Showing posts with label taxonomy. Show all posts
Showing posts with label taxonomy. Show all posts

Wednesday, January 21, 2015

Not So Simple: Social Evolution in Silk-Weaving Ants



Silk weaving ants. That in and of itself is really neat. Then you see this picture of Polyrhachis shattuck...I mean, look at her! How many cool points can one animal rack up? A new study in Behavioral Ecology and Sociobiology takes a look at these arboreal nesting and silk-weaving ants.

Let's begin with sociality. It is one of those subjects in biology that is considered its own discipline. When you think of social animals you probably think of herds of mammals or maybe schools of fish. Sociality reaches its peak in eusociality, a surprisingly complex and truly social organization. These animals live in groups, cooperatively care for juveniles, divide labor, and overlap in generations. Studies of these social systems has shed light onto broader concepts of collective decision making, even leading to advances in our own technology (traffic flow, communications networks, internet searches, etc.). However, as much as we know about the social mechanics, we know very little about the evolution of such systems.

Most eusocial animals are found in the phylum Arthropoda, with the order Hymenoptera being the largest and most well-known, and all ants classified as eusocial species. And ants are the focus of today's chosen study. Ant larvae spin individual protective cocoons of silk and, depending on the species, that silk is either allocated to the colony or sequestered for the larvae’s individual needs. Donated silk is used by the worker caste to weave together leaves into nests. The “lowest grade” of arboreal (a.k.a. tree-dwelling) ants, Dendromyrmex, have larvae that produce silk without any interaction or provocation from the worker ants. In “intermediate grade” ants, Camponotus senex and Polyrhachis ?doddi (re-described as Polyrhachis robsoni (Kohout 2006)), the workers hold larvae at the work site and, with simple ritualized behaviors, the workers collect the silk. In the “highest grade” genus, Oecophylla, the larvae donate their silk supply to the colony. A worker ant will use highly ritualized behaviors - bring the larvae to the work site, straddle a leaf seam, use antennae to tap the head of the larva (telling it to extrudes silk from its salivary glands), use silk to glue together the seam, repeat.

A comparison of ant genera in this way, simple to complex, is thought to represent possible evolutionary steps in nest-weaving behavior. However, molecular sequence data suggests that nest-weaving has evolved independently in each of the four genera in which it occurs. This new study focuses on Polyrhachis ants. This genus offers good within-taxa comparison of multiple life strategies as different species vary in their nesting locations, from intertidal to subterranean to arboreal, the presence of nest construction, and even silk sources.

A total of 37 specimens of ants from all 13 currently recognized (*grr*, an often frustrating term in insect taxonomy) subspecies and five outgroup taxa were used for this study. The researchers isolated total genomic DNA and amplified and sequenced DNA from six fragments using specific primers for each gene region. After they collected the sequences, they analyzed and aligned them using computer programs. In their complicated analysis (they used Bayesian…that always makes my eyes cross) they input the gene level data along with variables of nesting preference (ground = soil, logs, stones vs. arboreal = twigs or leaves in trees) and nest construction (silk weaving vs. no silk vs. other silk). All of this allowed them to construct phylogenies (like an evolutionary family tree) and infer relationships among the species and ancestral states for behavior.

Their results showed robust phylogeny with strong support for the monophyly of the genus Polyrhachis, further supported by the inclusions of nesting preference and nest construction.This is good because it provides a nice, solid ancestral reconstruction for the evolution of the different species and their relationships to each other. It also allows for the comparison of the different nesting strategies within the framework of evolution. The investigation turned up some very interesting results. Simply, their results do not support the stepwise evolution of simple to complex. They found that the production of arboreal silk nests is the ancestral state with at least two transitions to subterranean nesting and the loss of silk weaving as species become more derived. There is also some flexibility and reversal in the behavior. Basically, the ants evolve, abandon and then re-evolve the nest weaving practices. The loss of silk nest weaving seems to occur with the transition from arboreal to terrestrial nesting followed by the re-evolution of silk nest weaving. This suggests a strong but flexible link between nesting preference and nest construction.

To illustrate this evolve-abandon-re-evolve point, the researchers present the example of Hedomyrma, a subgenus within a larger clade of subterranean nesters. This larger clade has already lost both arborality and nest weaving. But there are 2 species of Hedomyrma (Polyrhachis argentosa and Polyrhachis fervens) that have reverted to arborality. The re-evolution of this nesting preference has come with the modification of building nests within the hollow internodes of bamboo sans silk. Another reversal pattern is seen in a third species of Hedomyrma (Polyrhachis turneri), which has larvae that retain all of their silk for their own cocoon-constructing needs. Rather, worker ants steal silk from spiders to build nests on the sides of rocks. So the nest construction characteristic is what has re-evolved, just with a different mechanism. Larval cocoons have been lost in 2 of the arboreal nest-weaving species studied, and the allocation of larval silk to colony rather than individual need is considered a more derived but decoupled characteristic of nest construction.

I think that both the flexibility and the rapid evolution (or re-evolution) of this system is what attracted me to this paper. We know that evolution is a complex concept that we often boil down to from-simple-to-complex, and in many cases it is exactly that. This study almost reads like a sequel, a what-happens-next sort of thing.


ResearchBlogging.orgRobson, S., Kohout, R., Beckenbach, A., & Moreau, C. (2015). Evolutionary transitions of complex labile traits: Silk weaving and arboreal nesting in Polyrhachis ants Behavioral Ecology and Sociobiology DOI: 10.1007/s00265-014-1857-x


(image of Polyrhachis shattuck, Maliau Basin, Sabah via AntWiki via California Academy of Science Ant Course)

Monday, September 24, 2012

Wednesday, September 19, 2012

Snakes, An Origin Story


Quite honestly, I should have been reading a plant paper for my upcoming lab meeting. But then I stumbled across a really cool snake paper and, well, that won out. I regret nothing. As with most people, I will most likely read the plant paper right before the meeting anyway.

A paper published online today in Biology Letters takes a look at the phylogeny of squamate reptiles (lizards and snakes). This group of reptiles is one of the most diverse and well-known vertebrate groups including approximately 9000 species among 61 families. As with many groups, taxonomists and geneticists are trying to reconcile morphology and molecular analysis. This paper is taking the molecular approach, specifically looking at sister groups and interrelationships of major snake clades and iguanian families. Being a well-studied group, molecular analyses have been conducted in the past. These studies have suggested that squamate molecular phylogeny results differ quite a bit from morphological ones. This study takes one gigantic step forward, increasing the sampling of taxa dramatically and doubling the number of genes studied.

The researchers sampled 161 squamate species and 10 outgroup taxa, including mammals (Homo, Mus, Tachyglossus), crocodilians (Alligator, Crocodylus), birds (Dromaius, Gallus), turtles (Chelydra, Podocnemis) and a rhyncocephalian (Sphenodon). Then they sequenced portions of 44 nuclear genes, targeting single-copy genes evolving at appropriate rates. The nucleotide sequences were then translated into amino acids to aid alignment. This alignment consisted of 33,717 base pairs! I’m not going to go into all of the bootstrapping, likelihoods, and Bayesian analyses that were used (even the word Bayesian makes my brain shut down in protest). But suffice it to say that the different analysis techniques that were used yielded similar phylogenies, providing strong support for the relationships found.

The results of this molecular analysis were found to be consistent with other, recent, similar studies. However, there were some interesting relationships discovered. The first of these was that dibamid (legless lizards found in tropical forests) and gekkotans (geckos and the limbless Pygopodidae) are together the sister group to all other squamates. They also found strong support for paraphyly of scolecophidian snakes (blind snakes). Scolecophidians have reduced eyes and are specialized burrowers. Considering these traits, the paraphyly of this group suggests that it is the ancestral form, that other snakes may have been burrowers ancestrally. This makes sense if you compare the morphology of snakes to other burrowing species such as limb-reduced lizards. They both have short tails and elongate trunks. Very good for tunneling their way through the earth.

Overall, a really interesting study that was huge in its scope. I look forward to more of these kinds of studies in the future.


ResearchBlogging.orgJohn J. Wiens, Carl R. Hutter, Daniel G. Mulcahy, Brice P. Noonan, Ted M. Townsend, Jack W. Sites Jr., & Tod W. Reeder (2012). Resolving the phylogeny of lizards and snakes (Squamata) with extensive sampling of genes and species Biology Letters, 4 (11) DOI: 10.1098/rsbl.2012.0703

If you are a non-scientist and I used too many biology-jargony words for you or you just need a refresher on phylogeny, then I recommend looking through these sites:
Fullerton’s Biology 261 course page on Interpreting Cladograms
Berkeley’s Understanding Evolution page on reading phylogenetic trees

Here is some more information on blind snakes:
ScienceBlogs article Scolecophidians: seriously strange serpents

Also:
ScienceShot article: Snakes' Slitherin' Subterranean Kin


(images from  Encyclopedia of Life and Neoseeker, respectively)

Tuesday, August 21, 2012

Freshman Survival Kit

OK, prepare yourself because I'm going to fly my nerd flag high. It is that time of year when college campuses around the country are being invaded by new and returning students. A labmate's daughter is starting her first year in college and so as a graduation present I put together a Freshman Survival Kit. I used the excuse of her being a science major to validate my nerd-out. Biologists love dichotomous keys and so why not put one together to tell her all about what is included in her kit. See? Nerd flag. Enjoy!








Friday, March 4, 2011

Attack of the Zombie Ant!


A couple of years ago a study was published in The American Naturalist about an interesting fungal parasite known as Ophiocordyceps unilateralis. This fungus infects ants in the tribe Camponotini (carpenter ants) but does not kill them outright. Rather, the ant remains alive for a short time but the fungus is in control. The fungus compels the ant to crawl down from its nest in the high forest canopy down to the small plants of the understory. Then the fungus has the ant crawl onto the underside of a leaf, clamp down its mandibles, and then die. There the ant body will stay while the fungus continues to grow inside of its body, producing a hyphae and stroma (fruiting body) that grows right out of the ant's head. The stroma then releases spores on to the forest floor, spores waiting to infect the next unsuspecting ant passerby. You can see where the nickname "zombie ants" and "zombie fungus" came from. Now, this was not a previously unknown species of fungus but rather an unknown effect of the fungus on ants, a previously unknown part of the life cycle. What is truly amazing is the accuracy to which the fungus directed the ant. The ants always clamped on to the underside of a leaf and almost always on a leaf vein. The chosen leaf was about 25 centimeters above the ground, with 94-95% humidity, and between 20-30 Celsius. The fungus directs the ant to a location with the parameters that it needs to survive and reproduce.

Now a new paper in the journal PLoS ONE describes four new species belonging to the O. unilateralis species complex from the Atlantic rainforest in Brazil. The species are named according to their ant host species (specifically Camponotus rufies, C. balzani, C. melanoticus, and C. novograndadensis). Ultimately, this paper is just recognizing and naming new species. However, it helps to draw attention to the south-eastern region (Zona de Mata) of the State of Minas Gerais in Brazil, one of the most heavily degraded biodiversity hotspot on the planet. A total of 92% of this rainforest is gone, and four new species have just been discovered. How many more are there to find and how many have already been lost?

Want more zombie animals? Check out these:
The nematode-ant relationship in Central America
The emerald cockroach wasp (Ampulex compressa)-cockroach relationship in the Polynesian Islands.
The spider (Plesiometa argyra)-wasp (Hymenoepimecis argyraphaga) relationship in Costa Rica.

The list goes on and on; pill bugs and spiny-headed worms (Plagiorhychun cylin-draceus), grasshoppers (Melanoplus sanguinipes) and the protist (Nosema acridophagus), the fluke (Dicrocoelium dendriticum) and the ant, the wasp (Glyptapanteles) and the caterpillar, the distome (Leucochloridium paradoxum) and the snail, the barnacle (Sacculina carcini) and the crab, etc. Wasps, ants, and caterpillars tend to have a lot of parasite-host stuff going on (there's even a whole group of parasitoid wasps), although admittedly not all that much zombism. It is an ever-so-interesting evolutionary arms race!

Read more about zombie animals here: http://www.newscientist.com/article/mg14018983.500-evolutions-neglected-superstars-there-is-nothing-glamorous-about-fleas-flukes-or-intestinal-worms-so-why-are-they-suddenly-attracting-so-much-attention.html
and here: http://discovermagazine.com/photos/04-zombie-animals-and-the-parasites-that-control-them

The original zombie ant study (online version of the paper contains a video):
Andersen, Sandra B., et al. (2009) The Life of a Dead Ant: The Expression of an Adaptive Extended Phenotype. The American Naturalist: 174(3), 424-433. (DOI: 10.1086/603640)

The new study, and because it is published in PLoS ONE it is free access (yay!):
Evans, Harry C., Simon L. Elliot, and David P. Hughes. (2011) Hidden Diversity Behind the Zombie-Ant Fungus Ophiocordyceps unilateralis: Four New Species Described from Carpenter Ants in Minas Gerais, Brazil. PLoS ONE: 6(3), e17024. (DOI:10.1371/journal.pone.0017024)

Online stories on this paper:
http://blogs.plos.org/everyone/2011/03/02/four-new-species-of-zombie-ant-fungi-another-step-forward-for-open-access-taxonomy/%20
http://www.physorg.com/news/2011-03-species-zombie-ant-fungi-brazilian.html
http://www.sciencedaily.com/releases/2011/03/110302171309.htm

Walking Cactus


"(An) armoured lobopodian with ten pairs of appendages. Trunk region with nine segments, bearing rows of transverse annulations each with some tubercles. Each region possesses a pair of robust and sclerotized spiny appendages with primary articulation. Anterior is extended, probably forming a proboscis. Posterior region bears a protrusion."

That's the description of a new species found in China and described in the journal Nature last week. The species name is Diania cactiformis, the genus name referring to the Chinese province of Yunnan and the species epithet refering to it's cactus shape. Since, it has garnered the nickname the "walking cactus." It belongs to the group Lobopodia, a now extinct group consisting of small, segmented animals dating back to the early Cambrian. The dorsal armored or sclerotized plates are characteristic of this group. This group of organisms resembles velvet worms (Onychophorans) which are terrestrial worms with legs.

The new species was nicknamed the "walking cactus" because of its many appendages and spiny appearance. The specimen dates from around 500 million years ago, is about 6 centimeters (2.4 inches) long, and has the long worm-like body characteristic of lobopodians. What makes this creature unique is its hardened, jointed legs. These joints are important because they provide a link between lobopodians and arthorpods. Sure missing links are always great to find, but in this case what makes this link so significant? Well, the group Arthropoda contains more than 80% of all known living animal species, we're talking all insects, crustaceans, etc. This newly described link gives insight into how this group evolved. For example, the hardened surfaces of the legs of D. cactiformis imply that arthropods developed hardened limbs before hardened bodies, effectively the first step in evolving the body plan from soft-bodied to an articulated exoskeleton.

The Field Museum in Chicago have imagined it to move something like this:



Read more and see pictures in the paper:
Liu, Jianni, et al. (2011) An armoured Cambrian lobopodian from China with arthopod-like appendages. Nature: 470, 526-530. (DOI: 10.1038/nature09704)

And some story links:
http://www.nature.com/news/2011/110223/full/news.2011.121.html
http://www.npr.org/blogs/krulwich/2011/03/01/134138005/cactus-walking-on-20-legs-found-in-china
http://news.nationalgeographic.com/news/2011/02/110223-walking-cactus-worm-new-species-fossils-animals/

Wednesday, December 8, 2010

Its a squid, its a worm, its a squidworm!

The Celebes Sea is a deep basin (approx. 6200 m) located between the Philippines and Indonesia, at the center of the Coral Triangle. Since its formation in the Eocene (44-42 million years ago) it has been isolated from surrounding deep water by relatively shallow sills. Due to density differences in the water in this basis in relation to the water around it, the water is thought to have long residence times. This area is considered to be a biodiversity hotspot because of the high diversity and endemism of shallow-water corals and fishes as well as being the center of geographical distributions and diversity of lanternfish, hatchetfish, dragonfish, and anglerfish. Considering the high diversity of these shallow water creatures it stands to reason that the deep water fauna may be equivalently diverse even though animal density typically decreases with increasing ocean depth. Finding and studying the creatures found that these depths can be very difficult as they are few and far between and because it is just plain difficult to get down that far.

Meet Teuthidodrilus samae, the squidworm:


This is a new and unusual genus and species of swimming polychaete (marine annelid or segmented worms) recently described in a paper in Biology Letters. T. samae belongs to Acrocirridae as a member of the swimming clade and sister to the "bomb"-bearing clade. As you can see from the picture, it sports a series of 10 large appendages near its head. Hence the likeness to a squid. It is slow moving and found in these very deep waters, and it is likely that similar species can be found in this unique region of the ocean.

Osborn, Karen J., Laurence P. Madin, and Greg W. Rouse (2010) The remarkable squidworm is an example of discoveries that await in deep-pelagic habitats. Biology Letters: published online. (DOI: 10.1098/rsbl.2010.0323)

Here's the ScienceShot:
http://news.sciencemag.org/sciencenow/2010/11/scienceshot-meet-the-squidworm.html?ref=hp

(Image Credit: Laurence Madin/WHOI, image from ScienceShot via Science Magazine)

Wednesday, April 21, 2010

What's in a name?

Drosophila melanogaster, a tiny little fly that is a monster in the world of genetics research. There isn't a biologist that hasn't heard of it, and there are thousands of papers about it. The average person is also familiar with this 2.5-millimeter-long fly. You can see it buzzing around trash cans and unripe or overripe fruit on a regular basis.

D. melanogaster has been used for over a century to study genetics. Thomas Hunt Morgan studied the fly in the early 20th century and was the first to discover sex-linkage and genetic recombination, earning him a Nobel Prize. His work, and the work of his students, solidified D. melanogaster as a model organism. This species is easy to obtain from the wild, small in size and easy to handle, is sexually dimorphic, has a short life cycle (10-12 days), is easy to rear in the lab, has fecund females, has a relatively small genome, and is relatively inexpensive to work on. Additionally, the entire genome has been sequenced and many of the genes identified, and there are a variety of mutants available to purchase for study. Exactly because of these reasons, and how much is known about this species, it is also being used in other fields such as behavior, development, neurobiology, biochemistry, and many others. Much of this research is directly related to human conditions and behaviors (are you listening Sarah Palin?).

However, a recent decision at the International Commission on Zoological Nomenclature (ICZN) may reclassify this organism completely. There are about 1,450 species in the Drosophila genus, and the genus Drosophila is part of a larger family of flies called Drosophilidae. As it turns out D. melanogaster (and potentially some other Drosophila species) may actually be more closely related to Samoaia, Captomyza, or Hirtodrosophila. Should this name change happen, will scientists adopt the new terminology? Will we be calling the fly Sophophora instead of Drosophila? Will it be like Brontosaurus to Apatosaurus and Pluto the planet to Pluto the dwarf planet? Perhaps these name changes just take time to take hold.

Kim Van der Linde, one of the very scientists who opened the debate, has argued to keep the name Drosophila attached to the species. A proposal to the ICZN states that the appellation "Drosophila melanogaster" be preserved to prevent confusion in the scientific literature, but that other species in the Drosophila genus be renamed/reclassified as they are less influential.

I can't really say that I completely disagree with her reasoning. I also recognize that, in the age of computers, the titles of already-published papers do not need to be changed, only a new tag added so they can be easily searched. Also, while D. melanogaster is the most widely used of the Drosophila species, to say that the other species are less influential ignores the thousands of studies that research these other species and even compare them to D. melanogaster. In fact, many (if not most) fly labs raise more than one Drosophila species.

Regardless of the name change this little fly will remain a giant in its field.

Here's more on the topic: http://seedmagazine.com/content/article/idrosophila_i_we_hardly_knew_ye/

Oh, and check these out because they are fantastic!!:
http://notsohumblepie.blogspot.com/2009/12/science-cookies-drosophila-melanogaster.html
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