There and back again: an angiosperm's tale

Eelgrass (Zostera marina) is the dominant seagrass in the northern hemisphere and provides the foundation of highly productive ecosystems that rival tropical rain forests and coral reefs in ecosystem services.

A seagrass meadow in foggy northern California © SA Krueger-Hadfield

A seagrass meadow in foggy northern California © SA Krueger-Hadfield


Zostera isn’t really a grass, but a monocot, like a tulip. It absorbs nutrients and pollutants and helps prevent erosion in near-shore marine ecosystems.
But it appears that seagrasses recolonized

the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet (Olsen et al. 2016).

A team led by Jeanine Olsen, Thorsten Reusch and Yves Van de Peer, recently published the Zostera marina genome in NatureThis genome represents a huge advance for evolutionary ecologists working at the land-sea interface.
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Haute cuisine: what mystery meat did the Explorers Club dine on in 1951?

What’s the weirdest thing you’ve eaten? Grubs? Alligator? Kudu? I bet nothing you’ve ever eaten comes close to what was purportedly on the menu at at the 47th Explorers Club Annual Dinner in 1951 — Wooly Mammoth.
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Welcome to the Rapture

This image of the rapture is not an accurate depiction of the underlying molecular biology. (Jan Luyken [Public domain], via Wikimedia Commons)

Typical depiction of the rapture. (Jan Luyken [Public domain], via Wikimedia Commons)

The advent of massively parallel, high throughput sequencing has undoubtedly revolutionized biology. However, have you ever wanted to run a parentage analysis, assess basic population structure, or perform any of the other countless applications where hundreds of thousands of SNPs simply aren’t necessary? Or maybe you have 5,000 individuals you need to genotype and can’t afford the bajillion dollars it would cost to use standard next-gen methods.
There are typically two main solutions to this problem.

  1. The first is sequence capture, a method that uses designed oligonucleotides to isolate specific regions of the genome. This method, while quite accurate in the genomic regions it can pull down, is relatively expensive, slow, and not scalable for use with many samples.
  2. The alternative method is a restriction enzyme-based approach (RAD, ddRAD, genotyping by sequencing, etc.). These methods use restriction enzymes to pull down only a portion of the genome and are relatively flexible in the degree to which they reduce complexity. While RAD approaches allow numerous samples to be genotyped at low cost, it is difficult to control the exact location and number of loci that will be sequenced.

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The Carnivorous Rodents of Southeast Asia

Two mouse-like rodents
Celænomys silaceus (Syn. Chrotomys silaceus) and Rhynchomys soricoides (Joseph Smit, 1883, via Wikimedia Commons)

Whoa, Wallace.

There be carnivorous rats on those islands. Sixty-two species, to be exact, across the broader Indo-Australian Archipelago. Among them are small- and large-bodied rats, worm-eaters with elongated snouts (“vermivores”), and even amphibious forms (Fig. 1), and they are all the subjects of a recent Evolution paper by Kevin Rowe and colleagues on the ecological and dietary evolution in this group.

Among orders of mammals, rodents are the most diverse. Like, its not even close. Their diversification in continental Southeast Asia and Indonesia has been spurred even further by island biogeographic dynamics, resulting in highly endemic faunal assemblages across different parts of the archipelego. The pattern appears in many other taxa as well. If you have so much as glanced at a biogeography book, you know the boundaries of these assemblages are demarcated in memorium: Wallace’s line, Huxley’s line, Lydekker’s line.
Many species of rodents worldwide are omnivorous. And even more will consume animal material opportunistically.

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Supergenes and Sparrows with Four Sexes

Supergenes are groups of tightly-linked genes that influence suites of traits relevant to fitness. While long a fixture of evolutionary genetics theory, their role in empirical studies of non-model organisms has been relatively limited, due to limitations in both our understanding of genomic architecture and the fitness consequences of traits.

In a recent Current Biology paper on the evolutionary history and implications of a chromosmal inversion-based “supergene” responsible for white and tan color morphs of White-throated Sparrows (Zonotrichia albicollis), Elaine M. Tuttle and her coauthors overcome this hurdle with what one tweeted was “25 years of fieldwork and a pile of genomics.”

Alternate color morphs in male and female sparrows differ at alternate supergene alleles on chromosome 2, which is highly divergent and potentially the result of hybridization followed by adaptive introgression. Figure 1 from Tuttle et al. 2016.
Alternate color morphs in male and female sparrows differ at alternate supergene alleles on chromosome 2, which is highly divergent and potentially the result of hybridization followed by adaptive introgression. Figure 1 from Tuttle et al.

Those 25 years of field work prompted an investigation of the genomic architecture of a fitness-linked supergene by first documenting perfect “dissociative” mating between tan and white color morphs of sparrow. In other words, any individual bird is restricted to mating only with another bird of both the opposite sex chromosome and color morph supergene (approximately 1/4th of the total population).

Different color morphs of the same sex also displayed remarkably different social behavior: white morph males were highly promiscuous, but tan morph males were monogamous and contributed more to caring for offspring, while a similar pattern was seen in females. Very rare assortative mating events also apparently had severe fitness consequences, as some hybrid individuals were much smaller, potentially as a result of less parental investment.

De-novo whole genome sequencing and population genomics revealed that this dissociative mating results in 99.7% of white morph sparrows being heterozygous for alternative supergene alleles on the second chromosome, while tan morph sparrows are always homozygous.
How did these alternate copies come to exist? A phylogenomic analysis demonstrated the inversion-based supergene originated prior to the divergence of the White-throated Sparrow from its sister species, Harris’s Sparrow (Z. querula). Tuttle et al. posit that its polymorphism is best explained by hybridization with an unknown sister species followed by adaptive introgression of one chromosomal copy. Interestingly, as a result of complete homozygosity and an absence of recombination, this copy may now be degrading, similar to patterns seen in some sex chromosome systems.

The upshot of all this: White-throated Sparrows have effectively four sexes, from their chromosomes to their reproductive behavior. It’s a striking finding that testifies to the power of using long-term field data to put genomics in the context of organismal biology.

References

Thompson, M.J., Jiggins, C.D. 2014. Supergenes and their role in evolution. Heredity 114. DOI: 10.1038/hdy.2014.20

Tuttle, E.M., et al. 2016. Divergence and Functional Degradation of a Sex Chromosome-like Supergene. Current Biology 26. DOI: 10.1016/j.cub.2015.11.069

Posted in adaptation, evolution, genomics, horizontal gene transfer, natural history, population genetics, selection | Tagged , , , , | 2 Comments

How the White Sands lizards lost their stripes

In molecular ecology, most of us work with study systems that are messy, uncooperative, or just plain difficult (note the fecal samples incubating on my lab bench). What I wouldn’t give for a nice, elegant study system — like the White Sands lizards featured in a recent article by Laurent et al.*
Laurent et al. work in the recently formed White Sands system, where ~275 square miles of white dunes are surrounded by the dark Chihuahuan Desert. Several species in this region (reptiles, arthopods, and mammals) have rapidly evolved blanched color morphs to blend into the white sands.
The White Sands system provides a ready-made opportunity to study the genomics of rapid adaptation, which is exactly what Laurent et al. did using two different species of White Sands lizards, each with light and dark color morphs.
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Single dispersal of modern humans to Eurasia

Dolne Vestonice burial 16, South Moravia, Czech Republic (Credit: Martin Frouz)

Dolní Věstonice burial 16, South Moravia, Czech Republic
(Credit: Martin Frouz)


In a typical ancient DNA study where the number of authors exceeds the number of specimens (actually, equals this time), Cosimo Posth and colleagues sequenced 35 pre-Neolithic modern humans from Europe.
By sequencing 35 mitochondrial DNA (mtDNA) genomes, Posth et al. tripled the currently available dataset of hunter-gatherers spanning in age from 35 ka (thousand years) to 7 ka, which covers most of time that hunther-gatherers were present in Europe. Continue reading

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New faces: Elin Videvall

(Elin Videvall)

(Elin Videvall)


This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who am I?
Elin Videvall, PhD candidate in Evolutionary Biology
Where am I?
I’m in the Molecular Ecology and Evolution Lab at Lund University, Sweden
What do I study?
I study host-microbe interactions in avian systems using genomic and transcriptomic tools. In one of my projects I analyse changes in gene expression of both the avian host and its malaria parasite during an ongoing infection, and in another project I study gut microbiome composition and how it relates to fitness in ostriches.
What do I do when I am not studying?
When I’m not working I like travelling, watching movies, enjoy good food and reading.

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New faces: Reid Brennan

(Reid Brennan)

(Reid Brennan)


This week we’re pleased to welcome a big group of new contributors to the blog. By way of introduction, I asked each of them to answer a few quick questions about him- or herself. —Jeremy
Who are you?
Reid Brennan
Where are you?
I’m a PhD candidate in Andrew Whitehead’s lab at the University of California Davis.
What do you study?
My work focuses on the mechanistic basis of local adaptation to abiotic environments. I work primarily on the killifish, Fundulus heteroclitus. These fish are typically found in marine habitats, but a few populations inhabit exclusively freshwater environments. I combine physiological, transcriptomic, and genomic approaches to understand how selection has shaped phenotypes in these different salinities.
What do you do when you’re not studying it?
When I’m not working I try to spend my free time enjoying the great landscape California has to offer. I like to backpack and hike as well as run, bike, and play soccer.

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How to build a mimic

Image from Wikimedia Commons, Source: Mattias Starkenberg

Image from Wikimedia Commons, Source: Mattias Starkenberg


The history of evolutionary and ecological studies on mimic species is deep and chock-full of familiar names (Bates, Darwin, Muller, Wallace are just a few). There has also been no limit on the number of jaw-droppingly gorgeous species that have been under investigation.
A new paper by Evan Twomey and colleagues presents an integrative view into the process of mimetic speciation in yet another beautiful taxon, a poison dart frog appropriately named Ranitomeya imitator.
This frog species is a mullerian mimic of four different members of Ranitomeya and is  interesting due to the multiple, independent instances of mimetic divergence that are in replicate across Peru.
Four Peruvian morphs of Ranitomeya imitator and their associated described in Figure 1 from Twomey et al (2015)

Four species of Ranitomeya dart frog and their associated Peruvian mimic as shown in Figure 1 from Twomey et al (2015)


The authors studied three transition zones in R. imitator by quantifying color phenotypes, genetic variation, and mate choice preferences. Hypothesizing that mimetic divergence is promoting reproductive isolation in these morphs, they predicted that:

  1. phenotype clines should be narrow
  2. genetic divergence among mimetic morphs should be apparent
  3. mimetic morphs should prefer to mate with their own morph

Whether or not these predictions held was dependent on which transition zone was in question, but most were contrary to expectations. While each transition zone varied in the phenotypic width, no transition zone showed any additional genetic differentiation that couldn’t be explained through isolation by distance alone. Additionally, most populations showed no mating preference for their own morph.
The authors used these results to pitch the idea of a speciation continuum among the different morph transition zones of R. imitator:
At the first stage of population divergence, only mimetic color pattern divergence is present (spotted-striped transition zone). In the second stage, clines get narrower, becoming divergent in multiple aspects of overall color pattern, and mating preferences appear among allopatric populations. Lastly, the final stage of the continuum (shown in the striped-veradero transition zone) includes narrow clines that are variable among color pattern components, preferential mating at the transition zone, and restricted gene flow.
The discovery of this continuum is still the beginning of explaining exactly how this differentiation came to be. Selection on single or multiple traits? Geographic barriers? Secondary contact? Differences in divergence time? The authors discuss these options and provide an argument for simultaneous selection on color pattern and body size that has created reproductive isolation during different time frames for each morph.
I just want to know if they need any field help.
 
Twomey, E., Vestergaard, J. S., Venegas, P. J., & Summers, K. (2016). Mimetic Divergence and the Speciation Continuum in the Mimic Poison Frog Ranitomeya imitator. The American naturalist, 187(2), 205. DOI: 10.1086/684439

Posted in evolution, population genetics, speciation | Tagged , | 1 Comment