Christopher Laumer, EMBL-EBI

Revealing the genome biology of Earth’s smallest animals

A large fraction of earth’s animal biodiversity is found in the so-called meiofauna. Such tiny creatures may contain only 100s or 1000s of nuclei per individual, but may contain high genetic diversity. These conditions frustrate current methods for genome assembly. I have developed a novel protocol to generate long read (10-20 kbp) libraries with minimal coverage bias from minute inputs, through optimized long-range PCR library amplification. Optional modifications allow the collection of full-length cDNA libraries and genomic linked-reads from the same specimen. A related method efficiently builds and amplifies libraries of chromosome conformation capture (3C) DNAs also from single specimens. Long-read sequencing of such amplified 3C-DNAs can scaffold assemblies to the chromosome scale, and potentially, enable true phased diploid assemblies. I have validated these methods using single Caenorhabditis nematodes, including both homozygous and heterozygous species. I will also discuss applications in non-model species, in particular, flatworms found in the Cam. For instance, the genome of a rhabdocoel, Castrella truncata, appears to be small and remarkably homozygous, potentially showing evidence of recent inbreeding, consistent with the natural history of this species. In contrast, the genomes of two facultatively asexual catenulids (Stenostomum spp.), while also small, are highly heterozygous, with low-accuracy nanopore reads giving assemblies nearly double the haploid size. Further comparative work, enabled by methods such as those presented here, will be needed to explain the mechanisms governing these and other forms of variation in the genome biology of meiofauna.

 

Erika de Castro, University of Cambridge

Unveiling the roles of cyanogenesis in the Heliconius evolution

Understanding how the interactions between species promote their diversification is one of the most fascinating questions in evolutionary biology. Heliconius butterflies and Passiflora plants are classical examples of antagonistic coevolution1. Curiously, both butterfly and plant contain toxic cyanogens. Heliconius biosynthesize cyanogens but can also sequester simple cyanogens from Passiflora plants2. In this talk, I will discuss the role of cyanogens in the biology of Heliconius, focusing on their: i) coevolution with Passiflora; ii) ecological divergence; and iii) life-cycle. By performing metabolomic analyses of 22 heliconiines and over 50 Passiflora species, we discovered that not only Heliconius but also other heliconiines can sequester cyanogens from Passiflora. In turn, some of these plants have modified their cyanogen structures to disable sequestration by heliconiines3. Moreover, we also reared the sympatric species H. melpomene rosina and H. cydno chioneus on different Passiflora and confirmed that host-specialization was important in their isolation4. H. c. chioneus is less efficient sequestering cyanogens and had the worst larval performance when reared on the favourite host of H. m. rosina. Finally, using CRISPR-Cas, we confirmed that CYP405As are responsible for first step of cyanogen biosynthesis in Heliconius. Our results also emphasize the importance of cyanogens for their life-cycle, as CYP405A-knockout larvae were not able to pupate. In fact, metabolomic analyses shown that Heliconius catabolize part of their cyanogens during pupation, possibly to retrieve nitrogen. Our results shed light on the evolution of cyanogen metabolism in Heliconius and the importance of these compounds in their speciation.

References:
1. Ehrlich, P. R. & & Raven, R. J. Butterflies and Plants : A Study in Coevolution Author. Soc. Study Evol. 18, 586–608 (1964).
2. de Castro, É. C. P., Zagrobelny, M., Cardoso, M. Z. & Bak, S. The arms race between heliconiine butterflies and Passiflora plants – new insights on an ancient subject. Biol. Rev. 93, 555–573 (2018).
3. de Castro, É. C. P. et al. Sequestration and biosynthesis of cyanogenic glucosides in passion vine butterflies and consequences for the diversification of their host plants. Ecol. Evol. 9, 5079–5093 (2019).
4. de Castro, É. C. P. et al. Plasticity in larval-diet and cyanogenesis in a specialist and a generalist butterfly – in prep to Biology Letter.

 

Marie Louis, University of St Andrews

Parallel evolution in bottlenose dolphins

Behavioral and ecological variation among groups can facilitate the evolution and maintenance of genetic differences through local adaptation to particular environments. However, linking genetic divergence to local adaptation is particularly challenging as genetic differentiation may also arise due to demographic history or other selective processes. Studying parallel evolution is a powerful approach to identify genomic regions under natural selection and rule out the action of stochastic processes. Two ecotypes of bottlenose dolphins (coastal and pelagic) have recurrently formed in multiple regions of the world. Coastal populations were inferred to have been founded from pelagic source populations. They are thus an excellent study system to test if the same molecular processes were involved in independent colonization of coastal habitat. To investigate this hypothesis, we sequenced 57 coastal and pelagic genomes from the North East Atlantic, North West Atlantic and North East Pacific. We first determined the relations of the ecotypes in these regions using multivariate, tree, demographic history and admixture analyses. We then tested for parallel adaptation to coastal waters. Our analyses revealed a complex population history involving admixture between oceanic regions, non-independence of the ecotype splits and archaic ancestries. We also showed that parallel demographic and selective processes were involved in the evolution of coastal populations. Selection was mainly diversifying between coastal and pelagic ecotypes, and mainly homogenising among coastal populations. Our results suggest that many alleles present as standing genetic variation in the pelagic populations were repeatedly selected for in coastal environments.

 

Levi Yant, University of Nottingham

Hotspots of adaptation to whole genome duplication (WGD) in ten independent WGDs

DNA repair and cell division represent essential, conserved processes not normally envisaged as undergoing rapid, adaptive evolution. However, when faced with intense selection, nimble shifts in the functioning of crossover regulation at meiosis are observed, as well as strong signatures of selection on DNA repair proteins mediating meiotic and mitotic divisions. Here we take advantage of the conserved – but adaptable—nature of these processes to test the hypothesis that evolution in essential proteins is constrained, resulting in convergence in independent adaptation events. We broadly test the predictability of evolution by focusing on ten independent cases of within-species WGD, a phenomenon that occurs in all eukaryotic kingdoms and is implicated in adaptation and speciation. Despite the evolutionary potential of WGD, sudden duplication of all chromosomes poses challenges to essential processes, especially meiotic chromosome segregation. Nonetheless, nature reveals solutions: various autopolyploid species with diploid-like meiosis show that early difficulties can be overcome. The mechanistic basis for this is coming to light: our work in autotetraploid Arabidopsis arenosa revealed clear WGD-associated selective sweeps on meiosis genes which functionally modulate crossover frequency and distribution. To probe the genomic factors underlying predictability and constraint, we systematically assess whether species (and lineages within species) that independently adapted to the challenges attending WGD evolved similar or identical solutions. To this end, we have thus far individually resequenced the genomes of over 800 individuals from 6 plant and one animal species, all of which harbour recent, within-species WGDs resulting in extant ploidy variation, and performed high-density genome scans for selection. We observe widespread functional convergence in conserved processes and partial parallelism at the molecular level, but minimal repeated evolution on orthologous loci. This work provides high-resolution, functionally testable alleles responsible for repeated evolution across a wide phylogenetic breadth. We further take advantage of the large number of populations, individuals, and species investigated to explore the roles of genomic, demographic, and molecular factors that influence the realization of convergent outcomes. These results are generating novel hypotheses about the predictability of evolution and the adaptability of polyploids, which we are testing with synthetic polyploid transgenics in evolve-and-resequence experiments. Further, this work provides insight into how organisms across kingdoms adapt to the altered cellular environment following WGD, a prevalent ongoing force in evolution.

 

Jaime Iranzo, Universidad Politécnica de Madrid

Gain and loss of accessory genes accelerates core gene sequence divergence and facilitates speciation in prokaryotes

Bacterial and archaeal evolution involves extensive gene gain and loss. Thus, prokaryotic taxa are characterized by large sets of accessory genes -i.e. genes that are present only in some strains and provide adaptation to specific environments- and much smaller sets of core genes – i.e. genes harbored by every genome from the same taxon and typically involved in housekeeping functions. How prokaryotic genomes remain cohesive in their core gene sequences while broadly varying in their accessory genes, and how large-scale changes in the accessory genome interact with mutations in core genes to drive diversification, are longstanding questions where microbial genomics, ecology, and evolution converge. To investigate those questions, we compared the dynamics of sequence divergence in highly conserved core genes with the dynamics of gene gain and loss for 34 groups of closely related bacterial and archaeal genomes. We found that sequence evolution in core genes is delayed with respect to gene content evolution, and that the extent of this delay widely varies across taxa. Mathematical modeling demonstrates that the delay in the evolution of core genes can result from sequence homogenization, which itself is caused by homologous recombination within the population. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Only after the evolving genomes become isolated by barriers that impede homologous recombination, do gene and genome evolution processes settle into parallel trajectories and genomes diverge. Our analyses reveal that the higher the gene turnover rate, the faster the barriers to homologous recombination are established. In consequence, gain and loss of accessory genes promotes sequence divergence and, eventually, speciation.

 

Daniel K. Fabian, EMBL-EBI

Evolution of transposable element load and expression as a response to
selection for longevity in Drosophila

Transposable elements (TEs) often inflict numerous negative effects on health and fitness as they replicate by integrating into new regions of the host genome. Even though organisms utilize powerful mechanisms to demobilize TEs, transposons become increasingly derepressed during ageing. The rising TE activity causes genomic instability and was suggested to be involved in age-dependent neurodegenerative diseases and the determination of lifespan. It is therefore conceivable that long-lived individuals have improved TE silencing mechanisms and consequently fewer genomic insertions relative to their shorter-lived counterparts. Here, we test this hypothesis by quantifying genome-wide TE insertions in populations of Drosophila melanogaster selected for longevity through late-life reproduction for 50- 170 generations from four independent studies. Surprisingly, we found that within studies, 46% to 77% of the ~120 present TE families were significantly more abundant in long-lived populations compared to non-selected controls, while only 12% to 31% showed a reduction. The TE accumulation in long-lived flies thus demonstrates a striking example of evolutionary repeatability with a to date unknown role in the evolution of aging. Moreover, RNA-seq analysis of one study revealed that long-lived populations evolved to downregulate expression of several TEs, suggesting that reducing TE transcription might be more important for longevity than regulating genomic copy numbers. Finally, we find little evidence of parallel selection on genes related to TE regulation and transposition. Our results provide a novel viewpoint proposing that reproduction at old age increases the opportunity of TEs to be passed on to the next generation with seemingly little impact on longevity.

 

Melanie Kirch, Friedrich Miescher Laboratory of the Max Planck Society

Standing genetic variation in ancient ~13,000 year old marine stickleback genomes

The dynamics of adaption to a changing environment remains an open question in evolutionary biology. One mechanism which enhances the rate of adaptation is the usage of pre-screened adaptive standing genetic variation (SGV). Threespine sticklebacks (Gasterosteus aculeatus) show repeated parallel evolution of freshwater ecotypes using SGV in marine ancestors. We collected contemporary sticklebacks as well as stickleback bones from the sediments of two freshwater postglacial isolation lakes, which transitioned from marine bays to isolated freshwater lakes after the Last Glacial Maximum. Both ancient samples are ~13,000 years old placing them in the same time period as the formation of the lakes. DNA extracted and sequenced from the bone pieces revealed these Late Pleistocene samples to be female marine Atlantic sticklebacks with a greater genetic affinity to contemporary marine than to contemporary freshwater fish from the same lake. Although both ancient samples are genetically identified as marine sticklebacks, freshwater-adaptive alleles are found in one of the ancient samples suggesting that SGV was also present in the marine stickleback population that first colonized this lake. Genome-wide variation was shared among sticklebacks from the same lake indicating coalescence during a bottleneck which was likely associated with the adaptation to the transitioning environment. We consider variation in mutational and ROH load between contemporary freshwater and marine stickleback populations, and the potential fitness cost to freshwater adaptation caused by rapid adaptation to a changing environment. Our results will offer an insight into the mechanisms and constraints of rapid adaptation and into the evolutionary potential of biodiversity.

 

Nathanael Walker-Hale, University of Cambridge

Evolution of L-DOPA-4,5-dioxygenase reveals multiple origins of betalain pigmentation in Caryophyalles

In plants, betalain pigments occur uniquely in Caryophyllales, and their evolution, restricted phylogenetic distribution and mutual exclusivity with more widespread anthocyanin pigments remain enigmatic. Extensive Caryophyllales-wide sampling of genomes and transcriptomes, together with fast and efficient in planta transient heterologous assays have enabled unprecedented understanding of the genomic evolution underpinning betalain pigmentation. With these approaches, we have revealed the roles of gene co-option, gene duplication, and the formation of operon-like genomic structures as mechanisms underpinning biosynthetic novelty. We have characterised the evolution of a core enzyme in the betalain biosynthesis pathway, showing that betalain-specific enzymatic activity arose multiple times independently, in concert with multiple origins of betalain pigmentation. Patterns of molecular evolution in the gene family are consistent with convergent evolution. However, while the central structure of the pathway has been determined, many downstream elements remain to be elucidated. We outline the use of site-directed mutagenesis to understand the phenotypic consequences of convergent mutations and examine the structure of the pathway across putative betalain origins using coexpression network approaches. Understanding the evolution of betalain pigmentation provides a unique insight into the genomic basis underpinning convergent origins of a complex biochemical trait.

 

Eleanor Miller, University of Cambridge

Bayesian Skyline Plots do not agree with range size changes based on Species Distribution Models for Holarctic birds

During the Quaternary, large climate oscillations had profound impacts on the distribution, demography and diversity of species globally.  Birds offer a special opportunity for studying these impacts because surveys of geographical distributions, publicly-available genetic sequence data, and the existence of species with adaptations to life in structurally different habitats, permit large-scale comparative analyses.  We use Bayesian Skyline Plot (BSP) analysis of mitochondrial DNA to reconstruct profiles depicting how effective population size (N_e) may have changed over time, focusing on variation in the effect of the last deglaciation among 102 Holarctic species.  Only three species showed a decline in N_e since the Last Glacial Maximum (LGM) and seven showed no sizeable change, whilst 92 profiles revealed an increase in N_e.  Using bioclimatic Species Distribution Models (SDMs), we also estimated changes in species potential range extent since the LGM.  Whilst most modelled ranges also increased, we found no correlation across species between the magnitude of change in range size and change in N_e.  The lack of correlation between SDM and BSP reconstructions could not be reconciled even when range shifts were considered.  We suggest the lack of agreement between these measures might be linked to changes in population densities which can be independent of range changes.  We caution that interpreting either SDM or BSPs independently is problematic and potentially misleading.  Additionally, we found that N_e of wetland species tended to increase later than species from terrestrial habitats, possibly reflecting a delayed increase in the extent of this habitat type after the LGM.

 

Astrid Böhne, Center of Molecular Biodiversity Research

Dynamics of sex chromosome evolution in a rapid radiation of cichlid fishes

Sex is an ancient and fundamental trait in eukaryotes, yet its determining factors comprise a variety of environmental and genetic mechanisms, including many different types of sex chromosomes. The degree of differentiation that sex chromosomes occupy and a counteracting force of differentiation, namely sex chromosome turnovers, are not equally distributed across the tree of life. Some groups of organisms seem to be particularly dynamic with respect to their sex-determining mechanisms. By focusing on a textbook example of rapid adaptive radiation, the one of cichlid fishes in East African Lake Tanganyika, we investigate when and how new sex chromosomes evolve on a short evolutionary timescale. Based on whole genome data comprising all species of the radiation (~240) and transcriptome data for ~80 of those, we identify sex chromosomal signatures in 90 species involving 11 different chromosomes with respect to the reference genome of a common out-group. We show that sex chromosome recruitments, i.e. which chromosome becomes a sex chromosome, are not random which supports the idea that particular chromosomes make better sex chromosomes than others. We demonstrate that cichlids have the highest rate of sex chromosome turnovers so far described with turnovers driven by a combination of mutational load and sexual antagonism.

 

Daniel Gebert, University of Cambridge

Evolution of piRNA clusters in the Drosophila genus

Piwi proteins and Piwi-interacting RNAs (piRNAs) are crucial for fertility and for the silencing of transposable elements (TEs) in the animal germline. In this system, piRNAs guide associated PIWI proteins to their targets by sequence complementarity to establish transcriptional and post-transcriptional repression. The vast majority of piRNAs in Drosophila is produced from a few large genomic loci, called piRNA clusters, which are enriched for TE sequences and are regarded as ‘master regulators’ of transposons. However, we show that the three largest germline piRNA clusters in Drosophila melanogaster, 42AB, 20A and 38C, which produce more than half of all unique piRNA reads, are dispensable, as deletion of these loci has no effect on viability, fertility, and germline development. This result challenges the previously assumed role of piRNA clusters and raises questions about their biological significance within the evolutionary anti-TE arms race. In order to shed light on this issue, we intent to reconstruct the evolutionary history of piRNA clusters and their TE content in ten species of the Drosophila genus, spanning about 50 million years of evolution. We use embryonic small RNA expression data to identify piRNA clusters and integrate de novo TE annotation for each Drosophila species. Through a synteny-based approach we will then be able to track piRNA clusters between species and compare TE contents and targets. By this, we aim to elucidate their emergence, degree of conservation and turnover rate and ultimately to better understand their role in TE repression, as their status as ‘master regulators’ is questioned.

 

Roberta Bergero, University of Edinburgh

Turnover of a highly degenerated Y chromosome

Turnovers of sex chromosomes – a phenomenon in which a new sex-chromosome evolves either by movement of the ancestral sex-determining region or by the formation of a new sex determining region – have been documented in several taxa.  Hypotheses to explain such a puzzling phenomenon include the ‘hot potato model’, which proposes that turnover events may occur after a sex chromosome becomes genetically degenerated⁴.  However, empirical evidence to support one scenario or another has remained elusive. Here we show evidence for a turnover event in which the sex determining function of a highly degenerated Y chromosome has been hijacked, with the X chromosome becoming a new Y chromosome. We compared the sex chromosomes in three species of the tropical fish genus Poecilia, P. reticulata (the guppy), and the guppy’s closest extant relatives, P. picta and P. parae. The sex determination in all three species is controlled by the same chromosome pair, but P reticulata Y chromosome carries homologues of most of the genes on the X chromosome whereas the Y chromosomes of the two sister species show high levels of gene loss on the Y chromosome. We use sequence divergence estimates for inferring the time of species split and show that the recent species split is incompatible with alternative hypotheses for the evolution of these three sex chromosome systems. A phenotypic guppy male carrying a recombinant sex chromosome that is part X and part Y provide further evidence for the turnover event. Our study describes for the first time a turnover event for a highly degenerated Y chromosome. This evolutionary scenario lends support to hypotheses that invoke genetic degeneration as the selective force favouring sex chromosomes turnovers.

 

Roman Kellenberger, University of Cambridge

The molecular basis of sexual deception in the South African daisy Gorteria diffusa.

One of the most sophisticated plant-animal interactions is plant sexual deception, in which flowers mimic female insects to attract males for pollination. Although plant sexual deception has fascinated biologists for centuries, it is still unclear how sexually deceptive structures can evolve from other non-deceptive traits.

We are investigating the molecular evolution of sexual deception in Gorteria diffusa, a South African daisy which produces orange flowers with black petal spots mimicking female flies. Within its natural habitat, G. diffusa has radiated into 16 morphotypes, which vary in strength of sexual deception.

Differential expression analysis of focal morphotypes identified four conceptually distinct gene sets underlying key petal spot traits: Set 1 are anthocyanin pathway genes and regulators, including a malonyl transferase. This confirms our biochemical analyses, which show that petal spots contain malonylated anthocyanins. Set 2 are genes of iron transport, an initially surprising group until elemental analysis revealed that petal spots have a six-fold increased iron concentration. Iron atoms chelate with anthocyanins, intensifying their coloration. Set 3 are genes involved in root development, including a usually root-specific Expansin. This module likely regulates the development of papillate cells, mimicking the surface of a female’s body. Set 4 are genes involved in developmental staging, most notably a SQUAMOSA Promoter-binding Like (SPL) transcription factor with a miR156 recognition motif in the 3′-UTR. We hypothesise that the petal spots develop in response to SPL.

These results elucidate the developmental genetic basis of complex phenotypic structures, and contribute towards an integrative understanding of pollinator-mediated diversification.

 

Past human migrations account for the origins of the major Eurasian linguistic families

Patrícia Santos, Université de Bordeaux & CNRS

Demographic events in human history leave traces in languages and genes, hence Darwin’s intuition that the best possible description of linguistic relationships among populations would be their phylogenetic tree.

Studies based on genetic and linguistic data have investigated the question of the origin of Indo-European (IE) and Uralic (UR) languages. At the basis of these studies lies Cavalli-Sforza’s hypothesis that a major demographic shift with a massive population turnover across a large geographic area be accompanied by the introduction of a new culture/language.

In the present study, we combined linguistic and genomic data to shed light on the origin and spread dynamics of the IE and UR linguistic families in Eurasia. We investigated the congruence between linguistic traits inferred from syntactic comparisons and human genome diversity, finding a general correlation with a few exceptions. Then we used genome-wide data to characterize the genetic background and phylogenetic relationships of modern populations in Eurasia speaking IE and UR. Finally, we compared modern and ancient DNA data to investigate the genetic ancestry of these populations.

We found that modern populations speaking UR in Europe are genetically closer to the modern and Bronze-Age populations from the Pontic steppes, than present-day IE speakers are. Our preliminary results suggest that the distribution of grammatical diversity of most languages in Europe is largely related to past human migrations, and to the different impact of their culture and genetic legacy during their expansion.