A taxonomic riddle: Where does the extinct Canary Islands Oystercatcher fit in?

Which living species is the closest relative of this extinct species?

The Canary Islands used to have their very own Oystercatchers. Members of this species (Haematopus meadewaldoi) has glossy black plumage with the exception of white patches on the wings. It closely resembled the African Oystercatcher (H. moquini), but the exact taxonomic position of the Canary Islands Oystercatcher remained a mystery. Recently, Tereza Senfeld and her colleagues sequenced the DNA of several Canary Islands Oystercatchers and compared it with the extant species. Their findings appeared in the journal Ibis.

Canarian_Oystercatcher

The Canary Islands Oystercatcher. Artwork by Henrik Gronvold (1858–1940) | Wikimedia Commons

 

Eight Specimens

Canary Islands Oystercatcher probably went extinct around 1940 (although it was officially declared extinct in 1994). The drivers of this extinction event are difficult to infer, but it was probably a combination of habitat disturbances and human activities (e.g., hunting by humans and predation by introduced rats and cats). Currently, there are eight specimens left: three at the Natural History Museum in Tring (UK), two at the Zoological Research Museum Alexander Koenig in Bonn (Germany), one at the Liverpool World Museum (UK) and two at the Manchester Museum (UK). The researchers managed to extract DNA from the specimens in Tring, Liverpool and Manchester.

 

Haematopus_ostralegus.jpg

Could the Canary Islands Oystercatcher be related to the Eurasian Oystercatcher? © Richard Bartz | Wikimedia Commons

 

Subspecies?

Analyses of several mitochondrial genes revealed that the Canary Islands Oystercatcher clustered with the Eurasian Oystercatcher (H. ostralegus). Despite its similarity to the African Oystercatcher, it is thus more closely related to the Eurasian Oystercatcher. The authors suggest that it might represent a local melanistic subspecies of the Eurasian Oystercatcher.

Another possibility is that the mitochondrial similarity between the Canary Islands and Eurasian Oystercatcher is due to hybridization. Perhaps the birds on the Canary Islands were an offshoot of the African Oystercatcher but obtained mitochondrial DNA after interbreeding with some visitors from Europe? Genomic analyses are needed to explore this scenario.

oc_tree

Based on mtDNA, the Canary Island Oystercatcher (H. meadewaldoi) clusters with the Eurasian Oystercatcher (H. ostralegus). From: Senfeld et al. (2019) Ibis

 

Mystery Bird

After figuring out the taxonomic position of the Canary Islands Oystercatcher, the researchers turned their attention to a mystery bird in the Tring collection. Specimen NMHUK.1938.11.15.1 was captured in Gambia in 1938. It was transported to the UK where it lived in captivity for several years. Due to artificial feeding, it developed an abnormally long beak. Beak morphology is an important trait to identify Oystercatcher species, so it became impossible to determine the species identity of this specimen. The black plumage of this bird suggests that it might be the last known Canary Islands Oystercatcher. However, DNA analyses showed that it concerns a vagrant African Oystercatcher, about 4500 kilometers outside of its range. Still a significant finding, but not as exciting as finding the last Canary Islands Oystercatcher. Perhaps it is still out there?

African_Black_Oystercatcher

The mystery bird turned out to be a vagrant African Oystercatcher. © Dick Daniels | Wikimedia Commons

 

References

Senfeld, T., Shannon, T. J., van Grouw, H., Paijmans, D. M., Tavares, E. S., Baker, A. J., Lees, A. C. & Collinson, J. M. (2019). Taxonomic status of the extinct Canary Islands Oystercatcher Haematopus meadewaldoi. Ibis. Early View.

A lesson in cladistics with the Plain-brown Woodcreeper

Genetic study indicates that the Plain-brown Woodcreeper is paraphyletic.

Every taxonomist enjoys a nice monophyletic group. Paraphyletic or polyphyletic groupings are best avoided. But what do these terms actually mean? We owe this wonderful terminology to the German entomologist Willi Hennig who published the book Phylogenetic Systematics. This book introduced cladistics, a new method to classify organisms based on their morphological differences and similarities. Cladistics came with a whole suite of new tong-twisting term, such as symplesiomorphy and autapomorphy. But let’s focus on the phyletic terms for now.

 

Cladistics for Dummies

The evolutionary relationships between different organisms can be depicted in a cladogram. The endpoints of a cladogram – the twigs if you will – correspond to living species, whereas the nodes represent extinct ancestors. A group of organisms (several twigs) is called a clade. A monophyletic clade comprises an ancestor and all of its descendants. For instance, in figure a, species D, E, G and H can be traced back to a common ancestor B.

We could decided to cluster species E and G (see figure b), but then we would create a so-called polyphyletic group. These species originate from different ancestors (C and F) that are not included in the group. We could also cluster species J and K (see figure c), but now we ignore the many descendants of their common ancestor (A). The result is a paraphyletic group.

phyletics

Examples of the different types of groupings in cladistics.

 

Fish do not exist

A famous example of a non-monophyletic group concerns fish. They share a common ancestor with all other vertebrates. By excluding these vertebrates from the fish-group, we are creating a group that does not include all descendants of this common ancestor. In other words, fish are paraphyletic. Technically, fish do not exist.

An example of a polyphyletic group can be found in the bible where birds and bats were grouped together: “These are the birds you are to regard as unclean and not eat because they are unclean: the eagle, the vulture, the black vulture, the red kite, any kind of black kite, any kind of raven, the horned owl, the screech owl, the gull, any kind of hawk, the little owl, the cormorant, the great owl, the white owl, the desert owl, the osprey, the stork, any kind of heron, the hoopoe and the bat (Leviticus 11:13-19).” A clear sign that the bible is not a science book…

paraphyletic_fish.png

Fish as paraphyletic and do technically not exist…

 

Woodcreepers

But let’s focus on birds (this is after all a blog about our feathered friends). A recent study in the journal Molecular Phylogenetics and Evolution reconstructed the evolutionary history of the Plain-brown Woodcreeper (Dendrocincla fuliginosa), which has been divided into 12 subspecies. Eduardo Schultz and his colleagues assessed the relationships between these subspecies using genetic data from over 200 individuals.

woodcreeper.jpg

The Plain-brown Woodcreeper (Dendrocincla fuliginosa) © Gail Hampshire | Flickr

 

Non-monophyletic

The genetic analyses revealed that two other species are embedded with the Plain-brown Woodcreeper, namely the Tawny-winged Woodcreeper (D. anabatina) and the Plain-winged Woodcreeper (D. turdina). This phylogenetic result renders the Plain-brown Woodcreeper paraphyletic because it does not include all descendants of the common ancestor. A possible solution is to elevate some subspecies to the species level, creating several monophyletic groups.

woodcreeper_tree

The Plain-brown Woodcreeper is paraphyletic due to the position of the Tawny-winged Woodcreeper (D. anabatina, top) and the Plain-winged Woodcreeper (D. turdina, bottom). From: Schultz et al. (2019) Molecular Phylogenetics and Evolution

 

Hybrids

The study also mentioned some possible hybridization events. The observation of a individual of the subspecies rufoolivacea within the range of the subspecies fuliginosa suggests ongoing gene flow. But this will need to be confirmed with denser sampling in that region.

Interestingly, rufoolivacea is known to interbreed with another subspecies (atrirostris). The paper describing this situation speculated that the hybrid zone originated because Amazonian rivers (Tapajos and Teles-Pires) split an ancestral population in two (a so-called vicariant event). However, the current study indicates that rufoolivacea and atrirostris are not each others closest relatives, suggesting that they established secondary contact due to changes in their distribution. No need for a vicariant event.

 

References

Schultz, E. D., Pérez-Emán, J., Aleixo, A., Miyaki, C. Y., Brumfield, R. T., Cracraft, J., & Ribas, C. C. (2019). Diversification history in the Dendrocincla fuliginosa complex (Aves: Dendrocolaptidae): Insights from broad geographic sampling. Molecular Phylogenetics and Evolution 140,106581.

Weir, J. T., Faccio, M. S., Pulido-Santacruz, P., Barrera-Guzman, A. O. & Aleixo, A. (2015). Hybridization in headwater regions, and the role of rivers as drivers of speciation in Amazonian birds. Evolution 69, 1823-1834.

Unraveling the origin of the Visorbearers

Did they originate by vicariant events or due to extinction of related lineages?

Hybrid hummingbirds are relatively common. Gary Graves has described numerous hybrid species combinations (see here for an overview). The widespread occurrence of hybridization – and possibly gene flow – complicates the taxonomic work on hummingbirds. In some cases, such as the Visorbearers (genus Augastes), the taxonomy is even complicated without hybridization. This genus houses two species: the Hyacinth Visorbearer (A. scutatus) and the Hooded Visorbearer (A. lumachella). They are probably closely related to the genus Schistes, but this remains to be confirmed. A recent study in the journal Ibis reconstructed the evolutionary history of the Visorbearers to settle this taxonomic issue.

Hooded_Visorbearer.jpg

The Hooded Visorbearer (Augastes lumachella) © Joao Quental | Flickr

 

Two Hypotheses

In addition to the mystery of the closest relative of the Visorbearers, their evolutionary history is still unclear. Two hypotheses have been put forward to explain the origin of these hummingbirds. Silva (1995) proposed that genus used to be widespread across South America, but that extinction of several ancestral lineages during the Pleistocene (less than 2 million years ago) resulted in the current two species. An alternative scenario was put forward by Vasconcelos and colleagues (2012): they envisioned that a barrier arose in Brazil, separating the two Augastes species.

Augastes_scutatus.jpg

The Hyacinth Visorbearer (Augastes scutatus) © Norton Defeis | Wikimedia Commons

 

Divergence Times

To figure out which scenario is more likely, Anderson Chaves and his colleagues sequenced several mitochondrial and nuclear genes to reconstruct the evolutionary history of the Visorbearers. The analyses confirmed the idea that these hummingbirds are closely related to the genus Schistes. Moreover, the researchers managed to date the divergence events: the genera Schistes and Augastes split about 7.34 million years ago, and the two Visorbearer species went their separate ways around 3.2 million years ago.

The latter divergence time is more consistent with the vicariance-hypothesis of Vasconcelos and colleagues. The timing corresponds to the uplift of the Brazilian plateau which may have resulted in distinct climatic conditions. The ancestral lineages probably adapted to the different climates and diverged into different species.

ibi12777-fig-0002-m.jpg

The phylogenetic relationships between Visorbearers (genus Augastes) and other hummingbirds. From: Chaves et al. (2019) Ibis

 

References

Chaves, A. V., Vasconcelos, M. F., Freitas, G. H., & Santos, F. R. (2019). Vicariant events in the montane hummingbird genera Augastes and Schistes in South America. Ibis. Early View.

Silva, J.M.C. 1995Biogeographic analysis of the South American Cerrado avifaunaSteenstrupia 2149– 67.

Vasconcelos, M.F.Chaves, A.V. & Santos, F.R. 2012First record of Augastes scutatus for Bahia refines the location of a purported barrier promoting speciation in the Espinhaço RangeBrazil. Rev. Bras. Ornitol. 20443– 446.

White-throated Sparrows influence gene expression in their offspring

Less parental care leads to an increased stress response in the nestlings.

Parents have a profound impact on the development of their offspring. In birds, the mother directly influences the condition of the offspring by adding particular hormones to the egg. Also, the location of the nest and the incubation schedules of the parents impact consequent egg development. Once the chicks crawl out of the egg, the feeding behavior of the parents determines the amount of stress the young birds experience. Not only will they have to compete with their siblings, they might also experience anxiety when left alone for too long. All in all, the parents cause a certain amount of stress on their offspring which affects their future development. A recent study in the journal Molecular Ecology investigated the effect of parental behavior on the stress experienced by young White-throated Sparrows (Zonotrichia albicollis).

white-throated-sparrows

An super-gene in the White-throated Sparrow genome results in two morphs: white-striped and tan-striped (from: https://www.northcountrypublicradio.org/).

 

Super-gene

The researchers choose White-throated Sparrows for a reason: these passerines show peculiar behavioral differences due to a genetic phenomenon. White-throated Sparrows come in two morphs: tan and white. These morphs are determined by a large super-gene (an inversion to be more specific, you can read more about it in this blog post). Tan morphs have the same version of the super-gene (i.e. they are homozygous) whereas white morphs have two different versions (i.e. they are heterozygous).

This super-gene contains more than 1000 genes that influence the morphology and behavior of the birds. White-morph males are promiscuous and provide little parental care. Tan-morph males, however, are great partners: they defend their nest and take care of their offspring. Compared to the male morphs, females typically provide intermediate care.

Interestingly, birds tend to prefer the opposite morph. This results in two pair types in terms of parental care. A white-morph male and a tan-morph female (W x T) will provide female-biased care. A tan-morph male and a white-morph female (T x W) will provide biparental care. Are you still with me?

wts.jpg

The different morphs of the White-throated Sparrow (A and B) prefer to mate with the opposite morph (see percentages in C). The differences between the morphs can be traced back to a super-gene (D). From: Campagna (2016) Current Biology

 

Stress

Daniel Newhouse and his colleagues took advantage of this situation to explore the effects of differential parental care on the offspring. They focused on patterns of gene expression in 32 nestlings. The analyses revealed 881 genes that were differentially expressed between the pair types. Detailed analyses of these genes revealed that nestlings raised by W x T pairs (female-biased care) expressed more stress-related genes than nestlings raised by T x W pairs (biparental care).

This finding raises another question: which mechanism is responsible for the differences in genes expression? Do females of different morphs deposit different amounts of hormones in the eggs? Or does the parental care influence gene expression? The authors argue that “the difference in parental provisioning is the most plausible explanation.” But – as always – more research is needed to confirm this idea.

 

References

Campagna, L. (2016). Supergenes: the genomic architecture of a bird with four sexes. Current Biology, 26(3): R105-R107.

Newhouse, D. J., Barcelo-Serra, M., Tuttle, E. M., Gonser, R. A., & Balakrishnan, C. N. (2019). Parent and offspring genotypes influence gene expression in early life. Molecular Ecology, 28: 4166-4180.

Taking advantage of hybridization to find a migration gene in warblers

A genetic study of Golden-winged and Blue-winged Warbler reveals the gene underlying their migration direction.

Every evolutionary biologist dreams of finding that one gene underlying a particular trait under selection. For example, extensive work on the Threespine Stickleback (Gasterosteus aculeatus) uncovered the genetic basis of armor-plating: marine forms of this fish are heavily armored while lake populations are not (probably because of the absence of predators). Stickleback in lakes have repeatedly lost pelvic hindfins, which is due to recurrent deletions of a pelvic enhancer of the Pitx1 gene. Mostly, however, things are not that straightforward. Human height, for instance, is determined by numerous genes of small effect instead one single candidate gene. A recent study in the journal PNAS attempted to find the genetic basis of another complex trait: the direction of bird migration.

Golden-winged_Warbler

Looking for the genes underlying migration in the Golden-winged Warbler © Bettina Arrigoni | Wikimedia Commons

 

Genomic Regions

Several studies have tried to pinpoint the genes underlying migratory behavior in birds. In the Swainson’s Thrush (Catharus ustulatus), researchers found a region on chromosome 4 that is strongly associated with the direction of migration. And a study on the Willow Warbler (Phylloscopus trochilus) uncovered three genomic regions – on chromosomes 1, 3 and 5 – that corresponded to different migratory strategies (see also this blog post). In both cases, large genomic regions, containing hundreds of genes, were identified. Certainly a step in the right direction, but there is still a long way to go.

David Toews and his colleagues focused on another study system: the Golden-winged (Vermivora chrysoptera) and the Blue-winged Warbler (V. cyanoptera). These species were chosen for a reason: due to extensive hybridization, their genomes are largely undifferentiated (mainly “plumage genes” seem to be different). This lack of genetic differentiation makes it easier to find genes related to migration. Compare it to finding a needle in a very small haystack.

 

Z-chromosome

Both species breed in North America and winter in two particular regions: South America (mainly Venezuela) and Central America (Panama to Guatemala). By linking these migration strategies to genomic sequences, the researchers attempted to find the genetic basis of migration. And they did: the analyses converged on a small region (120,000 base pairs) on the Z-chromosome. This region showed reduced genetic diversity in warblers migrating to South America and Tajima’s D (a statistic to identify selective processes) was also much lower in these birds.

This region contained only one gene: VPS13A. The function of this gene in birds is not known, but recent work showed that it is associated with mitochondria. The researchers speculate that “selection on VPS13A may enhance the capacity in SA wintering birds to more efficiently remove reactive oxygen species resulting from a prolonged migration.”

warbler_migration

The genomic region underlying migration direction in Golden-winged and Blue-winged Warbler. (A) The highly differentiated region on the Z-chromosome is highlighted with the arrow. (B) This region (marked in grey) has a low Tajima’s D (suggesting selection) and (C) contain one gene: VPS13A. From: Toews et al. (2019) PNAS.

 

Go Hybrids!

This study shows the importance of choosing the right study system to answer your research question. The undifferentiated genomes of these warblers provided the perfect background to find genes related to migration. And it also highlights the importance of hybrids: if Golden-winged and Blue-winged Warbler did not hybridize, their genomes might have been too diverged to easily find migration genes. Do not underestimate the power of hybridization!

 

References

Delmore, K. E., Toews, D. P., Germain, R. R., Owens, G. L., & Irwin, D. E. (2016). The genetics of seasonal migration and plumage color. Current Biology26(16), 2167-2173.

Lello, L., Avery, S. G., Tellier, L., Vazquez, A. I., de los Campos, G., & Hsu, S. D. (2018). Accurate genomic prediction of human height. Genetics210(2), 477-497.

Lundberg M, Liedvogel M, Larson K, Sigeman H, Grahn M, Wright A, Åkesson S, Bensch S 2017. Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks. Evolution Letters 1: 155-168.

Toews, D. P., Taylor, S. A., Streby, H. M., Kramer, G. R., & Lovette, I. J. (2019). Selection on VPS13A linked to migration in a songbird. Proceedings of the National Academy of Sciences, 116(37), 18272-18274.

Xie, K. T. et al. (2019). DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science363(6422), 81-84.

Songbirds have an extra chromosome in their germline

A recent study tried to figure out what this chromosome actually does…

Yesterday, you could read about the crazy sex-chromosomes of larks. It turned out that the sex-chromosomes of these birds consists of parts from several other chromosomes. Weird… A recent study in the journal Nature Communications revealed another chromosomal conundrum in songbirds: the so-called germline restricted chromosome (or GRC for friends). Let’s get acquainted.

Taeniopygia_guttata

What mysteries does the GRC of this Zebra Finch (Taeniopygia guttata) hold? © Peripitus | Wikimedia Commons

 

An Accessory Chromosome

The story of the GRC starts with two researchers investigating the karyotype of the Zebra Finch (Taeniopygia guttata). In the germline (i.e. cells in the testes and ovaries) of this bird, they found a big “accessory” chromosome. Surprisingly, in the rest of the body cells – the so-called soma – this chromosome was absent. Further investigations revealed that, in males, it is eliminated during the formation of sperm cells. In females, however, the chromosome is passed on to the offspring but gets eliminated in soma-cells. Good riddance, chromosome! Because this extra chromosome only resides in the germline, it was dubbed germline-restricted chromosome (GRC).

GRC_karyotype

The karyotypes seven biggest chromosomes and sex chromosomes (ZW) of Zebra Finch for (a) female soma, (b) male some, and (c) male germline. The big germline-restricted chromosome (GRC) is highlighted with the arrow. From: Pigozzi & Solari (1998) Chromosome Research

 

Which Genes?

The presence of the GRC raises a lot of questions. First of all, what kind of genes are on this chromosome? The researchers of the recent study predicted that the GRC would be enriched in repetitive elements, a kind of wastebasket for harmful “genetic parasites”. Surprisingly, the GRC contained numerous genes from other chromosomes (i.e. paralogs). Using a clever combination of the latest genome-sequencing techniques and some bioinformatic wizardry, they succeeded in pinpointing 115 high-confidence GRC-linked genes. These genes were copied to the GRC from 19 chromosomes (18 autosomes and the Z-chromosome).

GRC_chromosomes.jpg

The GRC contains gene from numerous other chromosomes. From: Kinsella, Ruiz-Ruano et al. (2019) Nature Communications

 

Expressed Genes?

The presence of these genes does not necessarily mean that they are actively used. Perhaps the GRC is a reservoir for decaying pseudogenes? To infer whether these genes are active, the researchers turned to transcriptomic (RNA) and proteomic (proteins) data. These analyses revealed that at least 6 genes were expressed in testes and 32 in ovaries. Because some GRC-genes are (almost) identical to their paralogs on other chromosomes, the researchers could not distinguish between them. Thus, there might be more active GRC-genes.

The divergence between some GRC-genes and their paralogs already indicates that different genes were copied to the GRC at different times. By comparing the DNA-sequence of GRC-genes and paralogs, we can deduce how the GRC changed over time. Some genes, such as bicc1 and trim71, were early additions during the diversification of songsbirds (more than 25 million years ago). Other genes were recently added to the mix. The figure below gives a nice overview of the gradual accumulation of genes on the GRC.

GRC_tree.jpg

The GRC captured different genes during its evolutionary history. From: Kinsella, Ruiz-Ruano et al. (2019) Nature Communications

 

What does it do?

The GRC is not restricted to the Zebra Finch. A recent study in PNAS found this chromosome in 15 other songbirds, suggesting that it plays an important role in the germline of these species. The presence of several germline developmental genes indicates that it might act as a germline-determining chromosome. The authors also speculate that “a GRC may allow adaptation to germline-specific functions free of detrimental effects on soma.” In other words, the GRC could prevent conflicts between germline and soma.

Finally, the observation of several species-specific genes on the GRC supports the idea that it might contribute to reproductive isolation during the formation of new species. Could the GRC explain the massive diversification of songbirds?

 

References

Kinsella, C.M., Ruiz-Ruano, F.J., et al. (2019) Programmed DNA elimination of germline development genes in songbirds. Nature Communications, 10:5468.

Pigozzi, M. I., & Solari, A. J. (1998). Germ cell restriction and regular transmission of an accessory chromosome that mimics a sex body in the zebra finch, Taeniopygia guttataChromosome Research, 6(2):105-113.

Torgasheva, A. A. et al. (2019). Germline-restricted chromosome (GRC) is widespread among songbirds. Proceedings of the National Academy of Sciences116(24), 11845-11850.

The crazy sex-chromosomes of the Larks

The largest sex-chromosome found in birds consists of parts from several other chromosomes.

Let’s talk about sex. To be more specific, let’s talk about sex chromosomes. Most people are familiar with the human system of sex-determination: if you have two X-chromosomes, you are female; and if you have an X and a Y-chromosome, you are male. In birds, the situation is slightly different. Males have two Z-chromosomes, whereas females have a Z and a W chromosome. However, a recent study on larks in the Proceedings of the Royal Society B shows that things are not always that straightforward.

Horned_lark

What happened with the sex-chromosomes of this Horned Lark (Eremophila alpestris)? © Tom Koerner | Wikimedia Commons

 

Evolution of sex-chromosomes

The sex-determining locus

Before we delve into the findings of that study, we first need to understand the evolution of sex-chromosomes. Who are they? Where do they come from? What drives them? It mostly starts with one genetic locus: the sex-determining locus. Most mammals carry the gene SRY (sex-determining region Y) on the Y-chromosome which is responsible for the start of male sex-determination. In birds, the gene DMRT1 (Doublesex and mab-3 related transcription factor 1) seems to be an important player. Sex chromosomes initially arise when a standard chromosome (i.e. an autosome) acquires a sex-determining gene.

 

Suppression of recombination

Next, recombination is suppressed around this gene. Recombination occurs during meiosis when homologous chromosomes line up and exchange sections of themselves. This genetic exchange results in new combinations of genetic variants that evolution can work with. The suppression of recombination between a pair of chromosomes allows them the become different from each other. This explains why the X and Y chromosome look so distinct.

Why did recombination become suppressed? The main hypothesis calls upon sexually antagonistic alleles: genetic variants that are under different selection pressures in males and females. For example, a particular variant might be beneficial in males but detrimental in females. By residing close to the sex-determining locus, these genes end up on different chromosomes and eventually spend most of their time in the sex they benefit.

As more and more sexually antagonistic alleles accumulate around the sex-determining locus, larger sections of the chromosome stop recombining. This recurring process gives rise to “evolutionary strata” on the sex-chromosome that started diverging at different time points.

 

Degeneration of sex chromosomes

Finally, the sex chromosomes stop recombining altogether, mostly leading to rapid degeneration of one chromosome. In humans, this happened to the Y-chromosome, while in birds, the W-chromosome is degenerating. Eventually, these chromosomes can disappear completely. The figure below gives a nice overview of the evolution of sex chromosomes that I just described.

sex_chromosome_evolution

The evolution of sex chromosomes: from a sex-determining locus to the degeneration (and potential loss) of one sex-chromosome. From: Vicoso (2019) Nature Ecology & Evolution

 

Sex-specific Signatures

Back to the larks! Previous studies already indicated that something fishy is going on with the sex-chromosomes of these birds. A cytogenetic study of Bimaculated Lark (Melanocorypha bimaculata) and Horned Lark (Eremophila alpestris) revealed extremely large sex-chromosomes. And a genetic study of the Razo Lark (Alauda razae) indicated sex-specific inheritance of markers on chromosomes 3 and 5. This prompted Hanna Sigeman and her colleagues to have a closer look at these species.

Genomic analyses of four species – Bimaculated Lark, Raso Lark, Eurasian Skylark (Alauda arvensis) and Bearded Reedling (Panurus biarmicus) – uncovered some interesting patterns. The researchers found sex-specific signatures on the entire Z-chromosome (what you would expect), but also on chromosomes 3, 4A and 5. The strength of these signatures varied between the species, suggesting that different parts of these chromosomes have been added to the Z-chromosome at different times.

lark_chromosomes

The sex-specific signatures in the genome of three larks and the Bearded Reedling. The red shading indicates decreased sequencing depth in females, and the blue shading points to female-specific genetic variants. From: Sigeman et al. (2019) Proceedings of the Royal Society B

 

Evolutionary Strata

Using the phylogenetic relationships between the species, the researchers could estimate when different chromosome-sections (or strata) were added to the sex-chromosomes. The first strata is the Z-chromosome itself, which arose about 140 million years ago in an ancestor of birds. The second oldest stratum – coming from chromosome 4A – formed when the suborder Sylvioidea split from all other songbirds, roughly 21-19 million years ago. About 19-17 million years ago, chromosome 3 contributed its first share to the sex-chromosome. A few million years later, between 17 and 14 million years ago (when the Larks and the Bearded Reedling parted ways), chromosome 3 made its second contribution. Finally, chromosome 3 (again!) and 5 were added to the mix between 14 and 6 million years ago. The final result is the largest avian sex-chromosome known to date: 195,300,000 DNA-letters long!

Eurasian_Skylark

The Eurasian Skylark (Alauda arvensis), owner of the largest sex-chromosome in birds. © Imran Shah | Wikimedia Commons

 

References

Sigeman, H., Ponnikas, S., Chauhan, P., Dierckx, E., Brooke, M. L. & Hansson, B. (2019) Repeated sex chromosome evolution in vertebrates supported by expanded avian sex chromosomes. Proceedings of the Royal Society B.

Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution, 1-10.

 

 

 

Islands in the Andes: Are populations of the Plumbeous Sierra-finch in Ecuador genetically distinct?

Recent study points to population expansion during the Last Glacial Maximum.

The sponge of the Andes. That is how the Páramo ecosystem is sometimes called. This collection of lakes, peat and grasslands can be found at 3500 meter above sea level and higher. These pockets of vegetation are separated by valleys and glaciers, giving rise to an ecological archipelago of Páramo islands. Birds (and other organisms) living on these “islands” might get isolated and gradually evolve into different species. A recent study in the Journal of Ornithology checked whether this is happening to the Plumbeous Sierra-finch (Geospizopsis unicolor).

Plumbeous_Sierra-finch.jpg

The Plumbeous Sierra-finch (Geospizopsis unicolor) © Allan Drewitt | Flickr

 

Haplotypes

Elisa Bonaccorso and her colleagues collected samples from 17 locations across the Ecuadorian Andes. Genetic analyses of two mitochondrial markers revealed no genetic differentiation between different Páramo islands. Indeed, the haplotype network shows that different islands (the colors) share the same haplotypes (the circles). If there was genetic differentiation, the circles would have distinct colors.

This pattern can be explained in several ways. Possibly, the finches are not isolated on their respective Páramo islands and they can travel between islands over low ridges (so-called “nudos”). This would result in gene flow between neighboring islands. Alternatively, the birds have been isolated for an insufficient amount of time to develop genetic differentiation.

finch_map_haplo.jpg

(A) Sampling locations in Ecuador and (B) the resulting haplotype network. The sharing of different haplotypes (the circles) by different islands (the colors) show that there is no genetic differentiation between the islands. From: Bonaccorso et al. (2019) Journal of Ornithology

 

Last Glacial Maximum

The second explanation (isolated for an insufficient amount of time) is supported by other analyses. The researchers used ecological niche modelling to reconstruct the range of the Plumbeous Sierra-finch during the Last Glacial Maximum (21,000 years ago) and the Middle Holocene (6,000 years ago). During these periods, the Páramo extended to lower elevations and connected the now isolated islands. This might have facilitated gene flow between different finch populations. Moreover, the genetic data indicated a population expansion between 14,000 and 28,000 years ago.

These findings support a scenario in which populations from different Páramo islands came into contact during the Last Glacial Maximum. However, the authors caution that more research with genomic data is needed to confirm this hypothesis.

 

References

Bonaccorso, E., Rodríguez-Saltos, C., Vélez-Márquez, A., & Muñoz, J. (2019). Population genetics of the Plumbeous Sierra-finch (Geospizopsis unicolor) across the Ecuadorian paramos: uncovering the footprints of the last ice age. Journal of Ornithology, 1-9.

Multispecies hybridization among Thrushes (genus Catharus)

Genetic study uncovers gene flow between several Catharus thrushes.

“Hybridization is not always limited to two species; often multiple species are interbreeding.” This is the first sentence of my recent Avian Research review on multispecies hybridization in birds. In that paper, I argue that hybridization between multiple bird species is probably a common phenomenon, but that we do not know how important it is from an evolutionary point of view. However, before we can assess the evolutionary importance of multispecies hybridization, we first need to know which species are hybridizing. A recent study in the journal Molecular Phylogenetics and Evolution provided some insights for thrushes of the genus Catharus.

Catharus_fuscescens_CT

A Veery (Catharus fuscescens) © Cephas | Wikimedia Commons

 

Twelve Species

The Catharus thrushes are small passerines that have been important in understanding the genomic basis of migration (see here). However, the evolutionary relationships between the 12 species in this genus remain contentious. Therefore, Kathryn Everson and her colleagues used a set of ultraconserved elements (UCEs, you can read more about these molecular markers here) to delve into the speciation history of these birds.

Analyses of over 2000 UCEs resulted in well-resolved species tree in which the position of Swainson’s Thrush (C. ustulatus) was rather surprising. In contrast to previous studies, this species clustered with the Veery (C. fuscescens), the Grey-cheeked Thrush (C. minimus) and the Bicknell’s Thrush (C. bicknelli).

Swainson's_Thrush_0777vv.jpg

A Swainson’s Thrush (Catharus ustulatus) © VJAnderson | Wikimedia Commons

 

Hybridization

However, a closer look at individual gene trees revealed extensive conflict between several genes. In other words, different genes tell different evolutionary stories. Moreover, the species tree (based on UCEs) did not match the mitochondrial tree. These results suggest that hybridization might have influenced the evolution of these thrushes.

Indeed, testing explicitly for introgressive hybridization (using the D-statistic, see here for more details about this test) showed extensive gene flow between several species. The phylogenetic tree below shows the different hybrid interactions between the thrushes. Clearly, multispecies hybridization.

catharus_tree

Phylogenetic tree of the genus Catharus. The arrows indicate gene flow between different species. Solid arrows show strong support (p<0.05), while dashed arrows show weaker support (p<0.1). From: Everson et al. (2019) Molecular Phylogenetics and Evolution

 

 

Mitochondrial Capture

The disagreement between UCEs and mtDNA can be explained by mitochondrial capture. The researchers suspect that an ancient hybridization event between Swainson’s thrush and the ancestor of the Ruddy-capped Nightingale-thrush (C. frantzii) and the Black-billed Nightingale-thrush (C. gracilirostris) might have resulted in the exchange of mtDNA.

Black-billed_Nightingale-thrush.jpg

A Black-billed Nightingale-thrush (Catharus gracilirostris) © Jerry Oldenettel | Flickr

 

Heteropatric Speciation

The results of this study are not only of interest to the question of multispecies hybridization, they are also relevant for the heteropatric speciation scenario. This model applies to populations that occur in the same area at some times during the year (when they can hybridize), but are geographically separated at other times. Migratory species, such as some of the Catharus thrushes, are an excellent study system to explore this speciation model. And the results from this study do fit the proposed scenario. Indeed, the authors write that “seasonal sympatry could promote hybridization and result in reticulate or networked genetic evolution among congeners.”

 

References

Everson, K. M., McLaughlin, J. F., Cato, I. A., Evans, M. M., Gastaldi, A. R., Mills, K. K., Shink, K. G., Wilbur, S. M. & Winker, K. (2019). Speciation, gene flow, and seasonal migration in Catharus thrushes (Aves: Turdidae). Molecular Phylogenetics and Evolution139, 106564.

Ottenburghs, J. (2019). Multispecies hybridization in birds. Avian Research10(1), 20.

 

Thanks to Kevin Winker for sending me this paper, which has been added to the Turdidae page.

Cultural evolution contributes to speciation in Crossbills

Divergence in call types results in reproductive isolation.

New species can arise despite ongoing gene flow. One possible route is ecological speciation where populations become reproductively isolation due to divergent natural selection on particular traits. A textbook example of such a scenario concerns Crossbill (genus Loxia). These birds have diversified in beak morphology because they specialized on eating the seeds from different conifer species. The different beak shapes lead to different call types which are used to form flocks. Because the birds pick their partner within a flock, there is reproductive isolation between the different call types. And it all started with a cone seed…

Red_Crossbills_(Male)

Two Red Crossbills in Oregon (USA) © Elaine R. Wilson | Nature’s Pic’s Online

 

Crossbills

A recent study in Proceedings of the Royal Society B focused on the Cassia Crossbill (L. sinesciuris) which recently diverged from the Red Crossbill (L. curvirostra). About 5000 years ago, the ancestors of the Cassia Crossbill colonized the South Hills. Because the dominant seed predator – the American Red Squirrel (Tamiasciurus hudsonicus) – was absent, the birds adapted to the lodgepole pine and developed larger bills compared to the Red Crossbills. More recently, a certain type of Red Crossbill – the Ponderosa Pine Crossbill – entered the South Hills. The secondary contact between the Cassia Crossbill  and the Ponderosa Pine Crossbill allowed the researchers to test ecological speciation scenario outlined above. They made two predictions:

  1. The calls of the Cassia Crossbill  and the Ponderosa Pine Crossbill should become more different over time.
  2. The birds should flock according to call type.

 

Divergence in call type?

To test the first prediction, the researchers analyzed more than 3000 recordings of Cassia Crossbills over a period of 20 years (1998-2018). The results show that the calls of these birds steadily become more and more different from the Ponderosa Pine Crossbill (orange line in figure). Next, they compared the calls of Cassia Crossbills with Lodgepole Pine Crossbills, a population that does not coexist with the Cassia Crossbills. Because these species do not interact, there should be not divergent selection on the call types. And indeed, the difference between calls of Cassia Crossbill and Lodgepole Pine Crossbills remained stable over the study period (purple line in figure).

Crossbill_change

Over time the calls of Cassia Crossbills and Ponderosa Pine Crossbill become more different (orange line) whereas the difference with the Lodgepole Pine Crossbill remains stable (purple line). Adapted from Porter & Benkman (2019) Proceedings of the Royal Society B

 

Flocking behaviour?

The first prediction is confirmed! What about the second one? Do crossbills flock according to call type? To assess the second prediction, the researchers performed playback experiments: they played recordings of Cassia Crossbills that were similar or dissimilar to Ponderosa Pine Crossbill calls. According to the ecological speciation scenario, more Cassia Crossbills should be attracted to the calls that sounded different from the Ponderosa Pine Crossbill. And this was indeed the case as shown in the barplots below.

Crossbill_flock.jpg

More Cassia Crossbills landed when the researchers played calls that did not resemble Ponderosa Pine Crossbills (left). And more Ponderosa Pine Crossbills landed when the researchers played calls that resemble Ponderosa Pine Crossbills (right). Adapted from Porter & Benkman (2019) Proceedings of the Royal Society B

 

Speciation

This case nicely exemplifies how cultural evolution can contribute to speciation. The calls are learned from the parents and can thus be considered a cultural trait. The authors conclude that “these increasingly divergent vocalizations are imitated by offspring, leading to call divergence at the population level and reduced heterospecific flocking. […] Because Crossbills flock year-round and choose mates from within flocks, increased reproductive isolation is probably a byproduct of character displacement in call structure.”

 

References

Porter, C. K., & Benkman, C. W. (2019). Character displacement of a learned behaviour and its implications for ecological speciation. Proceedings of the Royal Society B286(1908), 20190761.