Ancient DNA helps to place two extinct duck species on the Tree of Life

Mitochondrial DNA from Chendytes lawi and the Labrador Duck reveals some interesting evolutionary patterns.

The fossil record of birds is not great (to start with an understatement), but occasionally some wonderful fossils pop up. Some even contain traces of ancient DNA which can be used to pinpoint the phylogenetic position of these extinct species. On this blog, I have written about studies on ancient DNA from the Creighton’s Caracara (Caracara creightoni) and the Poūwa (an extinct Black Swan from New Zealand). Another recent paper in the journal Molecular Phylogenetics and Evolution took a closer look at two extinct waterfowl species: Chendytes lawi and the Labrador Duck (Camptorhynchus labradorius).

labrador duck

The extinct Labrador Duck © James St. John | Wikimedia Commons

 

Sea ducks or not?

The genus Chendytes was erected in 1925 to classify Holocene fossils from the California coast and nearby Channel Islands and holds two species. One species (C. lawi) is the size of a goose and shows degeneration of the wings. The second species (C. milleri) is smaller with larger wings. It might represent an intermediate form between a flying ancestor and the flightless C. lawi (similar to Tachyeres ducks, see this blog post). Based on several morphological traits, these extinct species were considered sea ducks (tribe Mergini).

In 2018, Janet Buckner and her colleagues managed to extract mitochondrial DNA from a C. lawi fossil. Comparing these DNA sequences with extant species revealed that Chendytes ducks are not sea ducks, but basal dabbling ducks (tribe Anatini). Hence, this lineage represents an independent evolution towards a diving lifestyle. The traits shared with sea ducks are thus the outcome of convergent evolution.

1-s2.0-S1055790317304621-fx1_lrg

The phylogenetic positions of two extinct species inferred from mtDNA. From: Buckner et al. (2018) Molecular Phylogenetics and Evolution

 

What about the Labrador Duck? In contrast to the Chendytes ducks, this species does belong to the sea ducks. Indeed, the Labrador Duck is closely related to the Steller’s Eider (Polysticta stelleri). This finding refutes the morphological work by Bradley Livezey, who considered the Labrador Duck a scoter in the genus Melanitta.

However, one should always be careful with mitochondrial phylogenies and ducks because of hybridization. Waterfowl are known for their high levels of hybridization and mtDNA can easily be transferred between species (i.e. mitochondrial capture, see for example Jacamars). The Labrador Duck might be closely related to the Steller’s Eider, but you never know whether hybridization mixed things up a bit.

 

References

Buckner, J. C., Ellingson, R., Gold, D. A., Jones, T. L., & Jacobs, D. K. (2018). Mitogenomics supports an unexpected taxonomic relationship for the extinct diving duck Chendytes lawi and definitively places the extinct Labrador Duck. Molecular phylogenetics and evolution122, 102-109.

This blog post was written to celebrate #BlackBirdersWeek. Check out the wonderful work of Janet Buckner on her website.

Cryptic Crows: Genetic study uncovers a wide hybrid zone between American and Northwestern Crow

These crow species represent distinct lineages but interbreed along the western coast of North America.

What is the difference between an American Crow (Corvus brachyrhynchos) and a Northwestern Crow (C. caurinus)? Some ornithologists argued that Northwestern Crows are clearly smaller, but that turned out to be a false impression. Perhaps they produce different sounds? That is also a tricky trait because these birds learn vocalizations from their social group. Morphology and sound are thus not sufficient to discriminate between these species. This raises the question whether they are even distinct species. A genetic approach might provide some crucial insights. A recent study in the journal Molecular Ecology explored the genomes of American and Northwestern Crows to shed some light on this ornithological mystery.

Vancouver Canada 2014

A Northwestern Crow in Canada © Gordon Leggett | Wikimedia Commons

 

Two Lineages

David Slager and his colleagues took a closer look at the mitochondrial and nuclear genomes of these crows. The mitochondrial analyses (based on the gene ND2) revealed two distinct lineages that diverged about 443,000 years ago. Similarly, the nuclear perspective pointed to two clusters that correspond to American and Northwestern Crows. These genetic results indicate that we are dealing with two separate lineages.

However, a closer look at the nuclear data showed that 34 individuals were actually hybrids: not first-generation hybrids (so-called F1s) but backcrosses and late-generation hybrids. These hybrid individuals could be traced back to a 900 kilometre-wide hybrid zone along the west coast of North America.

crow_cline

Genetic analyses uncovered a cryptic hybrid zone between American Crow and Northwestern Crow. From: Slager et al. (2020) Molecular Ecology

 

Cryptic Hybrid Zone

This study not only confirmed that there are two cryptic crow species, but also revealed the existence of a cryptic hybrid zone. Most hybrid zones have been discovered and described using morphological data. The absence of clear diagnostic traits in American and Northwestern Crows prevented ornithologists from detecting this hybrid zone earlier. This highlights the importance of genomic data in understanding speciation and hybridization. Who knows how many cryptic hybrid zones are still out there!

This finding raises a new question: what mechanisms prevent these crow species from merging into one species? The analyses did not uncover any genomic regions that were highly differentiated between the crows (so-called islands of differentiation). However, the researchers only covered a small percentage of the entire genome (they used a ddRAD approach). Whole genome analyses might be able to detect subtle differences, similar to European crows – Carrion Crow and Hooded Crow – where a large genomic region likely explains the plumage differences between these species. However, given that American and Northwestern Crow are morphologically indistinguishable other genomic regions might pop up. To be continued…

american_crow

An American Crow © Mr.TinDC | Flickr

 

References

Slager, D. L., Epperly, K. L., Ha, R. R., Rohwer, S., Wood, C., Van Hemert, C., & Klicka, J. (2020). Cryptic and extensive hybridization between ancient lineages of American crows. Molecular Ecology, 29(5): 956-969.

This paper has been added to the Corvidae page.

Does migratory behavior affect genetic diversity in the Golden-crowned Kinglet?

A recent study compared the genetic make-up of migratory and resident populations across North America.

In January 2016 I attended the Plant and Animal Genomics (PAG) meeting in San Diego. Obviously, I took some time off for bird watching and managed to add some new species to my life-list, including the Ruby-crowned Kinglet (Regulus calendula). However, this blog post will not focus on this red-capped beauty, but on a related species: the Golden-crowned Kinglet (R. satrapa). This small songbirds has a wide distribution across North America and displays an interesting behavior: populations in the center of the range migrate while the peripheral populations (on the east and west coast) are resident.

This situation provides ideal circumstances to study the effect of migratory behavior on genetic differentiation and diversity. Resident behavior is expected to reduce gene flow between populations, resulting in more genetic differentiation. In addition, the reduction in gene flow might increase the influence of genetic drift in isolated populations, which leads to loss of genetic diversity. Migratory behavior, on the other hand, will increase levels of gene flow, culminating in less genetic differentiation and more genetic diversity. A recent study in the Journal of Ornithology tested these predictions.

golden-crowned_kinglet

A Golden-crowned Kinglet in Washington © Francesco Veronesi | Wikimedia Commons

 

East and West

The researchers used seven microsatellites to probe the genetic make-up of migratory and resident populations of Golden-crowned Kinglets across North America. These genetic markers revealed a clear separation between eastern and western populations (in accordance with a previous study). This geographical pattern is probably a genetic signature of the Last Glacial Maximum when eastern and western populations of Golden-crowned Kinglets were isolated in distinct refugia. The population in Alberta showed some signs of admixture and could be a potential bridge for gene flow between east and west.

But what about migratory and resident populations? The authors start their discussion with the following statement: “We found no evidence to support our hypothesis that migratory behaviour influences neutral genetic differentiation and neutral genetic diversity for Golden-crowned Kinglets.” Indeed, there was no significant difference in genetic differentiation or diversity between migratory and resident populations.

Fst

There was no significant difference in genetic differentiation between migratory and resident populations of the Golden-crowned Kinglet. From: Graham et al. (2020) Journal of Ornithology

 

Genomics

It thus seems that the genetic population structure of these passerines is mainly determined by the glacial dynamics of the Pleistocene. Does this mean that migratory behavior has no effect on genetic patterns? Not necessarily, there are several explanations for this result. First, the resident and migratory behaviors might be a recent development that has not yet impacted the genetic make-up of these populations. Second, the genetic markers in this study (seven microsatellites) might be too variable to pick up subtle differences between resident and migratory populations. Moreover, the genetic variants associated with migratory behavior might be restricted to particular genomic regions, such as in warblers (see here and here). A genomic approach is warranted.

 

References

Graham, B. A., Carpenter, A. M., Friesen, V. L., & Burg, T. M. (2020). A comparison of neutral genetic differentiation and genetic diversity among migratory and resident populations of Golden-crowned-Kinglets (Regulus satrapa). Journal of Ornithology, 1-11.

Phylogenetics in the genomic era: Reconstructing the evolutionary tree of rails (family Rallidae)

A phylogenomic study reports some interesting new relationships.

The life of a “phylogeneticist” used to be so simple. You sequence a couple of genes, align them with your favorite software (mostly Clustal), and run some phylogenetic analyses (maximum likelihood, maximum parsimony and perhaps something Bayesian). Then genomic data arrived. Suddenly, there were thousands of genes and non-coding elements to take into account. What was worse, different genes often resulted in different gene trees! The life of the phylogeneticist – or should I say phylogenomicist – just became a whole lot more complicated and more exciting.

Obviously, I exaggerated here. Phylogenetics was never that simple. But the advent of genomic data did open up many avenues for further research. These new opportunities came with an expansive toolkit of software and analysis methods. You can check out the details in this recent paper in Nature Reviews Genetics: Phylogenetic tree building in the genomic age.  In this blog post, however, I would like to focus on two general methods to construct phylogenetic trees from genomic data, namely concatenation and coalescent-based consensus approaches.

 

Supermatrix or Supertree?

To explain both methods, I will borrow some text from a paper I published some years ago in Molecular Phylogenetics and Evolution.

In concatenation (or supermatrix) methods all sampled genes are concatenated and analysed as a single ‘‘supergene”. Supertree methods, on the other hand, involve separate analyses of the sampled genes and subsequent integration of the resulting trees into a species tree. Certain supertree methods incorporate the multispecies coalescent model to estimate the species tree from a set of heterogeneous gene trees.

In short, during a concatenation analysis you paste all the genes together and analyse them as if they are one big gene. In supertree methods, you generate a gene tree for each gene and then combine them into a species tree. Simple.

supermatrix_tree

The difference between supermatrix and supertree methods. From: Delsuc et al. (2003) Nature Reviews Genetics

 

A tree of rails

A recent study in the journal Diversity applied both methods to reconstruct the evolutionary history of the rail family. The researchers analyzed 393 loci from 63 species. In the abstract, they report that “Concatenated maximum likelihood and coalescent species-tree approaches recover identical topologies with strong node support.” That is good news and suggests that the phylogeny has been resolved reliably. There are several intriguing findings, so let’s have a look at a few unexpected results.

First, a bombshell: the family Rallidae (as we know it) is not monophyletic. The Forbes’ Forest rail (Rallicula forbesi) does not cluster with the other rails, but is more closely related to the flufftail (Sarothrura rufa). Together, these species are best classified in a distinct family: the Sarothruridae. Another new insight concerns the African Nkulengu rail (Himantornis haematopus). This species now occupies its own separate branch (which is in agreement with morphological data)

rail_tree

The phylogenetic relationships between different rail species. Notice the location of Rallicula forbesi outside the core family. Colors correspond to different genera. From: Garcia-R et al. (2020) Diversity

 

Unstable genera

The analyses revealed some other interesting relationships that rendered several genera non-monophyletic.

  • The African crake (Crex egregia) is more closely related to Rouget’s rail (Rougetius rougetii) than to its congeneric, the corn crake (C. crex).
  • The positions of the New Guinea flightless rail (Megacrex inepta) and the watercock (Gallicrex cinerea) break the monophyly of the genus Amaurornis.
  • The Inaccessible rail (Atlantisia rogersi) falls within the genus Laterallus.

Clearly, there is some taxonomic work ahead of us.

crex_egregia

Two African crakes © Derek Keats | Flickr

 

Stems and crown groups

Finally, the researchers also attempted to date the resulting phylogenetic tree. When did all these species arise? The answer to that question strongly depends on the placement of the Belgirallus fossil. This taxon represents the oldest known fossil of the Rallidae, but the exact relationship with extant species is unknown: it can be considered as a representative of the stem or the crown group. What is the difference, you ask? Well, a crown group is the smallest clade that includes all living members of a group and any fossils nested within it. A stem group is a set of extinct taxa that are not in the crown group but are more closely related to the crown group than to any other.

If you consider Belgirallus as part of the stem group, the Rallidae originated around 26 million years ago. But if you place it within the crown group, the origin of Rallidae shifts to about 33 million years ago. More fossils are needed to resolve this issue.

Fig.3.8

The difference between crown and stem groups. From: Noriyuki Satoh (2016) Chordate Origins and Evolution

 

References

Garcia-R, J. C., Lemmon, E. M., Lemmon, A. R., & French, N. (2020). Phylogenomic Reconstruction Sheds Light on New Relationships and Timescale of Rails (Aves: Rallidae) Evolution. Diversity12(2), 70.

Kapli, P., Yang, Z., & Telford, M. J. (2020). Phylogenetic tree building in the genomic age. Nature Reviews Genetics, 1-17.

Hybridizing hyenas and how to find them

Genomes of extant and extinct hyenas reveal a reticulated history.

Almost every study that uses genomic data to retrace the evolutionary history of particular species uncovers traces of hybridization. Hyenas are no exception. A recent paper in the journal Science Advances reported gene flow between African spotted hyenas and extinct Eurasian cave hyenas. Spotted hyenas (Crocuta crocuta) are large carnivores that currently occur in sub-Saharan Africa. Compared to their African cousins, cave hyenas have shorter limbs and blunter teeth, suggesting that they were mainly scavengers. Based on more suble morphological differences, cave hyenas have been split into European (spelaea) and Asian (ultima) subspecies.

The genomic data pointed to a deep divergence (about 2.5 million years ago) followed by bidirectional gene flow sometime before 475,000 years ago. The study nicely outlines the different analyses that led to this conclusion. Let’s have a look.

spotted-hyena-3474798_960_720

A Spotted Hyena © Alicave | Pixabay

 

Phylogenetics

We start with the mtDNA. Previous work with short mitocondrial fragments could not differentiate between spotted and cave hyenas. Using whole mitochondrial genomes did not markedly change this conclusion. The resulting evolutionary tree is a mixture of both hyenas, albeit with more resolution.

Perhaps nuclear DNA might help resolve this phylogenetic mess? The researchers constructed almost 500 phylogenetic trees based on DNA sequences of 2 million letters. Most of these trees supported a clear split between spotted hyenas and cave hyenas. The incongruence between nuclear and mitochondrial phylogenies already indicates that something interesting is happening here. Are we dealing with incomplete lineage sorting or hybridization?

Hyena

Incongruence between mitochondrial and nuclear DNA. (A) Phylogenetic analyses of mtDNA could be discriminate between spotted hyena (blue) and cave hyena (red). (B) Nuclear DNA, however, pointed to a clear split between both hyena types (Africa vs. Europe and Asia). Adapted from: Westbury et al. 2020 Science Advances

 

D-statistics and Simulations

Next, the researchers turned to everyone’s favorite test for ancient gene flow: the D-statistic (see this blog post for more information). They used an adjusted version of the D-statistic that infers the direction of gene flow. Calculating this statistic for different genomic regions revealed several instances of gene flow between spotted hyenas and cave hyenas. However, the patterns of gene flow depended on the individual genomes that were being compared. These results can be explained in two ways: (1) multiple gene flow events into spotted hyenas or (2) a single admixture event was followed sorting of the cave hyena loci.

To figure out which explanation was more likely, another approach was added to the mix: a coalescent modelling excercise. The researchers used Fastsimcoal to explore different scenarios of gene flow. These analyses suggested that gene flow was mostly bidirectional but with more gene flow from Europe into Africa in more recent times (as shown in the figure below). Given that the spotted and cave hyenas with mitochondrial haplotype A diverged about 475,000 years ago, these gene flow events probably happened after this split. More research is needed to pinpoint the exact timing.

hyena_tree

The most likely model of gene flow between spotted hyenas and cave hyenas. From: Westbury et al. 2020 Science Advances

 

Summary

The researchers nicely summarize their findings: “We suggest a bidirectional gene flow event between cave and spotted hyenas after the split of cave hyenas into the European and Asian lineages and a subsequent unidirectional gene flow event into northern spotted hyenas, followed by differential diffusion of the admixed loci within the other spotted hyena lineages”

 

References

Westbury, M.V. et al. (2020). Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena. Science Advances6(11), eaay0456.

Conservation genetics in China: Comparing genetic diversity of Siberian and Sichuan Jays

Is the low population size of the Sichuan Jay reflected in their genetic make-up?

Somewhere in the mountains of western China you might stumble upon a peculiar species: the Sichuan Jay (Perisoreus internigrans). Little is known about this corvid. A survey between 1999 and 2004 estimated about 1 individual per km2 in Jiuzhaigou (and the density was even lower in Zhuoni). These low densities are probably the result of habitat fragmentation: large patches of pristine forest have been removed. Moreover, the habitat of the Sichuan Jay has been influenced by the Pleistocene ice ages when forests were fragmented by advancing ice sheets. Taken together, we can expect that these events led to a significant reduction in population size and hence genetic diversity. A recent study in the journal Conservation Genetics put this expectation to the test.

Perisoreus internigrans

A Sichuan Jay in China © Tang Jun | Oriental Bird Images

Genetic Diversity

Kai Song and his colleagues collected samples from 58 Sichuan Jays and compared their DNA with 205 Siberian Jays (P. infaustus) from Sweden and Russia. As explained above, the researchers expected a clear reduction in genetic diversity in the Sichuan Jays. Suprisingly, this was not the case. Both species showed similar levels of genetic diversity, despite the more restricted range of the Sichuan Jay.

Moreover, the populations of Sichuan Jay showed clear population structure, separating into three clear clusters (see figure below). Unfortunately, the sampling locations of these birds have been lost, so it is currently not possible to relate this structure to particular geographical locations.

plot

The genetic analyses revealed clear population structure in the Sichuan Jay. From: Song et al. (2020) Conservation Genetics

Conservation

Does the high level of genetic diversity mean that we should not worry about the Sichuan Jay which is currently considered “vulnerable” by the IUCN? Not necessarily, the analyses were based on microsatellites, which are known to be very variable. It is thus possible that this study overestimated the amount of genetic diversity. In addition, the clear separation into three clusters suggests that the populations of Sichuan Jays are highly fragmented into small populations. This might make them more vulnerable to environmental changes.

Habitat loss seems to be the most important threat for this Chinese bird species. To prevent further population decline targeted habitat restoration is key. The protection and expansion of virgin conifer forest will not only benefit the Sichuan Jay, but numerous other species, such as Chinese Grouse (Tetrastes sewerzowi) and Sichuan Wood Owl (Strix davidi).

Perisoreus_infaustus

A Siberian Jay in Norway © Bouke ten Cate | Wikimedia Commons

References

Song, K., Halvarsson, P., Fang, Y., Barnaby, J., Germogenov, N., Sun, Y., & Höglund, J. (2020). Genetic differentiation in Sichuan jay (Perisoreus internigrans) and its sibling species Siberian jay (P. infaustus). Conservation Genetics, 21: 319–327.

Figuring out the evolution of forked tails in Swallows and Swifts

A recent study shows that both groups took different evolutionary paths to their deeply forked tails.

A warm summer evening is often accompanied by the acrobatic caprices of swifts and swallows. These agile fliers might look alike but they belong to vastly different bird orders that diverged about 85 million years ago. Swallows are songbirds from the order Passeriformes, while swifts are the closest relatives of hummingbirds in the order Apodiformes. The resemblance between these distantly related groups partly relates to their forked tails. But how did this feature evolve in both groups? A recent study in the Journal of Evolutionary Biology collected data for 72 swallow and 39 swift species to tackle this question.

Apus_apus

 A Common Swift (Apus apus) in Barcelona, Spain. © Pau Artigas | Wikimedia Commons

 

Selection

To put it bluntly, forked tails can be the outcome of two main evolutionary forces: sexual selection or natural selection. Previous studies have found evidence for both explanations. Male Barn Swallows (Hirundo rustica) with deeply forked tails are more successful with female birds, leading to higher reproductive output. This clearly fits the description of a sexually selected trait. However, other researchers have suggested that natural selection could have shaped these tails to ensure more efficient foraging.

In their study, Hasegawa and Arai put forward several predictions to disentangle the effects of sexual and natural selection. Sexual selection predicts that the fork in the tail will look deeper (i.e. the tail feathers look longer). This can be achieved by longer tail feathers (obviously) or by a shorter central tail feather (less obviously). However, a shortening of this central feather could impair flight in species that rely more on tail lift instead of wing lift. Hence, natural selection would select against a shorter central tail in these species.

Wire_tailed_swallowjpg

A Wire-tailed Swallow (Hirundo smithii) feeding a chick ©Manojiritty | Wikimedia Commons

 

Convergent Evolution

I will not dwell on the technical details – they used a phylogenetic comparative approach – but the results supported a main role for sexual selection in the evolution of forked tails. In both groups, the length of the central tail feather decreased with deeper tails. In swifts, this pattern was linear, while in swallows the relationship was concave (see figure below). This subtle difference is highlighted in the title of the paper: “Fork tails evolved differently in swallows and swifts.”

Moreover, the white spots on some swallow tails gave the impression that the tail is even longer. This optical illusion could relax the sexual selection on the central tail feather. Instead of shortening this feather (and potentially losing aerial maneuverability), swallows just add some white spots to let their tail appear longer. An alluring hypothesis that requires more research.

tail

The central tail feather (black dots) decreased with deeper forks. In swallows, the relationship is concave, whereas in swifts it is linear. From: Hasegawa & Arai (2020) Journal of Evolutionary Biology

 

Setting the Stage

So, does this study settle the debate: forked tails in swifts and swallows were shaped by sexual selection? You could definitely argue that the recent evolutionary history of this trait was mainly driven by sexual selection. The relationship between tail length and reproductive success is indeed very convincing. However, perhaps these forked tails first evolved in the context of aerial maneuverability and were later co-opted by sexual selection. In other words, natural selection set the stage for sexual selection*.

 

References

Hasegawa, Masaru, and Emi Arai (2020) Fork tails evolved differently in swallows and swifts. Journal of Evolutionary Biology. Early View.

* This scenario nicely contrasts with the evolution of feathers where sexual selection set the stage of natural selection. You can read more about it in this blog post.

Choosy Snowcocks: How habitat preference can affect genetic population structure

Genetic study reveals striking differences in population structure for two snowcock species in the Himalayas.

The Tibetan Plateau houses two species of snowcock: the Tibetan Snowcock (Tetraogallus tibetanus) and the Himalayan Snowcock (T. himalayensis). These partridge-like birds occur in the mountain ranges around the plateau, but occupy slightly different habitats. The Tibetan Snowcock prefers high-altitude areas (above 3000 meters) with dwarf shrubs, while the Himalayan Snowcock can be found in low-elevation regions that are drier and warmer. These differences in distribution can affect their genetic make-up. A recent study in the journal Avian Research used several microsatellites and a mitochondrial marker to probe the population genetic patterns of these species.

Himalayan Snowcock

Himalayan Snowcock © Subharanjan Sen | Oriental Bird Club Image Database

 

 

Population Structure

The genetic analyses by Bei An and colleagues revealed some interesting differences between the two species. Populations of Himalayan Snowcock showed a “divergent and structured” pattern whereas there was no clear phylogeographic pattern in the Tibetan Snowcock. The researchers speculate that this difference is due to the distinct habitat preferences of these snowcocks.

The high-altitude lifestyle of the Tibetan Snowcock might render it more resilient to extreme cold. Hence, this species might have been affected less by the glacial cycles of the Pleistocene. Populations did not have to survive the cold periods in separate refugia and so do not exhibit any clear population structure. The Himalayan Snowcock, on the other hand, occurred at lower altitudes where populations were fragmented by the waxing and waning of the Pleistocene ice sheets. This explanation makes intuitive sense, but will need to be tested (for example with some ecological niche modelling).

Tibetan_Snowcock

Tibetan Snowcock © Donald Macauley | Wikimedia Commons

 

Hybridization

The mitochondrial marker indicated that Tibetan and Himalayan Snowcock are clearly distinct. The haplotype network, however, uncovered an intruiging insight. One haplotype (H9) was shared by both species. This finding suggests that there might be occasional hybridization. Indeed, both species co-occur in some regions, such as the Kunlun Mountains and the Qilian Mountains. More dense sampling is required to investigate whether these species actually interbreed.

snowcocks

The mitochondrial marker shows that both species are clearly distinct. However, one haplotype (H9 in the network) suggests that they might interbreed. From: An et al. (2020) Avian Research

References

An, B., Zhang, L., Wang, Y., & Song, S. (2020). Comparative phylogeography of two sister species of snowcock: impacts of species-specific altitude preference and life history. Avian Research, 11(1), 1.

Woodcreeper species continue to exchange DNA until 2.5 million years after divergence

Recent study estimates the time window for introgression in birds.

One of my favorite avian hybrids is the Swoose, a cross between a Greylag Goose (Anser anser) and a Mute Swan (Cygnus olor). This particular hybrid is probably sterile, because its parental species diverged more than 20 million years ago. It has been estimated that bird species can still produce viable offspring after, on average, 21 million years of independent evolution. This is considerably longer compared to mammals, where it takes about 4 million years for hybrid inviability to develop. The time window for hybridization has thus been established for birds and mammals, but what about introgression? How long can hybridization result in the exchange of genetic material between species? A recent study in the journal Evolution tackled this question using the neotropical genus Dendrocincla.

Dendrocincla_fuliginosa

 

ABBA-BABA

Paola Pulido‐Santacruz and her colleagues collected genomic data for 87 specimens, representing all six recognized species in this genus. First, they reconstructed the phylogenetic relationships between these taxa. The resulting evolutionary tree served as the backbone for a series of ABBA-BABA-tests to infer introgression. For readers unfamilar with this approach, I copied the explanation from a previous blog post (D-statistics for Dummies).

The rationale behind this test is quite straightforward: it considers ancestral (‘A’) and derived (‘B’) alleles across the genomes of four taxa. Under the scenario without introgression, two particular allelic patterns ‘ABBA’ and ‘BABA’ should occur equally frequent. An excess of either ABBA or BABA, resulting in a D-statistic that is significantly different from zero, is indicative of gene flow between two taxa. A positive D-statistic (i.e. an excess of ABBA) points to introgression between P2 and P3, whereas a negative D-statistic (i.e. an excess of BABA) points to introgression between P1 and P3.

The figure below illustrates this procedure for several Dendrocincla subspecies. In this example, there is an excess of ABBA-patterns, suggesting introgression between the subspecies neglecta and ridgwayi (belonging to the Plain-brown Woodcreeper, D. fuliginosa).

ABBABA_dendro

The ABBA-BABA-test was used to infer introgression between different Dendrocincla (sub)species. Here, an excess of ABBA-patterns points to introgression between the subspecies neglecta and ridgwayi (indicated with black arrows). From: Pulido-Santacruz et al. (2020) Evolution.

 

Time Window

These analyses uncovered five introgression events, which is probably an underestimate because the ABBA-BABA-test only captures introgression between nonsister taxa. Nonetheless, the researchers were able to date these introgression events, which ranged from “a few hunderd thousand to about 2.5 million years following divergence”. These results suggest that the timeframe for introgression is much narrower than the timeframe for hybridization. In Dendrocincla woodcreepers, the species boundaries seem to become impermeable after about 2.5 million years of separate evolution. Whether this time window is the same for other bird species remains to be tested.

dendro_tree

The phylogenetic tree of the genus Dendrocincla with different introgression events indicated with colored arrows. From: Pulido-Santacruz et al. (2020) Evolution.

 

Genetic Snowballs

Another interesting observation in this study concerns the amount of genetic material than is exchanged between species. I explained the relevance of this pattern in a news article (a so-called digest) that accompanies the original study: “These proportions turned out to decline exponentially with the age of the hybridizing taxa. Interestingly, this pattern resembles the accumulation of genetic incompatibilities during the build-up of postzygotic isolation. These genetic incompatibilities do not increase linearly but instead seem to snowball because each new mutation is increasingly likely to be incompatible with a previous mutation.” However, this pattern is based on a few datapoints and will need to be confirmed with more data and other species.

dendro_curve

The relationship between the proportion of DNA exchanged (fhom) and the age at hybridization follows a snowball pattern, reminiscent of the accumulation of genetic incompatibilities. From: Pulido-Santacruz et al. (2020) Evolution.

 

References

Ottenburghs, J. (2020). Digest: Avian genomes are permeable to introgression for a few million years. Evolution.

Pulido‐Santacruz, P., Aleixo, A., & Weir, J. T. (2020). Genomic data reveal a protracted window of introgression during the diversification of a Neotropical woodcreeper radiation. Evolution.

Drum roll, please! The evolution of rhythm in Woodpeckers

Large-scale analyses show how current selection on woodpecker drums might influence subsequent evolutionary trajectories.

A walk in the woods is often accompanied by the occasional drumming of a resident woodpecker. Experienced birdwatchers – or perhaps better: “bird-listeners” – can discriminate between the drums of different species. In fact, visualizing the different drum solo’s revealed that each species’ pattern conforms to a particular mathematical formula (see the figure below for some examples). The beauty of nature captured in a few symbols.

Similar to bird song, the drum rolls of woodpeckers serve a dual function. Males use these drums to attract females and to defend their territories against other males. These functions are the hallmarks of sexual selection. But which components of the woodpeckers’ drum – such as speed, length, cadence – are under sexual selection? A recent study in The American Naturalist compared the drums of about 200 woodpecker species to figure this out.

black woodpecker

The Black Woodpecker has a low, vibrating drum. © Alastair Rae | Wikimedia Commons

 

Character Displacement

This woodpecker-wide comparison revealed that species that live in the same area (i.e. they are sympatric) tend to produce drums with very different rhythms. This suggests that sympatric woodpecker species use rhythm to find a partner of their own species and avoid – possibly detrimental – hybridization. In technical terms, rhythm is undergoing sexual character displacement. Interestingly, the same is not true for the speed and length of a drum. These components are under directional selection and might thus be more important in territorial competition among males.

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The variety of drums across the woodpecker phylogeny. The graphs on the right illustrate how different drums can be captured in a mathematical formula. From: Miles et al. (2019) The American Naturalist

 

Constraint and Potentiation

So, different rhythms allow the coexistence of certain woodpecker species. But these changes in rhythm have important implications for subsequent evolutionary trajectories. This is nicely illustrated by the Northern Flicker (Colaptes auratus) which contains two populations that might represent distinct species, namely the red-shafted (lathami) and yellow-shafted flicker (auratus). Individuals of the auratus population produce a linear cadence, while individuals of the lathami population have a constant rhythm. According to the estimates of this study, the lathami woodpeckers’ drum has the capacity to evolve more than ten times faster than the drum of auratus birds. In other words, the current drum rhythm “has introduced either a constraint on further signal evolution in auratus or a potentiation of further signal evolution in lathami.”

Colaptes_auratus_auratus1

A Northern Flicker of the auratus population. © USGS | Wikimedia Commons

 

Recursion

This phenomenon, where past selection influences the trajectory of future selection, is known as the recursive nature of evolution. This particular characteristic of the evolutionary process makes future evolutionary changes even harder to predict. Evolution is shaped by the interaction of deterministic and stochastic processes. Deterministic processes can be used to predict evolutionary outcomes, but the recursive feature of evolution can introduce stochastic elements in these deterministic changes, reshaping the evolutionary process in an unpredictable way.

You might be put off by this evolutionary quirk, but I think it only adds to the beauty of evolution. The authors capture this feeling nicely in their final sentence: “Altogether, out data illustrate how selection can be a source of contingency: it is a recursive process that modifies itself and, in doing so, leaves behind the exaptations and evolutionary ghosts that have fascinated biologists for decades.”

 

References

Miles, M. C., Schuppe, E. R., & Fuxjager, M. J. (2020). Selection for rhythm as a trigger for recursive evolution in the elaborate display system of woodpeckers. The American Naturalist, 195(5).