the future will be pre-released on arXiv.

I could speak at length on the specific results, but I would just be saying what is already in the abstract. So, I would like to bring up three points for potential conversation.

First, what does it mean for TEs to be at transposition-selection balance when we know different TE families show a signature of “boom and bust” in genome sequences? There may be one way to reconcile this apparent problem. Any particular TE family may in fact not be at transposition-selection balance. For example, the P element, which invaded Drosophila melanogaster only a few decades ago, is hardly at transposition-selection balance. Therefore, one must be careful in using insertion frequencies for P elements to describe general TE dynamics. However, by integrating over all TE families in the genome, one may in fact reach an approximation that might be reasonable for assuming equilibrium transposition-selection balance. But one must be careful of something I call “family ascertainment bias”. Sometimes the most recently activated TEs are the ones easiest to discover and annotate because these ones are easily cloned from insertion mutations or are most frequent in genome sequences.

Second, in this paper, we derive the probability distribution for each individual TE insertion frequency based on its age. We demonstrate that this provides a method for TE insertions that are either positively or negatively selected. In the case where we show allele frequencies are less than expected (i.e. predicted to be negatively selected), many of these are copies that have zero substitutions. In principle, all of these could have inserted one generation before the reference strain was collected for genome sequencing. The inference that selection is acting against these TEs implicitly assumes either: 1) this wasn’t the case for many of these insertions, and the posterior distribution of ages is a good representation of the true age distribution, or 2) it may have been the case, but natural selection has already acted to remove slightly older TEs from the population, therefore making them absent from the genome sequence.

Third, when putting the finishing touches on our analysis of TE insertion data in North America, we ran up against the issue that nobody has yet published an explicit demographic scenario for North American populations of D. melanogaster, similar to those that have been developed by Wolfgang Stephan‘s Lab and others for European and African populations. We found one paper by Yukilevich et al (2010) from John True’s Lab that generated similar findings to the demography of European populations, which is consistent with the idea that North America populations of D. melanogaster are mainly derived from European ancestors.  However, Yukilevich et al (2010) didn’t explicitly model the admixture with African populations, which is known to occur in North American populations as shown by Caracristi and Schlötterer in 2003. We were surprised that an explicit admixture scenario has not been published yet, especially since this is crucial for interpreting the data from population genomic projects like the Drosophila Genetic Reference Panel. This should be an important line of work for someone to pursue (if it isn’t being done already) and if anyone has information about this a demographic model for North American populations of D. melanogaster, we’d be keen to know more so we can see if might improve our analysis.

Justin and Casey

Genomic tests of variation in inbreeding among individuals and among chromosomes

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Genomic tests of variation in inbreeding among individuals and among chromosomes

Joshua G. Schraiber, Stephannie Shih, Montgomery Slatkin
(Submitted on 26 Sep 2012)

We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about inbreeding when a relatively small set of whole-genome sequences is available. Rather than focus on testing for deviations from Hardy-Weinberg genotype frequencies at each site, we analyze the entire distribution of heterozygotes conditioned on the number of copies of the derived (non-chimpanzee) allele. Using Levene’s exact test, we reject Hardy-Weinberg in both populations. We generalized Levene’s distribution to obtain the exact distribution of the number of heterozygous individuals given that every individual has the same inbreeding coefficient, F. We estimated F to be 0.0026 in Europeans and 0.0005 in Yorubans, but we could also reject the hypothesis that F was the same in each individual. We used a composite likelihood method to estimate F in each individual and within each chromosome. Variation in F across chromosomes within individuals was too large to be consistent with sampling effects alone. Furthermore, estimates of F for each chromosome in different populations were not correlated. Our results show how detailed comparisons of population genomic data can be made to theoretical predictions. The application of methods to the Complete Genomics data set shows that the extent of apparent inbreeding varies across chromosomes and across individuals, and estimates of inbreeding coefficients are subject to unexpected levels of variation which might be partly accounted for by selection.

Protein function influences frequency of encoded regions containing VNTRs and number of unique interactions

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Protein function influences frequency of encoded regions containing VNTRs and number of unique interactions

Suzanne Bowen
(Submitted on 25 Sep 2012)

Proteins encoded by genes containing regions of variable number tandem repeats (VNTRs) are known to be polymorphic within species but the influence of their instability in molecular interactions remains unclear. VNTRS are overrepresented in encoding sequence of particular functional groups where their presence could influence protein interactions. Using human consensus coding sequence, this work examines if genomic instability, determined by regions of VNTRs, influences the number of protein interactions. Findings reveal that, in relation to protein function, the frequency of unique interactions in human proteins increase with the number of repeated regions. This supports experimental evidence that repeat expansion may lead to an increase in molecular interactions. Genetic diversity, estimated by Ka/Ks, appeared to decrease as the number of protein-protein interactions increased. Additionally, G+C and CpG content were negatively correlated with increasing occurrence of VNTRs. This may indicate that nucleotide composition along with selective processes can increase genomic stability and thereby restrict the expansion of repeated regions. Proteins involved in acetylation are associated with a high number of repeated regions and interactions but a low G+C and CpG content. While in contrast, less interactive membrane proteins contain a lower number of repeated regions but higher levels of C+G and CpGs. This work provides further evidence that VNTRs may provide the genetic variability to generate unique interactions between proteins.

Our paper: Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution

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This guest post is by Daniël Melters [@DPMelters] and Keith Bradnam [@kbradnam] on their paper [along with co-authors]: Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution. ArXived here.

The centromere poses an interesting paradox; although its function is essential, its molecular components are fast evolving. Centromeres in many animal and plant genomes have been characterized by the presence of large tandem repeat arrays. Numerous studies have suggested that the composition and length of the repeat units that comprise these arrays vary between species.
In this paper we tried to answer three main questions:
1) Can we identify the candidate centromere repeat sequences in genomes from hundreds of different species?
2) Do candidate centromere repeat sequences from different species share any common properties (sequence composition, length, GC% etc)?
3) How do these tandem repeats evolve?
To answer these questions, we took advantage of the large number of species with publicly available whole genome shotgun sequence data from various sequencing platforms. In total we analyzed 282 animal and plant genomes for the presence of high copy tandem repeat sequences, with the assumption that the most abundant tandem repeat is a good candidate for the centromere repeat.

We found high copy tandem repeats in the vast majority of the 282 genomes that we analyzed. For the smaller number of species with published cytology data, we correctly identified the published repeat sequence in 38 out of 43 cases. This confirms our assumption that the most abundant tandem repeat in any genome is likely to be the centromere repeat. In the five cases were we did not find the published centromere tandem repeats, we did not have data from sequencing platforms that would have allowed us to identify these repeats.

If an individual sequencing read contains at least four tandem repeats, then there is the possibility of detecting higher order repeat (HOR) structure. I.e. where a tandem array is made up of two alternating types of related sequence (A and B) to produce an A->B->A->B structure. In these cases, the AB dimer is more similar to other AB dimers, than A is to B. We found that HOR structure was surprisingly common in the candidate centromere repeats of many different species. The very long reads from Pacific Biosciences (PacBio) sequencing allowed us to further characterize repeat structure in great detail (for a few selected species), and this revealed additional levels of HOR structure.

To address the important question of ‘how similar are centromere repeats in different species?’, we performed an all-vs-all comparison between the most abundant tandem repeat in every species. Surprisingly, we found only 26 groups of species that shared any significant sequence similarity in their candidate centromere repeat sequence. The species that make up these 26 groups were always closely related species which had diverged less than 50 million years ago. When comparing the repeat sequences in these groups of closely related species, we found that repeats evolve not only by accumulation of mutations, but also by the spread of indels or by repeat doubling.

These results are in line with the ‘library’ hypothesis, which aims to describe how ratios of repeat variants can change over time. In addition, PacBio sequencing found very long tandem repeats (~1,500 bp). Furthermore, in switchgrass (Panicum virgatum) we identified several centromere repeat variants, but PacBio sequences did not show any mixing of these repeat variants. In summary, tandem repeats are frequently associated with the centromere function and most probably evolve according to the “library” hypothesis (a.k.a. molecular drive).

This paper is dedicated to the late Simon Chan, who passed away on the 22nd of August 2012 at the young age of 38 (see here for more infomation).

Daniël Melters and Keith Bradnam
PS. Supplementary table can be provided upon email request.

Diversity and abundance of the Abnormal chromosome 10 meiotic drive complex in Zea mays

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Diversity and abundance of the Abnormal chromosome 10 meiotic drive complex in Zea mays
Lisa B. Kanizay, Tanja Pyhäjärvi, Elizabeth G. Lowry, Matthew B. Hufford, Daniel G. Peterson, Jeffrey Ross-Ibarra, R. Kelly Dawe
(Submitted on 25 Sep 2012)

Maize Abnormal chromosome 10 (Ab10) contains a classic meiotic drive system that exploits asymmetry of meiosis to preferentially transmit itself and other chromosomes containing specialized heterochromatic regions called knobs. The structure and diversity of the Ab10 meiotic drive haplotype is poorly understood. We developed a BAC library from an Ab10 line and used the data to develop sequence-based markers, focusing on the proximal portion of the haplotype that shows partial homology to normal chromosome 10. These molecular and additional cytological data demonstrate that two previously identified Ab10 variants (Ab10-I and Ab10-II) share a common origin. Dominant PCR markers were used with FISH to assay 160 diverse teosinte and maize landrace populations from across the Americas, resulting in the identification of a previously unknown but prevalent form of Ab10 (Ab10-III). We find that Ab10 occurs in at least 75% of teosinte populations at a mean frequency of 15%. Ab10 was also found in 13% of the maize landraces, but does not appear to be fixed in any wild or cultivated population. Quantitative analyses suggest that the abundance and distribution of Ab10 is governed by a complex combination of intrinsic fitness effects as well as extrinsic environmental variability.

Announcement: Genetics prepublication policy

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This guest post is by Chuck Langley on the policy of Genetics on preprint servers.

The journal GENETICS promulgates a formal new policy on prepublication.

Population genetics continues to be a prized element of the editorial purview of GENETICS. Creating value for and servicing this critical constituency is a high and ongoing goal of the editorial board and staff. The increasing use of preprint archives by our community and the perceived value of early, unfettered communication to the advancement of research prompted the GENETICS editors to adopt a policy that enables authors to submit drafts of manuscripts to preprint archives (such as arXiv) before or during the period that the manuscript is under review at GENETICS. In line with the journal’s role in scientific publishing, GENETICS asks two things of the authors: 1) the accepted version of a manuscript should not be submitted to an archive; GENETICS has an efficient “early access” mechanism via its website that makes the manuscript freely accessible within 2 weeks of its acceptance; 2) upon final publication in GENETICS, authors should insert a journal reference (including DOI), and link to the published article on the GENETICS website, and include the acknowledgment: “The published article is available at www.genetics.org.” For help with these simple updates to arXiv.org submissions, see here for details. Questions and comments on this and other journal policies can be directed to the Editor in Chief (Mark Johnston), the Executive Editor (Tracey DePellegrin Connelly) or any other member of the Editorial Board. Please submit your best work for publication in GENETICS, the peer-edited journal of the Genetics Society of America.

C.H. Langley

Non-stationary patterns of isolation-by-distance: inferring measures of genetic friction

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Non-stationary patterns of isolation-by-distance: inferring measures of genetic friction

Nicolas Duforet-Frebourg, Michael G. B. Blum
(Submitted on 24 Sep 2012)

The pattern of isolation-by-distance arises when population differentiation increases with increasing geographic distances. This pattern is usually caused by local spatial dispersal which explains why differences of allele frequencies between populations accumulate with distance. However, the pattern of isolation-by-distance can mask complex variations of demographic parameters. Spatial variations of demographic parameters such as migration rate or population density generate non-stationary patterns of isolation-by-distance where the rate at which genetic differentiation accumulates varies across space. Barriers to gene flow are particularly well studied examples that generate non-stationary patterns of isolation-by-distance. Using the concept of genetic friction, we develop a statistical method that characterizes non-stationary patterns of isolation-by-distance. Genetic friction at a sampled site corresponds to the local genetic differentiation between the sampled population and fictive populations living in the neighborhood of the sampling site. To avoid defining populations in advance, the method can also be applied at the scale of individuals. The proposed framework is appropriate for dealing with massive data because it relies on a pairwise similarity matrix, which can be obtained with computationally efficient methods. A simulation study shows that maps of genetic friction can detect barriers to gene flow but also other patterns such as continuous variations of gene flow across habitat. The potential of the method is illustrated with 2 data sets: genome-wide SNP data for the human Swedish populations, and AFLP markers for alpine plant species. The software FRICTION implementing the method is available at this http URL

Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution

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Towards the Recapitulation of Ancient History in the Laboratory: Combining Synthetic Biology with Experimental Evolution

Betul Kacar, Eric Gaucher
(Submitted on 23 Sep 2012)

One way to understand the role history plays on evolutionary trajectories is by giving ancient life a second opportunity to evolve. Our ability to empirically perform such an experiment, however, is limited by current experimental designs. Combining ancestral sequence reconstruction with synthetic biology allows us to resurrect the past within a modern context and has expanded our understanding of protein functionality within a historical context. Experimental evolution, on the other hand, provides us with the ability to study evolution in action, under controlled conditions in the laboratory. Here we describe a novel experimental setup that integrates two disparate fields – ancestral sequence reconstruction and experimental evolution. This allows us to rewind and replay the evolutionary history of ancient biomolecules in the laboratory. We anticipate that our combination will provide a deeper understanding of the underlying roles that contingency and determinism play in shaping evolutionary processes.

Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution

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Comparative Analysis of Tandem Repeats from Hundreds of Species Reveals Unique Insights into Centromere Evolution

Daniël P. Melters, Keith R. Bradnam, Hugh A. Young, Natalie Telis, Michael R. May, J. Graham Ruby, Robert Sebra, Paul Peluso, John Eid, David Rank, José Fernando Garcia, Joseph L. DeRisi, Timothy Smith, Christian Tobias, Jeffrey Ross-Ibarra, Ian F. Korf, Simon W.-L. Chan
(Submitted on 22 Sep 2012)

Centromeres are essential for chromosome segregation, yet their DNA sequences evolve rapidly. In most animals and plants that have been studied, centromeres contain megabase-scale arrays of tandem repeats. Despite their importance, very little is known about the degree to which centromere tandem repeats share common properties between different species across different phyla. We used bioinformatic methods to identify high-copy tandem repeats from 282 species using publicly available genomic sequence and our own data. The assumption that the most abundant tandem repeat is the centromere DNA was true for most species whose centromeres have been previously characterized, suggesting this is a general property of genomes. Our methods are compatible with all current sequencing technologies. Long Pacific Biosciences sequence reads allowed us to find tandem repeat monomers up to 1,419 bp. High-copy centromere tandem repeats were found in almost all animal and plant genomes, but repeat monomers were highly variable in sequence composition and in length. Furthermore, phylogenetic analysis of sequence homology showed little evidence of sequence conservation beyond ~50 million years of divergence. We find that despite an overall lack of sequence conservation, centromere tandem repeats from diverse species showed similar modes of evolution, including the appearance of higher order repeat structures in which several polymorphic monomers make up a larger repeating unit. While centromere position in most eukaryotes is epigenetically determined, our results indicate that tandem repeats are highly prevalent at centromeres of both animals and plants. This suggests a functional role for such repeats, perhaps in promoting concerted evolution of centromere DNA across chromosomes.

Chimeric protein complexes in hybrid species generate novel evolutionary phenotypes

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Chimeric protein complexes in hybrid species generate novel evolutionary phenotypes
Elzbieta M. Piatkowska, David Knight, Daniela Delneri
(Submitted on 19 Sep 2012)
Hybridization between species is an important mechanism for the origin of novel lineages and adaptation to new environments. Increased allelic variation and modification of the transcriptional network are the two recognized forces currently deemed to be responsible for the phenotypic properties seen in hybrids. However, since the majority of the biological functions in a cell are carried out by protein complexes, inter-specific protein assemblies therefore represent another important source of natural variation upon which evolutionary forces can act. Here we studied the composition of six protein complexes in two different Saccharomyces “sensu strictu” hybrids, to understand whether chimeric interactions can be freely formed in the cell in spite of species-specific co-evolutionary forces, and whether the different types of complexes cause a change in hybrid fitness. The protein assemblies were isolated from the hybrids via affinity chromatography and identified via mass spectrometry. We found evidence of spontaneous chimericity for four of the six protein assemblies tested and we showed that different types of complexes can cause a variety of phenotypes in selected environments. In the case of TRP2/TRP3 complex, the effect of such chimeric formation resulted in the fitness advantage of the hybrid in an environment lacking tryptophan, while only one type of parental combination of the MBF complex could confer viability to the hybrid under respiratory conditions. This study provides empirical evidence that chimeric protein complexes can freely assemble in cells and reveals a new mechanism to generate phenotypic novelty and plasticity in hybrids to complement the genomic innovation resulting from gene duplication. The ability to exchange orthologous members has also important implications for the adaptation and subsequent genome evolution of the hybrids in terms of pattern of gene loss.