Showing posts with label Darwin. Show all posts
Showing posts with label Darwin. Show all posts

Thursday, February 12, 2015

Darwin in images (Darwin Day 2015).

Feb. 12 is the anniversary of Charles Darwin's birthday, a celebration of a man who nearly single-handedly (not to ignore Alfred Russel Wallace and others) laid the foundations for modern ecology and evolution. He championed the idea that evolution was descent with modification, where natural selection was the main means of modification. Darwin's work furthered achievements in science, medicine, and philosophy, perhaps in part because he helped disentangle science, society and religion. One outcome of being such a prominent figure is the frequency with which Darwin ends up in images, cartoons and illustrations, beginning in his own lifetime. So here is a short tour of Darwin and his big idea via cartoons and illustrations. 

A famous Vanity Fair caricature from 1971.

The oft-repeated mantra that evolution means that man evolved directly from a monkey or beast was an early (and still popular) theme. Darwin often took the role of the monkey.
John Tenniel for Fun magazine (1872)
From 1882, Punch’s Almanack, Linley Sambourne


Even in his day, some cartoons supported rather than poked fun. See the speech on the wall, a plea avoid ignorance of Science. (Link)
"Puck Presents Archdeacon Farrar’s New Year’s Hint — A Needed Course of Instruction for Our Religious Instructors"(1890).

The "evolution of man" meme has a long history - what was originally satire is primarily now a visual joke. (Link)
Harper's Bazaar 1871
Modern concerns.

Darwin and evolution has been a repeated image in US politics, covering evolution and education, religious tension, science, and social darwinis, among other themes. (Link)
1925 SF Examiner
More recent, by Karl Wimer
Religion and Darwin have been unavoidable companions.
From pro-religion angles: 
1922 Moody's bible institute
And anti-religious:

Darwin pops up on motivational images and posters:

And evolution jokes remain eternally popular:
The Farside providing one of the better ones :)
source unknown

And finally, Darwin's own images have been incredibly influential. He was a talented naturalist and scientist and left many lovely illustrations. His sketches in his books, particularly the "tree of life" image has become an emblem for many scientists - of evolution and the origin of species, of immense intellectual accomplishment, of the birth of modern ecology and evolution.
The famous "I think" image - the tree of life.

To learn more about Darwin in images, this is a great resource.

Monday, July 7, 2014

Phylogeny, competition and Darwin: a better answer?

*Sorry for the low frequency of posts these days – I seem to be insanely busy this summer 

Oscar Godoy, Nathan Kraft, Jonathan Levine. 2014. Phylogenetic relatedness and the determinants of competitive outcomes. Ecology Letters.

Ecology is hard in part because of the things we can’t (at least easily) measure: fitness, interaction strengths, and the niche, all fundamental ecological concepts. Since we are unable to measure these concepts directly, ecologists have come up with proxies and correlates. Take Darwin’s hypothesis that competition should be greater between closely related species. It relies a chain of assumptions about proxy relationships – first that relatedness should correlate with greater similarity of traits, secondly that similar traits should correlate with greater niche overlap. The true concept of interest, the niche, is un-measurable (if it is an n-dimensional hypervolume) so instead shared evolutionary history provides possible insight into species coexistence.

Ecophylogenetic studies have adopted Darwin's hypothesis as an example of how  molecular phylogenies may provide information about evolutionary history which in turn informs current ecological interactions. Phylogenies ideally capture feature diversity, and so (all things being equal) should provide information about similarity between species based on their relationship.  Despite this, studies have been mixed in terms of finding the relationship predicted by Darwin between phylogenetic relatedness and competition. It is not clear whether this mixed result suggests problems with the phylogenetic approaches being used, or non-generality of Darwin’s hypothesis.

Oscar Godoy, Nathan Kraft, and Jonathan Levine attempt to explore this question once again, but through the lens of Chesson’s coexistence framework (2000). Chesson’s framework describes competitive differences between species not as a single quantity, but instead the outcome of both stabilizing niche differences and equalizing fitness differences between species. This framework predicts that competitive differences should be greatest when species have similar niches (low stabilizing niche differences) and/or when they have large differences in fitness. This divisions alters the predictions from Darwin's hypothesis: if closely related species have similar niches, they should compete more strongly, but on the other hand, if closely related species have similar fitnesses, they should compete less strongly. Darwin’s hypothesis as it has been tested may be too simplistic.

The authors used an experiment involving 18 California grassland species to look at first, whether competitive ability is conserved, and more generally to explore whether phylogenetic distance predicts “the niche differences that stabilize coexistence and the fitness differences that drive competitive exclusion?” Further, can this information be used to predict the relationship between phylogeny and competitive outcomes? To determine this, they quantified germination, fecundity, seed survival, and interaction coefficients for the 18 species based on competition with different competitors (both by identity and density), and quantified the strength of stabilizing and equalizing forces (as in previous works). With this information, they calculated for each species the average fitness and ranked species in a competitive hierarchy using a fully parameterized annual plant population model. Species’ competitive rank did in fact show a phylogenetic signal (Figure 1), and the strongest competitors were clustered in the Asteraceae and its sister node.
Fig 1. Relationship between competitive rank among the 18 CA grassland species.
Competitive rank was then decomposed into fitness differences and niche differences. Fitness differences showed the clearest relationship with phylogeny - distantly related competitors had significantly greater asymmetries in fitness, closely related species had similar fitnesses (Figure 2). However stabilizing niche differences showed no phylogenetic signal at all (Figure 3, solid line).
Fig. 2. Relationships between fitness differences and phylogenetic distance.
Fig 3. Solid line - observed niche distances as a function of phylogenetic distance. Dashed line, size of distances actually needed to assure coexistence.
The authors could then calculate, for a given pair of species with a given phylogenetic distance, the expected fitness difference (based on the fitness difference-phylogeny relationship), and given this, the amount of stabilizing niche differences that would be necessary to prevent competitive exclusion between pairs of species. When they did this, they found that the required stabilizing niche differences were much larger than those that actually existed between the plants. This was especially true between distant related species(dashed line, Figure 3). Darwin’s hypothesis, that closely related species should be more likely to coexist, seemed to be reversed for these species.

How should we interpret these results more broadly? Is this reinforcement of the use of phylogenetic information to answer ecological questions, provided the questions are asked correctly? One of the most interesting contributions of this paper is their discussion of the oft-seen, but poorly incorporated, increase in variation in a trait (here fitness differences) as phylogenetic distances increase. This uneven variance often leads to phylogenetic-trait correlations being labelled non-significant, since it violates the assumptions of linear models. In contrast, here the authors suggest that this uneven variance is important. “For example, even if on average, both niche and fitness differences increase with phylogenetic distance, the increasing variance in these relationships means that only distant relatives are likely combine large competitive asymmetries with small niche differences (rapid competitive exclusion), or large niche differences with small competitive asymmetries (highly stable coexistence). Overall, our results suggest that increasing variance in niche or fitness differences with phylogenetic distance may play a central role in determining the phylogenetic relatedness of coexisting species.”

This discussion is important for questions about phylogenetic relatedness and coexistence – variability is part of the answer, not evidence against the existence of such relationships. However, a few caveats seem important: Because fitness differences and niche differences as defined in the Chesson framework may not be easily associated with traits (since a single trait might contribute to both components), it seems that it will be a little difficult to expand these analyses to less rigourous experimental settings. This might also be important to hypothesize how fitness or niche differences per se become associated with phylogenetic differences, since traits/genes are actually under selection. But the paper definitely provides an interesting direction forward.

Chesson, P. 2000. Mechanisms of maintenance of species diversity. Annual Review of Ecology and Systematics 31:343-366.

Tuesday, March 11, 2014

The lifetime of a species: how parasitism is changing Darwin's finches

Sonia Kleindorfer, Jody A. O’Connor, Rachael Y. Dudaniec, Steven A. Myers,Jeremy Robertson, and Frank J. Sulloway. (2014). Species Collapse via Hybridization in Darwin’s Tree Finches. The American Naturalist, Vol. 183, No. 3, pp. 325-341

Small Galapagos tree finch,
Camarhynchus parvulus
Darwin’s finches are some of the best-known examples of how ecological conditions can cause character displacement and even lead to speciation. Continuing research on the Galapagos finches has provided the exceptional opportunity to follow post-speciation communities and explore how changes in ecological processes affect species and the boundaries between them. Separate finch species have been maintained in sympatry on the islands because various barriers maintain the species' integrity, preventing hybrids from occurring (e.g. species' behavioural differences) or being recruited (e.g. low fitness). As conditions change though, hybrids may be a source of increased genetic variance and novel evolutionary trajectories and selection against them may weaken. Though speciation is interesting in its own right, it is not the end of the story: ecological and evolutionary pressures continue and species continue to be lost or added, to adapt, or to lose integrity.

A fascinating paper by Kleindorfer et al. (2014) explores exactly this issue among the small, medium, and large tree finches (Camarhynchus spp.of Floreana Island, Galapagos. Large and small tree finches first colonized Floreana, with the medium tree finch speciating on the island from a morph of the large tree finch. This resulted in three sympatric finch species that differ in body and beak size, but otherwise share very similar behaviour and appearance. However, ecological and environmental conditions have not remained constant on Floreana since observations in the 1800s: a parasite first observed on the island in 1997, Philornis downsi has taken residence and has caused massive nestling mortality (up to 98%) for the tree finches. Since parasite density is correlated with tree finch body size, the authors predicted that high parasite intensity should be linked to declining recruitment of the large tree finch. If females increasingly prefer smaller mates, there may also be increased hybridization, particularly if there is some advantage in having mixed parental ancestry. To test this, the authors sampled tree finch populations on Floreana in both 2005 and 2010. Parasite numbers increase with high precipitation, and so by combining museum records (collected between 1852-1906, when no parasites were present), 2005 sampling records (dry conditions, lower parasite numbers), and 2010 sampling records (high rainfall, high parasite numbers), they could examine a gradient of parasite effects. They measured a number of morphological variables, collected blood for genotyping, estimated individual age, measured parasite intensity in nests, and observed mate choice.

Philornis downsi:
larval stage parasitizes nestlings.
(a Google image search will provide
some more graphic illustrations)
For each time period, morphological measurements were used to cluster individuals into putative species. The museum specimens from the 1800s had 3 morphologically distinguishable populations, the true small, medium and large tree finch species usually written about. In 2005 there were still 3 distinct clusters, but the morphological overlap between them had increased. By 2010, the year with the highest parasite numbers, there were only two morphologically distinguishable populations. Which species had disappeared? Although recent studies have labelled the two populations as the “small” tree finch and “large” tree finch, the authors found that the 2010 “large” population is much smaller than the true large tree finches collected in 1852-1906, suggesting perhaps the large tree finch was no longer present. Genetic population assignment suggested that despite morphological clustering, there were actually only two distinct species on Floreana in 2005 and 2010: it appeared that the large tree finch species had gone extinct, and the boundary between the small and medium tree finch species had become porous, leading to morphologically intermediate hybrids.

The question then, is whether the extinction of the large tree finch and the collapse of the boundary between small and medium tree finches can be attributed to the parasite, and the changing selective pressures associated with it. Certainly there were clear changes in size structure (from larger birds to smaller birds) and in recruitment (from few young hybrids to many young hybrids) between the low parasite year (2005) and the high parasite year (2010). Strikingly, parasite loads in nests were much lower for hybrids and smaller-bodied populations than for the larger-bodied population (figure below). Compared to their large-bodied parents, hybrids somehow avoided parasite attack even in years with high parasite densities (2010). When parasite loads are high, hybrid offspring have a fitness advantage, as evidenced by the large number of young hybrids in 2012. The collapse of the large tree finch population is also likely a product of parasite pressures as well, as females selected smaller mates with comparatively lower parasite loads. Despite the apparent importance of the parasites in 2010, the existence of only a few older hybrid individuals, and greater morphological distance between populations seen in the 2005 survey (a low parasite period) suggests that selection for hybrids varies greatly through time. Though the persistence of the Philornis parasite on Floreana may prevent re-establishment of the large tree finch, changing parasite densities and other selective pressures may continue to cause the boundaries of the remaining finch populations to overlap and retract in the future. The story of Darwin's finches is even more interesting if we consider that it doesn't stop at character displacement but continues to this day.
From Kleindorfer et al 2014: Philornis parasite intensity in nests sampled in 2005 (lower parasite) and 2010/2012 (higher parasite), for nests of the small-bodied (population 1), intermediate hybrid, and larger-bodied (population 2) individuals.

Friday, February 13, 2009

40% believe in evolution, but only 25% do not!

Gallup released a poll, that coincides with Darwin's birthday, which examines American's belief in biological evolution. It is a great poll, breaking down belief patterns across education attainment, age , religiousness, etc.

However, several reports and blogs about this poll disparage Americans for their lack of scientific sophistication, but I think that the results are far more positive then I would have guessed. Only 25% outright deny evolution! I would have thought a clear majority would take this stance as was shown in 2005. A further 36% do not have an opinion, and as scientists and educators, these folks are the reason why we educate and hold events like Darwin Day. Thank you to all those who work so tirelessly promoting science education and literacy, like those at NCSE.

Wednesday, February 11, 2009

Charles Darwin, founder of evolution AND ecology

Perhaps a good alternative title should be: “Why we need a second modern synthesis”

Darwin is rightfully seen (or vilified in some quarters) as the founder of modern evolutionary biology. He gave the naturalists of that era an observable and testable mechanism explaining species change and for understanding the similarities and differences among species. As we celebrate Darwin’s 200th birthday and the 150th anniversary of the publication of the Origin of the Species, it seemed right to think about Darwin’s contributions beyond just evolutionary change, namely ecological patterns and processes.

I’ve read Origin probably half a dozen times now and as an ecologist, I am always amazed by the depth and breadth of Darwin’s insights. Every time I read it, there are passages that directly relate to what I happen to be thinking about or working on at the time, which leads me to the conclusion that he thought a lot about what scientists would come to call ecology. Though the word “ecology” wouldn’t be invented for another seven years (by Ernst Haeckel in 1866) and the first ecology text book didn’t appear until 1895 (by Eugenius Warming, and which includes interesting Lamarckian invocations in the last chapter), Darwin thought and wrote about ecology extensively.

In the Origin (1st edition), Darwin makes predictions about ecological patterns. On page 109, he states, “a … larger number of the very common and much diffused or dominant species will be found on the side of larger genera”. That is community dominance likely relays on inherited traits linked to species success. This certainly sounds like the result of some recent, interesting papers (e.g., Strauss et al.*).

Almost the whole discussion in the Struggle for Existence chapter is about ecological interactions and the severity of negative interactions, which stems from the fact that populations, if unchecked, will increase exponentially (i.e., page 116). We all know from work by ecologists such as Connell and Huston that those negative, deterministic interactions can be overridden by non-equilibrium processes, especially disturbances. Here again Darwin’s observations lead him to this conclusion; “If turf which has long been mown …be let to grow, the more vigorous plants gradually kill the less vigorous” and he observes that diversity in a plot goes from 20 species to 11 when the disturbance is removed.

Further, we often think of Darwin’s view of the environment as a selective pressure (e.g., fur thickness), but he also saw the environment as a determinant of species interactions. Lush places support a lot of species and the control of populations is due to competitive interactions, whereas in harsh places, populations are controlled by “injurious action” of the environment (e.g., page 121). Thus there is a shift from biotic to abiotic controls on ecological processes.

I think that we have collectively forgotten that evolution directly informs our expectations and predictions of ecological patterns and processes. While ecological geneticists drove much of the modern synthesis in the mid 1900’s by incorporating ecology (namely selection) into evolutionary processes, the reverse, bringing evolution into ecology is only now really starting to happen. Lets hope this second modern synthesis completes Darwin’s vision.