Posts Tagged taxonomy

Sunday Spinelessness – Each thing by its right name David Winter May 06

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In Dr Zhivago Boris Pasternak describes an epiphany that sneaks up on one of his characters thus:

For a moment she rediscovered the purpose of her life. She was here on earth to grasp the meaning of its wild enchantment and to call each thing by its right name…

It’s probably not spoiling the story to tell that Lara doesn’t dedicate her life to taxonomy at this point of the novel.I can’t say I really know what Pasternak was getting at with these sentences, but I’ve always liked them because they really do describe the driving force that makes taxonomists and lovers of natural history seek to understand and even name the wild diversity of life on earth.

I’ve recently learned the name of two species that turned up on these pages unnamed. So, let me introdue you to Thalassohelix igniflua (last seen in “they’re alive!”):

And Phenacohelix pilula (seen in Incertae sedis)

The drive that naturalists feel to call each thing by its right name can seem oddly obsessive to people that aren’t pulled by the same forces. But species are the fundamental units of biodiversity, and thus a natural point of comparison for studies in ecology, evolution and many other fields. If we want to understand biology we need to know about species, and if we want to know something about a species the we need to have a name that uniquely identifies that species in any scientific work. The species above got its name from Lovell Reeve and, being a New Zealand endemic invertebrate, only a little information has been tacked on that name since. Even so, knowing the name of this species is enough for me to learn that it is widespread across New Zealand, and down here in the southern end of the South Island it can co-exist with a close relative called P. mahlfelda. (From this last fact we can infer that it’s likey that P. mahlfeldae and P. pilula occupy slightly different ecological niches, as it is generally though two species can’t co-habitate while trying to take up the same sopt in nature’s economy).
I can also look at an unpublished study by the late Jim Goulstone, who collected snails from all around Dunedin and the surrounding patches of bush, and learn that its a bit of a surprise that our urban garden (we are 400 m away from the Octagon, Dunedin’s answer to a town square) has such a thriving population of this snail. Goulstone only found P. pilula at two sites in Dundedin, both in old-growth forests on the slopes of Mt Cargill. In both of those sites he only records one shell for P. pilula. Land snail distributions are notoriously patchy, but it’s still interesting to wonder how what seems like a fairly rare and habitat-restricted species ended up as the only native land snail in our garden. 

On the radio David Winter Mar 23

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David McMorran from the Department of Chemistry here at Otago hosts a fortnightly radio show, which talks about postgraduate research in the Division of Science. I was the guest last week, so if you want to hear me talk about taxonomy, the challenge that the world’s biodiversity represents for scientists and a little bit about my land snails the audio for interview is up here.

I find it very hard to listen to recordings of my own voice, but I did manage to get through that audio once. So, I should say that “a bloke called Ernst Mayr” is perhaps taking the antipodean lack of reverence for important people a little too far. And I don’t know what I said the Galapagos has nightingales – it was the Galapagos mockingbirds that Darwin was interested in.

I was a little bit nervous about doing the interview, but in the end far the most difficult part of the whole process was trying to find three songs so share. Here’s one that missed the cut, decided it was just a bit too cute:


Sunday Spinlessness – Amphipods are not prawns (and it matters) David Winter Feb 19


A couple of weeks a go the internet was abuzz with the discovery of giant deep-sea amphipods off the coast of New Zealand.  Invertebrates, form New Zealand featuring in a story that once again highlights how little we know about life on earth - surely, this should be a story that brings me nothing but joy?

Sadly, the New Zealand Herald managed to take just a tiny bit of gloss of the story. They choose to call the creatures  ”prawns” and illustrated their story with this picture…

…which when clicked to achieve a larger view gives us this:

Quite some transformation. Needless to say, amphipods are not prawns and the creature in the larger photograph is only distantly related to the mega-amphipod in the smaller one.

Am I being ridiculously pedantic to care about this error? Is my life really so easy that I have time to worry about taxonomic and nomenclatural details associated with reports in the Herald? In fact, there’s more to this error than the name. The Herald’s conflation of these two distantly related groups highlights the way we fail to comprehend the true diversity of life on earth. So here’s my attemp to show what you miss when you call an amphipod a prawn.

The scale of biodiversity

Every cell in my body is the result of an unbroken-chain of cell division that stretches back 3.8 billion years. I find that an absolutely staggering fact, but I shouldn’t feel too special. Really, I ‘m just like every creature on earth – riding on the edge of one of the lineages that extends out from biology’s big bang at the origin of life. Plenty of people have tried to illustrate the history of life, here’s one more look, based on DNA sequences from living organisms:

Forget animals and plants as the ”two kingdoms” of life. For most of the history of life every creature on earth was a single cell. Even today, most of the lineages that extend out from the biology’s big bang are made entirely of singled-celled organisms. Because this tree is based on those species that scientists have sequenced the genomes of, it drastically over-represents animals, but even here all animals are represented by the little twig that descending from the black-labeled node.

Biodiversity is more or less fractal, if we zoom in on that node and look at the phylogeny of animals we get another tree with branches:

As I’ve said before, it’s very difficult to resolve the relationships among the different lineages of animals. No matter how the branches relate to each other, it’s clear there are a lot of different ways to be an animal, and that I’m never going to run out of subjects to write about for these Sunday posts. All the lions, tigers, bears, elephants, fish, fowl, lizards and frogs that make their way around the world with the aid of a backbone are part of the branch labeled Chordates above. The rest are invertebrates, and so fair game for me. But I’m meant to to be talking about amphipods, so let’s skip a couple of steps and move into the arthropods (jointed-limbed creatures including insects) then down further into crustaceans and in particular the class Malacostraca – a group that includes crabs, lobsters, shrimps, wood lice and indeed amphipods and prawns:

Now we can start to how broad a brush you’d need to paint amphipods into the same group as prawns. In fact, the lineages that went on to give rise to modern amphipods, on the one hand, and prawns on the other parted ways about 130 million years ago. That’s much more ancient than the divide between, say, mice and elephants. What’s more, the amphipods are a much more diverse and interesting group than the prawns into which they were lumped. 

So what is an amphipod?

I’m willing to admit that “amphipod” is not a term with which many people are familiar, and that the Herald had to find some way of explaining what a normal amphipod might look like. The only amphipod that most people are likely to be familiar with is the “sand hopper”. The little crustaceans that bounce away from beach-cast seaweeds when you pick them up are examples of typical amphipods. Most gardens in New Zealand will have species closely related to the sand hoppers living under logs (this one was actually living under a flower pot):

That’s the basic amphipod body plan – a relatively soft exterior divided into 13 sections, two large antennae , two compound eyes and lots and lots of legs divided into different sets for different jobs. By and large amphipods are scavengers, eating decaying matter where ever they get their limbs om it. The land-dwelling amphipods are the only ones you are likely to have seen up close, but most species live in the sea.

Most marine amphipods look more or less like their land-lubber relatives. The super giants that showed up in the Kermadek Trench are presumably from the genus Alicella, which is related to, and more less a scaled-up version of, your typical scavenging amphipod. Other groups of amphipods have remained small, but radically reworked their ancestral body plan. The most striking example of such a reimagining are the elongated caprellids or “skeleton shrimp”:

Caprella mutica. Photo is CC-BY-SA 3.0 from Hans Willewart

There is another radically different amphipod that I’m sure you’ve seen photos of, even though you don’t know it. Here’s a colony of them:

The bumps around the heads of right whales (called callosities) are part of the whale’s body, but the white colouration results from the thousands of cyamid amphipods which live on these bumps. Unlike barnacles, which also attach themselves to whales, cyamids don’t have a free-swimming larval stage, so they are only passed on from one whale to another through contact. Researchers have even used the genetic relationships between cyamids to learn about relationships among whale populations

Cyamids are commonly called “whale lice”, and indeed their flattened bodies are similar to those of their distant insect cousins:

By contrast with the diversity found within the amphipoda, prawns are pretty limited morphologically. I realise the Herald’s headline synonymising the first into the second reflected a general lack of understanding about the sorts of creatures that fill our biosphere, rather than a particular oversight on their behalf. But when the true picture is so much more interesting than the lazy shorthand they used, I think it’s worth pointing out the error.

All the trees here were made with iTOL, this first is their main tree drawn unrooted. The animal and Malacostraca trees are the NCBI taxonomy drawn to phylum and genus level respectively

Sunday Spinelessness – An online fungal foray David Winter Sep 04


One of my goals with these Sunday posts is to do a little to broaden the understanding of just how extraordinarily diverse the biological world is. In almost two years of writing about spineless creatures I’ve limited myself to animals, which, as amazing as we are, only comprise one twig in the tree of life. You can call that an institutional bias, since I’m from a Zoology Department (there are few that haven’t yet been swallowed by Schools of Life Sciences) and maybe it’s a necessary step to narrow the field of targets a little bit. But this is my blog, and my series, and today I want to write about fungi.

In fact, fungi are a prefect example of the gap between our everyday experience of the biological world and what’s really out there. Most of us only notice fungi when mushrooms start popping up in the autumn or when the fruit we bought, and were definitely going to eat this time, starts turning furry. In fact, there might be something like one and a half million species of fungi on earth; there are deep-sea fungi, forest fungi and freshwater fungi; there are fungi that live on tree roots and others that live on human skin; there are even mind-controlling fungi that hijack the nervous system of certain ant species for their own gain:

Some fungi play important roles in ecosystems, and probably the most important of all are a taxonomically diverse group that livr in or on the roots of plants. These so called ‘mycorrhizal’ fungi greatly increase their host’s ability to take up and process nutrients and water from the soil, while the fungi can take advantage of the plant’s ability to create sugars from carbon dioxide and sunlight. Between 80 and 90 per cent of plant species can form relationships with mycorrhizal fungi (Wang and Qui 2006 doi: 10.1007/s00572-005-0033-6) and, as you might imagine, the presence or absence of mycorrhiza can have a big impact on the health of individuals plants, crops and forests.

On Wednesday, I heard David Orlovich (@davidorlovich) speak about mycorrhiza in southern beech (Nothafagus) forests in New Zealand. Beech forests form a major part of New Zealand’s natural heritage, and some our most important conservation sites (Westland, Fiordland…) are covered almost exclusively by beech species. Without mycorrhizal fungi there would be no Southern Beech: seedlings raised in sterile soil simply fail to develop. David went as far as to say that we should see beech trees as giant antennae that fungi used to fix carbon from the atmosphere. I’m not sure I’d follow him quite that far, but his talk on using DNA sequences to quantify the number of fungal species associated with local silver beech forests and the the specificity of fungal species was really interesting.

It also got me thinking about a blog post by Rod Page (@rdmpage) in which he shows how we can take advantage of data that is stored in The Big DNA Database (called GenBank) but goes almost unused. Every record in GenBank has certain information attached to the DNA sequence in describes (the source of the sample, the name of the gene, a scientific paper the sequence is attached to) but the information in a given record is not limited to the required fields – researchers can add any pertinent information they want to. Researchers in biodiversity and related fields often wring their hands about the lack of any infrastructure to hold data collected on various species and taxonomic groups, but, as Rod has pointed out in the past, existing databases (and wikipedia) already contain considerably more information than we’re taking advantage off.

So, when I decided I needed a break from thinking about snails this Friday night, I set out to see if there was enough information about fungal hosts in GenBank for us to start examining the fungal diversity of New Zealand forests*. You could make a start at that project using the pointy-clicky web-interface but I decided to use Biopython (a library for the Python programming language), because writing code for a project is really the best way to document what you’re doing , helps make you research reproducible and allows you to pick up a project where you left it. So, the first step was finding records that corresponded to sequences from mycorrhizal fungi in New Zealand. As far as I can tell you can’t search within particular submitter-defined features of a file, so here’s how I did the search with Biopython’s Entrez.esearch() function.

The ‘ids’ object collected form that search is a list of unique identifiers for sequence records that matched our search, so let’s get all of those records in a sequence file and use SeqIO from Biopython to deal with them

Now the heavy lifting! We need to get the host information from each record which means looping through a bunch of attributes in the Biopython object representing that record. We want to store the data as a “one to many” relationship, since each host species might have multiple fungal species associated with it. There are couple of different ways of doing that, but I used python’s very cool “defaultdict” dictionary which can create a list for each host and add new information to that list when it encounters the host.

And this is where everything went wrong. Well not quite, the search term I used found 84 records, but they were all for fungi collected from silver beech (Nothofagus menziesii) trees. So much for comparing diversity between hosts! Still, those 84 records give us a change to estimate the taxonomic diversity of fungi associated with this tree, so lets count up all the unique taxonomic names among these records:

And (dropping python for R and ggplot2) a graph (click for a larger version):

I’m not finished with this little project, I have some ideas to widen the net for fungal species next time I get really sick of snails, but even this little exercise shows some interesting things. First, silver beech have lots of fungi on their roots, and they come from lots fo different groups! It would be fascinating to know if the fungal families represented above were playing different roles in the root-tip, or if each was competing with others. Or how that make-up of the fungal biota attached to a given tree or a given forests effects its health. More importantly, GenBank is potentially a really useful way for researchers to share more than just sequence data. If people working on mycorrhizal fungi decided on a de facto standard for the way they annotated their GenBank submissions then data from hundreds of published (and unpublished) studies could be almost effortlessly combined to create a big picture of the dynamics of these important fungi. Even as it is now, there is a source of data that is almost never used by researchers or people building the various “encyclopedia of life” projects, and it doesn’t take too much tinkering to see how it could be put to use.

*Yes, I’m the sort of person who takes a break from science by doing some other science. On a Friday night. What of it?

Sunday Spinelessness – Attack of the Killer Sponge! David Winter May 23

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Chondrocladia turbiformis, a ruthless carnivore hauled from bottom of the sea off new New Zealand by NIWA scientists, has been named among the top ten new species described last year. This abyssal predator isn’t a kraken, a plesiosaur that time forgot or even an improbable (but awesome) hybrid. It’s a sponge.

It may come as some surprise that a sponge can be a carnivore, or even that sponges are animals. Sedentary as they are, sponges tick all the boxes for inclusion in the kingdom Anamalia. They eat other organisms to make energy and build their body (differentiating them form plants and algae), they have cells enclosed by membranes (not cell walls like plants and fungi) and they are truly multi-cellular, with specialised cell-types (which sets them apart from protists). On the other hand, sponges are pretty unusual animals. Sponges have no nervous system, no gut, not circulatory system and their cells don’t form tissues. The relative simplicity of sponges helps us to understand the evolutionary history of animals, by plotting some of the characteristics of modern animals onto a phylogeny we can see what order those characters evolved in:

How the sponges relate to other animals. The protostomes and deuterostomes differ from each other in in fate of the blastopore, the first opening to form during embryonic development. In protostomes it becomes the mouth, indeuterostomes it becomes the anus.

So, sponges are useful in trying to understand the evolution of animals. But we shouldn’t view modern species as steps along a path toward more complex animals. Sponges are amazing creatures in their own right, for a start they’re the only animals that don’t have a mouth. Most sponges feed by drawing water into the their body through pores and absorbing bacteria and small algae from that water with specialized cells on the inner surface of their bodies. The cells of the inner surface have two sets of projections to help them with this task. The tail-like flagella which beat together to get water flowing over the absorbing cells and the hair-like micro-villi which increase the cells surface area and make them more efficient absorbers (the guts of more complex animals play the same trick on a larger scale). Most sponges further increase the efficiency of this process by taking the form, and the function, of a chimney. The tubular forms are help together by a mesh of small calcium carbonate structures called spicules.

Filter feeding works well in relatively nutrient-rich shallow waters, but scientists have pulled odd looking sponges up from the bottom of the ocean. Some of those sponges still had the characteristic sponge filter feeding system, but others had lost it all together. Quite how these strange sponges were getting by in the dark and unproductive abyss without even the normal sponge feeding system remained a mystery until 1995 when French researchers found a relative of the deep sea sponges in a relatively shallow submarine cave. Abestopluma hypoa gave scientists their first chance to observe these sponges, and what they saw was amazing: it was a carnivore. In life A. hypoa projects a set of filaments into the water. Those filaments are covered in tiny spicules which act like Velcro (that’s the author’s own simile) grabbing passing crustaceans and holding them in place. It takes a while for the sponge to get its meal, cells make contact with prey within an hour but the actual ingestion follows a period of cell growth and movement which completely covers the animal after a day. It takes another couple of days to completely digest the crustacean.

Since that first discovery scientists have discovered many more carnivorous sponges, with a surprisingly large number coming from sea mounts off New Zealand and in the Southern Ocean. The topic of today’s post (I knew I’d get to it eventually…), Chondrocladia turbiformis, is one of the newest killer sponges, and it looks a bit like a mushroom:

The Chondrocladia are a bit of a special case among the carinovore-sponges because they have retained the rudiments of their filter feeding system. They don’t appear to use it to supplement their diet, rather it’s been re-purposed to inflate a balloon like structure the sponge uses to help capture prey. (For a stunning example of this structure in a live sponge see the photo that illustrates Olivia Judson’s article here.). But the thing that really distinguishes C. turbiformis from the already amazing carnivorous sponges are its spicules:

Beautiful as they are, those symmetrical curved claws in D and E are run of the mill for Chondrocladia. The spinning top spicules in G and H are something quite different. It was only through the description of C. turbiformis and a related species C. tasminae that it became apparent these spicules, with have been named trochirhabds, are present in some modern Chondrocladia species. It’s not extactly clear what these cool little spiclues are doing in modern Chondrocladia but they give us a clue to the history of carnivorous sponges. Spicules just like the trochirhabds described from C. turbiformis have been found in marine sediments from the Jurassic period. It appears the carnivorous sponges that it took us until 1995 to learn about have been living in the oceans for at least 150 million years.

The rest of the this years top ten – including bombardier worms, amphibious sea slugs and giant web building spiders – can be found here.

Vacelet, J., Boury-Esnault, N., Fiala-Medioni, A., & Fisher, C. (1995). A methanotrophic carnivorous sponge Nature, 377 (6547), 296-296 DOI: 10.1038/377296a0

Jean Vacelet,, Michelle Kelly, & Monika Schlacher-Hoenlinger (2009). Two new species of Chondrocladia (Demospongiae: Cladorhizidae) with a new spicule type from the deep south Pacific, and a discussion of the genus Meliiderma Zootaxa (2073), 57-68

Sunday Spinelessness – The end of Drosophila melanogaster? David Winter Apr 25

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It looks like Drosophila melanogaster, the subject of a recent Sunday Spinelessness post, is about to be lost the world. The species itself isn’t under threat of extinction, you can still have them delivered to your door, it’s the name that looks set to go the way of the Brontosaurus.

One of the goals of taxonomy is to give scientists a precise set of terms that refer to a mutually understood group of organisms. The name D. melanogaster is a case in point, geneticists frequently refer to that species as “the fruit fly” but the common name “fruit fly” could equally be applied to the whole genus Drosophila (more than 1400 species), the family Drosophilidae (containing another 50 or so genera) or the related family Tephritidae. Believe it or not, the lack of precision conveyed by the term fruit fly became part of the USA’s 2008 presidential election. Sarah Palin made some snide and ignorant remarks about “fruit fly research” in one of her speeches which were interpreted by scientific types all over the world as a swipe at basic research. People wrote pieces on the importance of D. melanogaster research in understanding human disease and media picked up the story. But Palin wasn’t talking about Drosophila, she was referring to a project on an economically important Tephritid. She was still being ignorant and playing the “aren’t those scientists stupid” card, be she was doing it about a project that stood to help a multi-million dollar industry that employs thousands of people.

Combined phylogenetic tree (“supertree”) stolen from Michael Bok, who redrew it from van der Linde and Houle (2008)

When we say D. melanogaster instead of fruit fly we all know what we’re talking about, and in modern biology a species name can be a key to huge amounts of information. But there’s a problem with Drosophila. The genus as it is currently prescribed is a mess, species currently included in the genus come out in disparate groups in phylogenetic analyses like the one one the left. The solution is obvious, break up the big malformed genus into a set of smaller ones, giving all but one a new name. Such a process is pretty common in taxonomy, and the code used to my animal taxonomists explains how to go about doing it. Each genus has a “type species” which acts as the name bearer and when a genus is split, it’s the group with the type species that keeps the original name. In molecular biology D. melanogaster is very much the name bearing Drosophila (it’s frequently referred to just by that name or even as “the fly”) but the same isn’t true in taxonomy. The type species is D. funebris and no matter how Drosophila is broken up D. funebris and D. melanogaster are going to end up in different genera so melanogaster will lose its forename. But D. melongaster isn’t just any fly – changing that name would render thousands of textbooks, papers and databases out of date.

Kim van der Linde saw the coming of the Drospho-pocalypse, and applied to the International Committee of Zoological Nomenclature (ICZN) to have D. melanogaster installed as the type species, preventing any changes to the taxonomy of the group from changing the species name. A couple of weeks ago the ICZN made their decision: the application was turned down and D. melanogaster will almost certainly have it’s name changed. You can read the decision online – the committee make arguments for their decision with varying degrees of credibility. Perhaps the weakest justification revolves around this mosquito (I couldn’t have two Sunday Spinelessness posts in a row without one photo from me!):

Aedes aegypti  Stegomyia aegypti ?

This photo was taken on Mitiaro in the Cook Islands, and at the time I took I knew for sure that those white striped legs marked it out as Aedes aegypti. If that species of mosquito had bitten me on any other island in the Cooks I wouldn’t have calmly framed a photo, it’s a vector for dengue fever which is, by all accounts, a horrible disease to have (Mitiaro’s population of 200 people isn’t enough to sustain Dengue, and since the main features of the island are two huge brackish lakes fill of mosquito larvae you soon give up on swatting bugs and spraying DEET). But the point of me showing you this photo now is to tell you that mosquito is no longer Aedes aegypti. Some ICZN committee members cited the fact this species has recently been renamed to Stegomyia aegypti as evidence that renaming a widely studied organism isn’t the end of the world, which rather ignores that fact medical workers, ecologists, parasitologists and geneticists have ignored the reassignment entirely and some prominent journals have even issued editorials encouraging researchers to use the “old” name.

Surely in Aedes aegypti we have a model of what will happen when D. melnoagster gets its genus reassignment – taxonomists will refer to it by the new name and the rest of the world will cray on as if nothing had happened. By refusing to make a small change to the existing taxonomy of the group the ICZN runs the risk of driving a gap between the taxonomic community and other scientists. The only good thing to come from the whole ordeal is that “D. melanogaster” will almost certainly become Sophophora melanogaster which tranlates as “dark bodied bearer of knowledge”, a fitting name for such an important fly.

Plenty of other bloggers have been talking about this story, some with quite different takes than mine. You should check out Kim van der Linde who made the the application to the ICZN and has been blogging the aftermarth as well as Micheal at Arthropoda, Chris at Catalogue of Organisms and Dave at Seed.

The tree is from the following paper:

Kim Van der Linde, & David Houle (2008). A supertree analysis and literature review of the genus Drosophila and closely related genera (Diptera, Drosophilidae)Insect Syst. Evol., 39, 241-267

Link taxonomic names on any website to the Encyclopedia of Life David Winter Aug 24

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The Encyclopedia of Life is a project aimed at compiling information on each of the 1.8 million species that scientists have so far described and making that information available to students, scientists and anyone that wants to know a bit more about life on earth. The project is now a couple of years old (I actually wrote about its launch here) and is starting to build up information and some pretty cool tools to get at that information.

Earlier this month the EoL released NameLink, a service that searches a web-page for taxonomic names and then adds links to from those names to their records in various taxonomic databases. At present the only way for a user to get those links to show up is to copy page’s url, surf over to the NameLink page and paste it into their handy form. Which is fine, but I am very lazy so I wanted to be able to add the links while I was reading a page, thankfully the EoL include an API for NameLink that made it very easy to write a ubiquity command and some bookmarklets that allow me to be as lazy as I want.

If you have ubiquity installed you can follow this link and install the “taxonomize” command or you can drag the following links on to you bookmarks toolbar to get commands that will add links the EoL and the The Global Biodiversity Information Facility with a single click:

EoL Taxonomize!

GBIF Taxonomize!

The ubiquity command allows you to choose which database to link to by providing one of the following abbreviations after the taxonomise command:

col: Catalogue of Life
eol: Encyclopedia of Life
gbif: Global Biodiversity Information Facility
gni: Global Names Index
itis: Integrated Taxonomic Information System
namebank: uBio Namebank

The commands in action

Once you have your have a command or a bookmarklet ready to go then next time you find yourself reading a page rich in taxonomic names like this post on Dechronization about anole hunting in Haiti you’ll be able to use the command to get to this page which has all the species names linked:

From which point new information on the handsomely dewlapped Anolis distichys venosus is just a click away

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