Category Archives: Population genetics analysis

Our paper: The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

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This guest post is by Detlef Weigel (@WeigelWorld) and Hernán A. Burbano on their arXived paper [with coauthors] Yoshida et al. The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. arXived here and in press at eLife [to appear here].

This paper is the result of a great collaboration between a lab that specializes in ancient DNA (that of Johannes Krause from the University of Tübingen), an expert in pathogen systematics (the group of Marco Thines from the Senckenberg Museum and Goethe University in Frankfurt), two pathogen genomics labs (those of Sophien Kamoun from the Sainsbury Laboratory in Norwich and Frank Martin from the USDA in California), and our evolutionary genomics group at the Max Planck Institute in Tübingen (Hernán A. Burbano and Detlef Weigel).

 

Phytophthora infestans made history when it destroyed large parts of the European potato crop, beginning in 1845. Potato has its origin in the Andes, in the Southeast of modern Peru and Northwest of Bolivia, while the center of diversity of P. infestans is several thousand kilometers further north, in Mexico’s Toluca Valley. There, other Phytophthora species live on a broad range of host plants. At some point in its history, evolutionary events associated with repeat-driven genome expansion [1,2] endowed P. infestans with the genetic arsenal required to infect potato. The pathogen was introduced to Europe in 1845 via infected potato tuber from the United States, where potato blight had made its first appearance in 1843. In the ensuing European blight epidemic, Ireland was hit especially hard, because the virtual absence of independent farmers and a restrictive customs policy conspired with the disease caused by P. infestans, potato blight, to have disproportionately devastating effects. The Great Famine that struck Ireland was a decisive event in both European and American history. One million Irish died of starvation, and at least another million left the country – most of them to the USA.

 

This part of P. infestans history has been clear, but the relationship of the strain(s) that caused the nineteenth century epidemic to modern strains has been controversial. Before a range of genetically quite distinct P. infestans strains made their debut throughout the world some 40 years ago, the global population outside Mexico was dominated by a single strain, called US-1. Because of its prevalence, US-1 was long thought to have been the cause of the fatal outbreak in the nineteenth century. From the analysis of a single SNP in the mitochondrial genome, it was, however, concluded in 2001 that the nineteenth century strains were more closely related to the modern strains that prevail today [3].

 

In our new paper, we resolve this paradoxical view: While the historical pathogen strain, which we call HERB-1, indeed differs at this one position from US-1, which has a derived allele, HERB-1 is far more closely related to US-1 than to other modern strains. Molecular clock analyses show that both strains probably separated from each other only a few years before the major European outbreak. HERB-1 seems to have dominated the global population without many genetic changes, and only in the twentieth century, after new potato varieties were introduced, was HERB-1 replaced by US-1 as the most successful P. infestans strain. We do not know for sure why HERB-1 was replaced, but we noted that the modern strains tend to be polyploid, while HERB-1 was diploid. We speculate that the increased genetic diversity in polyploid lineages were important for the success of US-1 (and other modern strains).

 

Our conclusions are based on Illumina sequencing of 11 herbarium samples of infected potato and tomato leaves collected in Ireland, the UK, Continental Europe and North America and preserved in the herbaria of the Botanical State Collection Munich and the Kew Gardens in London. Both herbaria placed a great deal of confidence in our abilities and were very generous in providing the dried plants. The degree of DNA preservation in the herbarium samples was impressive, much higher than in other examples of ancient DNA, and the majority of recovered DNA was from the host plant, with some samples having in addition over 20% pathogen DNA. In contrast to recent studies of historic human pathogens, no target DNA enrichment was required. We compared the historic samples with modern strains from Europe, Africa and North and South America as well as two closely related Phytophthora species. Due to the 150-year long period over which the individual samples had been collected, we were able to estimate with great confidence when the various P. infestans strains had emerged during evolutionary time. Here, too, we found connections with historic events: the first contact between Europeans and Americans in Mexico falls exactly into the time window in which the genetic diversity of P. infestans experienced a remarkable increase. Presumably, the social upheaval following the arrival of the Europeans somehow led to a spread of the pathogen at the beginning of the sixteenth century, which in turn accelerated its evolution.

 

The historical HERB-1 type is so far not known from modern collections, but we now have many diagnostic markers with which we can type the hundreds of modern isolates to determine whether perhaps there is somewhere a reservoir of HERB-1. In addition, our work highlights that herbaria constitute a rich, so far untapped source for investigating real-time evolution.

 

Detlef Weigel, weigel@weigelworld.org

Hernán A. Burbano, hernan.burbano@tuebingen.mpg.de

 

Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany

 

 

1.         Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, et al. (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461: 393-398.

2.         Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, et al. (2010) Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science 330: 1540-1543.

3.         Ristaino JB, Groves CT, Parra GR (2001) PCR amplification of the Irish potato famine pathogen from historic specimens. Nature 411: 695-697.

 

 

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

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The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine
Kentaro Yoshida, Verena J. Schuenemann, Liliana M. Cano, Marina Pais, Bagdevi Mishra, Rahul Sharma, Christa Lanz, Frank N. Martin, Sophien Kamoun, Johannes Krause, Marco Thines, Detlef Weigel, Hernán A. Burbano
(Submitted on 17 May 2013)

Phytophthora infestans, the cause of potato late blight, is infamous for having triggered the Irish Great Famine in the 1840s. Until the late 1970s, P. infestans diversity outside of its Mexican center of origin was low, and one scenario held that a single strain, US-1, had dominated the global population for 150 years; this was later challenged based on DNA analysis of historical herbarium specimens. We have compared the genomes of 11 herbarium and 15 modern strains. We conclude that the nineteenth century epidemic was caused by a unique genotype, HERB-1, that persisted for over 50 years. HERB-1 is distinct from all examined modern strains, but it is a close relative of US-1, which replaced it outside of Mexico in the twentieth century. We propose that HERB-1 and US-1 emerged from a metapopulation that was established in the early 1800s outside of the species’ center of diversity.

Small ancestry informative marker panels for complete classification between the original four HapMap populations

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Small ancestry informative marker panels for complete classification between the original four HapMap populations
Damrongrit Setsirichok, Theera Piroonratana, Anunchai Assawamakin, Touchpong Usavanarong, Chanin Limwongse, Waranyu Wongseree, Chatchawit Aporntewan, Nachol Chaiyaratana
(Submitted on 16 May 2013)

A protocol for the identification of ancestry informative markers (AIMs) from genome-wide single nucleotide polymorphism (SNP) data is proposed. The protocol consists of three main steps: (a) identification of potential positive selection regions via Fst extremity measurement, (b) SNP screening via two-stage attribute selection and (c) classification model construction using a naive Bayes classifier. The two-stage attribute selection is composed of a newly developed round robin symmetrical uncertainty ranking technique and a wrapper embedded with a naive Bayes classifier. The protocol has been applied to the HapMap Phase II data. Two AIM panels, which consist of 10 and 16 SNPs that lead to complete classification between CEU, CHB, JPT and YRI populations, are identified. Moreover, the panels are at least four times smaller than those reported in previous studies. The results suggest that the protocol could be useful in a scenario involving a larger number of populations.

SARS-CoV originated from bats in 1998 and may still exist in humans

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SARS-CoV originated from bats in 1998 and may still exist in humans
Ailin Tao, Yuyi Huang, Peilu Li1, Jun Liu, Nanshan Zhong, Chiyu Zhang
(Submitted on 13 May 2013)

SARS-CoV is believed to originate from civets and was thought to have been eliminated as a threat after the 2003 outbreak. Here, we show that human SARS-CoV (huSARS-CoV) originated directly from bats, rather than civets, by a cross-species jump in 1991, and formed a human-adapted strain in 1998. Since then huSARS-CoV has evolved further into highly virulent strains with genotype T and a 29-nt deletion mutation, and weakly virulent strains with genotype C but without the 29-nt deletion. The former can cause pneumonia in humans and could be the major causative pathogen of the SARS outbreak, whereas the latter might not cause pneumonia in humans, but evolved the ability to co-utilize civet ACE2 as an entry receptor, leading to interspecies transmission between humans and civets. Three crucial time points – 1991, for the cross-species jump from bats to humans; 1998, for the formation of the human-adapted SARS-CoV; and 2003, when there was an outbreak of SARS in humans – were found to associate with anomalously low annual precipitation and high temperatures in Guangdong. Anti-SARS-CoV sero-positivity was detected in 20% of all the samples tested from Guangzhou children who were born after 2005, suggesting that weakly virulent huSARS-CoVs might still exist in humans. These existing but undetected SARS-CoVs have a large potential to evolve into highly virulent strains when favorable climate conditions occur, highlighting a potential risk for the reemergence of SARS.

Positive selection drives faster-Z evolution in silkmoths

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Positive selection drives faster-Z evolution in silkmoths
Timothy B. Sackton (1), Russell B. Corbett-Detig (1), Javaregowda Nagaraju (2), R. Lakshmi Vaishna (2), Kallare P. Arunkumar (2), Daniel L. Hartl (1) ((1) Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, USA, (2) Centre of Excellence for Genetics and Genomics of Silkmoths, Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India)
(Submitted on 29 Apr 2013)

Genes linked to X or Z chromosomes, which are hemizygous in the heterogametic sex, are predicted to evolve at different rates than those on autosomes. This faster-X effect can arise either as a consequence of hemizygosity which leads to more efficient selection for recessive beneficial mutations in the heterogametic sex, or as a consequence of reduced effective population size on the hemizygous chromosome, which leads to increased fixation of weakly deleterious mutations due to random genetic drift. Empirical results to date have suggested that, while the overall pattern across taxa is complicated, in general systems with male-heterogamy show a faster-X effect primarily attributable to more efficient selection, whereas systems with female-heterogamy show a faster-Z effect primarily attributable to increased drift. However, to date only a single female-heterogamic taxa has been investigated. In order to test the generality of the faster-Z pattern seen in birds, we sequenced the genome of the Lepidopteran insect Bombyx huttoni, a close outgroup of the domesticated silkmoth Bombyx mori. We show that silkmoths experience faster-Z evolution, but unlike in birds, the faster-Z effect appears to be attributable to more efficient positive selection in females. These results suggest that female-heterogamy alone is unlikely to be sufficient to explain the reduced efficacy of selection on the bird Z chromosome. Instead, it is likely that a combination of patterns of dosage compensation and overall effective population size, among other factors, influence patterns of faster-Z evolution.

Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al

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Timing of ancient human Y lineage depends on the mutation rate: A comment on Mendez et al
Melissa A. Wilson Sayres
(Submitted on 22 Apr 2013)

Mendez et al. recently report the identification of a Y chromosome lineage from an African American that is an outgroup to all other known Y haplotypes, and report a time to most recent common ancestor, TMRCA, for human Y lineages that is substantially longer than any previous estimate. The identification of a novel Y haplotype is always exciting, and this haplotype, in particular, is unique in its basal position on the Y haplotype tree. However, at 338 (237-581) thousand years ago, kya, the extremely ancient TMRCA reported by Mendez et al. is inconsistent with the known human fossil record (which estimate the age of anatomically modern humans at 195 +- 5 kya), with estimates from mtDNA (176.6 +- 11.3 kya, and 204.9 (116.8-295.7) kya) and with population genetic theory. The inflated TMRCA can quite easily be attributed to the extremely low Y chromosome mutation rate used by the authors.

The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees

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The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees
Andreas Sand, Mike Steel
(Submitted on 22 Apr 2013)

Evolutionary events such as incomplete lineage sorting and lateral gene transfer constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species tree. One particularly simple and efficient way to infer species trees from gene trees under such conditions is to combine three-taxon analyses for several genes using a majority vote approach. For incomplete lineage sorting this method is known to be statistically consistent, however, in the case of lateral gene transfer it is known that a zone of inconsistency does exist for a specific four-taxon tree topology. In this paper we analyze all remaining four-taxon topologies and show that no other inconsistencies exist.

Genomic and phenotypic characterisation of a wild Medaka population: Establishing an isogenic population genetic resource in fish

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Genomic and phenotypic characterisation of a wild Medaka population: Establishing an isogenic population genetic resource in fish
Mikhail Spivakov, Thomas O. Auer, Ravindra Peravali, Ian Dunham, Dirk Dolle, Asao Fujiyama, Atsushi Toyoda, Tomoyuki Aizu, Yohei Minakuchi, Felix Loosli, Kiyoshi Naruse, Ewan Birney, Joachim Wittbrodt
(Submitted on 16 Apr 2013)

Background Oryzias latipes (Medaka) has been established as a vertebrate genetic model for over a century, and has recently been rediscovered outside its native Japan. The power of new sequencing methods now makes it possible to reinvigorate Medaka genetics, in particular by establishing a near-isogenic panel derived from a single wild population. Results Here we characterise the genomes of wild Medaka catches obtained from a single Southern Japanese population in Kiyosu as a precursor for the establishment of a near isogenic panel of wild lines. The population is free of significant detrimental population structure, and has advantageous linkage disequilibrium properties suitable for establishment of the proposed panel. Analysis of morphometric traits in five representative inbred strains suggests phenotypic mapping will be feasible in the panel. In addition high throughput genome sequencing of these Medaka strains confirms their evolutionary relationships on lines of geographic separation and provides further evidence that there has been little significant interbreeding between the Southern and Northern Medaka population since the Southern/Northern population split. The sequence data suggest that the Southern Japanese Medaka existed as a larger older population which went through a relatively recent bottleneck around 10,000 years ago. In addition we detect patterns of recent positive selection in the Southern population. Conclusions These data indicate that the genetic structure of the Kiyosu Medaka samples are suitable for the establishment of a vertebrate near isogenic panel and therefore inbreeding of 200 lines based on this population has commenced. Progress of this project can be tracked at this http URL

Detecting the structure of haplotypes, local ancestry and excessive local European ancestry in Mexicans

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Detecting the structure of haplotypes, local ancestry and excessive local European ancestry in Mexicans
Yongtao Guan
(Submitted on 5 Apr 2013)

We present a two-layer hidden Markov model to detect structure of haplotypes for unrelated individuals. This allows modeling two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local ancestry for admixed individuals. Our method outperforms competing state-of-art methods, particularly for regions of small ancestral track lengths. Applying our method to Mexican samples in HapMap3, we found five coding regions, ranging from $0.3 -1.3$ megabase (Mb) in lengths, that exhibit excessive European ancestry (average dosage > 1.6). A particular interesting region of 1.1Mb (with average dosage 1.95) locates on Chromosome 2p23 that harbors two genes, PXDN and MYT1L, both of which are associated with autism and schizophrenia. In light of the low prevalence of autism in Hispanics, this region warrants special attention. We confirmed our findings using Mexican samples from the 1000 genomes project. A software package implementing methods described in the paper is freely available at this http URL.

Natural selection reduced diversity on human Y chromosomes

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Natural selection reduced diversity on human Y chromosomes
Melissa A. Wilson Sayres, Kirk E. Lohmueller, Rasmus Nielsen
(Submitted on 20 Mar 2013)

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.