Genetic distance predicts the spread of deadly fungal infections in bats

Little brown bat (Myotis lucifugus)


You’ve probably heard about White-Nose Syndrome (WNS), the particularly nasty fungal pathogen that has decimated North American bat populations over the last decade. Not only has WNS been extremely deadly, but the speed at which it’s spread has been alarming. Really alarming:

Yikes. Original map and more information here.


Understanding why WNS has spread so quickly is an obvious step towards predicting the future spread and potential control of the disease, but it is not easy task. Mainly, the spread of WNS hasn’t radiated out linearly from a starting point. Instead, outbreaks have hopscotched across eastern North America, often showing up in disjunct and distant populations from year to year:

For example, WNS appeared as far south as southern Virginia before it reached the western edge of New York. Previous analyses indicate that colony size, species composition, habitat patchiness and climate influence WNS risk and consequently the overall pattern of spread across the landscape (Maher et al. 2012; Thogmartin et al. 2012; Wilder et al. 2011).

But the movement of pathogens from population to population depends on dispersal of their host, right? While straight line distance might not be the best predictor for the spread of WNS, undetected barriers for bat dispersal might play a large role. A recently-accepted paper in Molecular Ecology by Aryn Wilder et al. (quoted above) provides a range-wide analysis of genetic structure of little brown bats (Myotis lucifugus) that shows how inferences of recent dispersal informs the spread of WNS.
Wilder and colleagues collected mtDNA and RADseq data from individuals that represented the entire North American range of little brown bats. The resultant genetic distances between populations were considered along with geographic distances between sites in a mixed-effects model that described the real-life spread of WNS across years. Predictably, the more distantly-related or distantly-located two populations were, the less likely their risk WNS introduction. However, the the highest level of predictability was demonstrated when genetic covariates are included in the model, showing that distance by itself had lower predictive power for the spread of WNS.
The impressive long-distance dispersal by little brown bats (regularly > 500 km; Norquay et al. 2013) and the paltry genetic differentiation across all sites measured with RAD loci (ΦST = 0.008) combines to paint a picture of WNS spreading through significant bat dispersal. However, the lack genetic structure seen in eastern North America (where WNS has spread the most) doesn’t carry over to populations in the west:

Our range-wide genomic data suggest that the spread of WNS by an important host is likely to be slower in western North America than in the eastern half of the continent, where a rapid geographic expansion of the disease has been observed over the past eight years. Given that the spread of WNS to date has been correlated with subtle patterns of genetic differentiation in eastern North America, the rate of dispersal of the fungal pathogen by little brown myotis should decrease as WNS moves into the Great Plains, where genetic differentiation among localities increases substantially.

 
Wilder, A. P., Kunz, T. H., & Sorenson, M. D. (2015). Population genetic structure of a common host predicts the spread of white‐nose syndrome, an emerging infectious disease in bats. Molecular Ecology. DOI: 10.1111/mec.13396

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Machine learning for model selection in population genomics

Machine learning. Image from www.toptal.com

Machine learning. Image from www.toptal.com


The application of model-based methods in phylogeography helped the field transition from a more qualitative, overlay-a-tree-on-a-map, discipline to one that tests hypotheses in robust statistical frameworks. Many researchers have embraced approximate Bayesian computation (ABC) for model selection since computing the likelihood of complex population models is often intractable. While ABC is easy to use and provides a posterior distribution, like all methods, it has its weaknesses. For example, ABC requires a very large amount of simulated data and the choice of what summary statistic and rejection threshold to use is difficult.
In a recent preprint posted on bioRxiv, Sara Sheehan and Yun Song present a likelihood-free inference framework for population genomics that applies deep learning, an active area of machine learning research. They aimed to jointly infer natural selection and changes in population size, processes that can leave similar signatures in the genome, by testing their method on simulated data and on empirical data for Drosophila melanogaster. Sheehan and Song provide accessible introductions to ABC and deep learning in their preprint that are well worth the read. Continue reading

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On background selection in Ficedula flycatchers

Several recent studies (including those I wrote about last week) use genome-wide scans of differentiation to understand evolutionary mechanisms behind high or low divergence. However, there has been contentious support for and against these differentiation islands being due to differential introgression, vesus low recombination and linked background selection. Burri et al. (2015) in a recent study use multiple populations of four black-and-white flycatcher sister species of the genus Ficedula to describe this phenomenon. Little hybridization is known in these species, particularly in Central Europe, and on Baltic Islands, despite hybrid female sterility, premating isolation, and male fitness reduction. They re-sequence 200 atlas flycatchers (F. speculigera) and semicollared flycatchers (F. semitorquata) to get at the evolution of differentiation islands.

Ficedula speculigera – Atlas flycatcher. Image courtesy: Wikipedia


Ficedula semitorquata – Semi-collared flycatcher. Image courtesy: IBC


 
 
 
 
 
 
Their study identifies more than 50 million variant sites, with highly heterogeneous genomic landscapes of differentiation, and interestingly, high correlation between all possible pairs of species. In other words, differentiation islands occur in the same genomic regions across species pairs, perhaps due to shared genomic features, rather than parallel evolution of the same set of loci. Major observations include reduced nucleotide diversity (and effective population sizes) across all the islands – suggesting a bottleneck event in the common ancestor, which is however incompatible with high differentiation at these islands between descendent lineages. Tests for homogenizing gene flow across populations reveal that sympatric populations are not less differentiated than allopatric populations, also supported by ABBA-BABA tests showing no excess of shared derived variants in sympatry. Instead, using a high-density recombination map, they determine that lineage-specific differentiation significantly increased with decreased recombination rate, and provide evidence for the dominating role of background selection, and divergent selection across lineages.

We conclude that the heterogeneous genomic landscape of differentiation in Ficedula flycatchers evolves mainly as a consequence of a heterogeneous landscape of recombination. It starts emerging in structured populations and, owing to the conservation of the recombination landscape among species, evolves recurrently in independent lineages across the speciation continuum due to effects of linked selection.

Reference:
Burri, Reto, et al. “Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.” Genome research (2015): gr-196485. DOI: http://dx.doi.org/10.1101/gr.196485.115
 

Posted in adaptation, Coevolution, evolution, genomics, natural history, population genetics, selection, speciation, theory | Tagged , , , , , , | Leave a comment

An unspoiled frontier

“An unspoiled frontier, an escape from industrialized Japan and a chance to connect with nature …” or so says the Rough Guide to Japan (6th edition, September 2014).
We had experienced a bit of the city-scene in Hakodate, but the rest of our sightseeing of this untamed island had been limited to flashes as we drove (albeit slowly at a max of 80 km/hr or 50 mph) to Akkeshi. All this changed as we headed north to our third Hokkaido field site.
Takefumi Yorisue, a researcher at the Akkeshi Marine Station, was our guide and translator.
D7000s_2849_Akkeshi
I’ll digress from Gracilaria for a moment to talk a bit about Take’s research on barnacle settlement pheromones. The proteinaceous pheromone SIPC induces conspecific larval settlement. This gregarious settlement becomes important for reproductive success as adults.
Take found variation in the SIPC genes and this variation might produce species specificity (Yorisue et al. 2012, Biofouling 28: 605-611). SIPC genes might also enhance the selectivity of settlement sites and thereby impact incipient speciation.
Take has now found SIPC genes under positive selection and potential links to diversification and adaptation in barnacles.
Contact Take if you are interested in the future directions of his work (yorisue@gmail.com).
Continue reading

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In the northern biosphere

As regular readers will know, I’ve spent the summer traveling around the Northern Hemisphere sampling the red seaweed Gracilaria vermiculophylla, an introduced alga in North America and Europe. I’ve rewound to the beginning of the summer in order to highlight our Japanese colleagues without whom our trips would not have been possible nor as enriching! Plus, who doesn’t want to look at some pictures on a (stormy if you’re in the Southeast) Friday?!
For just over a week at the beginning of our field expedition at the beginning of June, my greenhorn assistant and husband, Rob, and I completed a quasi-circumnavigation of Hokkaido.

Hokkaido, Japan © fentonqstuders.blogspot.com

Hokkaido, Japan
© fentonqstuders.blogspot.com


Our first stop was in Hakodate where we met up with my colleague Erik Sotka. Due to our late arrival, sampling was delayed and we ended up with a day of tourism.
Seaweed for sale in the fish market

Seaweed for sale in the fish market


Hakodate Ropeway

Hakodate Ropeway


Kimono at the Museum of Northern Peoples

Kimono at the Museum of Northern Peoples


We were then guided by Dr. Chikara Kawagoe to a beautiful rocky shore and our first glimpse of G. vermiculophylla.
Hakodate rocky shore

Hakodate rocky shore


Erik, Kawagoe-San and myself after an early morning field trip

Erik, Kawagoe-San and myself after an early morning field trip


In order to process our samples, we were pointed to the Muroran Marine Station. The station is one of the satellite campuses in the Field Science Center for Northern Biosphere. The Center was established in 2011 as one of the research facilities of Hokkaido University and integrated 16 research facilities affiliated with the Faculties of Agriculture, Sciences and Fisheries.
The research faculties focus on conservation, the mechanisms underlying biological diversity and ecosystem processes, sustainability and long-term monitoring of the diverse ecosystems comprising the Center (forests, rivers, lakes, agriculture and coasts).
FullSizeRender
There are six main divisions of research and education providing fantastic opportunities for students at Hokkaido University as well as foreign students and researchers. Research ranges from bio-resource development in order to reduce the environmental impact while improving agricultural practices for cold regions, such as Hokkaido, to phylogenies and life cycle strategies in plants. In addition to the main campus in Sapporo, there are a plethora of field stations. For example, in the Nakagawa Experimental Forest, a long-term tree census has been carried out since 1967 in order to establish appropriate methods for selective cutting and sustainable yields of timber.
Our visit to Muroran, one of the four aquatic stations, was a last minute addition to our itinerary. It was a perfect example of the hospitality of every single place we ventured throughout Japan. Even though it was a Sunday afternoon, we were welcomed with enthusiasm by Drs. Motomura, Nagasato and Tanaka.
Muroran Marine Station Back row: Rob, Chikako Nagasato, Atsuko Tanaka Front Row: Erik, me, Taizo Motomura, Nana Kinoshita, Yuki Katayama

Muroran Marine Station
Back row: Rob, Chikako Nagasato, Atsuko Tanaka
Front Row: Erik, me, Taizo Motomura, Nana Kinoshita, Yuki Katayama


The Muroran Marine Station was founded in 1933. It is located in an area of rich marine flora and fauna due to the cold Kurile Current and warm Tsugaru Current.
Botofurinai

Botofurinai rocky intertidal


Gliopeltis

Gliopeltis


The researchers at the lab focuses on algal fertilization and development, morphogenesis and improving gene transfer techniques. Drs. Motomura and Nagasato were contributors to one of the first algal genomes, Ectocarpus (Cock et al. 2010, Nature, Vol 465: 617-621).
Unfortunately, we did not find a population of Gracilaria vermiculophylla, but we did get to see local fishermen drying kelp right near the marine station.
D7000s_2690_kelp drying
 
D7000s_2697_kelp drying
Packed tightly into our Wingroad, we drove over 400 km to the Akkeshi Marine Station, arriving right at sunset.
IMG_0422
The Akkeshi Marine Station, one of the other aquatic stations of Hokkaido University, was founded in 1931 in order to explore marine organisms inhabiting cold-current ecosystems. The Akkeshi Bay is influenced by the cold Oyashio Current with a unique marine flora and fauna from all other marine stations in Japan.
We sampled a population of G. vermiculophylla very similar to the populations we see in the non-native range.
seaweed, seagrass and snails

seaweed, seagrass and snails


After field work

After field work


On our final night before heading north (and Erik heading to the US), we were treated to a dinner with all the students at the marine station hosted by our colleague and collaborator Dr. Masahiro Nakaoka.
Gyoza

Gyoza


All the students and faculty based at the Akkeshi Marine Station

All the students and faculty based at the Akkeshi Marine Station


Having never traveled in Japan, we were nervous about the language and cultural barriers making field work and our very tight schedule difficult. Yet, all those qualms easily washed away in the first few days due to the kindness and generosity of every single person we encountered, whether they were our hosts or the owners of a restaurant taking great pains to translate a menu for those of us without LTE.
I’ll be back next week highlighting some of the work of a post-doc at Akkeshi, Takefumi Yorisue, plus more images from our sampling in Hokkaido.

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Introgression history in sticklebacks and oaks

Speciation theory has many monikers for differential gene flow – migration, introgression, admixture, hybridization, secondary contact. As a homogenizing process, gene flow at large acts to reduce differentiation between populations post-divergence. However, selection and demography affect the rates of gene flow across genomic loci (see my detailed post about differential migration here). Recently, two studies in very different speciation regimes – oaks speciating in sympatry, and threespine sticklebacks in parapatry/allopatry detail differential introgression using large scale reduced representation sequencing.
The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments, Ferchaud and Hansen (2015), Molecular Ecology
Threespine sticklebacks have been described by numerous previous studies for their genomic and morphological adaptations to saline waters, in the presence (and absence) of gene flow from fresh waters. Ferchaud and Hansen (2015) address three phenomena with respect to heterogeneous gene flow and adaptive divergence – (1) genome-wide patterns of differentiation in riverine versus lake populations which freely exchange genes, versus lack gene flow with marine environments respectively, (2) footprints of demographic changes in population sizes (bottlenecks) across genomes, and (3) describing patterns of adaptive divergence in populations showing less drastic (than previously described studies) changes in morphology.

Sampling across a variety of environments, Ferchaud and Hansen use RAD sequencing of 177 sticklebacks and analyze LD, differentiation among populations, population structure, compare models of demographic history, and identify “outlier” loci – loci exhibiting significant differentiation across populations. Ultimately using >23k loci after filtering, their key findings include (a) highest diversity, and lower LD decay levels in marine environments, and lowest diversity and higher LD decay in smaller lakes (without inflow), with intermediate levels of diversity and LD in lakes with riverine inflow (b) high Fst (0.204) among all populations, with varying levels of differentiation among all pairs of populations with similar patterns uncovered by analyses of population structure, (c) stable population size history in marine environments, versus all freshwater populations exhibiting signatures of bottlenecks, all observations pointing towards the role of heterogeneous gene flow in population differentiation and adaptive divergence.
Historical introgression among the American live oaks and the comparative nature of tests for introgression – Eaton et al. (2015), Evolution

The Angel Oak Tree (Quercus virginiana), a species of American Live oak, believed to be over 1500 years old. American live oaks are termed a “worst case scenario for the biological species concept” by Coyne and Orr (2004). Image courtesy – Pinterest


Natural populations of American Live oaks (Quercus series Virentes) hybridize freely, and yet several extant species/subspecies exist across its distribution in a variety of climates and geographies. Eaton et al. (2015) use RADseq data to quantify genetic admixture, and ancestral demography in fourteen American clade oaks using five widely used methods – phylogenetic resolution into clades, inference of population structure under an admixture model, joint inference of tree topology and admixture, D-statistic (ABBA-BABA) tests, and  demographic models by comparison of site frequency spectra. Phylogenetic reconstruction recovered support for three major clades – southeastern US, southwestern clade, and a Central American clade, also obtained using analyses of population structure. Admixture analyses supported admixture edges between Central America, and southeastern US clades, and additional edges between southeastern and southwestern clades. ABBA-BABA tests (non-parametric) showed heterogeneity in patterns of admixture, with significant results restricted to geographically proximal clades. Analyses of SFS differences also reject a hybrid origin for Cuban populations, with indistinguishable support for Central American, and southeastern US origin.

Our analyses demonstrate the difficulty of inferring historical introgression over deep evolutionary time scales…Here, rather than focus on a specific number of individual, we stress the importance of attaining “phylogenetically relevant sampling,” which we define to include several geographic samples from both within species and across species to allow for contrasts that can reveal the presence and geographic extent of admixture.

References:
Ferchaud, AL, and Hansen MM. “The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments.” Molecular Ecology (2015). DOI: http://dx.doi.org/10.1111/mec.13399
Eaton, Deren AR, et al. “Historical introgression among the American live oaks and the comparative nature of tests for introgression.” Evolution (2015). DOI: http://dx.doi.org/10.1111/evo.12758
 
 
 
 
 
 

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

Paternity matters in polyploid plants


In the most basic definition, polyploidy is a numerical increase in whole chromosome number. The effects of this increase in genomic material often produce novel morphologies compared to parental species, and polyploids have become both a huge part of explaining the evolutionary history of biological diversity and a crucial aspect of agriculture.
However, polyploids are clearly not the result of simple math. Those genomes might be duplicates of one another or from two different species. There might be an odd number of genomes where one parental species dominates the other. There might be differing ploidy depending on tissue type.
The conflict between how many genomes an organism has (polyploidy) and where each of those genomes came from (hybridity) is a large confounding factor when trying to understand what genetic characteristics are most responsible a given phenotype. If you observe a difference in biomass between a diploid plant and an triploid plant hybrid, is that difference due to the extra genome, the heterozygosity contributed by the two parental genomes, or some combination of both?
A recent study by Fort et al. appearing in New Phytologist attempts to cleverly tease apart these factors. First, the authors acquired isogenic varieties of Arabidopsis that were either diploid and tetraploid. These plants were crossed and separated into those that were triploid with an additional paternal genome [3x(p)] or triploid with an additional maternal genome [3x(m)], producing a gradient of groups from 2N-4N that all have the same genetic background except for which parental donated a genome to the triploids. Second, the authors did the same with crosses between different genetic backgrounds, creating gradients of 2N-4N individuals with increased heterozygosity due to having divergent parents.
The authors show that the triploid plants with an additional paternal genome had the greatest increase in plant size when compared to diploids. The truly fascinating aspect of this result is that it didn’t matter whether those 3x(p) individuals were isogenic or hybrids.

Strikingly, our data indicate that paternal genome dosage increases in isogenic F1 triploid plants trigger positive heterosis outcomes, whereas maternal genome dosage increases in isogenic F1 triploid plants trigger negative heterosis outcomes. When paternal genome dosage is increased in an F1 hybrid context, the paternal genome dosage effect can act as an enhancer of hybridity-associated heterosis.

Plant size can be the result of multiple growth characteristics, and the authors indicate that increased seed size is mainly responsible for increased plant size, not growth rate. Hybrid individuals showed increased growth rates compared to diploids, but only early in development.

Figure 5 from Fort et al.

Figure 5 from Fort et al. (2015) that demonstrated the positive (black arrows), negative (gray arrows), and unknown (question marks) relationships between genome dosage and hybridity on phenotype.


The conclusion here is that genome dosage matters, even independent of the hybrid status of the genomes that make up a polyploid. However, the parental status of extra genomes produces different effects even when both parents are genetically similar, indicating that epigenetic effects are yet another layer to untangle among the complexity of polyploid genetics.
 
Fort, A., Ryder, P., McKeown, P. C., Wijnen, C., Aarts, M. G., Sulpice, R., & Spillane, C. (2015). Disaggregating polyploidy, parental genome dosage and hybridity contributions to heterosis in Arabidopsis thaliana. New PhytologistDOI: 10.1111/nph.13650
 

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Algae bring life to the world – marine forests and domestication

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The final two days of the European Phycological Congress included talks focused on the fate of marine forests in light of global climate change as well as other anthropogenic stressors, such as domestication.
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Algae bring life to the world – species, microbiomes and biodiversity

The first European Phycological Congress was held in Cologne, Germany in 1996. In the last 20-odd years, the meeting has been held every four years from Italy, to Northern Ireland, to Spain and Greece.
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This year the meeting was held in London and as a recipient of the FEMS Meeting Attendance Grant and a little bit of field work (see here and here), I was able to attend. Not only is this one of the best meetings to attend, in my opinion, it also served as a chance for me to meet up with friends and colleagues I hadn’t seen since returning to the US in 2013.

Mind the Gap

Mind the Gap


The sessions were as varied as Shedding new light on photosynthesis and its role in global biogeochemistry, Algae-microbiome interactionsPhylogenomics and Algae in stressful environments in coastal systems. Thus, it was a very full four days of conference talks, coffee breaks and dinners.
I wanted to highlight some of the excellent presentations, though this is by no means an exhaustive review of the excellent science that was on show in Hammersmith. There’s too much for one post, so I’m going to break it up into two awesome algal posts (Rob Denton, that’s for you)!
If you are a regular reader of TME and I did not highlight your presentation at EPC, by all means contact me for a follow up interview/article highlight!
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Measuring dispersal rate in Neotropical fishes in units of 'wallace'

Portrait of Wallace from his autobiography My Life, Vol. 1 (Chapman and Hall, London, 1905). Copyright © Royal Society.

Portrait of Wallace from his autobiography My Life, Vol. 1 (Chapman and Hall, London, 1905). Copyright © Royal Society.


Alfred Russel Wallace often gets second billing compared to Charles Darwin but in a paper recently accepted at Systematic Biology, Tagliacollo et al.  define a new term for their analyses (dispersal rate, D) and measure D in units of ‘wallaces‘ (wa) to honor the contributions of Alfred Russel Wallace to the field of biogeography.
This detail is a small part of a great paper that tests alternative hypotheses about how freshwater fish assemblages formed in Central America and the Greater Antilles (Cuba, Hispaniola, Puerto Rico, Jamaica, and the Cayman Islands). The authors used parametric biogeographic methods to estimate rates of coordinated dispersal in the two most species clades of freshwater fish in the Caribbean basin- the heroine cichlids and poeciliine live-bearers. Continue reading

Posted in methods, phylogenetics, phylogeography, Uncategorized | 1 Comment