Growing the evolutionary relationship between green algae and salamanders

Posted on 19 Nov, 2014 by Rob Denton

Spotted Salamander (Ambystoma maculatum) egg mass. Photo by Rob Denton

Spotted Salamander (Ambystoma maculatum) egg mass. Photo by Rob Denton


The presence of  green algae within the developing egg masses of amphibians has been recognized since the early 1900s, but only recently have researchers discovered that the these algae (termed “Oophila”) persist in animal tissues far after leaving the egg. The allure of an unexpected mutualism between an alga and a vertebrate animal (a solar salamander!) is undeniable for both scientists and science journalists, but many authors pump the brakes on coevolutionary explanations until more is understood about the relationship between algae and amphibians at a wider taxonomic level.
Eunsoo Kim and colleagues provide a new perspective on this evolutionary relationship in a new publication appearing in PLOS ONE. Kim and colleagues sampled algal DNA from eggs of four different amphibian species across North America, showing not only a single clade of amphibian-egg algae, but also a partial species-specificity among those algal groups.

We designate this group as the ‘Oophila’ clade, within which the symbiotic algae are further divided into four distinct subclades. Phylogenies of the host amphibians and their algal symbionts are only partially congruent, suggesting that host-switching and co-speciation both play roles in their associations.

These results are another important and encouraging step in fully explaining the beginnings and extent of algal/amphibian symbiosis, while laying the groundwork for some fascinating questions concerning how amphibians allow for this strange association during their development.
Kim E., Lin Y., Kerney R. & Blumenberg L. (2014). Phylogenetic Analysis of Algal Symbionts Associated with Four North American Amphibian Egg Masses, PLOS ONE, 9 (11) e108915. DOI: http://dx.doi.org/10.1371/journal.pone.0108915

Posted in Coevolution, phylogenetics, speciation | Tagged , , , | 1 Comment

From cats to rats: two studies on domestication and tameness

Posted on 18 Nov, 2014 by Noah Snyder-Mackler

Crazy Cat Lady (From The Simpsons)


Anyone who has ever read Charles Darwin is acutely aware of his fascination with domestication – particularly how he fancied fancy pigeons. Darwin drew on his domestication obsession while writing his book, The Variation of Animals and Plants under Domestication, in which he outlined his ‘provisional hypothesis’ of pangenesis (heredity). In the century and a half since, researchers studying the domestication of plants and animals have continued to advance our knowledge of the genetic mechanisms underlying heredity and selection. Here, I interviewed the authors of two recently published studies that elegantly examined the genetics of tameness and domestication in cats and rats.
Continue reading →

Posted in adaptation, association genetics, domestication, genomics, methods, next generation sequencing, phylogenetics, quantitative genetics | Tagged , , , , , | Leave a comment

Here, kitty, kitty. The cat genome sheds light on feline evolution and domestication

Posted on 17 Nov, 2014 by Melissa DeBiasse


Although this kitten looks fierce, Montague et al. recently uncovered the genes responsible for the taming of the house cat, Felis silvestris catus, which coincided with the development of agriculture about 10,00 years ago. Grain crops attracted rodents into human settlements and wildcats were not far behind.

There, many scientists suspect, they [cats] mostly domesticated themselves, with the friendliest ones able to take advantage
of human table scraps and protection. -David Grimm

In their 2014 Proceedings of the National Academy of Sciences paper, Montague et al. published the most complete reference genome for the domestic cat to date. Their research identified the genes responsible for the diversification of felines from other carnivores and the process of domestication in the house cat.
Cats have the widest hearing range of all carnivores and accordingly, Montague et al. identified six genes under positive selection that are thought to increase auditory acuity. The authors also identified signatures of positive selection in a suit of genes related to lipid metabolism in cats, likely related to their obligate carnivory and adherence to a diet high in saturated and polyunsaturated fats.
In terms of domestication in the house cat, the cat genome revealed 13 genes on 5 chromosomal regions that influence behaviors, such as the loss of fear, and responses to rewards, food rewards, in particular. Interestingly, cats appear to be less domesticated than dogs.

The number of genomic regions with strong signals of selection since cat domestication appears modest compared with those in the domestic dog, which is concordant with a more recent domestication history, the absence of strong selection for specific physical characteristics, as well as limited isolation from wild populations. -Montague et al.

This may explain why even the most docile lap kitty has a little bit of wildcat inside.
Montague, Michael J., et al. (2014) Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proceedings of the National Academy of Sciences. doi: 10.1073/pnas.1410083111
Grimm (2014) The genes that turned wildcats into kitty cats. Science. vol. 346. pg 799.

Posted in genomics, population genetics | Tagged , | Leave a comment

The forest resounding at rare intervals with the note of … reproductive isolation

Posted on 14 Nov, 2014 by Stacy Krueger-Hadfield

Hybrid zones are often used as a window with which to gaze upon the evolutionary process (Barton and Hewitt 1989). With the advent of genomic tools, it is possible to detect the genomic signatures and the architecture underlying reproductive isolation. In the case of the black-capped (Poecile atricapillus) and Carolina (P. carolinensis) chickadees, a narrow, but long zone of contact stretches from New Jersey to Kansas in which hybrids experience strong intrinsic selection.

Black-capped chickadee © Laura Meyers

Black-capped chickadee © Laura Meyers


Most studies investigating hybrid zones are snapshots of a particular time and place. Yet, as Taylor and colleagues (2014) highlight in their new Evolution article:

Stochastic processes (biological or from sampling) can, however, generate variation in genetic patterns among loci that can mimic forms of selection, including reproductive isolation and adaptive divergence.

This is especially relevant as stochastic processes can confound outlier approaches with which to detect non-neutral loci. However, utilizing different geographic and temporal samples, comprising different sets of admixed individuals, is one method whereby it is possible to determine whether patterns of differentiation and introgression are the result of selection or of stochastic variation.
In the case of these two chickadee species, the hybrid zone is moving northward at a rate closely matching natal dispersal distance.  Taylor and colleagues found:

consistently low introgression for highly divergent loci [with some localized on the Z chromosome] between  P. atricappillus and P. carolinensis in this moving hybrid zone.  This is strong evidence that these loci may be linked to genomic regions involved in reproductive isolation between chickadees.

Reduced geographic introgression and higher differentiation of sex-linked loci may be driven by lower recombination rates or a higher proportion of infertility alleles on sex chromosomes.  Undoubtedly, the genomic architecture of reproductive isolation between these two species is complex, but the sex chromosomes may be further along the speciation continuum than autosomes (see the comprehensive examination of genomic architecture in flycatchers by Ellegren et al. 2012).
Though fine-scale distribution within chromosomes was beyond the scope of this current study, it appears, nonetheless, that a small proportion of loci contribute to reproductive isolation.  Do other spatiotemporal studies also find consistency of genomic architecture?  Do relatively few loci contribute to reproductive isolation?
 
Barton, NH and GM Hewitt (1989) Adaptation, speciation and hybrid zones. Nature 341: 497-503. doi:10.1038/341497a0
Ellegren, HL, et al. (2012) The genomic landscape of species divergence in Ficedula flycatchers. Nature 491: 756-760. doi:10.1038/nature11584
Taylor, SA, RL Curry, TA White, V Ferrretti, I Lovette (2014) Spatiotemporally consistent genomic signatures of reproductive isolation in a moving hybrid zone. Evolution 68: 3066-3081. doi: 10.1111/evo.12510

Posted in adaptation, conservation, genomics, next generation sequencing, population genetics, speciation | 1 Comment

Admixture maps in R for Dummies

Posted on 13 Nov, 2014 by Arun Sethuraman

Before we get started, I’d like to point everyone to an excellent tutorial here by Kim Gilbert on making maps in R. I have been grappling with overlaying admixture plots, and migration routes on top of maps recently, and thought I’d put together a quick tutorial on that

What you will need:

1. GPS coordinates

Eg. gps.data

ID,Lat,Lon 1,33.72,-94.40 2,34.1682185,-111.930907 3,37.2718745,-119.2704153

2. Admixture proportions

Admixture proportions – these are routinely printed out as the “Q” matrix by STRUCTURE, and in a file suffixed with a “Q” by ADMIXTURE. I added a column with sample sizes to this, to proportionately resize the admixture pies.

Eg. admixprops.data

K1,K2,Num 0.836601,0.163399,12 0.565904,0.434096,16 0.508735,0.491265,18 0.111114,0.888886,9

3. The maps() and plotrix() packages in R

Continue reading →
Posted in howto, population genetics, R, software, STRUCTURE | Tagged , | 14 Comments

Is genetics a requirement for restoration?

Posted on 12 Nov, 2014 by Rob Denton

Image from Luc Viatour (www.Lucnix.be)


The fields of conservation and genetics have relied heavily on one another for quite a while now (they even made an aptly named journal together!). Using genetic information is now an accepted, and even expected, step in recognizing and protecting species at risk. However, less attention has been paid to the role of genetic information during ecological restoration, the applied steps of manipulating ecosystems to a more historical or resilient state.

Thus, the aim of this paper is to review how genetics has been utilised in restoration ecology to the present and to identify ways in which genetics could be better utilised to inform restoration ecology in the future.

Mijangos et al. cite multiple cases in which the ecological assumptions made based on a species’ life history don’t match up with their genetic signature (example: some clonal species defy expectations by having a combinations of low seed dispersal and high population genetic diversity). These examples provide compelling support for a combination of genetics, ecology, and ecosystem services when making all restoration decisions.

Genetics can facilitate the evaluation of a restoration project by, for example, quantifying gene flow or demographic changes in the targeted populations. The role of genetics is not only limited to indirectly evaluating population dynamics or ecosystem processes however, as genetics can directly influence the success of restoration projects.

The authors provide a comprehensive review of how basic population genetic inference (effective population sizes, migration rates, connectivity, etc.) can benefit restoration goals. While this shouldn’t be surprising, providing a useful document for both molecular ecologists and restoration practitioners to look over and see the benefit of collaboration is a valuable contribution for the future of this young field.
Mijangos J.L., Pacioni C., Spencer P.B.S. & Craig M.D. (2014). Contribution of genetics to ecological restoration., Molecular Ecology, DOI: 10.1111/mec.12995

Posted in community ecology, conservation, Molecular Ecology, the journal, natural history, population genetics | Tagged , , | 1 Comment

Bugs fighting bugs: the evolution of the arthropod immune system.

Posted on 11 Nov, 2014 by Noah Snyder-Mackler

Deer tick (Ixodes scapularis)
photo courtesy of the Agricultural Research Service via Wikipedia

Since the beginning of time, animals have needed to protect themselves from invaders. They primarily do so via their innate immune system, in which trained killer cells attack foreign pathogens – ranging from microscopic bacteria to macroscopic worms. While we know a fair amount about the innate immune system of most vertebrates and some insects, we know comparatively little about the immune system of arthropods. Here is where the new preprint by William Palmer and Francis Jiggins comes in.
Using the recently acquired sequences of multiple arthropod genomes, the authors characterized the immune systems of some pretty icky arthropods: the Water Flea, the Coastal Centipede, Chinese Scorpion, the House Spider, the Deer Tick, and the Western Orchard Predatory Mite, and the Red Spider Mite. Interestingly, the authors found:

… both remarkable diversification of the immune response across the arthropods, and unexpected conservation and similarities to mammalian genes… These include a group of arthropod toll-like receptors that share structural similarity with vertebrate TLRs and cluster with them phylogenetically.

This is important because it suggest that some components of the innate immune system, such as TLRs – which recognize foreign microbes and activate immune cell responses, have deep roots in our evolutionary history. The authors state:

Our results confirm an ancient origin for the innate immune system, predating the split between protostomes and deuterostomes. We find striking examples of conservation between vertebrates and arthropods, despite these two groups having diverged before the Cambrian explosion some 543 million years ago.

W. Palmer & F. Jiggins “Comparative genomics reveals the origins and diversity of arthropod immune systems” BioRxiv.
DOI: http://dx.doi.org/10.1101/010942

Posted in genomics, phylogenetics | 1 Comment

Different genetic paths lead to the same phenotypic destination

Posted on 10 Nov, 2014 by Melissa DeBiasse


Male field crickets (Teleogryllus oceanicus) on the Hawaiian archipelago sing to attract mates using acoustic structures on their wings. While singing makes the ladies swoon, it also gives away the male cricket’s location, making it vulnerable to fatal attacks by a parasitoid fly (Ormia ochracea). In the last decade, male crickets that have lost the ability to sing have appeared, first on Kauai and then later on Oahu.
In their 2014 Current Biology paper, Pascoal et al. tested whether the presence of the silent, ‘flatwing’ phenotype on Oahu resulted from migration and introgression from the Kauai population or independent evolution of the trait on each island. Morphometric analyses showed Kauai and Oahu flatwing phenotypes were four times more different from one another than any two normal-winged phenotypes were from one another. Interestingly, this means different wing shapes achieve the same result- silence. Breeding crosses between normal and flatwing crickets showed flatwing is inherited as a Mendelian, sex-linked mutation on both islands. The shared mode of inheritance presents the possibility that a single mutation could produce the different flatwing phenotypes due to the different genetic backgrounds of the Kauai and Oahu crickets. The authors collected RADseq data and used a bulk segregant analysis (BSA) to identify single nucleotide polymorphisms (SNPs) in linkage disequilibrium with the flatwing phenotype in each population.

 If the observed population-level morphological differences are caused by expression of the same sequence variant in different genomic backgrounds after introgression, then the majority of linked SNPs should be shared between the two populations. In contrast, if the two wing-silencing phenotypes are caused by sequence variants that affect genetically distinct regions of the X chromosome, then the BSA should recover nonoverlapping sets of linked SNPs for each island.

And what did they find? The genome-wide scans showed a distinct set of SNPs were linked with flatwing in each island population, indicating different genomic architectures are responsible for the silent phenotypes in Hawaiian crickets. Essentially, this silent, flatwing trait has evolved independently on each island.

Divergent wing morphologies linked to different loci thus cause identical behavioral outcomes—silence—illustrating the power of selection to rapidly shape convergent adaptations from distinct genomic starting points.

Pascoal S, Cezard T, Eik-Nes A, et al. (2014) Rapid convergent evolution in wild crickets. Current Biology 24, 1369-1374.

Posted in adaptation, population genetics | 1 Comment

Happy as a clam, despite genetic uniformity

Posted on 7 Nov, 2014 by Stacy Krueger-Hadfield

 

Corbicula fluminea. photo courtesy of Noel M. Burkhead - U.S. Geological Survey

Corbicula fluminea, photo courtesy of Noel M. Burkhead – U.S. Geological Survey


Introduced populations of non-native species are often associated with low genetic diversity, as measured by neutral genetic loci, and, thus, considered a paradox (but see Roman and Darling 2007). The study by Lise-Marie Pigneur and colleagues documents an extreme example of this putatively paradoxical phenomenon in the invasive clam genus Corbicula. The authors document four, undiversified genetic lineages in Europe and the Americas, whereas the native range, in the northwest Pacific, is characterized by higher levels of genetic diversity. Yet, the relationship between genetic diversity and invasion success is not as straight-forward as it might seem.

The apparent importance of the flexibility of reproductive mode to the success of low diversity invasions suggests that there is much to learn regarding how evolutionary history and life history characteristics affect the invasiveness of species. (Roman and Darling 2007)

The mixed mating system exhibited in the native range of these Corbicula clams may hold an enticing clue as to the success of the invasive lineages. The dioecious sexual lineages are strictly diploid, whereas the hermaphroditic asexual, or more specifically androgenetic (i.e., male parthenogenesis), lineages can be diploid, triploid or tetraploid. But, interestingly, the unreduced spermatozoon from one androgenetic lineage can fertilize an egg of another androgenetic lineage. The resultant progeny exhibit the nuclear genome from one and the mitochondrial genome from another lineage, a phenomenon termed egg parasitism or mitochondrial capture (e.g., Hedtke et al. 2008, Pigneur et al. 2012). Thus, despite reduced genetic diversity, androgenesis in Corbicula clams may combine clonality with the ability of rare genetic material exchange.

Associated with other life history traits of Corbicula lineages, it might have been a determinant mechanism that contributed to the invasiveness of undiversified populations of these clams. (Pigneur et al. 2014)

The role of life history traits coupled with labile reproductive systems in invasion success and invasive histories warrants further attention, especially in aquatic and marine environments.
J Roman and JA Darling (2007) Paradox lost: genetic diversity and the success of aquatic invasions. TREE 22: 454-464; http://dx.doi.org/10.1016/j.tree.2007.07.002
SM Hedtke, M Glaubrecht, DM Hills (2008) Rare gene capture in predominantly adrogenetic species. PNAS 108: 9520-9524; doi:10.1073/pnas.1106742108
L-M Pigneur, SM Hedtke, E Etoundi, K Van Doninck (2012) Androgenesis: a review through the study of the selfish shellfish Corbicula spp. Heredity 108: 581-591; doi:10.1038/hdy.2012.3
L-M Pigneur, E Etoundi, DC Aldridge, J Marescaux, N Yasuda and K Van Doninck (2014) Genetic uniformity and long-distance clonal dispersal in the invasive and androgenetic Corbicula clams.  Molecular Ecology 23: 5102-5116; doi: 10.1111/mec.12912

Posted in natural history, population genetics | Leave a comment

Highlights from the 2014 Ecological Genomics Symposium

Posted on 6 Nov, 2014 by Melissa DeBiasse

Ecological genomics is a rapidly growing field that aims to understand the genetic mechanisms responsible for the adaptive responses of organisms to their environment. I’m jumping into this area of research as a postdoc in the Kelly Lab at Louisiana State University and last weekend I attended the 12th annual Ecological Genomics Symposium hosted by the Ecological Genomics Institute at Kansas State University. The talks and posters presented at EGS covered a broad range of questions, critters, and data types- both phenotypic and genomic, but the common goal of many of the projects was to determine how genotype and environment influence the evolution of phenotypes. In this post I’ll highlight a small cross section of the exciting research I heard about at the meeting.
Dr. Zac Cheviron at the University of Illinois and Dr. Catherine Linnen at the University of Kentucky both study the (adorable) deer mouse Peromyscus maniculatus, but they focus on different adaptive traits that have evolved in this species. Deer mice have the broadest elevational distribution of any North American mammal, occurring from sea level to 4300 meters, and Zac studies how mouse populations have adapted to life at such extreme heights. His recent work has shown that under the hypoxic (i.e. low oxygen) conditions expected at high elevation, mice from the highlands outperform lowland mice by, generally speaking, using oxygen more efficiently. You can read about the very cool details of this work here and here.

The Deer mouse, Peromyscus maniculatus. Image courtesy of J. N. Stuart, Flickr

The Deer mouse, Peromyscus maniculatus. Photo courtesy of J. N. Stuart, Flickr


Deer mice found at lower elevation in the Nebraska Sand Hills have multiple traits, including light colored fur, that help them blend in with the light colored soil and avoid detection by avian predators. Catherine presented results from a recent Science paper showing that in light colored mice different phenotypic traits correspond to different mutations within a single gene called Agouti. This work is a great example of how single nucleotide polymorphisms (SNPs) can determine phenotype.
Continue reading →

Posted in adaptation, conferences, genomics | Leave a comment