Adaptation in Parrotbills fueled by standing genetic variation

“It is not the strongest of the species that survives, nor the most intelligent that survives. It is the one that is the most adaptable to change.”

– Leon C. Megginson (1963)

This quote is often attributed to Charles Darwin, but it actually originated from a speech by Leon C. Megginson. Whoever said it, adaptation is a key concept in evolutionary biology and scientists are still trying to figure out how it happens. The main prerequisite seems to be the presence of advantageous alleles. The sources of these alleles are new mutations, gene flow from other species (i.e. adaptive introgression) or standing genetic variation. The latter refers to ancestral variation that is already present in the population and can be utilized immediately. A recent study in PNAS argues that this standing genetic variation has been the main source for adaptation in the vinous-throated parrotbill (Sinosuthora webbiana).

vinous-throated parrotbill.jpg

The vinous-throated parrotbill (from: http://www.hbw.com/)

 

High and Low

The vinous-throated parrotbill is a small songbird from East Asia. You can find it on the Asian mainland and on the island of Taiwan. There, it occurs up to 3100 meters above sea level. Yu-Ting Lai and colleagues collected 40 individuals from four populations in Taiwan, two from the lowlands and two from the highlands (situated in the Central Mountain Range). Next, they sequenced the genomes of these birds and started comparing their genetic variants, namely single-nucleotide polymorphisms (SNPs).

 

Candidate Regions

The researchers looked for genomic regions that were different between the high- and lowland populations. This search uncovered 24 candidate regions which harbored several genes related to adaptation to high and low altitudes, particularly the use of oxygen and thermoregulation.

Interestingly, the SNPs in these regions were not located within these genes but rather in the regions between the genes (i.e. intergenic regions) or in the non-coding parts of the genes (i.e. introns). This suggests that adaptation might be due to regulatory changes because the switches that control gene expression are generally located in these intergenic and intronic sections of the genome.

Gene example.jpg

Example of the different genomic regions. The stretch of DNA between two genes is the intergenic region (blue). Genes code for proteins, but some parts – the introns (yellow) – are spliced out in the process of making a protein. In the PNAS study, all candidate SNPs were located in the intergenic or intronic regions.

 

Mainland Birds

Next, the researchers sequenced the genomes of 40 parrotbills from the mainland. If the candidate SNPs from the Taiwanese populations are absent from the mainland, then they are probably due to new mutations. However, if the candidate SNPs are shared between the island and the mainland, it points to standing genetic variation. And indeed, most of the candidate SNPs were also found in the mainland population, indicating that standing genetic variation is the main source for adaptation to different altitudes on Taiwan.

Vinous-throated_Parrotbill_07.jpg

The vinous-throated parrotbill (from: http://www.hbw.com/)

 

Anthropocene

The use of standing genetic variation allows for rapid adaptation to changing environments. This  is relevant given global climate change and habitat loss. The authors write that “these findings provide important context for understanding adaptation and conservation of species in the Anthropocene.” Although I am not a big fan of the term Anthropocene (it still feels like a trick to “sell” your papers), understanding how species adapt to rapidly changing environments is crucial if we want to protect them.

 

References

Lai, Y.T., Yeung, C.K., Omland, K.E., Pang, E.L., Hao, Y., Liao, B. Y., Cao, H.F., Zhang, B.W., Yeh, C.F., Hung, C.M., Hung, H.Y., Yang, M.Y., Liang, W., Hsu, Y.C., Yao, C.T., Dong, L., Lin, K. & Hung, H. Y. (2019). Standing genetic variation as the predominant source for adaptation of a songbird. Proceedings of the National Academy of Sciences, 116(6), 2152-2157.

 

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First report of hybridization in millipedes

Discordance between genetics and morphology suggests hybridization.

Introgressive hybridization seems to be an integral part of evolution. Surprisingly, it has not been reported in the Diplopoda, or millipedes. A recent study in the journal ZooKeys suggests hybridization between two Australian millipedes in the genera Pogonosternum and Somethus. The first report of hybridization in millipedes! Well, there have been other reports, but these turned out to be incorrect.

 

Discordance

Peter Decker (Senckenberg Museum of Natural History) collected specimens of P. nigrovirgatum and P. jeekeli in southern Australia, close to the presumed boundary between these species. Next, he sequenced several genetic markers and compared the morphology of these species. The results showed discordance between the genetic and morphological analyses. Could this be due to hybridization?

Pogonosternum nigrovirgatum.jpg

Pogosternum nigrovirgatum (from: https://lifeunseen.smugmug.com/)

 

Gonopods

The discordance was caused by specimens from the site Dargo. Based on the genetic markers, some individuals clustered with P. jeekeli, while others were grouped with P. nigrovirgatum. Morphologically, the Dargo specimens are closest to the latter species. Specifically, their gonopods are very similar to those of P. nigrovirgatum. Gonopods are specialized appendages of various arthropods used in reproduction or egg-laying. Moreover, in millipedes from Dargo you can see brushes on the legs until pair 9, just like in P. nigrovirgatum. In the other species, these brushes only occur until pair 7. It seems likely that these patterns are the outcome of hybridization.

gonopods.jpg

Different views of the gonopod from a Dargo specimen (from Decker, 2018 ZooKeys)

 

More Hybridization?

Next, the author compared species of the genus Somethus. In one location – Mount Osmond – he found three individuals of S. castaneus that form their own genetic cluster. These anomalous millipedes might be a distinct lineage of this species or they might have exchanged DNA with another species. More data are necessary to discriminate between these hypotheses, but I wouldn’t be surprised if there was some hybridization involved.

 

A Personal Note

Although this blog focuses on avian hybrids, I regularly write about hybridization in other taxa. Why did I choose to dedicate a blog post to millipedes? First, because introgressive hybridization has not been reported in this group of animals. When someone finds clues of hybrid millipedes, it is worthwhile to write about it. Second, the paper of this blog post cited my 2016 review on hybridization in geese. It is always nice to see your work cited by other scientists, especially when you least expect it. As a thank you to Peter Decker, I decided to wrote a blog post about his work. So, if you want your work featured on Avian Hybrids, just cite me. 😉

 

References

Decker, P. (2018) Phylogenetic and morphological discord indicates introgressive hybridisation in two genera of Australian millipedes (Diplopoda, Polydesmida, Paradoxosomatidae). ZooKeys 809:1-14.

 

 

Can divergence in sperm morphology reduce hybridization in nightingales?

Testing for reinforcement at the gametic level.

Hybridization can lead stronger reproductive isolation. This statement might sound contradictory, but bear with me. Imagine two geographically isolated populations coming into secondary contact. The separation has not been long enough for complete reproductive isolation to develop, so these populations interbreed and produce hybrids. These hybrids are fertile but perform worse compared to the pure individuals. In other words, the hybrids have a lower fitness. Because the fitness of an individual is partly determined by the fitness of its offspring, it is better to avoid having hybrid offspring. Individuals that avoid hybridization do better. Hence, there will be selection against hybridization. Traits that contribute to the avoidance of hybridization will diverge, think of plumage patterns or song. In the end, reproductive isolation will be stronger. Biologists call this process reinforcement.

 

Predictions

One of the predictions of reinforcement is that the traits under selection should be more different in sympatry (i.e. where species co-occur) than in allopatry (i.e. the geographically separated regions of the species). This prediction has been confirmed for particular traits in several species, such song in Ficedula flycatchers or body size in African tinkerbirds. But could this process also operate on sperm morphology? Are sperm cells of hybridizing species more different in sympatry compared to allopatry? Tomáš Albrecht and his colleagues explored this question in two interbreeding nightingale species. Their results recently appeared in the journal Evolution.

common nightingale

Common Nightingale (from: http://www.vogelwarte.ch/)

 

Nightingale Sperm

Common Nightingale (Luscinia megarhynchos) and Thrush Nightingale (L. luscinia) diverged about 1.8 million years ago and currently hybridize in Central and Eastern Europe. Although females are sterile, there has been some gene flow between these species. This system has been studied extensively and I have written about it before (see here and here).

The researchers collected and measured sperm from both species and their hybrids. Common Nightingale sperm was longer than Thrush Nightingale sperm but it had shorter heads. Given that sperm cells with smaller heads swim faster (less drag), this might increase the fertilization success of Common Nightingale males. Interestingly, most hybrids result from mating of male Common Nightingales with female Thrush Nightingales. And gene flow is stronger from Common to Thrush Nightingales. Sperm morphology might explain these patterns, but more research is needed here.

 

Sperm Head

But what about the reinforcement prediction? Did sperm differ between sympatric and allopatric populations? The answer is yes; the difference in sperm morphology was bigger in sympatry compared to allopatry. This change might reduce the level of hybridization by allowing females to choose sperm from the “right” males. Female birds store sperm in specialized organs (so-called tubules). If the morphology of the sperm does not match the shape of these organs, the sperm will not be stored. This might lead to a bias for sperm from one species. The bigger difference in sperm morphology prevents the storage of heterospecific sperm and thus reduces the incidence of hybridization.

thrush nigthingale

Thrush Nightingale (from http://www.hbw.com/)

 

Hybrid Sperm

The sperm length of hybrids was intermediate between the parental species and showed no obvious abnormalities. This supports the notion that male hybrids are fertile. This situation is quite different from Ficedula flycatchers where males have deformed sperm cells and are sterile. Surprisingly, these flycatchers diverged only 0.5 million years ago (compared to 1.8 million years for the nightingales). This shows that the evolution of hybrid sterility in birds is very variable.

 

Want to know more about speciation and sperm? You can also check out this blog post on Long-tailed Finches (Phoephila acuticauda).

 

References

Albrecht, T., Opletalová, K., Reif, J., Janoušek, V., Piálek, L., Cramer, E.R.A., Johnsen, A. & Reifová, R. (2018) Sperm divergence in a passerine contact zone: Indication of reinforcement at the gametic level. Evolution 73(2):202-213.

 

This paper has been added to the Muscicapidae page.

Protecting Penguins: Exploring population dynamics in several penguin species

Two recent studies use different genetic approaches to uncover the past and present population structure of several penguin species.

Penguin colonies are a goldmine for nature documentaries. Many viewers have followed the life story of an adolescent Emperor Penguin (Aptenodytes forsteri) or the romantic escapades of Adélie penguins (Pygoscelis adeliae). But did you ever wonder about the dynamics between different colonies of the same species? Do individuals move between breeding grounds or do they remain loyal to their colonies? A recent study in Molecular Ecology mapped the genetic structure across five penguin species, representing 32 colonies.

Emperor_penguins.jpg

Emperor Penguins on the lookout (from: https://www.penguins-world.com/)

 

Pelagic Penguins

Four of the five species showed low levels of genetic differentiation between the colonies, which could be thousands of kilometers apart. It concerns Emperor Penguin, King Penguin (Aptenodytes patagonicus), Chinstrap Penguin (Pygoscelis antarcticus) and Adélie penguin. All these species are pelagic, they spend at least some part of their life in the open ocean. This behavior facilitates exchange between colonies, resulting in gene flow which prevents genetic differentiation.

 

Coastal Lifestyle

The fifth species in this study – the Gentoo Penguin (Pygoscelis papua) – showed high levels of genetic differentiation between the colonies. These penguins have a coastal lifestyle, they rarely swim into the open ocean but prefer to stay close to the shore. In addition Gentoo Penguins tend to breed where they were born (biologists call this natal philopatry). These characteristics result in low levels of gene flow between the colonies, leading to genetic differentiation.

gentoo-penguin-chick.jpg

Gentoo Penguins tend to breed where they were born (from: https://ocean.si.edu/)

 

Oceanographic Fronts

Apart from life history traits, environmental factors can also determine patterns of gene flow. The Antarctic Polar Front is the boundary between cold Antarctic waters and warmer sub-Antarctic waters. This front acts as a barrier to dispersal for several penguin species, which is reflected in the genetic patterns. For example, King Penguins from South Georgia (the only breeding colony south of the front in this study) were the most divergent even though they were not the most distant colony in this species. Penguins from distant colonies, such as Crozet and the Falkland Islands (about 7500 km apart) were genetically more similar each other than each colony was to the penguins on South Georgia.

king penguin.jpg

Close-up of a King Penguin (from: https://www.smithsonianmag.com/)

 

Ancient DNA

Another recent study, published in the journal Molecular Phylogenetics and Evolutionfocused on population dynamics of the genus Eudyptes in New Zealand. The ranges of these penguins have contracted over the years, possibly affecting their population sizes. Here, the researchers took a different approach. Instead of sequencing only contemporary populations, they obtained ancient mtDNA from several bone samples and compared the results with present-day penguins.

 

Genetic Diversity

Looking at the distribution of haplotypes over time revealed no loss of genetic diversity. Moreover, the reconstructed population history of one species, the Fiordland Crested Penguin (Eudyptes pachyrhynchus), indicated constant population size over the last millennium.  Despite range contractions, the penguin populations seems to be doing fine. The authors write that “importantly, in cases where populations are genetically well connected, range contractions do not necessarily result in substantially reduced population sizes and genetic diversity.”

1200114_MG_8355.JPG

The Fiordland Penguin does not seem to suffer from recent range contractions (from: http://nzbirdsonline.org.nz/)

 

Conservation of Penguins

Both studies provide important insights for penguin conservation. Pinpointing the barriers of dispersal can inform which populations are connected by gene flow and could potentially be managed as one unit. In addition, the use of ancient DNA can provide a perspective on the evolutionary history of population and how it has dealt with previous changes. Together these approaches can improve the way conservationists make decisions.

 

References

Clucas, G. V., Younger, J. L., Kao, D., Emmerson, L., Southwell, C., Wienecke, B., Rogers, A.D., Bost, C.-A., Miller, G.D., Polito, M.J., Lelliot, P., Handley, J., Crofts, S., Philips, R.A., Dunn, M.J., Miller, K.J. & Hart, T.  (2018). Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins. Molecular ecology, 27(23), 4680-4697.

Cole, T.L., Rawlence, N.J., Dussex, N., Ellenberg, U., Houston, D.M., Mattern, T., Miskelly, C.M., Morrison, K.W., Paul Scofield, R., Tennyson, A.J.D., Thompson, D.R., Wood, J.R., Waters, J.M. (2018) Ancient DNA of crested penguins: Testing for temporal genetic shifts in the world’ s most diverse penguin clade. Molecular Phylogenetics and Evolution.

 

Monophyletic Manakins? Not according to mtDNA…

Complex patterns of introgression between three Manakin species.

Gene trees are not species trees. When you construct an evolutionary tree for a particular gene, it might deviate from the actual species tree. This might sound like an annoyance (and it is for some scientists), but it also provides the opportunity to explore the evolutionary forces that underlie this incongruence. A recent study in Molecular Phylogenetics and Evolution shows how “wrong” gene trees can provide important insights.

 

Three Manakins

The relationships in the Manakin genus Lepidothrix remain poorly resolved. Particularly, the exact configuration of the following three species is still a matter of debate: Opal-crowned Manakin (L. iris), Snow-capped Manakin (L. nattereri), and Golden-crowned Manakin (L. vilasboasi). A phylogenetic study in 2013 reported Opal-crowned and Snow-capped Manakin as sister species. However, this analysis did not include specimens of Golden-crowned Manakin.

A recent genomic assessment of these three species revealed that Golden-crowned Manakin probably originated from hybridization between the other two species. In other words, it is a hybrid species (see here for a blog post about this particlar case, and here for hybrid speciation in general).

manakins.jpg

The three Manakins (drawings from http://www.hbw.com/)

 

Not Monophyletic

Cleyssian Dias and colleagues revisited this case and sequenced two mitochondrial and three nuclear genes. Analyses of these five markers revealed some striking patterns. Particularly, the Opal-crowned Manakin was polyphyletic, meaning that the specimens were scattered across the phylogeny. Some specimens (belonging to the subspecies iris) clustered with the some Snow-capped Manakins, while other specimens (belonging to the subspecies eucephala) grouped with Golden-crowned Manakin and the remaining Snow-capped Manakins.

 

Exchanging mtDNA

What could explain these peculiar patterns? A glance at the haplotype network for mitochondrial DNA might provide some clues.  You can see that the eucephala subspecies (blue) groups with Golden-crowned Manakin (orange), whereas the iris subspecies (pink) is closer to Snow-capped Manakin (green). You can also see some hints of blue in the green circles. So, the eucephala subspecies also shared DNA with the Snow-capped Manakin. These networks suggest pervasive introgression of mtDNA among these three species (similar patterns have been reported in Jacamars).

networks

Haplotype networks for two mitochondrial genes: (A) ND2 and (B) COI. Based on Dias et al. (2018) Molecular Phylogenetics and Evolution.

 

Sexual Selection?

What could cause this exchange of mtDNA? That question remains unanswered for the moment. It could be sex-biased dispersal (mtDNA is only passed on through the female lineage) or sexual selection at leks. Currently, there is no data on lek behavior of these species. It would be interesting to see what happens when male Manakins meet to battle it out. Here is already a taste of what might go down at these leks; have a look at this Red-capped Manakin (Ceratopipra mentalis).

 

References

Dias, C., de Araujo Lima, K., Araripe, J., Aleixo, A., Vallinoto, M., Sampaio, I., Schneider, H. & Senda do Rego, P. (2018) Mitochondrial introgression obscures phylogenetic relationships among manakins of the genus Lepidothrix (Aves: Pipridae). Molecular Phylogenetic and Evolution, 126:314-320.

This paper had been added to the Pipridae page.

Crossing the Atlantic: How the Glossy Ibis colonized North America and hybridized with the native White-faced Ibis

Genetic study uncovers gene flow patterns among three species of Ibis.

Six thousand kilometers. That is approximately the distance between Europe and North America. Quite a distance, but that didn’t stop the Glossy Ibis (Plegadis falcinellus) from crossing it. In the 1800s, this waterbird – which occurs in the Old World and Australia – managed to reach North America (either by flying there or by hitchhiking on a boat). The first record of this species was a specimen collected in New Jersey in May 1817. The Glossy Ibis is, however, not the first Plegadis species in North America. The White-faced Ibis (P. chihi) already roamed the American wetlands before the arrival of their close relative. But did the colonization of the Glossy Ibis result in hybridization and introgression with the native White-faced Ibis? A recent study in Molecular Ecology set out to answer this question.

Glossy_ibis.jpg

The Glossy Ibis crossed the Atlantic Ocean in the 1800s (from: http://www.wikipedia.com/)

 

Few Hybrid Reports

The first documentation of putative hybrids between Glossy and White-faced Ibis was reported in Oklahoma in 2002. Since then several other cases have been published (see here and here). The few and recent reports of hybrids are probably due to the difficulty of detecting hybrids between these morphologically similar species. Given the relative scarcity of hybrids, could there be genetic exchange between these species? To assess the possibility of introgression, Jessica Oswald, Michael Harvey and their colleagues sequenced ultraconserved elements (UCEs, read more about these markers here) of both species. In addition, they also included samples from the South American Puna Ibis (P. ridgwayi), the third member of this genus.

White-faced_Ibis.jpg

White-faced Ibis, the native Plegadis of North America (from: http://www.audubon.org/)

 

Gene Flow

The genetic analyses revealed introgression between Glossy and White-faced Ibis. Genes were primarily flowing from White-faced into Glossy Ibis. This pattern conforms with the expectations of a colonization model described by Currat et al. (2008) in which gene flow occurs from the local to the invading species. I have described the rationale behind this scenario in my PhD thesis: “Initially, the expanding species is outnumbered and is thus more likely to engage in heterospecific matings. As the expansion proceeds, the resident species and previously produced hybrids are engulfed by the expanding species, thereby overturning the numerical imbalance. Consequently, hybrids have a higher chance of backcrossing into members of the expanding species, resulting in a genetic wake of introgressed genes following the wave front of the expanding species.

Surprisingly, the analyses also pointed to introgression between Puna and White-faced Ibis. This signal is possibly due to recent contact or an older admixture event.

puna ibis.jpg

Puna Ibis, the third member of the Plegadis genus (from: http://www.wikipedia.com/)

 

Genomic Landscape

Although these three Ibis species look very similar, genetically they are clearly distinct. Genome scans revealed that divergence between the species is spread across the genome. This pattern contrasts with many other bird species where divergence is concentrated in specific genomic regions (see for example wood-warblers). However, this result could be due to the use of UCEs which only represent a small part of the genome. A whole genome analysis is needed to confirm these patterns of divergence.

 

References

Oswald, J.A., Harvey, M.G., Remsen, R.C.,  Foxworth, D.U., Dittmann, D.L. Cardiff, S.W. & Brumfield, R.T. (2019) Evolutionary dynamics of hybridization and introgression following the recent colonization of Glossy Ibis (Aves: Plegadis falcinellus) into the New World. Molecular Ecology

 

This paper has been added to the Pelecaniformes page.

 

Hybridization with Painted Stork threatens the already endangered Milky Stork

Genetic study assesses the amount genetic mixture between both species.

Hybridization can lead to extinction. When an endangered species hybridizes with a closely related species, it might get absorbed into that species. There are several examples of rare bird species being threatened by hybridization, such as the Chinese Crested Tern (Thalasseus bernsteini) and Golden-winged Warbler (Vermivora chrysoptera). A recent study in the journal Biological Conservation assessed the situation of the endangered Milky Stork (Mycteria cinerea) in Singapore.

milky stork.jpg

Milky Stork (from: http://www.hbw.com/)

 

Endangered

The Milky Stork occurs in coastal mangroves, mudflats and estuaries across Southeast Asia. There are currently about 1500 wild individuals left and the population is declining due to hunting and habitat destruction. In addition, Milky Storks might be interbreeding with their sister species, the Painted Stork (M. leucocephala). This adds another problem to the already precarious situation of this endangered species.

 

Captive Hybrids

In the Malay Peninsula, Milky Storks have been held in captivity since the 1980s. Unintentionally, hybridization with Painted Stork occurred in these captive populations. A few hybrids escaped into the wild and have possibly interbred with wild birds. To quantify the influence of hybridization on the wild Milky Stork populations, Pratibha Baveja (National University of Singapore) and her colleagues genotyped several individuals using RADseq. The results are worrisome.

painted stork.jpg

Painted Stork (from: http://www.wikipedia.com/)

 

Pure Species?

The researchers write that “the majority of sampled individuals carried a signature of different degrees of introgression from Painted Storks.” In other words, hybrids have become an integral part of the wild Milky Stork populations. The genetic analyses revealed 18 “pure” Milky Storks and 3 “pure” Painted Storks. The remaining 25 individuals had different proportions of genetic material from both species.

The genomic transition from Milky Stork to Painted Stork is mirrored by morphological traits, such as the presence of pink wing coverts (a trait of Painted Stork). These morphological cues can help detect and remove hybrid individuals from the population. And this removal has to happen quickly, because the authors conclude that “the genomic composition of the Milky Storks in Singapore is highly compromised by hybridization, and immediate conservation action is warranted.”

admxiture stork

Genomic transition from Milky Stork (blue) to Painted Stork (red). Hybrids have different proportions of genetic material from both species. Pictures show morphological variation of several individuals (from Baveja et al., 2019 Biological Conservation)

 

References

Baveja, P., Tang, Q., Lee, J.G.H. & Rheindt, F. (2019) Impact of genomic leakage on the conservation of endangered Milky Stork. Biological Conservation, 229:59-66.

 

This paper has been added to the Ciconiiformes page.

 

 

Doing it in the Dark: Hybridization in Bats

Two studies explore possible hybridization events in bats.

Hybrid bats. It could be the title of a horror movie, but it is actually serious science. Two recent papers explored the genetics of several bat species to figure out whether there is (or has been) any hybridization. The findings were not too bat…

bat.jpg

A Natterer’s Bat (from: https://www.nederlandsesoorten.nl/)

 

Bat Complex

The first paper appeared in the Journal of Biogeography. Emrah Çoraman and his colleagues focused on the Natterer’s bat (Myotis nattereri) complex, which is distributed in Northwest Africa, Europe and parts of the Middle East. Based on one mitochondrial and four nuclear markers, the researchers reconstructed the evolutionary history of this bat complex. The analyses revealed four main groups. Let’s have a look at them. The colors in the text correspond to the figure below.

 

Four Lineages

A central lineage (yellow), ranging from Ireland to Ukraine, probably survived the last glacial period in three refugia: western Balkans, Greece and western Anatolia. After the ice ages, these populations expanded into Europe. We find the second lineage (blue) in Italy. Here, there are two separate groups: one in northern Italy and one in southern Italy. They meet and probably hybridize in the central Appenine Mountains. The third lineage (green) houses bats from the Iberian Peninsula and Northern Africa. Finally, the fourth lineage (reddish brown) represents the lesser known eastern part of the distribution. This lineage is comprised of four subgroups, which have an interesting history that we will explore in more detail.

bat phylogeny.jpg

The (a) evolutionary history and (b) distribution of the Myotis nattereri complex (from Çoraman et al. 2018 Journal of Biogeography)

 

Hybridization Events

As you can see in the figure above, the evolutionary history of this bat complex is quite…well…complex. It involves several hybridization events, resulting in a reticulated phylogeny. For example, there has been gene flow between the blue and yellow lineages. Probably, the blue lineage expanded out of Italy and come into contact with the yellow one.

Another hybridization event occurred in the eastern part. Expanding population first came into contact with the local lineage in Anatolia. They acquired the mtDNA from this lineage and continued their expansion to Israel where they obtained mtDNA from the resident populations. Interestingly, the Israeli populations went extinct but their genes live on in another species.

 

Cryptic Species

The second paper – in the journal Ecology and Evolution – delved into the genetics of three cryptic species of long‐eared bats (Plecotus auritus, P. austriacus, and P. macrobullaris). Cryptic species are reproductively isolated, but morphologically they are identical. Tommy Andriollo and his colleagues postulated that the extensive phenotypic overlap and observation of morphologically intermediate individuals may hide rampant hybridization. To test this idea, they sampled 349 individuals and genotyped them with a mitochondrial marker and microsatellites. Surprisingly, no sign of hybridization was detected suggesting that these three species are biologically separated. Hybridization is a common phenomenon, but that doesn’t mean you will always find it.

Plecotus auritus.jpg

A Brown Long-eared Bat (from: http://www.freenatureimages.eu/)

 

References

Andriollo, T., Ashrafi, S., Arlettaz, R. & Ruedi, M. (2019) Porous barriers? Assessment of gene flow within and among sympatric long‐eared bat species. Ecology and Evolution, 8(24):ece3.4714.

Çoraman, E., Dietz, C., Hempel, E., Ghazaryan, A., Levin, E., Presetnik, P., Zagmajster, M & Mayer, F. (2019) Reticulate evolutionary history of a Western Palearctic Bat Complex explained by multiple mtDNA introgressions in secondary contact. Journal of Biogeography, 46:343-354.

A Little Brown Job: Unraveling the Chiffchaff complex

Genetic study clarifies relationships between different subspecies of the Common Chiffchaff.

LBJ. Bird watchers will know what this abbreviation stands for: Little Brown Job. It refers to the large number of small brown passerines that are difficult to distinguish. A nice example of a LBJ is the “Chiffchaff complex”. This collection of small birds used to be considered one species, but detailed studies – based on genetics, acoustics and morphology – revealed the presence of four species: Common Chiffchaff (Phylloscopus collybita), Iberian Chiffchaff (P. ibericus), Mountain Chiffchaff (P. sindianus) and Canary Islands Chiffchaff (P. canariensis). In addition, these species can be divided into several subspecies. As the name already implied, the situation is quite complex. A recent study in the journal PLoS One tried to unravel the complicated relationships in this group of birds.

canary islands

The Canary Islands Chiffchaff (from: http://www.wikipedia.com/)

 

Two Genes

Marko Rakovic and his colleagues sampled across the range of the Chiffchaff complex, from western Europe to Siberia. Next, they sequenced two genes (the mitochondrial ND2 and the Z-linked ACO1I9). Analyses of these markers confirmed the delineation of the four recognized species.

However, some Z-linked alleles were shared between Common Chiffchaff and Canary Islands Chiffchaff. Moreover, based on the ND2-gene, one individual from the Canary Islands was located within the Common Chiffchaff group (see orange group in the figure below). Could it be that these species occasionally hybridize?

journal.pone.0210268.g003.PNG

Relationships within the Chiffchaff complex based on the ND2-gene. All four species form separate clades (from: Rakovic et al. 2019 PLoS One).

 

Common Subspecies

Let’s have a closer look at the patterns within these Common Chiffchaff. This species is generally divided into several subspecies:

  • collybita
  • abientus
  • tristis
  • brevirostris
  • caucasicus
  • menzbieri

Based on the mitochondrial ND2-gene, all these subspecies form distinct clades. However, this was not the case for the other genetic marker. Genetic variation is shared between the subspecies abientus and collybita, which are known to hybridize in Sweden (see for example Hansson et al. 2000). The data did not reveal hybridization between abientus and tristis, altough recently a hybrid zone was discovered in the Urals (see for example Shipilina et al. 2017 and this blog post).

common chiffchaff

The Common Chiffchaff (from: http://www.wikipedia.com/)

 

Southern Chiffchaffs

Less is known about the southern subspecies of the Common Chiffchaff. The Anatolian Peninsula of Turkey houses brevirostris, while caucasicus breeds more to the east in Armenia. Finally, menzbieri is known from eastern Iran and the border with Turkmenistan. The genetic analyses clustered brevirostris and caucasicus. In the eastern part of their range, they might hybridize with menzbieri.

map

Distribution of the Common Chiffchaff subspecies. Notice the overlap between the brevirostris/caucasicus group (light blue) and the mezbieri subspecies (dark blue). The size of the pie charts indicates the sample size (from: Rakovic et al. 2019 PLoS One).

 

Another Subspecies?

The researchers also sampled in a region that is normally not included in the distribution of the Common Chiffchaff: Mount Hermon (situated near the border between Lebanon and Syria). This population turned out to be a mix of brevirostris, caucasicus and colybita. Probably these birds use Mount Hermon as a wintering area. Interestingly, this population also contained alleles that were not present in any of the other subspecies. Perhaps this population might represent a yet unnamed taxon. Things just got a bit more complex again…

 

References

Rakovic, M., Neto, J.M., Lopes, R.J., Koblik, E.A., Fadeev, I.V., Lohman, Y.V., Aghayan, S.A., Boano, G., Pavia, M., Periman, Y., Kiat, Y., Ben Dov, A., Collinson, J.M., Voelker, G. & Drovetski, S.V. (2019) Geographic patterns of mtDNA and Z-linked sequence variation in the Common Chiffchaff and the ‘chiffchaff complex’. PLoS One 14(1):e0210268.

 

This paper has been added to the Phylloscopidae page.

Scientific Sherlocks: The Case of the Imperial Pheasant

How scientists figured out the origin of this mysterious bird.

In 1923, Jean Delacour stumbled upon a pair of captive pheasants during a trip in Vietnam. Unknown to science, these birds were shipped to Delacour’s estate in France where they reproduced. The species was named Imperial Pheasant (Lophura imperialis). After this discovery, several ornithologists set out to observe them in the wild, but failed. There was no sign of this peculiar bird species. Until 1990, when a bird was trapped in a lowland forest. About 10 years later, another individual was found. Only four specimens observed in nearly 100 years time, this must be a critically endangered species! Or is there something else going on here?

The Imperial Pheasant, an extremely rare species?

The Imperial Pheasant, an extremely rare species?

 

Gathering Evidence

A interesting hypothesis was raised in 1997, what if the Imperial Pheasant was a hybrid between Silver Pheasant (L. nycthemera) and Edwards’ Pheasant (L. edwardsi), two species that co-occur in Vietnam? This idea was tested following three lines of inquiry: morphology, experiments and genetic analyses.

All known museum specimens of the Imperial Pheasant and numerous photographs were gathered. Alain Hennache started a hybridization experiment at the Zoological Park of Clères in France (nice detail: Delacour’s former estate). And Ettore Randi took care of the genetic analyses.

Silver Pheasant (above) and Edwards'  Pheasant

Silver Pheasant (above) and Edwards’ Pheasant

 

Captivating Consilience

All studies pointed towards a hybrid origin of the Imperial Pheasant. The museum specimens were intermediate in size between Silver Pheasant and Edwards’ Pheasant. Similarly, the hybridization experiment produced Imperial Pheasant-like birds that closely matched the original descriptions by Delacour. Finally, the genetic analyses showed that the Imperial Pheasant shared alleles (i.e., particular versions of genes) with its hypothesized parent species. The conclusion was clear: the Imperial Pheasant is not a species, but a hybrid of Silver Pheasant and Edwards’  Pheasant.

This beautiful study also exemplifies a characteristic of evolutionary theory, namely consilience of evidence. The principle that evidence from independent, unrelated sources leads to the same conclusions. In evolution, many disciplines (e.g., paleontology, genetics, morphology, embryology, biogeography, …) support the idea that life has evolved. Doubting this would just be silly….

 

References

Hennache, A., Rasmussen, P., Lucchini, V., Rimondi, S. & Randi, E. (2003). Hybrid origin of the imperial pheasant Lophura imperialis (Delacour and Jabouille, 1924) demonstrated by morphology, hybrid experiments, and DNA analyses Biological Journal of the Linnean Society, 80 (4), 573-600 DOI: 10.1111/j.1095-8312.2003.00251.x