On background selection in Ficedula flycatchers

Posted on 8 Oct, 2015 by Arun Sethuraman

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

Posted on 6 Oct, 2015 by Stacy Krueger-Hadfield

“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

Posted on 2 Oct, 2015 by Stacy Krueger-Hadfield

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

Posted on 1 Oct, 2015 by Arun Sethuraman

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

Posted on 30 Sep, 2015 by Rob Denton


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 Phytologist. DOI: 10.1111/nph.13650
 

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Algae bring life to the world – marine forests and domestication

Posted on 28 Sep, 2015 by Stacy Krueger-Hadfield

Slide1
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.
Continue reading →

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Algae bring life to the world – species, microbiomes and biodiversity

Posted on 25 Sep, 2015 by Stacy Krueger-Hadfield

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.
Slide1
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 interactions, Phylogenomics 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!
Continue reading →

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Measuring dispersal rate in Neotropical fishes in units of 'wallace'

Posted on 25 Sep, 2015 by Melissa DeBiasse

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

Sweptaway – Part 3 – Adaptation genomics of White Sands Lizards

Posted on 24 Sep, 2015 by Arun Sethuraman

Recent colonization events offer juicy insights into the adaptive evolution of species in response to natural selection of novel habitats – however, they are confounded by demographic changes (eg. bottlenecks, differential migration). In a recent study, Laurent et al. (2015) analyze the population genomics of convergent color morphs (dark and light, adaptations for crypsis against predators) of two lizard species – Sceloporus cowlesi and Aspidoscelis inornata in the White Sands, southern New Mexico.

‘Dark’ morph of A. inornata – image courtesy: Simone Des Roches, http://evoecowhitesandslizards.blogspot.com/ Do check out her blog for more cool pictures from the White Sands lizards project.


Using a sequence capture assay, and screening for the Mc1r gene clones across fosmids generated from dark and light populations of both species, Laurent et al. analyze diversity, differentiation and genetic structure, demography, and selective sweeps between them. Additionally, they also estimate allele ages, and selection coefficients for putatively selected mutations in both species. Using >20k SNP’s in S. cowlesi, and >13k SNP’s in A. inornata, they determined (a) similar levels of nuclear diversity amongst three sampling locations in both species, (b) genetic structuring among locations (3 subpopulations in S. cowlesi, >2 in A. inornata), and (c) support for a model of no migration between populations in S. cowlesi, versus one of migration between all three locations in A. inornata.
Mc1r regions showed high differentiation (compared to other genomic regions) in both species, with lower nuclear diversity in light color morphs, predicting reduction in diversity following a sweep. Mc1r regions also showed negative values for Tajima’s D in the lighter morphs, versus darker morphs, and high frequency white alleles in the lighter morphs. The mutant “white” allele was also dated to be very young in both species (900 – 1200 years).

Our study provides a number of important insights into the process of parallel ecological adaptation in a novel and geologically young environment. While the times of colonization may differ between the focal species, both appear to have colonized the White Sands area after their geological formation, utilizing different genetic mechanisms within Mc1r.

 
Reference:
Laurent, Stefan, et al. “The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards.”Molecular ecology (2015). DOI: http://dx.doi.org/10.1111/mec.13385
 

Posted in adaptation, Coevolution, evolution, genomics, natural history, population genetics, selection | Tagged , , , , , | 1 Comment

Landscape genetics shows that Tanzanian forest monkeys feel the heat of human influence

Posted on 23 Sep, 2015 by Rob Denton


A new publication appearing in Heredity applies new methods for associating population genetic data with landscape resistance to an tropical, endangered species.
The authors utilize multiple measurements of landscape resistance, like forest cover and distance from the nearest village, to select the best-fit model of resistance for the microsatellite genetic data from five forest blocks of endangered Udzungwa red colobus monkeys (Procolobus gordonorum). Methods that use landscape resistance values are often complicated by the subjective nature of choosing relevant variables or the scale/direction of effect, but the methodology used by Ruiz-Lopez, Barelli et al. (ResistanceGA) selects models of resistance with no a priori assumptions and can use both categorical and continuous resistance surfaces (cool!).
While genetic diversity among forest blocks was similar, genetic differentiation was apparent. The genetic distance between these blocks was best explained by both the distance to the nearest village and the density of fire events. This result fits nicely into a “humans did it” narrative, but the authors show caution when making interpretations of variables that have both contemporary and historical contributions:

Although it is tempting to conclude from these results that human-mediated forest fragmentation is the primary driving force of Udzungwa red colobus monkey genetic differentiation, this is not necessarily the case. In fact, it is possible that some of the fragmentation is natural and quite old, but in such cases human settlement and activity in the intervening matrix habitats has likely maintained fragmentation and is contributing substantially to driving genetic differences among forests.

Ruiz-Lopez, M. J., Barelli, C., Rovero, F., Hodges, K., Roos, C., Peterman, W. E., & Ting, N. (2015). A novel landscape genetic approach demonstrates the effects of human disturbance on the Udzungwa red colobus monkey (Procolobus gordonorum). Heredity.

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