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Cats aren’t evil, but they are a problem David Winter Jan 22

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It seems Gareth Morgan has declared a war on cats. It will, I’m sure, come as a great surprise to you that Morgan’s description of cats as ruthless and sadistic killers that we must eventually purge from the land  has met some opposition. Invoking outrage is pretty good way to get free advertising in New Zealand, and if you measure the campaign’s success in tweets, comments and talkback calls I guess Morgan is on to a winner. But I’d like to think we can do better than simply setting up an argument between supporters of Morgan’s Maoist purge and cat lovers who think their moggie can do no harm.

Cats are a problem

Most of the reaction to Morgan’s campaign has been to basically treat it as a joke. We should be clear then, that introduced predators are the number one threat to New Zealand species. Stoats, weasels possums and rats all contribute the decline of birds and lizards (and invertebrates, though we don’t monitor those species closely enough to track their progress). Cats are certainly part of that problem. They have contributed to the extinction of at least 6 bird species  in New Zealand, and many more populations and subspecies have been lost partly as a result of predation by cats (Merton, 1978). Cats continue to pose a threat to our wildlife. The impact of feral cats on shorebirds  (plovers, dotterels, oystercatchers) and kakapo is well documented (Karl and Best, 1981 doi: 10.1080/03014223.1982.10423857). In the space of a week one cat managed to kill 102 native short tailed bats.

The problem isn’t restricted to wild cats. Pet cats will attack and kill native birds and lizards when they have the chance. In Dunedin the impact of tame cats is large enough that it’s been estimated local bird populations (including natives) wouldn’t survive if they weren’t replenished by migrants from around the fringes of the city (van Heezik, et al. 2010. doi: 10.1016/j.biocon.2009.09.01)


Getting rid of cats isn’t necessarily a solution

It’s clear then, that cats are a problem for the conservation of native wildlife. But it’s not nearly as clear that simply getting rid of cats will be much help. Every study of the diet of cats in New Zealand has found that cats kill a lot of mice and rats. These rodents are themselves predators of birds so removing one predator from our country may simply let another run amok. When feral cats were removed from Little Barrier island it led to an outbreak in kiore (Pacific rat), which threatened Cook’s Petrel populations on that island (Rayner et al, 2007 avaliable via PMC ).

Should we phase out cats in New Zealand?

So, if Morgan’s plan was actually do-able, should we do it? I have to honest here and tell you, I don’t know. It’s abundantly clear that cats, both feral and domestic, can kill native animals. It’s clear that in at least some cases that killing can have a major impact on populations, but removing cats might not help all that much. If you want to know whether the impact of your typical urban moggy justifies Morgan’s campaign, especially given the abundance of rats in New Zealand, you’d have to ask a conservation biologist. That’s something no news organization has bothered with yet, as far as I can tell.

Is this the conversation we should have started?

It’s fairly obvious that Morgan’s website, with its strange anthropomorphism (cats are predators sure, sadists? no) was designed to draw headlines and “start conversations”. But what hope is there for environmentalists in conversation where our side wants to take people’s kittens away?

Introduced predators are the biggest threat to New Zealand’s biodiversity, so the goal of eventually controlling these predators so tightly that they no longer pose a threat is a very worthy one. But the sort of change required to get us from today, where only 12% of the conservation estate is managed for predators, to that goal has to come from the ground up. Picking fights like this will get you headlines, but I don’t think it will change anyone’s mind.


Merton, Donald V. “Controlling introduced predators and competitors on islands” pp 121-128. In Temple, S.A. (ed.) Endangered birds: management techniques for preserving threatened species 1978

(image at the top via Pauline Dawson/ArtAndMyLife)

Sunday Spinelessness – 5 down…. quite a few to go David Winter Jan 20

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I got some good news this week – a paper I’m an author on was accepted for publication pending some minor revisions. That’s great because career advacement in academia rests largely on what we publish, and this is a good paper that I’ll be happy to add to my CV. It’s also quite happy about his particular paper being (almost) accepted because it’s about serpulids, segmented worms of the phylum Annelida (relatives of earthworms). A new phylum for me.

Biology is about diversity. I know I always go on about this, and end up affecting the overly-enthusiastic style of the guide in Douglas Adams’s Hitchiker’s Guide to the Universe:

Biological is diverse. You just won’t believe how vastly, hugely, mind- bogglingly diverse it is. I mean, you might think there are lot of creatures in your average David Attenborough documentary, but that’s just peanuts to the true diversity of biological systems, listen…

Well, I don’t know to put in words, so let’s try a picture. All that biological diversity got here because life evolves. When populations break up they are free to evolve apart from each other and develop entirely new functions or features and so become different. In this way, life is a tree, forming new branches as populations split. When we come to deal with the diversity of life, biologists try to reconstruct that tree, giving names to those tips and twigs which belong to a particular branch. In that  system of classification the phylum (plura phyla) is the one of the deepest divisions.

 Creatures in separate phyla have usually been evolving apart from each other for 600 million years or more, and represent entirely different ways to deal with the trials of life. The annelid paper will mean I’ve published on 5 different phyla. That’s exciting for me – it’s nice to think I’ve added a little to our knowledge of decent sampling of the tree of life. But the truth is, biology is just so diverse that I’ve not even made a dent the tree of life. Here’s a picture of all the Eukaryotic phyla (that is, creatures with cells like ours, but not bacteria and archaea) with only those I’ve published at least one paper on labeled:




Tree was drawn and shaded with iTOL‘s nifty interfact to the NCBI taxonomy. There’s a couple of things to note here. Because this is the NCBI taxonomy it’s a curated tree rather than the result of any particular analysis. Although we aim to create biological groups “natural”, in the sense they are a single branch in the tree of life, the rank giving to a particular branch is somewhat arbitrary and will differ between different groups (so green plants, which traditionally had “divisions”  rather than phyla are certainly underrepresented here). Protists (single-celled eukaryotes) are certainly diverse, but Psi Wavefunction tells me protistologists have almost given up on rank-based taxonomy so this might not be a fair representation of them.
In any case, it’s certainly a spur to me to get back to work and fill in a few blanks on the figure!

Measuring population differentiation in R David Winter Aug 09

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ResearchBlogging.org

This is a little bit different than most posts here. I have a paper out today in Molecular Ecology Resources:  “mmod: an R library for the calculation of population differentiation statistics” (doi: 10.1111/j.1755-0998.2012.03174.x). Looking around the web, there aren’t many simple expositions of just what a “differentiation statistic” might be, and why the “modern measures of differentiation” my little R package can calculate might improve on the more traditional ones. So,  I thought I’d have a go here. 

Biologists often want to be able to measure the degree to which a population is divided into smaller sub-populations. This can be an important thing to quantify, because sub-populations within highly structured populations are, to some extent, genetically distinct from other sub-populations and therefore have their own evolutionary histories (and perhaps futures).

To illustrate this point I’ve run some simulations. Imagine if we had 5 subpopulations, each with a thousand individuals. In each population we will follow the fate of a locus with two alleles, R and r that have no effect on survival or reproduction and start with frequencies 0.8 and 0.2 respectively (these numbers motivated by this post). In the absence of gene flow between these populations (Panel 1) the frequency of the r allele bounces around due to genetetic drift (evolutionary change, after all, is inevitable). Crucially though, changes in one population can’t effect other populations so we end up with substantial among-population differences in allele frequency. In the next two panels, in each generation a proportion of each population’s individuals (0.001 and 0.01 respectively) are drawn from the other populations in the simulation. Now that the populations are sharing genes the lines that represent their allele frequencies pull together  (that is, the among-population variation is reduced). 




 

One way to quantify the among-population variation displayed in these simulations is to look at the number of heterozygotes you expect to observe across the entire population. The final values for P(r) in the first simulation were {0.33, 0.47. 0.88. 0.10. 0.33} with a mean frequency of 0.42 (so the frequency of the R allele would be 0.58). Knowing our Hardy Weinberg, if we had one big population with two alleles, one being at a frequency of 0.42 we’d expect to get 2pq = 2 * 0.42 * 0.58 = 0.40 heterozygotes. We can call that number Hfor expected total heterozygosity. But thats not what we’d actually see in this case. The sub-populations that make up this larger population have their own allele frequencies, when we calculate the expected proportion of heterozygotes for each of these populations by themselves we end up with {0.44, 0.49, 0.21, 0.18, 0.44} for a within-population expected heterozygosity (HS) of 0.35*. This lack of heterozygotes within sub-populations compared with the total population expectation will always arise when genetic drift makes sub-populations distinct from each other. 
Masatoshi Nei  used this pattern to propose a statistic to quantify population divergence called G
ST, which he defined like this:

 GST = (HT HS HT

Nei’s motivaton with GST was to generalise Sewall Wright‘s FST **, which was defined for diploid organisms and two-allele systems, so that it could be used for any genetic data. But there’s a problem with this formulation. Because HT  is always larger than H and can’t be greater than one, the maximum possible value of 
GST  is 1-HS. This dependency on the within-population genetic diversity means comparisons between studies, and even between loci in one study, are difficult (since Hwill likely be different in each case). This is particularly worryingly for highly polymorphic makers like microsatellites, which can give values of HS as high as 0.9, severely constraining the possible values of GST.


Although the problem of 
GST‘s dependence on HS has been known for a while, it’s taken some time for new statistics that get around this problem to be developed. Philip Hedrick (doi: 10.1554/05-076.1) along with Patrick Meirmans (doi: 10.1111/j.1755-0998.2010.02927.x) introduced G”ST  - a version of GST that is corrected for the observed value of HS as well as the number of sub-populations being considered. Meirmans used a similar trick to define φ’ST  (doi: 10.1111/j.0014-3820.2006.tb01874.x), another FST analogue that partitions genetic distances into within- and between-population components. Most recently, Lou Joust introduced an entirely separate statistic, D, that  directly measures allelic divergence (doi 10.1111/j.1365-294X.2008.03887.x). 


The statistical programming language R is becoming increasingly popular among biologists. Although there is a strong suite of tools for performing population genetic analyses in R, code to calculate these “new” measures of population divergence have not been available. My package, mmod, fills this gap.  I won’t give too many details of the package here, as that’s detailed in the paper and the package is will documented. Briefly, mmod has functions to calculate the three statistics described above (and Nei’s 
GST ), as well as pairwise versions of each statistic for every population in a datastet. It also allows users to perform bootstrap and jacknife re-sampling of datasets, the results of which are returned as user-accessable objects which can be examined with any R function (there is also a helper function to easily apply differentiation statistics to bootstrap sample and summarise the results) . The library is on CRAN, so installation is as easy as typing “install.pacakge(“mmod”)”, the source code is up on github. If want to use the package I’d suggest reading the vignette (“mmod-demo”) before you dive in.



I’m keen to hear about bugs or feature requests from users, just email them to




Reference:


Winter, D.J. (in press). MMOD: an R library for the calculation of population differentiation statisticsMolecular Ecology Resources : dx.doi.org/10.1111/j.1755-0998.2012.03174.x

* mmod actually uses nearly unbiased estimators for these parameters, to deal with the way small population samples can mis-represent the actual allele frequencies in populations.

** I don’t want to write an entire history of F-statisitcs here, because it’s a big and murky topic, but I did want to make the point that the formulation I gave for GST  is often presented as “Wright’s FST ” in genetics courses. Wright was certainly aware that his statistic was related to the proportion of heterozygotes you expect to get in a populaiton, but, when he introduced F-statistics in general, and FST  in particular, he was really dealing with correlation among gametes at various levels of population structure. Unfortunately, there are now many many definitions of FST  floating around, and it’s probably pointless to argue about a “right one”. If you use my package I encourage you to be explicit about, and cite, the particular statistic that you are using. For each of the the FST  analogues that the package calculates the in-line help contains the correct reference. 

Sunday Spinelessness – How snails conquered the land (again and again) David Winter Aug 05

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Christie Willcox wrote a nice article this week on how one small group of organisms called “vertebrates” first evolved to live on land. Since you are a vertebrate who lives on land, you should probably go and read Christie’s piece. I wouldn’t want you, however, to go around thinking those first fish to leave the ocean behind were pioneers making a uniquely difficult transition. By my figuring, onycophorans (velvet worms like peripatus), tardigrades, annelids, nematodes, nemerteans (ribbon worms) and quite a few arthropod lineages have also taken up a terrestrial lifestyle. Many of those lineages were already breathing air before Tiktaalik, Ichthyostega and your other long-lost relatives came along to join them on land. But if you want to talk about transitions from marine to terrestrial lifestyles then you really want to talk about snails. You can find snails living in  almost every habitat between the deep ocean and the desert, and snails have adapted to life on land many different times. In fact, a litre of leaf litter taken from a New Zealand forest can contain snails representing three separate transitions from water to land.

Almost all the land snails I’ve talked about here at The Atavism are descendants from just one invasion of the land. We call these species the stylommatophorans and you can tell them from other landlubber-snails because they have eyes on stalks (as modeled here by  Thalassohelix igniflua):

These snails are part of a larger group of air-breathing slugs and snails (including species living in fresh water,  estuaries and even the ocean) called pulmonates or “lung snails”. As both the common and the scientific names suggest, pulmonates breathe with lungs. Specifically, the mantle cavity, which contains gills in sea snails, is perfused with fine veins that allow oxygen to permeate the snails’s blood. In relatively thin-shelled species you can often see this “vasculated” tissue in living animals:

Blacklight photo of Cepaea nemoralis showing ‘vascularised’ lung. Photo is CC BY-SA via Wikipedian Every1Blowz
The pulmonates can also regulate the amount of air entering their lungs with the help of an organ called the pneumatostome or breathing pore –  an opening to the mantle cavity that the snail can open or close at will:

A leaf-veined slug from my garden – the small opening near the “centre line” of the slug is the pneumatostome. Interestingly, leaf-veined slugs don’t have lungs, the pneumatostome opens to a series of blind tubes not unlike an insect’s respiratory system

So that, along with a whole load of adaptations that prevent a fundamentally wet animal from drying out, is your basic land snail. But those little leaf-litter snails I’ve been talking about for the last couple of weeks provide a good reminder that other snail lineages have left the life aquatic. Here’s a species you find almost everywhere there is native forest in Otago, Cytora tuarua:

Holotype of Cytora tuarua B. Marshall and Barker, 2007. Photo is from Te Papa Collectons onlne, and provided under a CC BY-NC-ND license
Cytora is from the superfamily Cyclophoroidea, a group of snaisl that have indepedantly adapted to life on (relatively) dry land. (The weirdly un-twisted Opisthostoma is in this post is another cyclophoroid).  Cyclophoroids share some stylommatophoran adaptations to life on land, they’ve lost their gills and replaced them with a heavily vesculalised mantle cavity. Slightly oddly, cyclophoroids also breathe with their kidneys. Or, at least, the nephridium, an organ which does the same job as a vertebrate kidney, includes “vascular spaces” that the snail can use to collect oxygen from the air. Cyclophoroids don’t have an organ equivalent to the breathing pore to control the flow of air into the mantle cavity. Instead the mantle cavity is open and air enters by diffusion, or in larger species, as the result of movements of the animals head. 
For the most part, the respiratory and excretory systems in cyclophoroids are not as well adapted to life on land as those in their stylommatophoran cousins. For this reason, most cyclophoroids are only active in very humid conditions. In my limited experience, Cytora species are usually found deep in moist leaf litter and soil samples, and I’ve never seen one crawling about. Nevertheless, some species can survive in drier situations, and these are certainly terrestrial snails.
Local leaf litter samples reveal a third move from the water to land. I don’t have nice photo of Georissa purchasi, and I can’t find anything else on the web either, so you’re stuck with a crumby drawing from my notebook:




I did warn you that it was a crumby drawing. In life G. purchasi have an orange-red sort of a hue, and you can often see patches of pigment from the animal through the shell.  Georissa species are from the family Hydrocenidae and are quite closely related to a group of predominantly freshwater snails called nerites. Just like the other lineages discussed, the Hydrocenidae have given up their gills and breathe through a vasculated mantle cavity. Very little is known about the biology of these snails. G. purchasi is sometimes said to be limited to very wet conditions, but I’ve collected (inactive) specimens form the back of fern fronds well above ground so it can’t be completely allergic to dry . 
So, in a handful of leaf litter collected from a Dunedin park you might have cyclophoroids, hydrocenids and  stylommatophorans – descendants from three different moves from sea to land. If we look a little more broadly,  there are are many more examples of this transition.  I’ve written about the the helicinids before, then there are terrestrial littorines (perwinkle relatives) some of which have both gills and lungs. Plenty of other pulmonate lineages that have also taken up an entirely terrestrial lifestyle. Because some of these groups have adapted to life on land multiple times, there have probably been more than 10 invasions of the land by snails.

Most of the description of Cyclophoroids here is taken from:

Barker, GM (2001) Gastropods on land: phylogeny, diversity and adaptive morphology In Barker (Ed.),  The biology of terrestrial molluscs (pp 1146) CABI Publishing.

Sunday Spinelessness – Hairy snails David Winter Jul 29

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Here’s another of these tiny native snails I talked about last week. Aeschrodomus stipulatus:


 
Not the best photo I’ll admit, but it records enough detail to see the two things that set Aeschrodomus apart from most of its relatives in New Zealand. It’s tall and hairy. I’m not sure if there is an accepted definition of “hair” when it comes to snail shells, but plenty of different land snails groups have developed processes that extend form the shell. In New Zealand we have the fine bristles of Suteria ide, the filaments of Aeschrodomus and the spoon-shaped processes of Kokopapa (literally ”spoon-shell”):
 

K. unispathulata Photo is from David Roscoe / DoC and is under Crown Copyright

I try very hard to avoid the sloppy thinking that presumes there is an adaptive explanation for every biological observaton, but it’s hard to see how these hair-like processes would evolve if they didn’t serve a purpose. The larger hairs are presumably made from the same calcium carbonate minerals as the rest of shell, and calcium is a precious resource for snails (so much so that empty shells collected from the field often show signs of having been partially eaten by living snails). In those species with finer projections, the hairs are an extension of the “periostracum”, a protein layer that covers snail shells.  If we presume that snail hairs come at a cost, in either protein or calcium, what reward are they hairy snails reaping from their investment?

Markus Pfenninger and his colleagues asked just that question by looking at snails from the Northern Hemisphere genus Trochulus (doi: 10.1186/1471-2148-5-59). This genus contains many species that sport very fine and soft hairs. Pfenninger et al.collected ecological data for each species, and used DNA sequences to estimate a the evolutionary relationships between those species. From these data, they were able to infer the common ancestor of modern Trochulus species was probably hairy, and three separate losses of hairyness can explain all the among-species variation in this trait. Moreover, it appears the loss of hairs in Trochulus is associated with a switch for wet to dry habitats. Given this finding, Pfenninger’s team hypothesised that, in Trochulus at least, hirsute snails might stick to host plants more effectively than their bald brethren. Indeed, in experiments it took more force to dislodge a hairy shell from a wet leaf than non-hairy one.

Pfenninger’s study makes a neat case for the maintenance of hairy shells in Trochulus, but I don’t think adherence to leaves can explain all the hairy snails we know about. In New Zealand, most snails with shell processes are limited to leaf litter, a habitat that would seem to make adhering to leaves a positive hindrance to getting around. I don’t know if we’ll ever have a simple answer as to why some of our snails sport these attachments, but Menno Schilthuizen‘s work might give us a couple of clues as to why these sorts of shell sculpture arise and stick around. In 2003, Schilthuizen proposed many shell features may arise because those individuals that have them are more likely to procure a mate (or perhaps a desirable mate) (doi: 10.1186/1471-2148-3-13). Although there is quite a lot of evidence for sexual selection in land snails, I don’t know of a study testing Schilthuizen’s hypothesis on shell sculpture. On the other hand, Schilthuizen’s group has found evidence that elebaroate shell sculpture can arise as a response to predation (doi: 10.1111/j.0014-3820.2006.tb00528.x). Opisthostoma land snails from Borneo have extradonary shells, with unwound shapes, ribs and spines:

Opisthostoma mirabile
In Borneo, Opisthostoma species live alongside a predatory slug that attacks these snails by boring a hole into their shells. The unique shape and ornamentation of Opisthostoma shells appears to have evolved to hinder slug attacks. Even more interestingly, geographically distinct populations of slug appear to attack snails in different ways. This local variation in predator behavior could well be a response to local variation in the shell ornamentation – a so called Red Queen process in which each population evolves rapidly while maintaining more or less the same relative fitness

There are certainly plenty of snail-eating animals in New Zealand. Several species of Wainuia land snail appear to specialise in eating micro snails, which they scoop up and carry off using a “prehensile tail” (Efford, 1998 [pdf]). It’s entirely possible that the relatively small projections that some our snails sport are preforming the same job that those weirdly distorted Opisthostoma shells serve.

You can’t ban redheaded sperm David Winter Jul 11

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It’s the first week of semester two down here at Otago, which means I will helping with undergraduate labs for the first time this year. I suspect most students end up not liking me all that much, because I find my self teaching in the parts of the genetics program that undergrads like the least. Population genetics, as the name suggests, is the study of the way genes behave in populations, and in many ways its the base from which our understanding of evolution is built. So it’s important, but it’s also pretty mathsy.


It seems quite a few students have planned their high school and unversity careers in the hope that studying biology meant that could leave maths behind. So, when they are confronted with “p2 + 2pq + q2 = 1” and asked to do something with it, they are unhappy.

That particular formula is for something called the Hardy-Weinberg equilibrium and a significant proportion of students roll their eyes and slump their shoulders when you tell them they are going to need to use it for a problem. They think its arbitrary and irrelevant to anything the least bit important, and what’s more it looks a little like it’s already solved. So, I’m always looking for ways to convince people that Hardy-Weingberg isn’t just simple, but actually intuitive and important. So here’s my attempt to explain why knowing a little population genetics is helpful.

You may remember last year  a Danish sperm bank had started turning away would-be donors with red hair, since there is little demand for sperm that might contribute to the creation of a readhead. It turns out, if you know a little bit about population genetics you can see that policy will have little effect on the number of red heads the sperm bank helps to bring into the world.

Hair colour is partially controlled by a gene called MC1R. There are different versions of MC1R floating around in human populations, and one of them has a mutation that stops melanin (a dark pigment)  passing into hairs as they grow. Geneticists call different versions of a gene “alleles”, so we’ll call this flavour of MC1R the “red hair allele” and give it the symbol r.As I’m sure you know, you have two copies of most of your genes, one inherited from your mother and the other from your father. Red hair is a recessive trait, which means in order to have red hair both of your copies of MC1R need to be the r allele: if you have one or two copies of the “normal” MC1R allele (which we’ll call “R”) you have some pigment passing into your hair and it will be another colour. We call the total genetic make-up of a person their “genotype”, and their physical characteristics their “phenotype”, so here’s a table showing the genotypes and the phenotypes we’re talking about in this post:

Genotype 
r/r
r/R
R/R
Phenotype (hair colour)
Red Hair
Not Red Hair Not Red Hair

I know there are a lot of technical terms there (Carl Zimmer will not be happy...), but we do need to be precise when we talk about genetics because, strange as it may seem, there isn’t a single definition of the word gene. Once you’ve got your head around the terms, it’s all pretty straight forward: you need two copies of the r allele to have red hair. Think what this means for the Danish sperm bank though. Turning away red headed sperm donors doesn’t turn away red headed sperm since there will still be “carriers” with only one copy of r (and, thus, non-red hair) donating sperm and half of those sperm will be “red headed sperm”.

How big a problem is this likely to be? First we need to work how common the r allele is, and we can use the frequency of redheads to find that. By long tradition, the frequency of a recessive allele is denoted by “q“, so, in a population where one quarter of the alleles are r we’d say q = 0.25. We know that in order to have red hair you need both your copies of the MC1R gene to be the r allele and that you inherit each allele separately. When probabilities are independant we can mutiply them, so the chace someone in this population is a redhead is q x q = q2  = 0.06 .Following the same logic, the frequency of the R/R genotype must be the frequency of R squared (by convention, the frequency of a dominant allele is called “p“, so that’s p2).

Knowing this relationship, we can work backwards and find the frequency of r if we know the proportion of redheads in a population. In most of Northern Europe, about 4% (0.04) of the populaiton are redheads so  q2 = 0.04 and q = √0.04 = 0.2. As you can see, red hair genes can be a lot more common than redheads:

To understand how the sperm bank’s policy will we work, we need to know about those ‘carriers’ with the mixed genotypes (called “heterozygotes” by genetics geeks). It doesn’t matter which order your genes come in, so the probability of being a carrier in the population above will be the chance of getting an R then and r (p x q) plus the chance of getting and r followed by an R (q x p). You can simplify that to 2pq. You might recognize that term, because with it we’ve rediscovered the one in the first paragraph ”p2 + 2pq + q2 = 1“. The Hardy-Weinberg equation is just away of moving from allele frequencies to genotype frequencies (or the other way around) and it’s based on some very simple observations about the way populations work. We saw that in a population with  4% redheads you get q = 0.2, so p=0.8 and 2pq = 2 x 0.2 x 0.8 = 0.32. Almost a third of the population are carriers, and that’s eight times the number of redheads! While the frequency of the red hair allele is low, only a small proportion of the red haired alleles in a population will actually in red haired people:

That’s why the sperm banks policy, while prefectly sensible if there really is no demand for sperm from redheads, will do little prevent the creation of red-headed babies.  In the typical case, where 4% of the population are redheads the probability that a donated sperm carries the r allele only moves from 20% to 17% when you exclude red haired donors

It’s easy to calculate how the policy would work in populations with more or less redheads:

So, that annoying equation we make the undergrads learn actually tells us something about the world. Obviously, the example I’ve talked about here is a pretty silly one, but the basic ideas we’ve discovered above can help us understand some important ideas. Like why genes that cause debilitating diseases aren’t completely removed by natural selection, and why inbreeding is a bad idea.

A lot of rare diseases are caused by recessive alleles. They remain rare for the obvious reason that people with such diseases are unlikely to pass on their genes. But they remain present in populations because, as we’ve found, once recessive alleles get rare the overwhelming majority of them are found in carriers. In this way, rare recessive alleles are seldom exposed to selection so they stick around for a long time.*

Because disease causing genes stick around in populations, there is a pretty good chance that you carry a few alleles that would cause a debilitating disease in someone who had two copies of them. The same applies to anyone you might be hoping to have children with. Thankfully, its very unlikely that your prospective mate with have disease-causing alleles for the same genes that you do. That is, as long as you look beyond the family tree when you look for a mate. If you have a child with someone who is closely related to you, you will have each inherited some of your genes from the same source, which increases the chances you share disease alleles.



*In fact, they often reach a point called “mutation-selection balance” in which the frequency of the allele remains static because new mutations re-create the allele as quickly as selection removes it. JBS Haldane was the first person to notice this, and he used his theory to create a very accurate estimate of the human mutation rate well before we knew what genes were made of!

Sunday Spinelessness – Cuttlefish in drag deceive their rivals David Winter Jul 08

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One awesome mollusc deserves another, so let’s follow up last weeks octopus post with one on that group’s close relatives the cuttlefish.

Cuttlefish are relatively small (the largest grow to 50cm) squid-like cephalopods that present a nice soft and digestible meal to predatory fish and marine mammals. Having lost the shell that most molluscs use to protect themselves cuttlefish have had to develop other defences. Most strikingly, cuttlefish are masters of camouflage

.

The deceptive patterns that cuttlefish put on come from their remarkable skin, and are controlled by a pretty impressive nervous system. The skin is covered in cells called chromatophores which contain granules of pigment. When a cuttlefish decides it’s time to disappear it looks around its surroundings and, with the aid of nerves that lead from the brain to the the skin, stretch and twist the chromoatophores  on the skin’s surface in such as way as to change the colour of their cells, and ultimately their whole bodies. 
That impressive trick is principally used for camouflage, but cuttlefish and also use their skin as a sort of billboard to signal to other members of their own species, and even put on a strobing light show (possibly used to startle their own prey):

Just this week, researchers have reported evidence for a other trick that cuttlefish can pull off. When males of the Austrian Mourning Cuttlefish (Sepia plangon) see a female they put on a show, producing striped patterns that evidently impress the female. But these animals form male-dominated groups, and rival males often interrupt would-be woo-ers  in mid-display. So, when they spy a receptive female, males want to put on their flamboyant show for her to judge, but also want to make sure they don’t attract the attention of rival males that might want to spoil the party. The male Mourning Cuttlefish’s answer to this problem? Using only half of his body to put on the female-impressing show, and throwing would-be spoilers off the scent by mimicking a female with the other half.

This gender-splitting  tactic seems to be pretty common. In aquarium experiments about 40% of males would  attempt the deceptive signal when they were displaying in the presence of a rival. Just as the cuttlefish camouflage response requires information from the physical environment, the gender-splitting trick is influenced by what the male can learn of the social environment. If more than one female is available the male will display to both  without bothering to hide his intentions for observers (probably because working out an angle from which he could excite two females while staying under the radar is just not possible). Likewise, if more than one rival male is about that don’t bother with the deception – since it wouldn’t be possible to maintain the illusion for two rivals viewing from different positions.


Brown, Garwood & Williamson (In press) It pays to cheat: tactical deception in a cephalopod social signalling system. Biology Letters. http://dx.doi.org/10.1098/rsbl.2012.0435w

Sunday Spinelessness – Even their eggs are spikey David Winter May 27

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I really like the leaf vein slugs (Athoracophoridae) that live in our garden and  have featured here in the past. Here’s the latest one to pass under my camera:

As much as I like them, I have to admit these guys are actually one of the more boring leaf vein slug species in New Zealand. Some of their relatives are much larger or more colourful and quite a few of them sport large wort-like growths (technically called papillae) that pattern their bodies in various ways. Te Ara and Soil Bugs both have galleries that let you get an idea of their diversity.

A couple of weeks ago I made a little discovery. Some of these slugs also have eggs that are covered in papillae

Not the greatest photo I’ll admit. But it’s hard work taking photographs in the dense New Zealand bush at the best of times, and I found these eggs in the low-growing cloud forest that covers the Leith Saddle on Mt Cargill. These are certainly slug eggs, so  I did a bit of snooping among Astelia and ferns and other likely looking roosts for these nocturnal animals. I couldn’t find any parents-in-waiting, but the ferns were utterly covered in what people that follow mammals might call “sign”, so clearly there’s a big population in the area. 

Sunday spinelessness – live-bearing land snails David Winter Apr 29

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People seemed to like the idea of a marsupial land snail, so today I thought I’d go one step further, and introduce you to land snails that give birth to live young. 
I was lucky enough to spend a little time in Vanuatu a while ago, and, although I was really there to relax and see in a new year, I couldn’t travel that far and not spend a little of my time looking for snails. As it turns out the island on which we stayed  is heavily modified, and there is not much natural habitat left for native land snail species. In fact, the only really interesting snails I found were living on the side of our host’s house. I collected a few of those snails, transported them to the fridge in our lab and forgot about them for the best part of year.
More recently it dawned on me that these snails would be useful for a project I am working on, so I grabbed them from the fridge, set them up under the microscope ready to dissect away a tissue sample for genetic work and saw this:
 

Embryos developing inside the shell of their mother. 
We sometimes think of live-bearing as being a trait that sets the mammalian branch of the tree of life apart from other animals, but that’s wrong. Most of the major groups of animals have some species that give birth to live young – there are live-bearing frogs, snakes, lizards, insects, fish, crustaceans and star fish. In fact, the only large group without live-bearing species that I can think of is birds (and, it seems, dinosaurs, a group that contains birds). Most land snails lay a clutch of many eggs, each containing a single-celled zygote which is left to develop on its own. A few species, like theses ones, have evolved a different reproductive strategy: producing fewer eggs than their relatives, but retaining those eggs within their shell before giving birth to much more developed young.

This behaviour seems to be particular common in snails that live in rocky outcrops, and those that live in the tropics, especially the Pacific. I’m not sure about what species the snail depicted above fall into – but they are from the sub-family Microcystinae, which is one of the dominant groups of land snails in the Pacific and is made up entirely of live-bearing species. The large evolutionary radiations that used to live in Hawai’i and the Society Islands were also all live-bearers.

So why give birth to live young? It is easy to see why live-bearing is an advantage to snails living in rocky habitats with few places to deposit eggs. It’s less clear why the Pacific is full of live-bearers. It has been suggested that tropical weather can lead to unpredictable patterns of boom and bust – with snails that can hold on to and grow their offspring in the bad times and release them “ready to go” when conditions are better having an advantage over egg-layers. As far as I know no one has ever come up with a way of testing that idea, so the reasons for the prevalence of live-bearers in the Pacific remains an open question.

Sunday Spinelessness – Flightless flies David Winter Apr 15

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What do you call a fly with no wings? If you are someone’s Dad you are probably compelled to answer “a walk”, but, in fact, there are hundreds of species of fly that have given up on flight. What do you call a fly with no wings? Well, it could be a female phoird, or a hippoboscid, or perhaps a Mystacinobia. So here’s a brief survey of a few flies that have taken a brave stand against nominative determinism and given up on flight.

So what is a fly

You might be wondering how you can given the name “fly” to a flightless creature. Taxonomic groups reflect the evolutionary history of life. So for instance the great ape family contains orangutans, gorillas, humans and chimps because all these species descend from a shared common ancestor. When entomologists talk about “flies” they are referring to the taxonomic order Diptera – a group of insects that share a common ancestor that lived approximately 250 million years ago. Of course, organisms don’t come with little tags telling us where they came from, it’s the job of taxonomists to find characters that can be used to reconstruct that evolutionary history. The character that most sets flies apart from other branches of the insect tree of life is the presence of “halteres” – the stubby yellow structures  this predatory robber fly is modelling (more on that fly here).

Diptera means “two winged” and the name refers to the fact that most flies get about with one pair of wings, having reduced their second set into the flight-satablising halteres. This little innovation has allowed dipterans to become precision fliers, and one of the most successfully groups of organisms on earth with about 150 000 species (maybe 10% of all species are flies).

The true flies in order Diptera all descend from an ancestor which flew with two wings, but many of the species that descend from that ancestor have given up their wings. Because taxonomic groups are reflections of evolutionary history even wingless species are still flies – you can call them the apterous members of Diptera (wingless two-winged insects).

Flightless hippoboscids

Flies in the family Hippoboscidae are blood suckers. Many of these parasites fly from hosts to host, but a number of species have become so intimately associated that they’ve given up on flying – moving from one animal to another only while those hosts are in physical contact. The flightless hippboscids are generally called “louse flies” or “keds” and the most well known examples include species that specialise in drinking from pigeons, cattle and sheep. 
The “sheep ked” was once considered a pretty serious pest in New Zealand, but evidently it has been controlled thanks to “dip” and “pour on” insecticides that lambs are treated with. Besides the direct impacts, hippoboscids are potentiral vectors for blood borne disease, they have been implicated in the spread of avian malaria and are suspected for spreading other dieases. 

Bat flies, Bat flies, Bat flies

Bats seem to attract flies like… well they seem attract flies. At least three different lineages of flies have evolved a close relationship with bats. The largest group are, unsurpsingly, called “bat flies” (the taxonomy of this group is uncertain, but it includes the family Nycteribiidae). I have a soft-spot for most bugs, but even I have to admit bat flies are pretty gruesome looking creatures:


 Photo is CC 2.0 by Gilles San Martin

The bat flies have lost their eyes as well as their wings, by have made up for those loses in other body parts. The massive spider-like legs end in tiny claws that let the flies grip on the bat’s fur and move about. Once stuck on a bat these flies drink blood.


 

The fauna of New Zealand is very keen of flightlessness. Charasmatic mega-fauna like moa, kiwi and kakapo are the obvious examples, but we are also one of only two places on earth to have flightless perching birds (our three wrens are now extinct, as is the Canary Island Bunting). There are no truly flightless bats, but our short tailed bat is probably the closest thing – spending most of its time crawling around the forest floor. Our terrestrial bat hosts its own flightless flies. Apparenlty Mystacinobia zelandica descends from a blowfly but its association with the short talied bat has changed its body so greatly that is was not originally considered to be a fly at all, and thought to represent a unique order of insects. I couldn’t find any photos of Mystacinobia avaliable with a permissive license, but check out the New Zealand Geographic story and Te Ara’s article, which even has a video.

Mystacinobia has been placed in a family that is endemic to New Zealand, but there is one fly family with an even more restricted range. As far as we know, the family Mormotomyiidae is represented by a single species (Mormotomyia hirsuta) which is only known from a particular site in on one mountain in Kenya. As you may have guessed the site is a bat roost, and the animal, despite being only distantly related to the other bat flies discussed above, has taken on the spidery form that is associated with flies that spend their lives with bats.

 
Photo AFP

Mormotomyia doesn’t have the hooks that other species use to cling on to bats, so it may be a little more free-living than than the species discussed above.

Phorids

The family Phoridae might be the strangest group of flies . Hell, one genus is made up entirely of flies that burrow into the heads of ants, decapitate them, and use the severed head as a cocoon.

Photo from USDA (public domain)

Those flies can fly, but there is a phorid species within an even stranger life history. Male Aenigmatias lubbockii looks like a prefectly normal, albeit tiny, fly:

 
The female is something all together different:

A.lubbockii is a parasitoid of ants, the females live within an ant nest and lay eggs in the ants pupae. It is though that the rounded body, with relatively few jointed segments for ants to hang on to, helps them move around within a nest. But, of course, for that to work females need to be able to move on from the nest in which they are born. That’s where the winged male comes in, Alubbockii males airlift their females into ant nests. The males pick up females and carry them, mating on the wing, before dropping them off to infiltrate a new nest.

So, so many more

I’m going to end this brief survey of here, but I want to emphasise that these are just a few of the flies that go against their name. I could have talked about “snow fleas“, or “bee lice“,  in fact the flylogeny project records about 40 families with at least some flightless members. When the Daily Mail ran a story on the rediscovery of the Kenyan bat fly Mormotomyia hirsuta one of that newspaper giant page-view creating algorithm’s readers felt they needed to add this opinion to the ensuing discussion:

That looks nothing like a fly. How come this evolved into a ‘walk’ ? It makes no sense. If I could fly I wouldn’t evolve into something flightless. Evolution is flawed

I’ve heard some interesting critiques of evolutionary theory, but a lineage not evolving in the way a particular person would in the same situation might be the strangest. Even comical misunderstandings of evolution give us an insight into more common ones, and I’m sure this commenter’s confusion arises from a widespread “cartoon” version of evolutionary biology, in which changes within lineages is always progressive and moving towards more and more complexity. The “walks” discussed above, and the many more that I skipped over, are a good reminder that the only metric in evolution is “what works”. When these species took up lifestyles that don’t require wings they soon lost them – either because maintaining  wings and the muscles required to drive them was a cost they could profitably avoid, or because the “stabilising selection” that protects useful features from the ravages of mutation was no longer present.



The description and photos of A.lubbockii came from

Dupont S, Pape T. 2007. Fore tarsus attachment device of the male scuttle fly, Aenigmatias lubbockii. 8pp. Journal of Insect Science 7:54, available online: insectscience.org/7.54

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