Resolving the avian tree of life: Part II

In my previous post I talked about a landmark paper in avian systematics, that of Hackett et al. (2008), who reconstructed the first phylogeny based on DNA sequence data that included all major bird clades, and all the major Passerine families (aka 'perching birds': things like sparrows, flycatchers, warblers, etc., a clade that includes half of the world's bird species). This phylogeny revealed some broad trends in avian evolution, but only included 169 bird species, chosen to represent the full range of avian variation. There are actually about 10 000 known species of bird. This may seem like a lot, but compared to plants and insects, it's virtually nothing, so reconstructing a full species-level molecular phylogeny for birds is theoretically quite doable. This is the task that Walter Jetz and colleagues took up, and achieved, publishing their findings last year in the journal Nature. Here it is:

The full phylogeny reconstructed by Jetz et al. (2012), with frequency distribution of diversification rate (in centre), and diversification rates plotted per species

If there is a more recent, more complete phylogeny of birds, then you may rightfully ask, why did I even bother mentioning the 2008 study by Hackett's team? The answer is twofold. First, the two papers had different aims. The Jetz study, combining their phylogeny with distribution data for the world's birds, aimed to map the global distribution of bird diversification through time (more details to follow). Second, and somewhat connected, is the fact that the Jetz phylogeny is actually not a truly independent creation. In fact, the authors only had sequence data for 6 663 species, roughly two-thirds of the total. To place the remaining species, they relied purely on previous taxonomic classifications. Also, they did not use the molecular data to reconstruct the full phylogeny. Instead, they relied on an older, less detailed, broad phylogeny of birds. Yip, you guessed it, it's back to Hackett. Jetz et al. used the Hackett phylogeny to assign species to particular clades, and then simply added further detail to that 'backbone'. There are various reasons to be cautious about the results stemming from this approach, as Robert E. Ricklefs and Mark Pagel point out in their respective commentaries on this article in the same issue of Nature. But first, let's have a look at what those results were.

The main aim of the study was to explore the evolutionary history of birds as a whole. As the title of the paper ('The global diversity of birds in space and time') suggests, this involved both a temporal and a spatial aspect. Firstly, they plotted species richness, and diversification rate, against time, and showed that both have increased, particularly in the last 50 million years. This has been driven by certain groups, particularly the passerines, which originated about 60 Ma, as well as gulls, woodpeckers, and waterfowl (ducks and geese). Jetz et al. calculated a diversification rate (DR) per species, which initially seems nonsensical. however, their technique was based on the branch lengths of each species. Although the full story is far more technical, the upshot is that more recently diverged species (i.e. those with shorter branch lengths) will have higher DR values. Thus their next step was to examine the distribution of species with high DR.

Spatial diversity: a, b and c show diversification rate, whereas d and e show relative and absolute richness of the top 25% diversification rate species, respectively. f shows species richness for all birds.

The map above shows their results. One of the key findings is that diversification rate, and areas with a high proportion of rapidly diversifying lineages, do not correlate well with latitude across the globe. Instead, temperate areas, rather than highly diverse tropical areas, seem to be hotbeds of radiation, but only in some areas (e.g. compare southern South America with southern Africa in maps a and d). This suggests that tropical areas are stores rather than major generators of recent diversity, and that birds are continuing to speciate in more recently emerged temperate areas. However, many feel that certain aspects of this study provide good reason to regard it as preliminary, and its results tentative.

One of the strongest criticisms is levied by Pagel, against the use of branch length data to infer DR. There are serious reasons to be skeptical of lineage age estimates, and this approach makes the results highly susceptible to changes in this regard. A further criticism relates to the way in which the phylogeny was constructed. Because the method relied so heavily on a prior phylogeny, we have no way of assessing how confident we can be in this one. As a result, any inferences drawn are based on faith in the older phylogeny, and the molecular data currently available are not put to full use.

While both Ricklefs and Pagel present a strong cautionary viewpoint, both also admit that this is at least a very important first step towards providing answers to the most fundamental questions about avian evolution. Answers that may in turn reveal trends applicable to larger and more inclusive sections of the tree of life.

Resolving the avian tree of life: Part I

Since an early age, one of my major passions (some might call it an obsession!) has been birding. I watch birds, I study them, I plan holidays around them, I think and talk about them ad infinitum. But I often get the feeling that birders, myself included, often engage with them in a somewhat more superficial manner than we could be doing. That's a sparrow, that's a lark, that's an eremomela... As with anything, I suppose, we like to group things according to their obvious features. Thus, small, dull, hard-to-identify species are often called 'LBJs' - Little Brown Jobs. Likewise, birds like falcons and eagles are called 'raptors' or 'birds of prey'. But what isn't always obvious is the evolutionary history of birds that reveals the true links between them, which are often quite surprising - it's the stuff that's going on 'behind the scenes', if you will.  Yet it's the stuff that really matters, in a biological sense. Figuring out the true appearance of the tree of life provides us with invaluable insight into the evolution of the species we currently share the planet with, and with new molecular techniques and growing DNA sequence databases, it is now possible to do so not just for a few meagre twigs of the tree but for great, hulking branches of it.

So it was that Hackett et al. (2008) took on the challenge of reconstructing the phylogeny of living birds. Not all of the nearly 10 000 species of them, mind you. That task was taken up more recently, and will be the topic of my next post. Rather, Hackett and colleagues chose a select group of birds to represent all of the major orders within class Aves, including all bar three of the non-passerine families and all of the major passerine clades. The Passeriformes are a huge order containing over half of all bird species and at least 110 families - their taxonomy is ever-shifting. So it's understandable that Hackett et al. didn't include them all. As it was they analysed a total of 32kb of DNA code from 19 nuclear loci and 171 species (including two crocodilians as outgroups). DNA sequencing is generally held as the most reliable means of reconstructing phylogenies. Previous attempts at doing so for birds had been based on techniques now regarded as being unreliable. In addition, the birds themselves aren't playing along. Results from previous studies, corroborated by that of Hackett et al., suggest that birds underwent a rapid divergence very early on in their history. Because there's been so much time for change, telling who's related to who, and how, is a real challenge: there's very little to link the various highly distinct groups.

Yet despite this, Hackett et al. recovered a remarkably robust phylogeny that revealed some unexpected relationships, and supported others that had been suggested but regarded by most as pretty wacky. Notably, they showed that passerines are sister to parrots (Psittaciformes), and that this clade is sister to falcons (Falconidae). Previously falcons were thought to be sister to eagles, hawks and other raptors in Accipitridae. They also showed that flamingos and grebes are sister to each other, a fact that I remember being very surprised about when I first heard of it. They uncovered some important clues about the evolution of some real enigmas too, such as the fact that the Kagu (Rhynochetos jubatus) of New Caledonia and Sunbittern  (Eurypyga helias) of South America, both bizzare and unique birds of monotypic genera, are sister species. And buttonquails (Turnix), of which our own Turnix hottentotta occurs in the Cape of Good Hope Nature Reserve, and which have been variously thought to be part of Gruiformes and Turniciformes, are in fact nestled within Charadriiformes, sister to gulls.

However, some mysteries couldn't be solved. The totally bizarre Hoatzin (Opisthocomus hoazin), familiar to many a seasoned wildlife documentary watcher and renowned for its possession of claws in the juvenile stage, and the somewhat less familiar but equally strange Cuckoo Roller (Leptosomus discolor) of Madagascar, remain incertae sedis. Interestingly, fossil relatives of the Hoatzin have been found in Namibia (Mayr et al. 2011) from long after the break-up of Gondwana, and further evidence suggests that the lineage evolved in Africa, and then dispersed to South America. I wonder what that might imply about its evolution? The fact that these birds still defy classification is, I think, quite amazing, and it remains an exciting challenge for avian systematists.

Some of the bizarre and enigmatic birds dealt with by Hackett et al. (2008). Clockwise from top left: Sunbittern, Kagu, Hoatzin, Cuckoo Roller.

The phylogeny also shows some very interesting ecological pattern, providing us with food for thought about bird macroevolution. For example, the tinamous are nested within the ratites (Struthioniformes - ostriches, emus, kiwis, etc.), rather than being sister to them, as previously thought. This suggests that either that they regained the power of flight from flightless ancestors, or that their ancestors were flighted, meaning that flight was lost at least three times in ratites, which contradicts the traditional vicariance hypothesis of global ratite distribution (Harshman et al. 2008). They also found that large clades correspond to broad ecological niches: there are well-supported 'water bird' and 'land bird' clades, although there are some exceptions (of course!). So for the most part diversification has proceeded within the bounds of these broad niches, but some groups have bucked the trend, such as flamingos and grebes, which are aquatic but not part of the water bird clade, and the uniquely African turacos, which fall well outside the land birds and are in fact sister to water birds.

The list of interesting insights goes on, and will continue to stimulate research into avian macroevolution. As we'll see in Part II of this post, a recent study attempted to reconstruct a complete species-level bird phylogeny, building directly from Hackett et al. It provided some fascinating results, but did the authors go too far, too soon?

References

Hackett SJ et al. 2008. A Phylogenetic Study of Birds Reveals Their Evolutionary History. Science. 320: 1763-1768.

Mayr G et al. 2011. Out of Africa: Fossils shed light on the origin of the hoatzin, an iconic Neotropic bird. Naturwissenschaften. 98: 961-966.

Harshman J et al. 2008. Phylogenomic evidence for multiple losses of flight in ratite birds. PNAS. 105 (36): 13462–13467.

What is a ring species? What is a species?

A Greenish Warbler in the hand (c) Paul J Leader

Ring species show speciation in spite of gene flow, and also raise interesting questions about the nature of species. In a paper published in Science entitled 'Speciation by Distance in a Ring Species', Irwin et al. (2005) present the results of a detailed study on the Greenish Warbler Phylloscopus trochiloides, an Asian bird with a very intriguing biogeographic history. The warbler occurs in Asia, from the southern foothills of the Himlayas to the the extensive forests of Siberia to the north. However, the birds carefully (and for good reason) avoid the barren and inhospitable Tibetan plateau - no place for a minute tree-loving warbler (check out the map below). This peculiar scenario drew the attention of Irwin and collaborators, for two reasons. First, the ring-like shape of the species' distribution is an immediate sign that things could be interesting. Second, there are multiple subspecies of Greenish Warbler, two of which co-occur in parts of Siberia. You might think of this zone of overlap as the crucial connection point of the ring. But what is the nature of this link? Have the 'atoms' in the ring fused, resulting in a seamless transition from two disparate parts to one, united whole? Or is the link more tenuous, fragile, and, ultimately, more intriguing?

The global distribution of Greenish Warbler. Different colours represent subspecies; colour gradients show regions where subspecies intergrade. The blue/red hatched area shows the zone of overlap of P. t. viridanus (blue) and P. t. plumbeitarsus (red). The break in north=eastern China is likely to be due to recent habitat destruction. Taken from Irwin et al. (2005). 

Crucially, the two subspecies of Greenish Warbler that coexist in Siberia do not interbreed. In a previous paper on this species, Irwin et al. (2001) showed that there is a northward trend of increasing song complexity and length, but that this has occurred differently in P. t. plumbeitarsus and P. t. viridanus, with the former having many short phrases, and the latter, few long phrases. Further, they showed that females of one subspecies do not recognise the song of males of the other. Other traits have also been shown to vary with the same pattern,, suggesting that there is gene flow from one subspecies to the next. However, as all of these traits are likely to be under selection, it isn't really feasible to take this as conclusive evidence for gene flow. As a result, Irwin et al. (2005) turned to AFLP, which is a way of looking at variation across an individual's entire genome. They hoped to show that even though there is continuous gene flow around the ring, the two northern subspecies are still reproductively isolated, by sheer force of distance. And that is exactly what they did.

The implications of this are interesting in two ways. Firstly, in its own right, showing that populations can become reproductively isolated simply by being far enough away from each other, even if other populations of the same species occur in the intervening space, is of great significance. You don't always need a mountain range or a river or any of the other textbook examples, all you need is mileage.

But the other implication, which I find equally interesting, is that it challenges our concept of what a species even is. The discipline of systematics aims to reconstruct the ways in which the diversity of life has come about, but is dependent on its sister-discipline, taxonomy, to give names to that diversity. But what of the Greenish Warbler? In a way its rather vaguely descriptive common name is reflected in its nature: as a species, it is pretty vaguely defined. Being a birder, I am well aware of the dual challenge of not only identifying species (which occurs on a day-to-day basis), but also of just being able to tell when two things are in fact distinct species (which applies in a more general sense). Avian taxonomists are constantly 'splitting' and 'lumping', either adding more names to the tree of avian life, or culling them from it. But I don't think any taxonomist would really know what to do with the Greenish Warbler. Any naturalist tromping through the woods of Siberia, finding the two northern subspecies occurring together, would confidently call them different species. If that naturalist never travelled to the Himalayan foothills, and never studied the Greenish Warblers there, he or she would, in blissful ignorance, happily continue to do so. And if the 'intermediate' subspecies did not exist, so would we.

One could argue that this has occurred for many sister species in the past - the intermediates are now extinct, and we are seeing the end result. But what if this is the end result? Irwin et al. (2005) argue that in fact this system is likely to be stable, rather than progressing towards eventual speciation, and that only new processes such as habitat change have the potential to lead to what you might call 'full speciation'.

In my opinion, there is actually no solution to this problem. But that needn't worry us. It simply reflects the fact that the real world, the natural world, is immensely complex, and that sometimes our attempts at imposing order on it will be thwarted. We're just going to have to live with the Greenish Warbler being a sort-of species. I think that's great.

Cultural evolution via public information. The case of the Melodious Lark?

In my previous blog I focused on a paper that aimed to outline some of the most important current questions in the study of speciation. One of these was 'What is the role of phenotypic plasticity?' Plasticity is variation in phenotype that is determined by environment rather than genetic make-up. How, then, can plasticity cause species to diverge? The idea seems nonsensical, and indeed plasticity is often viewed as an obstacle to speciation. If individuals of a species can adapt to different environmental conditions regardless of their genotype, then surely this cannot lead to speciation. That is, unless plastic phenotypic traits are heritable.

This is where we come to the idea of cultural evolution. Through its development into a global internet phenomenon, the concept of the 'meme' has firmly entered the public consciousness, at least among the younger generation. Memes are the essential unit in cultural evolution, analogous to genes in genetic evolution. However, they differ from genes in that not only can they be transmitted vertically through generations (i.e. from parents to offspring), they can also spread horizontally through the 'meme pool', and obliquely, that is, between unrelated individuals from one generation to the next. For vertical and oblique inheritance of memes to take place, you need overlapping generations. But for any kind of meme exchange, organisms need some way of gathering non-genetically acquired information from other organisms. As Danchin et al. (2004) explain, in an article published in Science, public information (PI) is an important way in which organisms achieve meme transfer.

The concept of public information is simple, but let's first take a step back before we delve into it. There are two types of non-genetically acquired information: personal and social. Non-private personal information generates social information, which itself consists of cues (inadvertent social information [ISI]), and signals (deliberate communication). Danchin et al. (2004) divide ISI into location cues and performance cues, and define the latter as PI. Organisms can learn by making use of PI provided by other organisms, usually members of their own species, and make use of it to enhance their own ecological performance by making better decisions, for example about where to breed or forage. If this process results in a lastingly altered phenotype, then PI can help to generate culture (i.e. shared traditions and information that vary among groups or populations). Culture can then affect the evolution of species, as well as speciation, as it is passed from one generation to the next. Figure 1 provides a neat summary of this.

Figure 1: The types of non-genetically acquired information and their influence on culture, biological evolution, and each other. The blue text and boxes represent topics covered by Danchin et al. (2004). Taken from Danchin et al. (2004).

Danchin et al. (2004) provide a list of examples of how PI is used by various organisms across a broad taxonomic range, and at times it reads like something out of a David Attenborough production. For example, PI is used by various organisms to assess the level of predation risk in an area. In many fish species, when an individual is predated upon, it releases chemicals that provide PI that other fish can use to assess danger levels and decide on the appropriate response. Even plants seem capable of this, as shown from experiments with wild tobacco. When growing alongside another plant species that has been clipped, tobacco plants produce more flowers than when growing among unclipped members of the same species. The perceived greater predation risk (and hence shorter life expectancy) induces plants to divert more resources to reproduction rather than growth.

Habitat copying, whereby individuals use PI about breeding success of other individuals to choose where to breed, and mate-choice copying, whereby females choose which males to breed with based on the choices of other females (which indicate quality; usually used in situations where females struggle to distinguish fitness levels among competing males), are other examples of the importance of PI in evolution. Habitat copying might lead to the evolution of coloniality in birds. Mate-choice copying might explain how sexual selection causing increasingly exaggerated male traits can be reversed (as observed in some phylogenies), if a mutant female with a preference for drab males is copied by other females, as has been observed in experiments with guppies.

It was one example in particular that got me thinking about a potentially very interesting local case of PI and cultural evolution. 'Eavesdropping', whereby individuals make decisions based on the outcomes of others' interactions, is an example of PI use that has implications for a variety of situations. The authors suggest that PI could play a role in cultural evolution if eavesdropping leads to males adopting the songs of successful males more often than unsuccessful males. In South Africa there is a bird that has been observed engaging in some very unusual behaviour. It's called the Melodious Lark Mirafra cheniana, and males are extraordinarily accomplished mimics. Roberts Birds of Southern Africa (Hockey et al. 2005, p.861), provides the following list of bird groups recorded amongst its vocal repertoire: 'kites, kestrels, francolins, guineafowl, lapwings, coursers, go-away-birds, cuckoos, bee-eaters, swifts, shrikes, swallows, warblers, larks, chats, sunbirds, pipits, longclaws, starlings, weavers, waxbills and canaries.' In his insightful and informative guide to Southern Africa's larks and other 'little brown jobs', Faansie Peacock (2012) notes that each male can probably mimic over 50 different species of bird, and mentions another interesting aspect of its behaviour that I can find no other reference to. Males often gather and sing in loose aggregations, and interestingly, will often simultaneously mimic the same species as other males in the group. Clearly, this 'copycatting' behaviour involves the transmission of ISI between singing males - their singing is certainly not directed at one another. But what purpose does it serve? And might PI and culture play a role in this behaviour?

Melodious Lark

Many species of bird engage in group display behaviour known as 'lekking', which can often be amazingly well coordinated. Blue Manakins are a fantastic example of this. Groups of four or so males display to females as a 'team', leapfrogging over one another while rapidly 'buzzing' their wings to create a spectacular effect. In the end, only one male will mate with any suitably impressed females, but the 'losers' on his team stand a chance to take over as 'team leader' in the future, and so their sacrifice in the short-term is offset by their potential benefit in the long run. 

The copycatting behaviour of male Melodious Larks might be a form of lekking. However, an interesting question is whether it is genetically or culturally determined. Do males learn to copycat other males, or is it a genetically determined trait? Melodious Lark males are often found displaying singly, meaning that this lekking behaviour isn't the only means by which males attract mates. If they do learn, then what kind of information do they employ in the learning process? As a first step, it would be interesting to compare breeding success between males displaying in lekking groups and males displaying singly. Do males that lek have higher paternity? Does a single male 'win out' within lekking groups and breed with the majority of females in the area? Also, is competition for mates (i.e. sexual selection) stronger among lekking males? This last question could potentially be answered by comparing the vocal repertoires of males that do and don't lek. The question of whether lekking males have higher quality territories would also be interesting to explore in this regard. One might hypothesize that males that lek can mimic more species, perhaps because they are more experienced (i.e. older and hence fitter, and able to maintain a hold on higher quality territories), or perhaps because they are more likely to be shown up as being pretenders if they can't 'keep up' with the other males. This is where the possibility of cultural evolution comes into play, but it's something that I can't quite get my head around. Is copycatting a meme used by males to fool females into thinking that 'I'm as fit as the next guy', or is it an honest, genetically determined signal used by females to more efficiently distinguish the fittest males in (perhaps) the highest-quality territories? I think it would be fascinating to do an in-depth study on the breeding biology of these birds, and particularly to delve into the 'Why?' and 'How?' of their curious copycatting behaviour.  

References

Danchin E, Giraldeau L, Valone TJ and Wagner RH. 2004. Public Information: From Nosy Neighbors to Cultural Evolution. Science. 305: 487-491. 

Hockey PAR, Dean WRJ and Ryan PG (eds). 2005. Roberts - Birds of Southern Africa VII^th
ed. The Trustees of the John Voelker Bird Book Fund. Cape Town.

Peacock F. 2012. Chamberlain's LBJs. Mirafra publishing. Pretoria.

On the origin of the study of speciation...

In a recent, thought-provoking paper published in Trends in Ecology and Evolution, and entitled 'What do we need to know about speciation?', members of the Marie Curie Speciation Network (2012) outline some important themes and questions that should, among others, be central to future studies on speciation.

Darwin's famous scribble. (c) www.fossilmuseum.net

What struck me most about this article was how fundamental some of these questions are, and yet how far we seemingly are from even beginning to answer many of them. As I came to discover, this is partly because answering any general questions about speciation is a task fraught with challenges. However, scientists also need to take some of the blame, for two reasons: Firstly, many arguments and lines of thinking that have passed their sell-by date are still followed by many; secondly, studies of speciation were surprisingly rare up until surprisingly recently.

But first, let's have a look at some of the questions that illustrate just how much we have yet to learn about speciation. Bear in mind that the authors restricted themselves to questions concerning speciation in sexually reproducing eukaryotes; the fundamental differences in how asexually reproducing eukaryotes and prokaryotes diversify, and even in how we define the term 'species' for them, is yet another illustration of the complexity of speciation. Even excluding them, the scope of the issue is enormous.

Their first question asks which barriers are most important in restricting gene flow between populations. In other words, which barriers evolve first? Prezygotic isolation is often cited as generally being more important, firstly because there are many examples where species can produce viable hybrids but generally do not interbreed, and secondly because an organism must anyway first mate outside its own population before any postzygotic effects come into play. However, this doesn't account for the fact that sometimes the first step in speciation is reduced fitness of hybrids in the context of differential adaptation, i.e. postzygotic isolation. 

Such uncertainty is caused by the tricky nature of the task of figuring out which barriers are involved, and to what extent. For example, measuring behavioral reproductive isolation between populations seems simple: How often do members of different populations mate? However, the fact that mating events between members of separate populations are generally rare and field observations cannot be made continuously means that such events are easily overlooked. Furthermore, lab experiments are hindered by the fact that experimental design can have a huge impact on their outcome, and that for most species we don't know which experimental conditions are most appropriate.

The theme that I find most interesting in this paper is that on connecting speciation to patterns of biodiversity. For example, question 12 asks what factors contribute to variation in speciation rate (i.e. how quickly clades diversify). One of the biggest problems in answering this question relates to the fact that ecological and genetic factors can influence both speciation rate and extinction rate, both of which affect our current 'snapshot' view of biodiversity. This has been a central theme in the recent debate surrounding the origins of the latitudinal diversity gradient.

The authors also ask what we no longer need to know about speciation. In other words, what questions can we safely leave behind? Among the three arguments that they identify is that surrounding the geographic basis for speciation. They argue that the traditional distinction between allopatric, parapatric and sympatric speciation processes is now redundant. For example, rather than focusing on whether speciation can take place in sympatry, we are advised to rather focus on whether it can occur in the face of gene flow. As the authors say: 'The criteria for ‘proving’ sympatric speciation can be made so exacting that an unambiguous case is almost impossible' (p. 35), and that rather than viewing spatial context as central to the speciation process, it should be viewed as merely a single factor influencing it. I agree entirely with these sentiments. Perhaps in undergraduate courses it should be made clearer that while this argument has in the past been useful in studying speciation, it is no longer so.

The title of this blog post borrows from one of the most famous titles in any field. Yet there is a contrast here. Where the title of Darwin's seminal work alluded to its implications for our understanding of how new species arise, its focus, and that of many subsequent decades of evolutionary research, was on the nature of change within species rather than their origin. Only in the past 25 years has the study of speciation really taken off (Santini et al. 2012). In keeping with this philosophy, the title of this blog post is also somewhat out of sync with its focus. Understanding the nature of the study of speciation is vitally important for those who wish to engage in it. Yet its origins have been crucial in shaping its current state. Put simply, there is still much we need to know, and plenty of lost time to make up for. 

Key Reference

The Marie Curie Speciation Network. 2012. What do we need to know about speciation? Trends in Ecology and Evolution. 27 (1): 27-39.

Further Reading

An informative online discussion forum on this paper can be found here.

Santini F, Miglietta MP and Faucci A. 2012. Speciation: Where Are We Now? An Introduction to a Special Issue on Speciation. Evolutionary Biology. 39: 141-147.