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Showing posts with label evolution. Show all posts
Showing posts with label evolution. Show all posts

Monday, September 3, 2018

Goats of Hawai'i

Group of five goats at the side of a curved road. Three goats are brown and two are black. Behind the goats are piles of dark brown lava stone and scattered clumps of dried grasses.
I visited Hawai'i last year for a horticulture conference. Well, my spouse was attending the conference. I was just going along for vacation. I spent a lot of time driving and hiking during the days when the conference was in session.

Much of the north-west side of the island where the conference was being held is dry-land, with exposed rock from several different ages of lava flows. I came across the bleached bones of pigs and other large animals among the lava, but rarely saw any sizable living creatures.

One day I was driving out to a nearby park to do some hiking and I saw a group of goats crossing the road. I lucked out and was able to capture a few photos like the one above. What immediately struck me about the goats was that they were colored just like many of the aged lava stones I had been seeing the previous few days. They didn't have any of the white markings so common on goats I've seen almost every where else.




It made me think the goats might have been under a pretty severe hunting pressure and that their colors represented adaptive camouflage, protecting them somewhat from visually-hunting humans. If the goats had been resting among the rocks as I drove by, I likely would have thought they too were just rocks.


Goat hunting on the Big Island is allowed year-round in some places, with defined seasons in other areas. There have been intense and largely successful goat eradication efforts in the larger fence-enclosed parks on the island. This represents a fairly high level of hunting pressure, which would definitely be expected to select for traits that help the animals avoid predation.

Unfortunately, I have been able to find no research on the topic of the evolution of wild goats of Hawai'i due to human hunting. This might be a nice topic for a PhD for some motivated student living on the island. Let me know if you come up with anything.


References:

Monday, February 5, 2018

Speculative Biology: 3-Way Reproduction

The other day I found myself thinking about what would be the fundamental biological characteristics of a species having a system which depended on three individuals, instead of the two or one we're used to, for each reproduction event. (This is a distinctly different concept from a species having multiple sexes or genders. See references at end for examples of these.)

To simplify the discussion, I'm going to start with a big assumption that the hypothetical organism only differs from what we see here in that it has a 3-way reproduction system. It is carbon based, it has DNA organized into chromosomes, etc. Breaching that huge assumption would introduce far more variables into the discussion, when I'm only interested in the basics of sexual reproduction for this discussion.



There are different ways for Earth biology to control the sex of individuals. Sex in some species is driven by genetic differences (mammals and birds). In some it is driven by the number of chromosomes (bees and wasps). In some it is driven by temperature differences (reptiles and amphibians). In others the sex changes with age or social situations (some fishes). In large groups, there are almost always exceptions to the general patterns.

Almost all of these cases involve some chromosomes being contributed to an offspring by both a female and a male. Haplodiploidy in bees/wasps is an interesting exception. (Males grow from unfertilized eggs, while females grow from fertilized eggs.)



For our 3-way reproduction discussion, lets start by assuming each of the three individuals contributes chromosomes equally to each offspring. (Later we'll examine a more complicated case.)

We can easily enough abstract the concept of a Punnett square into higher dimensions, though it does get difficult to simply convey the results in a 2D format. In the regular version, the possibilities for a single chromosome contributed from each parent are aligned along the top and side edge of the table. For a 3D version we'll do the same, but split the contributions from the third parent into three sub-tables (left to right) with the third parent contribution at the upper-left corner of each. (I've added some color highlights to help visualize the contributing parent for each chromosome as well as the sexes of the potential offspring.)

Punnett square (and "cube") for 2-way and 3-way crosses.


The first observation that stands out from this is the difference in predicted sex ratios of the offspring. In our 2-way system, the calculations implies a 1:1 ratio. In the 3-way system, the calculations implies a 1:2.5:1 ratio between the three sexes of offspring.



Next lets discuss something analogous to the haplodiploidy of bees/wasps, where males only contribute chromosomes to their daughters.

Punnett square (and "cube") for 2-way and 3-way crosses, with haplodiploidy.

This shows the same possibilities for sex ratios of offspring. Since we're using bees as a model here, it's a good time to introduce the idea that a creature doesn't have to produce offspring at the ratios suggested by such simple calculations. Bees produce very few males, and only when needed for fertilization of new queens. Similarly, a hypothetical 3-way reproducing species could easily adjust the sex ratio of its offspring to be different from what the above calculations suggest.

An abstraction from Fisher's Principle (http://the-biologist-is-in.blogspot.com/2015/12/evolutionary-battle-of-sexes.html) suggests most species would evolve towards a 1:1:1 ratio between the three sexes. Cases where this wasn't the case would be interesting.



I imagine one sex evolving into an approximation of female (with a large immobile gamete), while the other two sexes evolving into an approximation of male (with smaller, more mobile gametes). It gets much more difficult to make predictions beyond this point, though a couple examples inspired from fiction and biology come to mind.

Maybe the two male-equivalents would actively court each other and then seek out the a female-equivalent together as a pair. This seems to be the pattern described for the fictional Pierson's Puppeteers (though their sexual biology is rarely detailed in the author's stories about them).

Maybe the male-equivalents would independently seek out the female-equivalent. I imagine something similar to the Deep-sea Anglerfish, with smaller male-equivalent individuals fusing to a larger female-equivalent and waiting for the opportunity to contribute to offspring when all three sexes have joined the party.



In the grand scheme of things, I expect biological systems requiring three individuals for reproduction would be rare in the cosmos. At an early evolutionary stage, any organisms which only required two partners to reproduce would probably out-compete those requiring three partners simply because it would be easier to arrange appropriate matings. This isn't to say it wouldn't happen, since all sorts of strange things happen in biology.

The Red Queen hypothesis (http://the-biologist-is-in.blogspot.com/2014/04/oxalis-and-red-queen.html) suggests why larger species don't simply have one sex. Yet, we do see this from time to time.


References

Tuesday, October 31, 2017

Sex Chromosomes of the Triturus Newt

Salamanders and newts are an interesting group of animals. They're amphibians, like the frogs and toads you're probably familiar with, but they have an elongated body form that looks more like a lizard. They're generally rather small and tend to live in places where you don't, so you probably won't see one unless you go a bit out of your way in search of them. Both salamanders and newts start out life as a submerged egg that hatches into a swimming tadpole. As they grow up, they both generally metamorphose into a form adapted for crawling around on land (though they do prefer moist places). Salamanders typically live out the rest of their lives in this stage, while newts return to an aquatic life once they reach full maturity. Adult newts develop a flattened tail that helps them swim and then they go about their quiet lives underwater.

Figure illustrating relationships between species in genus Triturus, with two representative salamanders at right.
Fig1. Adapted from Grossen et al. and photos by @Blackmudpuppy.
Hidden within these shy critters is some really interesting biology. One group, the Triturus newts (the marbled and crested newts), have some peculiar chromosome weirdness going on that results in the death of 50% of their eggs. Evolutionarily, this is a very strange situation. You'd expect any trait that resulted in such a high rate of offspring loss would quickly disappear from a population. You definitely wouldn't expect the trait to become a permanent fixture of most species in the genus, as is observed.



Two very young juvenile newts, with dark body stripes and long extended gills.
Fig 2. Triturus babies.
Photos by @Blackmudpuppy
My initial thought was that maybe the dead eggs were fed upon by their surviving siblings. Kin selection could then explain why such an apparently "wasteful" trait would stick around. If the additional nutrition gained from eating a sibling resulted in at least a 2x increase in genetic fitness (survival and offspring), then the trait could be maintained by this mechanism.

The problem with this idea is that the newts lay their eggs individually, folding a bit of underwater leaf over them for protection from predators. Any given hatchling wouldn't be expected to find a separately stashed egg, so the dead eggs would probably be consumed by other organisms. If the eggs were laid in small clusters, the story might be different, but for now we have to abandon this hypothesis.



Fig 3. Hypothetical lethal male.
The next thought I had is about the 50% loss. That specific number implies a limited set of possible genetics patterns. The first I thought of is the way our biology (generally) uses chromosomes to determine our sex. The male gametes come in X and Y versions, while the female gametes are all X. The result is that 50% of our kids are XX and 50% are XY. (There are lots of subtleties and complications to this story, but for now I'm just going to use this simple model.) If the Triturus newts were doing basically this (without the sex-determination thing the way we do it), but one version of the sperm always resulted in dead embryos... Well, that chromosome would very quickly disappear from a population. This is another hypothesis we have to abandon.

Fig 4. Balanced lethal chr1 in Triturus.
At this point I dug up a 2012 paper by Grossen et al., which described what was going on and described a model for how it might have come to be. It turns out every one of these newts has two distinct versions of their chromosome 1 (the largest chromosome). The two versions have a region of sequence with inversions and deletions relative to the other. These differences mean the two regions don't recombine during meiosis like the comparable regions of most chromosomes. This is significant because each version of this region has a recessive lethal allele that is paired to a functional allele on the other version. (Probably some of those deletions I mentioned earlier.) If any egg is fertilized with a sperm carrying the same version of this chromosome, one of the recessive lethal traits is expressed. This results in the death of 50% of embryos, and leaves the survivors all heterozygous for chromosome 1. This is a pattern that can continue through generations.



The difficulty arises when we consider how this arrangement could come to be. If either recessive lethal allele was present without the other, then it would be selected out of the population. The chromosome version without a lethal allele would quickly dominate in the population (and we wouldn't see a 50% death rate among the babies).

The Grossen et al. paper goes into some really cool details about how sex-determination works in these newts. They have an XY sex-chromosome system kind of like ours, but they're also strongly impacted by temperature. If baby newts are raised up in water that's too warm, they'll become functionally male. If they're raised up in water that's too cold, they'll become functionally female. If the temperatures are extreme enough, they'll all grow into one sex without respect to what their sex-chromosomes look like. (This happens with lots of cold-blooded creatures, though what sex is produced at what temperature varies by species.)

In this context, they propose that the 1a/1b chromosomes that are causing so much trouble started out as two versions of an ancestral Y-chromosome. Y-chromosomes tend to collect recessive lethal mutations (deletions and such) and different lineages of Y-chromosome will end up with different mutations. If a population of ancestral Triturus newts experienced a significant cold spell, some of the chromosomally male newts would have grown up female. They could then breed with more typical males to produce offspring with two Y-chromosomes. If the two Y-chromosomes have the same mutations, the offspring would die. But if they had sufficiently different versions, they could survive. (This has been shown experimentally in a few species, as described in Haskins et al. 1970.) Grossen et al. go into some detail simulating how this initial case could lead to the chromosome dynamics now seen.



Fig 5. Model for evolution of
balanced lethal Ys.
While I was reading the Grossen et al. paper, I was thinking of a slightly different version of the model. In this version, we see a female-promoting mutation develop instead of the male-promoting one that was modeled. In the associated figures to the right, I've included Punnett squares for all the possible chromosome combinations involved in matings at each stage of the model. The color of the progeny squares represents their sex, as determined by the interaction between genetics and temperature. (Red=female; blue=male; purple=either; black=dead.)
  1. The population beings with XY males and XX females. Multiple Y lineages coexist.
  2. As the temperature drops, the offspring of all XY*XX crosses develop as female. Sooner or later a XY female of the newer generation meets up with an XY male from the previous generation. If the Y-chromosome versions are the same, every baby again develops as female because the double-Y babies die. If the Y-chromosome versions are different, a fourth of the babies will develop as YaYb males.
  3. The older males eventually die off, leaving only YaYb males. There are still XX females around from the last generation, but all of their offspring will now be XYa or XYb.
  4. The XX females eventually die off, leaving only XYa and XYb females.
  5. The temperature drops a bit further. Now YaYb embryos can develop as either male or female.
  6. Some YaYb females meet up with some YaYb males and the first clutch of eggs is laid that experiences a 50% chromosomal-induced fatality rate.
  7. The newt population has been experiencing a major catastrophe and has dropped to very small numbers. The X chromosome carrying females die out, due to either random chance or some minor benefit the YaYb females have.
Fig 6. Model for evolution of
new sex chromosomes.
At this stage in the story, there are no further X chromosomes and half of every clutch dies due to incompatible Y chromosomes. We shouldn't really call them Y chromosomes anymore, so lets call them chromosome 1s for simplicity. The population is now in a stable evolutionary configuration, but only for as long as the temperatures remain consistent.
  1. The temperature starts to rise back up and new 1a1b babies start developing as males. Some very few of the females happen to have a mutation on another chromosome (2*) that encourages female development. The offspring carrying this mutation develop female at these warmer temperatures.
  2. All the older females die off, leaving only those carrying the mutation. The temperatures are still rising and some newts carrying the mutation start developing male.
  3. Some males with the mutation meet up with females also carrying the mutation. The first newts with two copies of the mutation are born and develop female.
  4. The temperatures are still rising. Newts born with only one copy of the mutation start developing male. The only newts that develop female have two copies of the mutation.
  5. The older females die off, leaving only those with two copies of the mutation. The only new males are those born with one copy of the mutation. The older males die off, leaving only those with one copy of the mutation.
At this stage in the story, a new pair of sex chromosomes has evolved. The copy with the mutation is now an X chromosome and the copy without the mutation is now a Y chromosome. The residual chromosomes from the original sex chromosome pair are still causing 50% of babies to die in early development.



I could extend my model using a simulation-based approach similar to Grossen et al. to make a better comparison, but I don't expect I will. With complex evolutionary history like this, it might never be possible to ascertain exactly how the process unfolded. There could be many equally-probably historical scenarios that would have led to the evolution of the situation we see today. It's educational to study how these systems could potentially have evolved, even if we can't sort out the exact path they took to get where they now are.

I don't often write about published papers, but when I do I prefer to carry the discussion past where the paper ended. Discussing an alternate model is in no way an attack against the one proposed in Grossen et al.. It's an honest reflection of what I was thinking of while reading and is part of an exploration of the ideas discussed in the paper. Frankly, if their writing didn't give me any new ideas to play with, I wouldn't find it anywhere near as interesting to read. Good science answers a question. Great science answers a question and then draws you in to ask your own new questions.



This post was inspired by an interesting conversation over on Twitter. (You can follow me there as @thebiologistisn.)
The photos of the Triturus newts were loaned to me for this blog post by photographer (and newt wrangler) @Blackmudpuppy.


References:

Saturday, November 26, 2016

Future of the Guinea Worm

Guinea worm (Dracunculus medinensis) is one of those parasites that nightmares are made of. Juvenile worms infect freshwater copepods, which invariably end up getting ingested [by humans] when drinking contaminated water. The adult female grows up to a few feet long. It migrates to the skin (usually in the lower leg) and induces an extremely painful blister about a year after infection. The blister is described like being set on fire. The pain is alleviated best by standing in water, which is exactly what the worm wants. When the blister is in water, the female worm releases hundreds or thousands of babies into the water.

Former US President Jimmy Carter has been leading an organization working to make the worm go extinct. As a disease organism, few people are going to lament its extinction. When I first learned about this organism, it was invariably described as infecting humans only. This would make the process of wiping it out so much simpler. Unfortunately, the story isn't quite so simple. The worm has other plans.

Hind leg of a dog with a parasitic worm hanging off the side.
Figure 1 from paper.
Increasingly, dogs in Chad are being found with lower-leg lesions that have worms hanging out of them. Genetic analysis has shown it is the same species as the Guinea worm which infects people. Even if we prevent all human infections for long enough to interrupt the parasite's life cycle, it can still persist in other animals. It looks like it would take continuing diligence to keep it from erupting into an active human disease again.

Figure showing increased incidence of parasite in each of four years.
Adapted from page.
Over the last several years, the number of infections observed in dogs has been going up and up, while human infections have been minimal. This pattern of yearly increases suggests the worms have been adapting to their new hosts.

The researchers did find evidence for human behavior that helped give the parasite the opportunity to make this transition. At the end of the dry season, the locals do a mass harvest of fish. The fish are processed and dried/smoked for later use. The guts and other undesirable bits are discarded for the dogs, chickens, etc. to deal with. The dogs are then getting infected by eating the fish guts. It also appears that uncooked/undercooked fish are responsible for the human cases of infection.

Figure showing life cycle of parasite through copepods to fish/humans/dogs and back to living in the water where they infect new copepods.
Adapted from Figure 9 of paper.
Historically, most human infections by this parasite were due to ingestion of water contaminated by infected copepods (an host to an earlier stage of the worm). With increasing knowledge about this mode of transmission, it became dramatically less useful of a pathway for the parasite. At the same time, any alternate pathway for the parasite to get into its main host would have been positively selected. Essentially, we've just seen a parasite go from a life-cycle with one intermediate host to a life-cycle with two intermediate hosts.

Many parasites are known to have complicated life-cycles passing through several intermediate hosts, but this is the first case I've come across that helps to illustrate how those complex life-cycles could have evolved.



Better control of the fish discards will help minimize the infection pathway through dogs, but it won't necessarily get rid of the problem. While adapting to their new hosts, the worms have had to evolve to better escape notice by the canine immune system. A consequence of this is that they will be better prepared to infect dogs later by other pathways, even if fish discards aren't available. Maybe dogs will start getting infected by ingesting infected copepods like humans used to. Maybe dogs will start getting infected by eating scavenged fish that died in the dry season. I can't predict what will happen exactly, but I understand the power of natural selection and very much believe the worm will find another way to survive even if we completely prevent transmission to humans in the near future.


References:

Monday, June 27, 2016

Metals in Biology

For any regular readers, I'm sorry to have missed posting last week. I was knocked offline by my computer spraying sparks (from a failed video card). After some troubleshooting, I determined that increasing amounts of sparks would be generated each time I applied supplementary power to the video card. So, now I have a nice and new video card and can once again do computery things.



Even though such things seem to be more in the realm of science-fiction than biology, I really like the idea of metals being used in biological systems. Specifically, metals being used for their structural characteristics, not simply as ions in protein complexes (hemoglobin, chlorophyll, cytochromes, etc.).

If the sauropod dinosaurs had built their bones from steel, they might have been able to grow far larger than they did. If turtles grew iron into their shells, they would be protected from even the most determined of [existing] predators. Organisms with metal threads through their skin might be able to perceive and/or generate radio waves. Essentially anything our technology uses metals for would potentially be within the realm of evolutionary biology (since it all comes down to physics in the end). The world would be a very different place.



It turns out that some organisms actually do grow metal in specialized tissues. Well, not exactly metal, usually, but more like heavily metal-reinforced tissues.
Metal-infused tissues have appeared sporadically in a range of lineages. In every example I've been able to find, the tissues are directly involved in predation or defense. The ever-present biological arms-race between predator and prey has drove the evolution of advanced [metal] weaponry and armor. Maybe one of the lineages will adapt to use metal more generally and evolve into a space-living creature that can migrate to other star systems and thus survive the death of our sun. Maybe I should read less science-fiction before bed-time.


References

Tuesday, March 15, 2016

From Weeds to Trees and Back Again (and Again)


In a post a few weeks ago, I discussed the evolution of trees and gave a few examples illustrating how simple it is (evolutionarily) to transition from a tree to a weed or back. "Evolutionary time" is generally interpreted to mean "a very long time" and probably "a long time ago". Most of the interesting evolutionary transitions people think about took place long in the past, so these interpretations aren't entirely without cause.

However, evolution definitely happens over very short time frames, we just have to pay attention for long enough to notice it. The image at right is a composite of a the flowers from a bunch of different individual specimens of the California Wild Radish. This population is derived from hybridization between feral Garden Radish (Raphanus sativus) and wild Jointed Charlock (Raphanus raphanistrum) in the central valley of California.

During the process of forming this hybrid population, the ancestral species were absorbed and eradicated. (Well...  garden radishes still exist just fine, but they're not actively reproducing in the wild of California any more.) The population is full of plants with all sorts of lovely shades of color (including nice combinations with both pink and yellow pigment) because the genetics of the population is still sorting itself out.

One specific plant caught my interest. Its flowers were pretty, but didn't stand out from the many others I'd already seen that day. What did stand out... was that this plant was a woody shrub which has been growing for several years. Both R. sativus and R. raphanistrum (the parent species) are annual weedy plants.

How long did it take for this [small] tree to have evolved from the weedy ancestors? The weedy parents merged together over just an estimated hundred years. So, it took something less than a hundred years for an albeit small tree to have evolved from its herbaceous weedy ancestors. I think that's a pretty quick transition.



Almost every reference I can find talking about the California Wild Radish only talk about herbaceous weedy forms. At best, there is the occasional reference to some plants being short-lived perennials. I haven't found any descriptions of woody perennial California Wild Radish plants growing as shrubs. The next time I visit this part of the country, I hope to spend some time looking for more specimens like this. If I'm lucky, I'll be able to collect some seeds and then grow out such a plant for a more detailed examination in the lab.


References:

Tuesday, March 1, 2016

Vavilovian Mimicry

Vavilovian mimicry is a form of mimicry where an agricultural weed begins to take on characteristics of a domesticated agricultural crop due to the selective forces present in the agricultural system.

The first example is involving wheat. Well, really, it involves both wheat and barley. During the early phases of domestication of these grains, they weren't distinguished as separate plants. Initially, the large seeded grasses were collected from the wild and planted closer to home. The now-farmers would then collect the large seeds from the grasses they grew, eat most and protect some, and then plant what was left the following year. You could say that wheat and barley are Vavilovian mimics of each other, because we really don't know which was the first grass to enter domestication.

At some point while the wheat/barley agricultural system was developing, other weedy grasses invaded the prime growing habitat found in the fields. Two of these weeds evolved to become what we call "rye" and "oats". They developed larger, non-shattering seed heads and an annual life-cycle. This allowed their seeds to be collected, saved, and planted as contaminants to the main crop. Both rye and oats are more tolerant of cold conditions and poor soils. Because they had become mimics (and contaminants) of the major crop, when farmers tried to establish the crop system in marginal conditions, these mimics can come to predominate as the major crop.
Wheat/Barley -> Wheat (Triticum spp.)
Wheat/Barley -> Barley (Hordeum vulgare)
Wheat/Barley -> Rye (Secale cereale)
Wheat/Barley -> Oats (Avena sterilis)


Another often-cited case of Vavilovian mimicry is found in the agriculture of lentils (Lens culinaris). A common weed in lentil fields is the Common Vetch (Vicia sativa). The Common Vetch seeds are bitter, so farmers are able to sell their crop for less if there is too much vetch contamination. As farmers have increased the selection pressure on the vetch by mechanical (and computer-vision) assisted seed sorting, strains of the vetch have evolved so that their seeds mimic the lentils in color and size, as well as the characteristic flattened lens-shape.

A. Lens culinaris. B. Vicia sativa, wild and mimic.
(from: www4.ncsu.edu/~fgould/pdfs/Gould1991.pdf)
Lentil (Lens culinaris) -> Common-Vetch (Vicia sativa)
Lentil (Lens culinaris) -> Black-Pod-Vetch (Vicia sativa subsp. nigra)
If farmers could impart some selective force on the mimic vetches such that they would lose their bitter flavor, they would have effectively created a new crop. This new crop might grow better in some conditions where lentils don't thrive, thus spreading the useful area of agriculture.



The selection force involved in the development of Vavilovian mimicry can be mechanical (as in Flax weeds) or manual (as in Rice weeds). What is key is that the selection force separating weeds from the crop has to progressively get more and more stringent over time. This allows the weed population to always have some individuals that will escape the selection force applied to them.
Flax -> False-Flax (Camelina sativa linicola)
Flax -> Flax-Dodder (Cuscuta epilinum)
Rice (Oryza sativa) -> Early-Baryard-Grass (Echinochloa oryzoides)


An interesting case that I think is related to Vavilovian mimicry is the complex of Andean tuber crops. I don't know which crop was first domesticated in this region, but since before modern history, five species of tuberous crops have been traditionally grown together in fields. Growing several different crops together in this agricultural system mean that there will always be production, even if any given plant doesn't produce in some year (due to weather, disease, or other factors).
Potato (Solanum tuberosum) -> Maca (Lepidium meyenii)
Potato (Solanum tuberosum) -> Oca (Oxalis tuberosa)
Potato (Solanum tuberosum) -> Mashua (Tropanolum tuberosum)
Potato (Solanum tuberosum) -> Ullucus (Ullucus tuberosus)
Though I doubt any of these species entered the agricultural system as weeds, I expect that each species will undoubtedly have evolved towards a set of traits similar to those of the most common plant grown in the fields. Any individual plants that didn't prosper in the agricultural system would have contributed less to the next generation and the species would shift to a form that did prosper. This shifting of the traits of one species to align with another, due to the selection forces favoring the majority plant species, is a characteristic common between Vavilovian mimicry and whatever this case should be referred to as.


References:

Tuesday, February 23, 2016

From Weeds to Trees and Back Again

The evolution of the first plants into the modern trees included the incorporation of numerous evolutionary novelties. I'm going to focus on the ones that I think are important for the story I'm trying to tell, though I'll likely get them in the wrong order. It has been many years since I took a course emphasizing this topic and it is likely I also won't be able to find links discussing all the fossils from which this knowledge originally came. In the end, this first section below is really about setting context.



The first novelty was water transporting tissue (tracheids) that let plants grow taller (a few inches) than water diffusing through previous tissues would reach. The size of these early plants was then limited by how thick their stems could grow from their apical meristems (called primary growth). The ability to restart growth from tissue previously laid down by the apical meristems, called secondary growth, allowed plants to grow thicker (and taller, since the thicker stems could support greater height). Eventually the plants were again limited in size by their strength. The evolution of the first true wood (thick cellulose cell walls reinforced with lignin) allowed what we would first recognize as trees to develop.

The trunks of these first trees could only grow to a certain size, however, because of a quirk of their secondary growth. They grew outwards by dividing their outer cells parallel to the outer surface (periclinal division). As the trunk grew, the outer cells got thinner and and wider. Eventually the cells were too thin to divide further. The growth of the trunks slowed to a stop. Eventually, a group of trees developed the ability for its outer cells to divide in half from side to side (anticlinal division). By mixing periclinal and anticlinal divisions, these trees could grow beyond the limited size of their ancestors with only periclinal divisions. They could grow thicker, stronger, and thus taller.

from: www.mun.ca/biology/desmid/brian/BIOL3530/DEVO_07/devo_07.html

At this stage we effectively have modern trees. There are lots of other interesting developments to talk about (vessel cells, seeds, leaves, flowers, etc.), but for some other time.



So, now that I've discussed the context...  what is the main topic I want to discuss?

Modern flowering plants (angiosperms) all count some of those ancient trees as ancestors. They range from the exceedingly tiny (Wolffia borealis), to the stupendously huge (Ficus benghalensis, others). Though most families of flowering plants don't range to such extremes, they generally count trees and small herbaceous plants among their members.

The milkweed family (Asclepiadaceae) is mostly small herbaceous species (such as Cynanchum barbigerum and Asclepias involucrata), but includes at least one moderately sized tree (Calotropis Procera). The dogwood family (Cornaceae) is most woody shrubs and trees (such as Cornus florida and C. kousa), but includes at least one herbaceous weed (C. canadensis).

If a tiny weed is introduced to an island, it can in a reasonably short time (from an evolutionary perspective) evolve into shrubs and large trees. This isn't just a story, an idea that sounds nice. The ecologies of isolated islands are often filled with very closely related plants filling wildly divergent ecological roles. Early on the geologic history of the Hawaiian islands, a tarweed seed managed to find a foothold and grow. It's descendants now fill the island in the form of weeds, vines, shrubs, and trees. On the Galapagos islands, a member of the common cactus genus Opuntia has evolved into a tree (Opuntia megasperma). On the channel islands, a member of the common herbaceous weedy genus Coreopsis has evolved into a tree (Coreopsis gigantea).

Coreopsis gigantea (from plants.usda.gov/core/profile?symbol=COGI)

Numerous other examples can likely be found where a tree has quickly evolved from an herbaceous group (or an herbaceous plant from a tree group) by examining the flora of the various isolated islands around the world.

Though the evolution of a flowering herbaceous plant into a tree or the reverse is interesting (and would make for really neat garden specimens), it doesn't require any dramatic evolutionary changes. Every flowering plant inherited the genetic/developmental toolkit necessary for growing as an herbaceous plant or as a tree from its ancestors among the very first trees. If an organism is missing some trait that its ancestors had, it is likely that the organism still carries most of the genetic tools needed to quickly evolve that trait in the future.


References

Tuesday, January 19, 2016

Micro insects

I haven't been feeling up to writing much lately. Most of my free time has been occupied with working on an academic project in meta-genomics. I'm aiming for this to be published in a science journal, so I won't be discussing the details of it here (for now). I'm also experiencing some anxiety surrounding what my job currently is, where it is going, and where I want it to go.

All together, this is leading to a pretty solid writer's block. I've got a collection of interesting topics that I haven't managed to pull together into full posts, so I'll probably be posting a few of these over the next several weeks. Today, I want to point you towards some readings about extremely, bizarrely, tiny insects.



Micro-wasp with aneucleate nerves
Micro beetle.
Features found in both micro-insects.
  1. Reduced number of neurons, but a relatively larger nervous system.
  2. Reduction in number of organ parts. Reduction in Malpigian tubules, spicules, etc.
References:
  1. Polilov, A. (2008). Anatomy of the smallest coleoptera, featherwing beetles of the tribe nanosellini (Coleoptera, Ptiliidae), and limits of insect miniaturization. Entomological Review 88:26-33.
  2. Polilov, A. (2011). The smallest insects evolve anucleate neurons. Arthropod Structure & Development In press. doi:10.1016.j.asd.2011.09.001
  3. Niven, J. E., and S. M. Farris (2012). Miniaturization of Nervous Systems and Neurons. Current Biology 22:R323-R329.

Tuesday, December 22, 2015

The Messy Science of Tardigrades

[Image source.]

Recently there has been some controversy in the news about the evolution of genomes in tardigrades. In particular, one recent paper claimed to see evidence for large-scale horizontal transfer of genes from bacteria/etc. into tardigrades, while another recent paper claimed to see no evidence for horizontal transfer.

The meat of the issue comes down to exactly how each group assembled the genomes they analyzed and published about.

Group 1:
  1. Illumina-seq (shotgun sequencing) with paired-ends.
  2. Notice lots of bacterial, etc. genes.
  3. Re-sequence genome using PacBio extremely-long-reads.
  4. Validate presence of bacterial/etc. sequences in tardigrade genome.
  5. Publish paper!
Group 2:
  1. Illumina-seq (shotgun sequencing) with paired-ends.
  2. Notice lots of bacterial/etc. sequences.
  3. Filter out bacterial/etc. sequences before constructing final genome.
  4. Publish counter-"paper"!

The first group first sequenced with paired-end reads using Illumina technology, then did re-sequencing using the extremely-long-reads of PacBio technology. This two-method sequencing allowed them to more reliably validate if the bacterial/etc. sequences were actually found contiguously in the DNA of the tardigrade or not. Any artifacts from one technique would likely not be found in the second independent technique. Any results shared between them thus have a higher confidence. The PacBio sequencing wasn't as comprehensive as the Illumina sequencing, so there wasn't complete validation of all cases of horizontal gene transfer. There is the potential that they've over-estimated the level of horizontal gene transfer. However, their methodology would allow them to see the difference between massive horiztonal gene transfer in the tardigrade's evolutionary history vs. the presence of contaminating DNA in the sample being sequenced.

The second group didn't put the same level of rigor into their sequencing. They used Illumina technology (as the first group), followed by intensive filtering of sequences which seemed to have an origin from contamination. They argue the bacterial/etc. genes seen in the first group's genome assembly were due to contamination. However, their result is exactly what would be expected from their methodology whether there was actually massive horizontal gene transfer in the tardigrade's history or not. I'm not convinced that their method would have been able to tell the difference.



A detail of the first group's results that lends credence to their interpretation over that of the second is that the bacterial/etc. genes found in the tardigrade's genome were not simply a random selection of genes as would be expected from a contamination origin. Instead, they were a selection of genes involved in DNA repair and stress response. These are exactly the sort of genes that would be expected to favor the survival of the tardigrades that had incorporated them.

Another section of the first group's results which were overlooked by the second was that the bacterial/etc. genes found in the tardigrades show evidence of having evolved inside the tardigrades for an extended period of time. The bacterial/etc. genes show a shift in the codon usage to be more like that of native tardigrade genes. As well, the bacterial/etc. genes have gained introns (something not found in bacteria). Both of these classes of changes would be very unexpected in a scenario where contamination was the source of the DNA.



The first group probably over-estimated the level of horizontal gene transfer in the tardigrade. The second group probably under-estimated the level of horizontal gene transfer in the tardigrade. So...  what is going on? This entire event shows very well how science is done in real life. Someone will have an interesting result. Someone else will produce an apparently contradictory result. Over time, the new results get closer and closer to telling us what the reality is.

The real world is messy. Science is, at its best, an attempt to understand what is happening in the world. It isn't telling people what should be, or what might be, but what actual is. The apparent uncertainty seen in regards to the tardigrades may confuse people who might be used to watching fictionalized representations of science that always seems to get everything right on the first try, or those who trust in science to get the right answer without realizing the extended process that getting the right answer can be. In the end, it is a good thing. All the interest the results in these papers has produced will likely inspire more research to be done which will add further clarity to what is going on in these interesting little creatures.


References:

Tuesday, December 8, 2015

More Convergence on the Seaside

Cakile maritima on a southern California beach.
(I know this one is tasty, in real life.)
In a previous post (the-biologist-is-in.blogspot.com/2015/03/convergence-on-seaside.html), I discussed two seaside plant species that both have succulent, edible (and reportedly tasty) leaves.
Cakile maritima (Sea Rocket). [Brassicaceae, annual]
Crambe maritima (Sea Kale). [Brassicaceae, perennial]
Since then I've found a selection of other seaside plant species that all have succulent, edible leaves.
Blutaparon vermiculare (Silverhead, Saltweed). [Amaranthaceae, perennial]
Cakile edentula (Sea Rocket). [Brassicaceae, annual]
Cakile lanceolata (Sea Rocket). [Brassicaceae, annual]
Crithmum maritimum (Sea Fennel, Rock Samphire). [Apiaceae, perennial]
Eryngium maritimum (Sea Holly). [Apiaceae, perennial]
Limbarda/Inula crithmoides (Golden Samphire). [Compositae, perennial]
Salicornia bigelovii (Marsh Samphire, Dwarf Glasswort). [Amaranthaceae, perennial]
Salicornia europaea (Marsh Samphire, Glasswort). [Amaranthaceae, perennial]
Salicornia virginica (American Glasswort, Pickleweed). [Amaranthaceae, perennial]
Salsola soda (Barba di Frate, Agretti, Liscari Sativa). [Amaranthaceae, annual]
Sarcocornia quinqueflora (Beaded Samphire, Beaded Glasswort). [Amaranthaceae, perennial]
Sesuvium maritimum (Annual Sea Purslane). [Aizoaceae, annual]
Sesuvium portulacastrum (Sea Purslane). [Aizoaceae, perennial]
Tecticornia arbuscula (Shrubby Glasswort). [Amaranthaceae, perennial]
Tecticornia pergranulata (Blackseed Glasswort, Blackseed Samphire). [Amaranthaceae, perennial]
What is it about the seaside environment which is selecting plants to be succulent and edible? I've got some thoughts that I think lead to a partial answer. Let's break down the question into two parts.

Why are they succulent? The seaside substrates where these plants grow is typically composed of sand, gravel, or rock. These substrates don't hold water at all. Even though there is an ocean very nearby, any small plant growing above the high-tide line is effectively growing in the middle of a desert. Two main strategies for this situation are 1) grow extremely deep roots and 2) hold onto any water that they find. The first strategy is typified by Creosote (Larrea tridentata) and Mesquite (Prosopis spp.), neither of which would be described as edible. The second strategy of holding onto their water, means a plant will be succulent in some way or other. There are plenty of both toxic and edible succulent plants, so there is more to the story.

Why are they edible? Some of the plants are perennial, while others are annual. Before I started looking into it, I was thinking they were all weedy species. Weedy plants (or animals) are those that invest a lot of their energy in reproduction, while investing very little in self-defence of any specific individual (r-selected). For plants, this means they're typically annuals (or short-lived perennials) that don't invest much biological energy into growing spines, fibers, or poisons. In short, r-selected plants are more likely to be edible to generalist herbivores like ourselves. Now, that none of these species would count as a long-lived perennial (like a woody shrub or tree) may perhaps mean that the weediness argument has some value in understanding this group of plants.

Before I started looking up these species, I had never heard the name "Samphire" before. The name seems to be used generally for any succulent (and edible) weed growing on a rocky seaside of the northern British Isles. Several of them are described as being easy to grow in a garden setting. Some of the plants can grow directly in sea-water. These may be a bit trickier to grow in the home garden. I like growing interesting plants, so hopefully I'll be able to try growing some of them over the next several years.


References: