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I've always rather liked ducks, ever since we hand-reared some ducklings back when I was still a school-kid. Mind you, the innocent me of those days didn't know what I know now about the effects of sperm competition and sexual selection on their reproductive organs. (Those of an enquiring mind will learn more - much more! - in this excellent piece by Ed Yong.) I liked them enough to make mallard behaviour the focus of my Honours dissertation, before moving on to swans.

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Ducks were domesticated multiple times by humans perhaps beginning around 4,000 years ago in Egypt, but dated to around 500BC in China (Zhou, Li, Cheng, Fan et al., 2018). Domestic breeds - with the exception of Muscovy ducks - are all derived from the mallard, Anas platyrhynchos. Selection by humans has given rise to quite a range of different phenotypes, with breeds differing most obviously in size and colouration. One of the most striking is the Pekin duck breed (image below), with its white feathers, very large size relative to the ancestral mallard, and its excellent rate of egg production. (Those yummy duck legs in the supermarket chiller are quite likely from Pekin ducks.) These characteristics made the Pekin duck an ideal focus for Shuisheng Hou, Yu Jiang, and their colleagues in their just-published search for the 'fingerprints' of artificial selection in domesticated waterfowl.  (However, as we'll see, their work has wider relevance.)

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The paper is based on a large sequencing exercise: the team carried out whole-genome resequencingA of 40 wild mallards, 36 ducks from 12 different indigenous domesticated breeds in Southern China, and 30 Pekin ducks from three separate populations, plus another 1026 individuals produced by crossing mallards and Pekin ducks.

It seems that in China there were two phases of artificial selection during duck domestication. The first saw the development of the various indigenous domestic breeds, and the second, the specific development of Pekin ducks. There appears to have been a genetic bottleneck at the point where that breed first formed, followed by either quite a bit of genetic drift, or else artificial selection targeting those desirable white feathers and large bodies.

The researchers identified 45 'candidate divergent regions' (CDRs) on the ducks' chromosomes that appear to be related to domestication, some of which were 'markers' for various genes. For example, two CDRs were closely associated with genes involved in reproduction and nervous system activity: bear in mind that the behaviour of domesticated animals differs from that of their wild brethren.

One CDR was used to identify a gene (MITF) involved in the production of melanin. Mutations in this gene result in a loss of pigment, apparently by down-regulating the activity of all other genes downstream of it in the melanin-producing metabolic pathway. Further genomic work led the team to decide that a mutation in MITF is the underlying cause of the striking white plumage of Pekin ducks, one that would have been strongly selected for once it appeared as the down, in particular, is much valued for quilts and padded clothing.

And other CDRs appeared to be associated with a part of the genome linked to body size - traits such as the weight of various body parts & of the body as a whole. Additional genomic work traced this to a 'growth factor' gene (IGF2BP1) that's "consistently expressed in Pekin ducks but ... barely expressed in mallards" from hatching to at least 8 weeks of age. And feeding studies suggested that the Pekin duck form of IGF2BP1 affected both the feed intake of the birds and the efficiency with which they converted food to body mass, resulting in their bigger body size.

This finding has implications beyond the ducks, though: the researchers feel it's likely that

consistent postnatal expression of IGF1BPa in other animals may also enlarge their body size. Therefore, IGF2BP1 is a strong performance target for meat production ... in animals.

And from an evolutionary point of view, it's notable how quickly these genetically-controlled traits - white plumage and larger body size - became fixed by artificial selection in just over 2,500 years of duck domestication.

 

A This technique's also been used in a recently-published study on domestication of cattle in East Asia.

 

Z.Zhou, M.Li, H.Cheng, W.Fan, Z.Yuan, Q.Gao, Y.Xu, Z.Guo, Y.Zhang, J.Hu, H.Liu, D.Liu, W.Chen, Z.Zheng, Y.Jiang, Z.Wen, Y.Liu, H.Chen, M.Xie, Q.Zheng, W.Huang, W.Wang, S.Hou & Y.Jiang (2018) An intercross population study reveals genes associated with body size and plumage colour in ducks. Nature Communications. DOI: 10.1038/s41467-018-04868-4

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Polyploidy - the duplication of chromosome sets - is relatively common in plants, and can result in the development of new species. (Many modern food crops are polyploids.) It's much less common in animals, although found in some frogs & salamanders (amphibians) & leeches (annelids). 

So it was with a mix of excitement, surprise, & alarm that I read about a triploid crayfish species: excitement, because I hadn't heard about a polyploid crustacean; surprise, because it's a triploid organism; & alarm, because it's an invasive pest across its range.

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Image: Wikimedia commons; photo by Zfaulkes

Procambarus virginalis, the marbled crayfish, was first found in Germany in the mid-1990s but is now widespread in Europe & Africa, including Madagascar. In a paper published this month, Frank Lyko & his colleagues reported on their study of the species' genome (Gutekunst, Andriantsoa, Falckenhayn, Hanna et al., 2017). They found that it has 3 copies of each of its 92 chromosomes (276 chromosomes in total), and that all the chromosomes come from the slough crayfish (Procambarus fallax), but from two individuals that weren't closely related. The team suggested that the marbled crayfish originated from a mating between 2 slough crayfish, where one parent contributed a normal, haploid, gamete (one copy of each chromosome) & the other, a diploid gamete with 2 copies of each chromosome, produced by non-disjunction during meiosis. Their genomic analysis pointed to the aquarium trade in Germany as the source of the new species. 

Now, triploid organisms are usually sterile, because they're not able to produce viable gametes via meiosis. (The same would be true of a pentaploid, with 5 copies of every chromosome.) Yet this crayfish has rapidly become an invasive species, & that means it makes lots of baby crayfish. How does it do this? 

By parthenogenesis. That is, this is a clonal species. (The researchers describe the Madagascan population of P.virginalis as "genetically homogeneous and extremely similar to the oldest known stock of marbled crayfish founded in Germany in 1995.)

Every marbled crayfish is female, producing 'apomictic' eggs by mitosis. No sperm necessary. And because every individual is capable of producing eggs and - in this species, a lot of them - in ideal conditions the species' population can grow much faster than that of a sexually-reproducing species. This gives the marbled crayfish quite an advantage over other, competing, species when it's introduced into a new ecosystem, which is why it has been able to expand quickly across Europe & Africa - having likely arrived in these countries via the aquarium trade. And again, because they are parthenogenetic, you need just a single individual to begin a new invasive population. In Madagascar their spread was enhanced by human activity in terms of moving animals around to establish new food populations, the warmer temperatures (compared to those in Europe), and the ready availability of suitable freshwater habitats, and there's concern that endemic crayfish species, and their unique ecosystems, are threatened by the exotic invader.

But there's much more to this story than a tale of an unusual crayfish. I found it fascinating that that understanding how the marbled crayfish genome evolves over time may have applications to cancer research:

The generation of genetic diversity will be shaped by a complex set of factors, including the intrinsic mutability of the genome, environmental mutagens, genetic drift and selective pressure. All these factors are known to play an important role in the evolution of tumour genomes. The analysis of mutations in marbled crayfish populations provides an opportunity to detect the generation, fixation and elimination of genetic changes with particularly high sensitivity and robustness and could therefore disentangle the specific contributions of individual factors. As such, it will be interesting to further explore marbled crayfish as a model system for clonal genome evolution in cancer.

 

J.Gutekunst, R.Andriantsoa, C.Falckenhayn, K.Hanna, W.Stein, J.Rasamy & F.Lyko (2017) Clonal genome evolution and rapid invasive spread of the marbled crayfish. Nature Ecology & Evolution doi:10.1038/s41559-018-0467-9

 

Interested readers will also enjoy this summary of the paper, with commentary from other scientists. 

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Students often get to look at hydras - tiny, fresh-water members of the group that includes sea anemones, jellyfish, corals, and the Portuguese man'o'war. All these cnidarians have a simple body-plan: two layers of true tissue with a jelly-like layer between them, a sac-like gut with a single opening that acts as both mouth and anus, and the characteristic stinging cells - cnidocytes - that give the taxon its name. And many of them rely on endosymbiotic algae for their survival, using some of the sugars that the algae produce by photosynthesis. The image below shows part of a hydra's tentacle - you can see not only its green algal symbionts, but also a halo of discharged stings.