Sunday, January 26, 2014
A Very Special edition of Sunday Spinelessness
Wow, it's been a long time since I wrote something here. Let's see if I can remember how this goes: I find a weird-looking bug and take some photos. Then I enthuse about that bug for a few paragraphs, hoping some broader point will emerge from all my geekery..
All right then, here's a neat creature I found recently in the Wellington Botanic Garderns. It's Helpis minitabunda the Australian Bronze Jumping Spider:
OK, so just this once the vertebrates might be the most interesting things in these photos. In November Ana, who has for many years put up with me turning over leaves and rolling rocks in search of interesting critters, and I got married. Since Ana made the most beautiful bride, and we had a wonderful day in the Botanic Gardens I can't help but share a few more photos:
Since getting married Ana and I have set out on another adventure. We've moved from the green and pleasant land in those photos to the endless sun and aridity of the Sonoran desert:
I am a doing a postdoc with Reed Cartwright at Arizona State University, where I am working to develop new techniques for detecting mutations from sequencing data and applying those methods to a very cool experiment .
Ana and I are starting to settle in to life here in the desert (I don't think we'll really be integrated into Phoenician life until we have a car, but that will happen soon), so I hope The Atavism will spring back to life soon. There certainly shouldn't be a shortage of topics to cover - I have a whole new invertebrate fauna to nerd out over, life in the desert to learn about and a whole new science system to try and understand!
Labels: sci-blogs, sunday spinelessnes
Monday, June 17, 2013
Sequencing the tuatara genome
Things have been quite around here for a while. Largely for the typical boring reasons, the pressure to get work done and on to journals that might publish it leaving little spare time. On top of that the non-science time I've had lately has taken up by what I think will be a very important piece of science communication: a blog documenting The Tuatara Genome Poject.
I'll keep trying to find time to share my thoughts here, but I really encourage all my readers to read and follow the tuatara blog - we're going to be discussing everything from why we'd want to sequence a genome, to actual process we'll use to it and some of the results that we'll gather. I won't be writing every word, in fact, one of the goals is to get the researchers on the project to describe their work in their own words. Hopefully we'll all learn a bit about reptiles, genome sequencing bioinformatics and a whole lot more.
I'll keep trying to find time to share my thoughts here, but I really encourage all my readers to read and follow the tuatara blog - we're going to be discussing everything from why we'd want to sequence a genome, to actual process we'll use to it and some of the results that we'll gather. I won't be writing every word, in fact, one of the goals is to get the researchers on the project to describe their work in their own words. Hopefully we'll all learn a bit about reptiles, genome sequencing bioinformatics and a whole lot more.
Labels: blog blogging, sci-blogs
Sunday, February 17, 2013
Sunday Spinelessness - Mostly True Facts about land snails
The ailing laptop on which I write these posts has developed a new symptom - a non-deterministic keyboard. So, I hope you'll excuse me if I just paste a link and get on with something less annoying than trying to write a post via a cellphone.
It's a pretty good link too. Ze Frank's "True Facts" series of zoological oddities has finally got to the best creatures on earth, land snails:
Pretty much everything Frank says about snail mating is true so, laptop permitting, I'll use next week's post to expand on how anatomy and behaviour have co-evolved to give us produce these mating habits, and how they effect evolutionary processes in land snail populations.
It's a pretty good link too. Ze Frank's "True Facts" series of zoological oddities has finally got to the best creatures on earth, land snails:
Pretty much everything Frank says about snail mating is true so, laptop permitting, I'll use next week's post to expand on how anatomy and behaviour have co-evolved to give us produce these mating habits, and how they effect evolutionary processes in land snail populations.
Labels: land snails, sci-blogs, snails, sunday spinelessness
Tuesday, February 12, 2013
Darwin and New Zealand
February the 12th is the anniversary of Charles Darwin's birth.
Across the world people will be marking the day by remembering Darwin the discoverer of evolution by natural selection, Darwin the cautious husband, Darwin the barnacle boffin and maybe even Darwin the geologist who explained the origin of coral atolls. I might be the only person who takes some time today to remember Darwin as a grumpy young traveler.
Darwin visited New Zealand in 1835, and he really didn't like it.The New Zealand visit came four years into the HMS Beagle's voyage, and at the end of a four thousand kilometer journey from Tahiti. Darwin and the Beagle's crew had loved their time in Tahiti (Darwin records that "every voyager ... offered up his tribute of admiration" to the island p 416). With the memory of Tahiti in mind, the sight of fern-clad hills, a few European houses and a single waka to act as a greeting party was a disappointment for Darwin:
Now, it is obvious that Darwin meet New Zealand at a bad time. The capital, Kororareka, had well and truly earned its nickname as the "Hell Hole of the Pacific", Maori where adjusting to life alongside Europeans, and the impact of the Musket Wars and the native flora and fauna was already in decline thanks to the introduction of pests and the clearing of forests. But when you consider that Darwin was in the Bay of Islands in summer time I don't think I'm being too parochial to suggest Darwin was being just a tad grumpy when he decided there was nothing to like in our country:
He developed contacts in New Zealand and his correspondence with other scientists has many references to our plants and animals. The presence of flightless birds, bats and the effects of glaciation all come up multiple times. But New Zealand's most important influence on Darwin's thinking came via his best friend, Joseph Hooker .
Like Darwin, and many other Victorian naturalists, Hooker started his career by jumping on a ship and sailing to the other side of the world. For Hooker, that meant the HMS Erebus and trip to Antarctica via South America, New Zealand and Australia. Hooker had read Darwin's Journey of the Beagle in proof before he set off, and when he returned to England the two stayed in contact.
In 1844 Darwin "confessed" his ideas about the origin of species to Hooker. That letter contains references to the New Zealand flora, in which Darwin is fishing for facts that might support his ideas about species moving from one land to another. In the same year, Darwin started a discussion with Hooker about the distribution of Kōwhai (Sophora). The yellow-flowering Kōwhai will be familiar to all New Zealanders, but it may come as surprise that some of the "Kōwhai" species sold in garden centres aren't from New Zealand at all, but are Chilean Sophora species. The species are similar enough they'll happily hybridise given the chance.
These Chilean Kōwhai are an example of a common pattern - the floras of New Zealand, Tasmania South American and the sub-Antarctic seem to be closely related. Hooker thought this pattern arose because all these island where connected in a southern super continent. Darwin didn't like the idea of creating new land to explain a biological pattern, and instead proposed that that chance dispersal (by wind or rafting) could explain the distrbution of these species. Darwin was a keen experimentalists, and so, he set about dropping seeds in salty water and attempting to germinate them. These experiments took place in Darwin's house in Down, and apparently his children counted each germination as a victory for their dad over Hooker.
It seems Hooker couldn't provide Kōwhai seeds for Darwin's experiments, but Darwin took a record of just three equally-sized Kōwhai trees on the Chatham Islands (some seven hundred kilometers from the mainland) as evidence for long-range dispersal, and perhaps a suggestion that Kōwhai seed could survive a trip from Chile to New Zealand.
It turns out Darwin was right about Kōwhai although he got the direction wrong. Molecular studies have shown that Sophora arose in the Northern Pacfic, dispersed down to New Zealand and arrived in Chile via the Antarctic's strong circumpolar current, all in the last few million years (Hurr et al, 1999 doi: 10.1046/j.1365-2699.1999.00302.x).
Darwin got a lot right, and foresaw many developments in the study of evolution. But evolutionary biology is much more than 21st century 'Darwinism'. Darwin didn't know what a gene was, so is unlikely to teach us much about genomics. For me, the most important thing to learn from Darwin's writing is the way he set out about understanding the world. Darwin sought out evidence for each sub-hypothesis in his Big Idea, sometimes that meant writing to colleagues like Hooker and Haast and sometimes that meant doing experiments like his salty seeds.
Darwin never got a Kōwhai seed to experiment with, but, in his 1958 lecture on Darwinism in New Zealand, AC Flemming mentioned a study that found they can survive 4 months of immersion in salt water. That's a little shorter than the time you'd expect a seed pod set adrift from New Zealand to take before it washed up on a Chilean beach. Right now, highschool students are starting another year of biology classes - and teachers are probably preparing another re-hash of the "plant study" they've taught to Year 13 students since they were called Seventh Formers. Wouldn't it be a fitting tribute if some of those classes did something a little different, and honoured Darwin's approach to undestanding the biological world by dunking Kōwhai seeds and running an experiemnt he never got to?
Quoted passages are from Darwin's Voyage of the Beagle. Links go the the Darwin Online Fascimile.
*Forget about the finches
Across the world people will be marking the day by remembering Darwin the discoverer of evolution by natural selection, Darwin the cautious husband, Darwin the barnacle boffin and maybe even Darwin the geologist who explained the origin of coral atolls. I might be the only person who takes some time today to remember Darwin as a grumpy young traveler.
Darwin in New Zealand
Darwin visited New Zealand in 1835, and he really didn't like it.The New Zealand visit came four years into the HMS Beagle's voyage, and at the end of a four thousand kilometer journey from Tahiti. Darwin and the Beagle's crew had loved their time in Tahiti (Darwin records that "every voyager ... offered up his tribute of admiration" to the island p 416). With the memory of Tahiti in mind, the sight of fern-clad hills, a few European houses and a single waka to act as a greeting party was a disappointment for Darwin:
Only a single canoe came alongside. This, and the aspect of the whole scene, afforded a remarkable, and not very pleasing contrast, with our joyful and boisterous welcome at Tahiti. (p 417)Closer inspection of the land around the Beagle's mooring in the Bay of Islands didn't do much to improve the young Darwin's opinion of New Zealand
In the morning I went out walking; but I soon found that the country was very impracticable. All the hills are thickly covered with tall fern, together with a low bush which grows like a cypress; and very little ground has been cleared or cultivated .. (p 418)And if the plants weren't enough, introduced predators had already removed much of native fauna:
I saw very few birds.. It is said that the common Norway rat, in the short space of two years, annihilated in this northern end of the island, the New Zealand species. In many places I noticed several sorts of weeds, which, like the rats, I was forced to own as countrymen. (pp 427-8)In nine days of traveling around the Bay of Islands Darwin found very little to like. In comparison to the Tahitians the Māori were "of a much lower order" (p 420) and the Europeans inhabitants where "the very refuse of society" (p 420). In fact, the only place he liked was William Williams' attempt to remake England at the Mission house in Waimate North. (pp 425-30).
Now, it is obvious that Darwin meet New Zealand at a bad time. The capital, Kororareka, had well and truly earned its nickname as the "Hell Hole of the Pacific", Maori where adjusting to life alongside Europeans, and the impact of the Musket Wars and the native flora and fauna was already in decline thanks to the introduction of pests and the clearing of forests. But when you consider that Darwin was in the Bay of Islands in summer time I don't think I'm being too parochial to suggest Darwin was being just a tad grumpy when he decided there was nothing to like in our country:
Left: Pahia beach, CC 2.0 by Fras1997 . Right: Tapeka Sunrise, CC2.0 by Chris Gin
New Zealand in Darwin's thinking
Darwin didn't think much of New Zealand while he was here, but I suspect he ended up regretting the brevity of his visit. About 30 years after he gladly left our islands behind, Darwin wrote a letter to Julius Von Haast to thank him for some information he'd provided, addingI really think there is hardly a point in the world so interesting with respect to geographical distribution as New ZealandDarwin spent a lot of time thinking about the geographical distribution of species. His first written account of where species might come from was spurred by thinking abut the distribution of Galapagos and Ecuadorian mockingbirds*. More importantly, if Darwin was going to do away with the popular idea that each continent's species arose more or less in their current place, he had to work out how plants and animals could get from one place to another.
He developed contacts in New Zealand and his correspondence with other scientists has many references to our plants and animals. The presence of flightless birds, bats and the effects of glaciation all come up multiple times. But New Zealand's most important influence on Darwin's thinking came via his best friend, Joseph Hooker .
Like Darwin, and many other Victorian naturalists, Hooker started his career by jumping on a ship and sailing to the other side of the world. For Hooker, that meant the HMS Erebus and trip to Antarctica via South America, New Zealand and Australia. Hooker had read Darwin's Journey of the Beagle in proof before he set off, and when he returned to England the two stayed in contact.
In 1844 Darwin "confessed" his ideas about the origin of species to Hooker. That letter contains references to the New Zealand flora, in which Darwin is fishing for facts that might support his ideas about species moving from one land to another. In the same year, Darwin started a discussion with Hooker about the distribution of Kōwhai (Sophora). The yellow-flowering Kōwhai will be familiar to all New Zealanders, but it may come as surprise that some of the "Kōwhai" species sold in garden centres aren't from New Zealand at all, but are Chilean Sophora species. The species are similar enough they'll happily hybridise given the chance.
These Chilean Kōwhai are an example of a common pattern - the floras of New Zealand, Tasmania South American and the sub-Antarctic seem to be closely related. Hooker thought this pattern arose because all these island where connected in a southern super continent. Darwin didn't like the idea of creating new land to explain a biological pattern, and instead proposed that that chance dispersal (by wind or rafting) could explain the distrbution of these species. Darwin was a keen experimentalists, and so, he set about dropping seeds in salty water and attempting to germinate them. These experiments took place in Darwin's house in Down, and apparently his children counted each germination as a victory for their dad over Hooker.
It seems Hooker couldn't provide Kōwhai seeds for Darwin's experiments, but Darwin took a record of just three equally-sized Kōwhai trees on the Chatham Islands (some seven hundred kilometers from the mainland) as evidence for long-range dispersal, and perhaps a suggestion that Kōwhai seed could survive a trip from Chile to New Zealand.
It turns out Darwin was right about Kōwhai although he got the direction wrong. Molecular studies have shown that Sophora arose in the Northern Pacfic, dispersed down to New Zealand and arrived in Chile via the Antarctic's strong circumpolar current, all in the last few million years (Hurr et al, 1999 doi: 10.1046/j.1365-2699.1999.00302.x).
Honouring Darwin Day in New Zealand
I'm not quite sure how I feel about Darwin Day. There is not doubt that Darwin was a genius, an exellent naturalist and the founder of a field of study that lives on today. But there is something a bit odd about the annual veneration of Darwin, and the rush to connect modern ideas in evolutionary biology with things Darwin wrote 150 years ago.Darwin got a lot right, and foresaw many developments in the study of evolution. But evolutionary biology is much more than 21st century 'Darwinism'. Darwin didn't know what a gene was, so is unlikely to teach us much about genomics. For me, the most important thing to learn from Darwin's writing is the way he set out about understanding the world. Darwin sought out evidence for each sub-hypothesis in his Big Idea, sometimes that meant writing to colleagues like Hooker and Haast and sometimes that meant doing experiments like his salty seeds.
Darwin never got a Kōwhai seed to experiment with, but, in his 1958 lecture on Darwinism in New Zealand, AC Flemming mentioned a study that found they can survive 4 months of immersion in salt water. That's a little shorter than the time you'd expect a seed pod set adrift from New Zealand to take before it washed up on a Chilean beach. Right now, highschool students are starting another year of biology classes - and teachers are probably preparing another re-hash of the "plant study" they've taught to Year 13 students since they were called Seventh Formers. Wouldn't it be a fitting tribute if some of those classes did something a little different, and honoured Darwin's approach to undestanding the biological world by dunking Kōwhai seeds and running an experiemnt he never got to?
Quoted passages are from Darwin's Voyage of the Beagle. Links go the the Darwin Online Fascimile.
*Forget about the finches
Labels: Darwin, Darwin Day, history of science, sci-blogs, science and society
Sunday, February 3, 2013
Sunday Spinelessness - Cannibalism in the garden
The most common jumping spider in our garden, Trite auricoma, with the remains of it most recent meal... a smaller T. auricoma:
Cannibalism, animals eating members of their own species, is a pretty common and widespread behavior. Species in almost every phylum have been shown to occasionally (or frequently) eat members of their own species. Even herbivores like monarch butterfly caterpillars will eat any monarch eggs they encounter.
In spiders, the most well-studied form of cannibalism relates to mating. In a very few species male spiders will offer themselves as a meal to their mate. In so doing, males make sure their offspring get the best start in life, by providing their mother with a nutrition meal. They are often also posthumously rewarded by female, who reject other suitors and ensure the sacrificial male's legacy. The best example of this behaviour comes from the Australian red back spider (Latrodectus hasseltii). In this species males actually pirouette their way into their mate's fangs, and females take up the offer about 65% of the time. New Zealand's endemic red back relative, the katipo, does not exhibit this behavior (nor does the North American black widow, despite the name).
Such sexual cannibalism isn't known from jumping spiders (although females will certainly eat unwary males), and a wider (and earlier) shot lets you see that this was a case of a mature spider taking a younger one (males and females are about equally sized in T. auricoma).
Cannibalism, animals eating members of their own species, is a pretty common and widespread behavior. Species in almost every phylum have been shown to occasionally (or frequently) eat members of their own species. Even herbivores like monarch butterfly caterpillars will eat any monarch eggs they encounter.
In spiders, the most well-studied form of cannibalism relates to mating. In a very few species male spiders will offer themselves as a meal to their mate. In so doing, males make sure their offspring get the best start in life, by providing their mother with a nutrition meal. They are often also posthumously rewarded by female, who reject other suitors and ensure the sacrificial male's legacy. The best example of this behaviour comes from the Australian red back spider (Latrodectus hasseltii). In this species males actually pirouette their way into their mate's fangs, and females take up the offer about 65% of the time. New Zealand's endemic red back relative, the katipo, does not exhibit this behavior (nor does the North American black widow, despite the name).
Such sexual cannibalism isn't known from jumping spiders (although females will certainly eat unwary males), and a wider (and earlier) shot lets you see that this was a case of a mature spider taking a younger one (males and females are about equally sized in T. auricoma).
Labels: arachnophilia, environment and ecology, jumping spiders, photos, sci-blogs, sunday spinelessness
Thursday, January 31, 2013
Elsewhere
A couple of links that might be of interest for readers of The Atavism:
- I've been really remiss in linking to interview I did with Veronika Meduna for Radio NZ's Our Changing World. The bugs Veronika and I visited will all be familiar to readers here
- The online Evolutionary Biology Journal Club is getting back together for "Season 2". If you don't know, a journal club is basically a bunch of geeks getting together to discuss recent (or no so recent) papers in a shared area of geekiness. As the first paper in this season's line up is one I already know pretty well I wrote a quick summary of it to serve as a jumping-off point. The discussion will be on Tuesday morning NZ time, and anyone who is keen can jump in (and if next week doesn't work there will be plenty more sessions this year).
Labels: blog blogging, sci-blogs
Sunday, January 27, 2013
Sunday Spinelessness - Native bees again
Last year, at about this time, I wrote a little about our native bees. Though I'm glad to have done my little bit to promote the existence of these all too anonymous members of our natural heritage I've always felt a little embarrassed by the photos in that post. As I admitted at the time the photos are staged. Photographing our twitchy little bees is hard - apart from being small, they zip about from flower to flower much more quickly than I can line up, let alone focus, shots.
So, to illustrate the original post I used half-drowned bees, scooped out from a swimming pool. The time it took the bees to dry out gave me a chance to take the photos, but I set them up on exactly the type of flower they'd never visit in the wild. So, not only did I cheat, but the photos I took actively misled about the true nature of bees!
So, here are some much worse photographs of native bees that do a much better job of representing their lifestyles. First off, a bee perched on a favourite flower, a hebe, and deciding on its next move:
So, to illustrate the original post I used half-drowned bees, scooped out from a swimming pool. The time it took the bees to dry out gave me a chance to take the photos, but I set them up on exactly the type of flower they'd never visit in the wild. So, not only did I cheat, but the photos I took actively misled about the true nature of bees!
So, here are some much worse photographs of native bees that do a much better job of representing their lifestyles. First off, a bee perched on a favourite flower, a hebe, and deciding on its next move:
and another collecting pollen from the same plant:
These hebes, and a few parsley plants left to go to flower, make my parent's house in the Wairarapa a mecca for native bees. They certainly make their mark around the garden, if you don't notice them drowned in the pool or visiting flowers you can see their nests in the soil:
Labels: bees, environment and ecology, native bees, photos, sci-blogs, sunday spinelessness
Tuesday, January 22, 2013
Cats aren't evil, but they are a problem
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)
Labels: cats, conservation, new zealand, sci-blogs, science, science and society
Sunday, January 20, 2013
Sunday Spinelessness - 5 down.... quite a few to go
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:
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:
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!
Labels: my research, phylogenetics, sci-blogs, science, sunday spinelessness
Sunday, January 13, 2013
Sunday Spineless - On the Wing
Just a photo today, but a pretty awesome one I reckon. An inbound bumble bee from my parents' garden in the Wairarapa:
(~50 out of focus shots from same session not shown!)
Labels: bee, bumblebee, environment and ecology, photos, sci-blogs, sunday spinelessness
Sunday, December 9, 2012
Sunday Spinelessness - A Clearwing moth
At last, Dunedin has managed to arrange a proper summer day for a weekend.
The extra heat and sun saw plenty of bugs out and about, and I spotted plenty of familiar critters (native bees, cicadas, drone flies and magpie moths) for this first time this year. The real find of the weekend though, was something entirely new to me:
You might be a little surprised to learn that you are looking at a moth.
I'm helping design an undergraduate lab on systematics and taxonomy at the moment. Since the new lab is about insects I've suddenly become very aware of the traits that distinguish various insect groups. Moths, along with butterflies, make up the order Lepidoptera. You can see a few lepitoperan characters in the above photo: a mouth designed for siphoning nectar from flowers and a body covered in fine scales.
"Lepitoptera" actually mans "scaley wing", and, indeed most butterflies and moths have scales on their wings. This species, though, has got rid of most of it's wing scales (there are plenty of scales on the trialing edge though):
I'm helping design an undergraduate lab on systematics and taxonomy at the moment. Since the new lab is about insects I've suddenly become very aware of the traits that distinguish various insect groups. Moths, along with butterflies, make up the order Lepidoptera. You can see a few lepitoperan characters in the above photo: a mouth designed for siphoning nectar from flowers and a body covered in fine scales.
"Lepitoptera" actually mans "scaley wing", and, indeed most butterflies and moths have scales on their wings. This species, though, has got rid of most of it's wing scales (there are plenty of scales on the trialing edge though):
Synanthedon tipuliformis * is member of the "clear wing" moth family Sesiidae. Although I think this one is pretty neat, the family contains some striking species, the most interesting of which are wasp-mimics
Labels: environment and ecology, lepidoptera, moths, photo, sci-blogs, sesiidae, sunday spinelessness, Synanthedon tipuliformis
Sunday, December 2, 2012
Sunday Spinelessness - Bark Lice
I should have known that the little challenge I put up last week wouldn't so much as wrinkle the brow of the bug-blogo-sphere's best. The Atavism's two homes means there were two winners. Ted MacRae of Beetles in the Bush chimed in at he blogspot version, correctly identifying the insect as a "bark louse" or psocopteran, and recognizing those stubby white protrusion as yet-to-be expanded wings . Morgan Jackson of Biodiversity in Focus did the same at SciBlogs.
*This is not a botany blog... I really have no idea what the tree is
Thanks too to Deborah from Bee of a Certain Age, who hazarded a guess that those white protrusions might be eggs. Certainly a more reasonable guess that my own first thoughts at seeing these bugs crawling over the the Big Tree* in our garden. The plump abdomens and long antennae made me think of the large (but certainly not GIANT) springtails. Ripping up a couple of pieces of bark revealed a whole colony of these odd-looking bugs, and evidence for just how wrong I was.
The adults have wings, which they hold tent-like over their bodies. Insects are the only invertebrates with wings, so, since spring tails aren't insects, my first guess was horribly inaccurate (glossing over about 400 million years of evolutionary divergence).
As Ted and Morgan worked out, these are "bark lice", members of the order Psocoptera. Although they are related to the "true lice" (Order Phthiraptera), psocopterans are not parasites. Rather, they wander around their trees eating algae, fungi and whatever detritus might be clinging to the bark. The only species that could be considered pests are the "book lice" - small flightless psocopterans that sometimes turn up in old books where they eat the paste that binds pages together. (I have it on good authority that book lice can also destroy botanical collections, so certainly a pest)
A couple of weeks ago I gave Veronika Meduna a tour of our garden and its bugs, and I gather you can hear the result on Radio New Zealand's Our Changing World next week. While I was catching my breath between talking about the mating habits of spiders, and how our native slugs are much more sluggish then their introduced counterparts she asked the obvious question - "why?". Why do I care so much about odd little creatures like bark lice and slugs and spiders? I'm not sure I managed a coherent answer at the time, but I can tell you now, spineless creatures need evangelists because most people have a very skewed view about the way biology works. If your vision of biodiversity is limited to pandas and dolphins and lions and tigers then you are missing out on millions of other ways to be alive.
Take bark lice as an example. I'll admit that I'd never given these creatures a moments thought before running into them last week. But, in researching this post I found out there are more than four thousand psocopteran species. That is to say, there are almost as many bark lice species as there are mammals - all the lions, tigers, bears, dolphins, whales, marsupials, rodents and bats in the world add up to about 5 400. That matters because species are the fundamental units of biological diversity. Each species represents a distinct evolutionary lineage - free to take up different ecological niches, develop new morphological features or occupy a different geographic range.
To try an illustrate how diverse these unassuming little critters really are, I've put together a "treemap". In the plot below, each of the stained-glass window panels represents the number of species in one psocopteran genus, nested within a family (the heavier lines, with labels ending in -DAE) which in turn is nested within a suborder (the very heaviest lines, labeled -MORPHA). These higher taxonomic ranks are not fundamental units in the way species are. Even so, species placed within a taxonomic group share evolutionary history, and are united by particular morphological characters which they share. It turns out there are quite a few ways to be a bark louse:
As Ted and Morgan worked out, these are "bark lice", members of the order Psocoptera. Although they are related to the "true lice" (Order Phthiraptera), psocopterans are not parasites. Rather, they wander around their trees eating algae, fungi and whatever detritus might be clinging to the bark. The only species that could be considered pests are the "book lice" - small flightless psocopterans that sometimes turn up in old books where they eat the paste that binds pages together. (I have it on good authority that book lice can also destroy botanical collections, so certainly a pest)
A couple of weeks ago I gave Veronika Meduna a tour of our garden and its bugs, and I gather you can hear the result on Radio New Zealand's Our Changing World next week. While I was catching my breath between talking about the mating habits of spiders, and how our native slugs are much more sluggish then their introduced counterparts she asked the obvious question - "why?". Why do I care so much about odd little creatures like bark lice and slugs and spiders? I'm not sure I managed a coherent answer at the time, but I can tell you now, spineless creatures need evangelists because most people have a very skewed view about the way biology works. If your vision of biodiversity is limited to pandas and dolphins and lions and tigers then you are missing out on millions of other ways to be alive.
Take bark lice as an example. I'll admit that I'd never given these creatures a moments thought before running into them last week. But, in researching this post I found out there are more than four thousand psocopteran species. That is to say, there are almost as many bark lice species as there are mammals - all the lions, tigers, bears, dolphins, whales, marsupials, rodents and bats in the world add up to about 5 400. That matters because species are the fundamental units of biological diversity. Each species represents a distinct evolutionary lineage - free to take up different ecological niches, develop new morphological features or occupy a different geographic range.
To try an illustrate how diverse these unassuming little critters really are, I've put together a "treemap". In the plot below, each of the stained-glass window panels represents the number of species in one psocopteran genus, nested within a family (the heavier lines, with labels ending in -DAE) which in turn is nested within a suborder (the very heaviest lines, labeled -MORPHA). These higher taxonomic ranks are not fundamental units in the way species are. Even so, species placed within a taxonomic group share evolutionary history, and are united by particular morphological characters which they share. It turns out there are quite a few ways to be a bark louse:
And that's just bark lice!
For me, this chart is the best answer to "why?". How can you know you share the world with all this extraordinary diversity and not want to want to spend your time working out how it got here?
For me, this chart is the best answer to "why?". How can you know you share the world with all this extraordinary diversity and not want to want to spend your time working out how it got here?
*This is not a botany blog... I really have no idea what the tree is
Labels: bark lice, environment and ecology, psocoptera, sci-blogs, sunday spinelessness
Sunday, November 25, 2012
Sunday Spinelessness - An ID challenge
OK, here's a chance for the bug nerds to show off. A photo of a strange-looking beast I recently ran into:
The challenge to readers is to answer the two questions that went through my head when I first uncovered the creature (1) What the hell is that? (2) What's going with those opaque white projections?
Unlike others, I can't often you anything cool as a prize for being right, but surely an electronic record to your entomological know-how will be enough?
Labels: environment and ecology, mystery, photos, sci-blogs, sunday spinelessness
Sunday, November 18, 2012
Sunday Spinelessness - Shocked from sloth by a beautiful spider
Regular readers will know that I've been pretty slack in posting here in recent weeks. Just the same old boring reason - lots of "real" work to get done and, as much as I enjoy it, blogging necessarily floats to the bottom of TODO lists.
But I was shocked from my sloth this afternoon when I passed that accursed agapanthus and saw a spider I really had to share with the world:
It's an orb-weaving (araneid) spider, a relative of the familiar garden spiders like the very common Eriophora pustulosa that spin orb-shaped webs and catch unlucky flying insects. I can't be sure on the identification of this one, but I reckon (with some support from twitter's resided spider experts, [1], [2]) its a species a species of Novaranea. According to Ray and Lyn Foster's Big Spider Book New Zealand Novaranea species are most commonly encountered in in grasslands and tussocks, so perhaps this one blew in from the tall grass that covers some the abandoned gardens in our block.
However it made it our garden, I'm very happy to have encountered a such a neat looking spider, and even done a half-decent job capturing some of its beauty:
But I was shocked from my sloth this afternoon when I passed that accursed agapanthus and saw a spider I really had to share with the world:
It's an orb-weaving (araneid) spider, a relative of the familiar garden spiders like the very common Eriophora pustulosa that spin orb-shaped webs and catch unlucky flying insects. I can't be sure on the identification of this one, but I reckon (with some support from twitter's resided spider experts, [1], [2]) its a species a species of Novaranea. According to Ray and Lyn Foster's Big Spider Book New Zealand Novaranea species are most commonly encountered in in grasslands and tussocks, so perhaps this one blew in from the tall grass that covers some the abandoned gardens in our block.
However it made it our garden, I'm very happy to have encountered a such a neat looking spider, and even done a half-decent job capturing some of its beauty:
Labels: environment and ecology, photos, sci-blogs, sunday spinelessness
Tuesday, September 25, 2012
All the media!
Oh, hi there. Yeah, it's been a while h'uh? Just been crazy busy lately you know - one thing after another with manuscripts and datasets to analyse, then I got a whole bunch of lab reports to mark. We should totally like, get back to writing/reading about science though. I'll put something up in a bit and...*
So, things have been a little quite here lately. That wasn't a plan to have me an that ridiculous hat up on the front page for a few weeks - just the result of having little spare time. As it turns out, a few things that might be of interest to readers here have been published over that fallow period, here's the links:
I guess to complete the set I'd need to make a TV appearance, though I can't see that happening!
*For people with whom I've had exactly this conversation lately - it's true, I have been busy, I am a terribly friend and we will catch up soon!
So, things have been a little quite here lately. That wasn't a plan to have me an that ridiculous hat up on the front page for a few weeks - just the result of having little spare time. As it turns out, a few things that might be of interest to readers here have been published over that fallow period, here's the links:
- I'm in a book! As I related last year, my post on the partulids land snails of Society Isalnds was selected for The Best Science Writing Online which is now available from all good book sellers. I'm ridiculously excited by this. There is also a short review in The Listener
- My latest little piece for stuff.co.nz deals with Colin Craig and his idea that research tells us sexual orientation is a choice, and that this is relevant to marriage equality.
- I was on the radio - an hour of talking about science, peer review and skepticsm on Radio One, the student radio station.
I guess to complete the set I'd need to make a TV appearance, though I can't see that happening!
*For people with whom I've had exactly this conversation lately - it's true, I have been busy, I am a terribly friend and we will catch up soon!
Labels: blog blogging, sci-blogs
Tuesday, August 28, 2012
Graduation, nerd blogging and a talk
The most dedicated readers of The Atavism may have noticed a few Sundays have passed without celebration of a spineless creature. Well, you know how blogging is sometimes. A few of the things that have kept me from blogging might be of interest to readers here. This weekend was dedicated to the wearing of silly hats, posing somewhat awkwardly and the conferring of my PhD. It was almost a big enough event to make me wear a tie:
So far I've rested the urge to change the name that appears under these posts to Dr David Winter, we'll see how long that lasts.
I've also been working a little on some more software for evolutionary biology. Since I very much aim this blog at a lay-level, and there is no reason on earth why a lay-person ought to care about the computer programs scientists use to collect and analyse their data, I've decided to set up a dedicated nerd blog. The first post their introduces an R library that can help researchers quickly download data from molecular biology and medical databases.
Finally, I should say their probably won't be a new post here this weekend either, as I'll be at the New Zealand Skeptics Conference, right here in Dunedin. I'll be giving a talk about how the the creation-evolution "debate" as it usually plays out has very little to do with evolutionary biology, and how getting past popular misconceptions about the way evolution works makes most creationist objections to evolution into non-starters. I'll also say why I think good old fashioned creationism is a more respectable position than "intelligent design", so that ought to be fun. If you're in Dunedin you can still register for the whole meeting, my talk is on at 9:50am on Saturday in Archway 3 (the best, and perhaps only, way to find this lecture theatre is to walk into the Archway building and wander around opening doors at random).
I've also been working a little on some more software for evolutionary biology. Since I very much aim this blog at a lay-level, and there is no reason on earth why a lay-person ought to care about the computer programs scientists use to collect and analyse their data, I've decided to set up a dedicated nerd blog. The first post their introduces an R library that can help researchers quickly download data from molecular biology and medical databases.
Finally, I should say their probably won't be a new post here this weekend either, as I'll be at the New Zealand Skeptics Conference, right here in Dunedin. I'll be giving a talk about how the the creation-evolution "debate" as it usually plays out has very little to do with evolutionary biology, and how getting past popular misconceptions about the way evolution works makes most creationist objections to evolution into non-starters. I'll also say why I think good old fashioned creationism is a more respectable position than "intelligent design", so that ought to be fun. If you're in Dunedin you can still register for the whole meeting, my talk is on at 9:50am on Saturday in Archway 3 (the best, and perhaps only, way to find this lecture theatre is to walk into the Archway building and wander around opening doors at random).
Labels: blog blogging, sci-blogs
Thursday, August 9, 2012
Measuring population differentiation in R
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 HT for 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 GST, which he defined like this:
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 HT for 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 GST, 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 HS 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 HS will 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 david.winter@gmail.com
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
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 david.winter@gmail.com
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.
Labels: my research, population genetics, sci-blogs, science
Sunday, August 5, 2012
Sunday Spinelessness - How snails conquered the land (again and again)
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 1—146) CABI Publishing.
Labels: molluscs, native snails, photos, sci-blogs, science, sunday spinelessness
Sunday, July 29, 2012
Sunday Spinelessness - Hairy snails
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
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.
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?
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.
Labels: molluscs, native snails, new zealand, sci-blogs, science, sunday spinelessness
Sunday, July 22, 2012
Sunday Spinelessness - New Zealand microsnails
When I tell people I study snails for a living I get one of two replies. There's either some version of the "joke" that goes "that must be slow-going" or "sounds action packed", or there's "oh, you mean those giant killer ones we saw when we went tramping?". I guess the joke is funny enough, but I want to make it clear that those giant killer snails from the family Rhytidae, cool as they might be, are not the most interesting land snails in New Zealand.
The local land snail fauna displays a pattern that is quite common for New Zealand animals - we have a very large number of species but those species are drawn from relatively few taxonomic families. Since taxonomic groups reflect the evolutionary history of the species they contain, that pattern most likely arises because New Zealand is (a) quite hard to get to, so few would-be colonists make it here and (b) full of ecological niches and geographic pockets that can drive the formation of new species. In total, there are are probably about 1200 native land snail species in New Zealand - about ten times the number found in Great Britain, which is approximately the same size. That diversity extends to the finest scales - individual sites in native forest might have as many as 60 species sharing the habitat. New Zealand forests probably have the most diverse land snails assemblages in the world (although tropical ecologists, who generally hold that diversity in terrestrial habitats almost invariably increases as you approach the equator, have argued against this conclusion).
You may now be asking why, if this land snail fauna is so diverse, have you never seen a native snail. Well, you've probably walked past thousands of them without noticing. Most of our native land snail species are from the families Punctidae and Charopidae, groups that are sometimes given the common name "dot snails". Meembers of these families are usually smaller than 5 mm across the shell, and are restricted to native forest and in particular to leaf litter. But in native forests, where there's leaf litter there's snails. Grab a handful of leaves, or pull up a log and you're likely to find a few tiny flat-spired snails going about their business. Hell, down here in Dunedin you can even find charopids living under tree-fuschia in a suburban garden.
Like so many native invertebrates, we know very little about our land snails. Lots of people have dedicated substantial parts of their lives to documenting and describing the diversity of these creatures, but even so we don't have a clear understanding of how the native species relate to each other or to their relatives in the rest of the world, or even where one species starts and another ends. Without such a basic understanding, its very hard to ask evolutionary and ecological questions about these species, so for now we remain largely ignorant of the forces that have created the New Zealand land snail fauna.
For the time being I can tell you that a lot of them are really quite beautiful. Since most people don't have handy access to a microscope to see these critters, I thought I would share a few photos from this largely neglected group over the next few weeks. The 2D photographs, with the relatively fine depth of field, don't quite record the beauty of these 3D shells, but I hope it's at least a window into the diversity of these snails.
Let's start with a snail that is very common in Dunedin parks and forests. This is a species from the genus Cavellia (the strong, sine-shaped ribs being the giveaway) but I won't be able to place it to species until a new review of that genus is published.
This particular shell is from an immature specimen, and is about 2mm across. When flipped, you can see an open umbilicus that lets you see straight through to the apex of the shell.
The local land snail fauna displays a pattern that is quite common for New Zealand animals - we have a very large number of species but those species are drawn from relatively few taxonomic families. Since taxonomic groups reflect the evolutionary history of the species they contain, that pattern most likely arises because New Zealand is (a) quite hard to get to, so few would-be colonists make it here and (b) full of ecological niches and geographic pockets that can drive the formation of new species. In total, there are are probably about 1200 native land snail species in New Zealand - about ten times the number found in Great Britain, which is approximately the same size. That diversity extends to the finest scales - individual sites in native forest might have as many as 60 species sharing the habitat. New Zealand forests probably have the most diverse land snails assemblages in the world (although tropical ecologists, who generally hold that diversity in terrestrial habitats almost invariably increases as you approach the equator, have argued against this conclusion).
You may now be asking why, if this land snail fauna is so diverse, have you never seen a native snail. Well, you've probably walked past thousands of them without noticing. Most of our native land snail species are from the families Punctidae and Charopidae, groups that are sometimes given the common name "dot snails". Meembers of these families are usually smaller than 5 mm across the shell, and are restricted to native forest and in particular to leaf litter. But in native forests, where there's leaf litter there's snails. Grab a handful of leaves, or pull up a log and you're likely to find a few tiny flat-spired snails going about their business. Hell, down here in Dunedin you can even find charopids living under tree-fuschia in a suburban garden.
Like so many native invertebrates, we know very little about our land snails. Lots of people have dedicated substantial parts of their lives to documenting and describing the diversity of these creatures, but even so we don't have a clear understanding of how the native species relate to each other or to their relatives in the rest of the world, or even where one species starts and another ends. Without such a basic understanding, its very hard to ask evolutionary and ecological questions about these species, so for now we remain largely ignorant of the forces that have created the New Zealand land snail fauna.
For the time being I can tell you that a lot of them are really quite beautiful. Since most people don't have handy access to a microscope to see these critters, I thought I would share a few photos from this largely neglected group over the next few weeks. The 2D photographs, with the relatively fine depth of field, don't quite record the beauty of these 3D shells, but I hope it's at least a window into the diversity of these snails.
Let's start with a snail that is very common in Dunedin parks and forests. This is a species from the genus Cavellia (the strong, sine-shaped ribs being the giveaway) but I won't be able to place it to species until a new review of that genus is published.
This particular shell is from an immature specimen, and is about 2mm across. When flipped, you can see an open umbilicus that lets you see straight through to the apex of the shell.
Labels: molluscs, native snails, photos, sci-blogs, snails, sunday spinelessness
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