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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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I'm starting to gear up for some Schol Bio preparation days in the regions (hi, Hawkes Bay! See you in 4 weeks!) and realised that I haven't written anything specifically focused on those exams for a while. So I thought that putting something together would be a good way to spend a rather wet Sunday. At these days we usually put quite a bit of time into working on answers to the previous year's questions, so in this post let's look at one from the 2015 paper.

In 2015, the examiner based question #1 on a statement by then-Opposition MP Trevor Mallard that he felt that it could be possible to bring moa back to our national parks

... the moa will be a goer, but we're talking 50-100 years out

and expressed a desire to see

small ones that "don't weigh much more than turkeysA ... ones that I could pat on the head rather than ones that are going to bowl us over...

After providing some other contextual material (as is the norm for Scholarship Biology - be aware that you'll need to factor a reasonable amount of reading time into your planning on the day), the examiner asked students to

Analyse the information provided in the resource material and integrate it with your biological knowledgeB to discuss:

  • the evolutionary and ecological factors that contribute to declining population numbers that may result in the extinction of species AND account for the very large increase in the rate of extinction of species in modern times. Use named examples to support your discussion
  • how humans could manipulate the transfer of moa DNA to restore a moa population to the Rimutaka Forest Park AND analyse the biological implications of this. Give your justified opinion on whether the 'moa is a goer'.

There are a number of factors that could feed into a decline in population size. High on most lists would be a reduction in the genetic diversity of the population, something that could be due to genetic drift. If the population is isolated, there would be little or no gene flow due to migration or breeding with individuals from other populations, which would also have a negative impact on genetic diversity and result in the phenomenon of inbreeding depression. (Think of NZ's black robins, as an extreme example.) This is why those managing endangered species such as takahe & kakapo are careful to mix breeding up where possible.

Then, if a species is a specialist, environmental change could pose a problem if the resources the organisms rely on diminish or disappear; they may lack the flexibility to change to others. Specialists are then perhaps more likely to feel the effects of loss of habitat due to climate change or a natural disaster; if they're a non-migratory species then the problem is compounded. Either way, the population sizes of such species are likely to decline. That environmental change can include the arrival of exotic predators, competitors, & diseases - something that's certainly had a significant negative effect on NZ's native fauna & flora. Takahe, for example, have suffered from competition with deer, but were also badly affected by the arrival of stoats. Mustelids, rats, & feral cats kill native birds, reptiles, and insects much faster than the prey species can replace their losses. And chytrid fungus infections pose a threat to amphibian species worldwide, including our own ancient native frogs.

Ultimately their population size may become too small to be sustainable - this is where the concept of 'effective population size' comes into play. If the total size is large, but most individuals are past their normal breeding age, then the effective population size is small. This means that at the population level, reproductive outputs decline. And once death rate exceeds the birth rate, extinction is on the horizon. In addition, in a small, isolated population inbreeding becomes common, and any harmful recessive alleles may be more likely to be expressed. 

It may not be only that species that's affected, either. Removal of one species from an ecosystem can have ramifications for the entire ecosystem - this relates to the concept of a keystone species.

In all of this, we should not forget or underestimate the impact of our own species. Habitat destruction accompanies human settlement, as does the introduction of new species (in NZ, rabbits, possums and pigs along with the deer, rats, cats, dogs, and mustelids). Humans are reasonably efficient predators themselves: it's estimated that moa became extinct here within 200 years of first human arrival. (Research suggests that human arrival & expansion, coupled with climate change, is implicated in megafaunal extinction in Patagonia & elsewhere.)

So, could we bring 'the moa' back? (I really dislike this whole 'the' thing: there were around a dozen different species of moa in NZ, with their own ecological niches.) In theory, yes, we could. It's possible to extract DNA from moa bones, and Massey University researchers used this aDNA to work out how many species of moa once existed here. Mind you, to bring any species of moa back you'd need to ensure you had its full genome!

Then, you'd need to identify a suitable surrogate parent, remove the nuclear DNA from eggs from that host, replace it with your moa DNA, and implant the egg into the surrogate. What would that surrogate be? Perhaps another ratite, such as an emu? Or - if we're going with Mr Mallard's wish for small & manageable moa - perhaps a turkey, given the similarities in size. You'd need to do this multiple times, with the remains of multiple individuals of your target species, and to clone both male and female moa (using the sex chromosomes to identify them), in order to end up with a genetically-variable breeding population. 

Easy to say. But in reality things are likely to be more complex, & more difficult, than that. It's debatable, for example, whether scientists could find a large enough number of P.geranoides individuals to be able to reconstitute that genetically-variable population. In that case, the threats related to inbreeding & genetic drift would still be there, and the species could well spiral back into extinction. 

From an ecological perspective, moa were reasonably large, and each individual would eat a lot of vegetation each day. Given that the Rimutaka Forest probably isn't the same as it was when moa were in their hey-day, would re-introducing moa have a negative effect on the current ecosystem, particularly on the other herbivores? We need to be able to answer that one, to avoid inadvertently causing further changes to the forest community's species composition. 

So, what would be your final opinion? You could argue, along with Mr Mallard, that yes, "the moa is a goer". Remember that you need to justify that opinion: bringing moa species back could help to re-establish the natural biodiversity of ecosystems that human actions have damaged.

Or, you could say - as I would - that no, this isn't a viable proposal. Firstly, as far as I'm aware, birds have yet to be cloned successfully. (There's a list of cloned species, plus a lot more information, at this FDA link.) And secondly, this seems to be a diversion from a more pressing problem: the need to use that money & scientific effort to conserve those ecosystems and species that we currently have.

 

A Mr Mallard was wise to limit the size of the species he wanted resurrected. After all, the giant moa species, Dinornis robustus & D.novaezelandiae, stood over 2m tall & weighed around 250kg. The much smaller Mantell's moa, Pachyornis geranoides, was under 0.5m tall & would have tipped the scales at 20kg ie roughly turkey-sized. Much less alarming, should you meet one in the bush!

B This reminds me that I also need to write something on what the examiner is looking for, in giving an instruction like this.

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Pangolins are strange little creatures, with their diet of ants and termites, and the entire outer surface of their bodies covered with armour-like scales (face, belly & the inner surfaces of the limbs are either hairy or naked). When in danger, pangolins are able to roll up in a ball, presenting only that armoured surface to a predator.

Actually, some of them aren't so little: from nose tip to tail tip, they range from 75 cm to more than 1.5 m in length, with their strong tails making up about half of that. Arboreal species tend to be smaller, just a couple of kilos in weight, but apparently the giant pangolin can weigh in at over 30kg. 

Ground Pangolin at Madikwe Game Reserve

Image by David Brossard (Scaly Anteater exits stage left) [CC BY-SA 2.0 (https://creativecommons.org/licenses/by-sa/2.0)], via Wikimedia Commons

In taxonomic terms pangolins have their own order (Pholidota), with a single family (Manidae) and genus, Manis; there are 4 species in Africa and 4 in Asia. Like giant anteaters they are toothless (edentate), & indeed, they converge with the giant anteaters in a number of ways and for a while the two groups were thought to be closely related. However, it seems that molecular data (from DNA & amino acids) places the pangolins' order as a sister group to the carnivores. So, the toothless state characteristic of both types of anteater has evolved more than once, as has the heavy musculature and massive claws of their forelimbs. 

I hadn't really thought before about how pangolins manage to digest their diets of termites and ants, after licking them up with those sticky, extrusible tongues. (Here's something else I didn't know: a pangolin's tongue is as long as head & body combined ie half their total body/tail length. It's folded back into a throat pouch when not in use, and the animals produce so much sticky saliva that they have to drink frequently.) It turns out that the stomach is rather like a bird's gizzard: its walls are hardened and it contains sand or very small pebbles, which help to grind up those crunchy meals as the muscles in the stomach wall contract and relax.

It seems that yesterday was World Pangolin Day. It would be nice to think that drawing attention to the plight of these strange little creatures would change the fact that they are currently the most trafficked mammal in the world. After all, they range from vulnerable to critically endangered status and are supposedly protected by both national and international legislation. Sadly I think that greed & stupidity will push them over the edge. 

Why? Because, as this article in The Independent says, pangolins are poached on a huge scale 

for their meat, which is considered a delicacy in China and Vietnam, and their scales, which are used as ingredients in traditional Asian medicine. 

Practitioners believe scales are capable of treating a range of ailments including asthma, rheumatism and arthritis.

That defensive habit of rolling up in a ball is useless against poachers, who can just pick the animals up. So, people are prepared to pay a lot of money for the meat and the scales of these creatures, which is where both greed and stupidity come into it.

Greed: well, money talks. In December 2016, Chinese customs made their largest-ever confiscation of scales - a mind-boggling 3.1 tons from an estimated 7,200 pangolins. Their worth: about $US2 million. Research by TRAFFIC, a network that monitors the international wildlife trade, suggests that around 20 tonnes of pangolins, & pangolin parts, are trafficked each year.

And stupidity, because those hugely expensive scales are made of keratin - nothing more and nothing less than the protein that makes up our own hair and nails. People consuming the pangolin's scales might as well chew their own fingernails, for all the good it would do them. I guess they'll have to, when the pangolins (and rhinos, whose horns are keratin too) are gone from the world.

 

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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.

File:Procambarus fallax forma virginalis.jpg

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.