The danger of few genetic markers: Revisiting introgression between Chukar and Red-legged Partridge

In contrast to previous studies, genomic analyses point to little gene flow between these species.

For decades, people have been releasing the non-native Chukar Partridge (Alectoris chukar) and farm-reared hybrids into the range of the native Red-legged Partridge (A. rufa). Conservationists feared that these practices would impact the genetic integrity of European Red-legged Partridge populations. And indeed, several genetic studies reported extensive introgression from the Chukar into the Red-legged Partridge (see the Galliformes page for an overview). However, the introgression patterns were based on a limited set of genetic markers, such as microsatellites. These markers only capture a fraction of the genetic variation. Genomic data will tell a more complete story that might be very different. The possible discrepancy between microsatellites and genomic data was nicely illustrated by Mallards (Anas platyrhynchos) and American Black Ducks (A. rubripes). Analyses of microsatellites suggested that hybridization between these duck species might lead to the genetic extinction of the latter species. However, genomic studies of this system revealed little gene flow between the species, indicating that hybridization is not threatening the genetic integrity of the American Black Duck. A recent study in the Proceedings of the Royal Society B investigated whether a similar scenario applies to the Chukar and Red-legged Partridge situation.

Limited Introgression

Giovanni Forcina and his colleagues sequenced the genomes of 81 birds (75 Red-legged Partridges and 6 Chukar Partridges) and obtained almost 170,000 molecular markers. Analyses of this large dataset indicated that introgression from the non-native Chukar into the native Red-legged Partridge was quite limited. Specifically, the authors reported the following patterns for several subspecies (rufa, intercedens and hispanica) of the Red-legged Partridge:

While most populations within the ranges of A. r. rufa and A. r. intercedens showed a low yet detectable level of A. chukar introgression, those of A. r. rufa from Corsica and A. r. hispanica turned out to be probably unaffected.

All in all, the genetic impact of restocking practices appears to be relatively minor. Although there are clear signs of introgression from the Chukar Partridge, the genetic integrity of the Red-legged Partridge is not in serious jeopardy. It is possible that lower fitness of hybrids prevents most of them from mating and contributing to the next generation.

A principal component analysis clearly separated the Chukar Partridges (white squares) from the Red-legged Partridges (colored dots). More detailed analyses pointed to limited introgression between these species. From: Forcina et al. (2021).

Genomic Landscape

The observation of limited introgression between these partridges is certainly good news, but why did previous genetic studies point to high levels of gene flow? In a recent review, I warned about the use of a few markers (such as microsatellites) in conservation because of the so-called genomic landscape of differentiation. When comparing the genomes of closely related species, we generally observe that genetic differences are heterogeneously distributed across the genome. Some genomic regions will be drastically different, while others are largely undifferentiated. The random selection of a few genetic markers might result in a marker set that only captures the undifferentiated section of the genome, giving the impression that the studied species are genetically similar. When the species interbreed, researchers can be quick to conclude that this similarity is due to introgressive hybridization. However, a genomic perspective might lead to very different conclusions, as we have seen with the partridges. Do not underestimate the power of genomic data.

References

Forcina, G., Tang, Q., Cros, E., Guerrini, M., Rheindt, F. E., & Barbanera, F. (2021). Genome-wide markers redeem the lost identity of a heavily managed gamebird. Proceedings of the Royal Society B288(1947), 20210285.

Featured image: Red-legged Partridge (Alectoris rufa) © Juan Lacruz | Wikimedia Commons

A chicken and egg situation: did the Red or the Green Junglefowl evolve first?

Two genomic studies tried to solve this mystery.

Although the domestic chicken is one of the most studied birds ever, the evolutionary history of its genus (Gallus) is still a mystery. The four species in this genus – Sri Lanka Junglefowl (G. lafayetti), Grey Junglefowl (G. sonneratii), Green Junglefowl (G. varius) and Red Junglefowl (G. gallus, the ancestor of the domestic chicken) – can be arranged in no less than 15 different topologies. Early genetic studies, using mitochondrial DNA or a few nuclear markers, reported evidence for six of these topologies. And a recent analysis of ultraconserved elements (UCEs) added a seventh possibility to the list. You can see an overview of these seven evolutionary arrangements in the figure below.

The discordant results among previous genetic studies can be explained by several factors. First, introgression can lead to patterns that deviate from the main evolutionary history (i.e. the species tree). Extensive gene flow from one species into another can pull distantly related species together in an evolutionary tree. Second, the random sampling of gene trees can cause issues. It is known that different genes tell different evolutionary stories. If you happen to sample a set of molecular markers that do not follow the species tree, you will draw the wrong conclusions. Third, some genetic markers might have too little phylogenetic information to confidently resolve phylogenetic relationships. These three issues can be addressed with whole genome sequences: there is plenty of data available and detailed analyses of gene trees can detect signatures of introgression and random sampling biases.

An overview of different topologies for the genus Gallus. The abbreviations corresponds to Sri Lanka Junglefowl (laf), Grey Junglefowl (son), Green Junglefowl (var) and Red Junglefowl (gal). From: Tiley et al. (2020) Avian Research.

Different Datatypes

Recently, two genomic studies appeared that tried to resolve the Gallus phylogeny. The first study – published in the journal Avian Research – focused on the effects of different datatypes. George Tiley and his colleagues performed phylogenetic analyses on different molecular markers, namely protein-coding exons, introns, UCEs and conserved non-exonic elements (CNEEs). Interestingly, all markers converged upon the same topology in which the Green Junglefowl diverged first, followed by the Red Junglefowl. The remaining two species – Sri Lanka Junglefowl and Grey Junglefowl – are sister species.

Moreover, the researchers took a closer look at the distribution of the gene trees. As expected, the most common gene tree (36%) reflected the topology described above. The remaining topologies can provide important insights into introgression dynamics. If there has been no introgression, two minor gene trees are expected to occur in roughly equal frequencies (similar to flipping a coin). Introgression, however, leads to a bias towards one minor gene tree. Additional analyses on gene tree distributions revealed several of such biases that pointed to introgression between Red Junglefowl and Green Junglefowl, and between Red Junglefowl and Grey Junglefowl.

Phylogenetic analyses of different genetic markers all converged on the same topology. From: Tiley et al. (2020) Avian Research.

NJ vs. ML

To answer the question in the title: the Green Junglefowl evolved first. Well, not so fast. Because a second genomic study in the journal Molecular Phylogenetics and Evolution suggests otherwise. Phylogenetic analyses of more than 20,000 gene sequences resulted in two main topologies depending on the applied method. A Neighbor-Joining (NJ) approach indicated that the Green Junglefowl evolved first, whereas a Maximum Likelihood (ML) approach pointed to Red Junglefowl as the first species to diverge. Introgression analyses on the NJ-tree – using the popular D-statistic – revealed extensive gene flow from the Green Junglefowl into the ancestor of the Sri Lanka Junglefowl and Grey Junglefowl: no less than 27.6%. The researchers consider this amount of introgression unlikely, which invalidates the NJ-topology. Hence, the ML-tree with more realistic levels of introgression – and where Red Junglefowl evolved first – represents a more likely scenario.

Introgression patterns across the two main topologies, based on (a) Maximum Likelihood and (b) Neighbour-Joining. The extremely high level of introgression (27.6%) in the NJ-tree makes this an unlikely scenario. From: Mariadassou et al. (2021) Molecular Phylogenetics and Evolution.

Species Tree?

So, now what? The two genomic studies report contrasting results and we still don’t know which species evolved first. Personally, I find the first study more convincing because it took different datatypes into account and provided a detailed overview of the gene trees. The second study, on the other hand, analyzed all autosomal gene trees in one go and did not report the distribution of these gene trees (I am very curious to see it). My bet would thus be on the Green-Junglefowl-first-scenario.

However, until now we assumed that the evolutionary history of the genus Gallus can be captured in a bifurcating tree. This is not necessarily the case. The high levels of ancient and recent introgression between these species might be better depicted in a phylogenetic network (see for example here). Trying to find the “true” species tree could be seen as a wild goose (or chicken) chase. And the question which junglefowl species evolved first becomes a bit nonsensical.

References

Mariadassou, M., Suez, M., Sathyakumar, S., Vignal, A., Arca, M., Nicolas, P., … & Tixier-Boichard, M. (2021). Unraveling the history of the genus Gallus through whole genome sequencing. Molecular Phylogenetics and Evolution158, 107044.

Tiley, G. P., Pandey, A., Kimball, R. T., Braun, E. L., & Burleigh, J. G. (2020). Whole genome phylogeny of Gallus: introgression and data-type effects. Avian Research11(1), 1-15.

Featured image: Green Junglefowl (Gallus varius) © Panji Gusti Akbar | Wikimedia Commons

Across Asia and beyond: The evolutionary story of the Common Pheasant

Genetic study reconstructs the Asian diversification of the Common Pheasant.

When I visit my family in Belgium, we often go for walks with our dog Mira (a Hungarian vizsla). While strolling through the local nature reserves, we sometimes disturb a Common Pheasant (Phasianus colchicus) hiding in the tall grass. Females mostly fly off with a loud alarm call, whereas males tend to run away in a seemingly random direction. These colorful birds – the males anyway – are not native to this part of Europe, but were introduced for hunting purposes. Common Pheasants originated in Asia where they display an amazing diversity of male plumage, resulting in a proliferation of more than 30 subspecies.

A recent study in the Journal of Biogeography focused on the native range of the Common Pheasant and reconstructed its evolutionary history based on a handful of genetic markers. The researchers found that this species diversified into eight distinct lineages during the Late Pleistocene. Let’s explore the Asian expansion of the Common Pheasant.

Spreading across Asia

Simin Liu and colleages sampled more than 200 individuals across the range of the Common Pheasant, which extends from the Black Sea to Korea. Analyses of seven nuclear and two mitochondrial genes revealed that the diversification within this species started at the end of the Pleistocene, between 700,000 and 200,000 years ago. Our evolutionary story starts at the eastern edge of the Qinghai-Tibetan Plateau from where several lineages spread in different directions.

One population expanded to the Chinese mountain ranges in the south-east, giving rise to the elegans-lineage. Because the climate remained relatively stable in this region, this lineage shows a stable population size of time and did not diversify into more sub-lineages. A second expansion to the east brought pheasants into a more unstable area where periods of drought promoted diversification into multiple lineages. Here, we currently find the torquatus and strauchi–vlangallii lineages that were occasionally connected by gene flow. One population traveled further east and became isolated on the island of Taiwan (the formosanus-lineage). Finally, a third movement to the west resulted in the evolution of several Central Asian lineages: tarimensis,, mongolicus, principalis–chrysomelas and colchicus. The exact evolutionary relationships between these lineages remain to be disentangled.

The genetic analyses pointed to eight distinct lineages (see phylogeny on top) that spread across Asia from the Qinghai-Tibetan Plateau (map below). From: Liu et al. (2020) Journal of Biogeography.

Taxonomic Decisions

This study nicely shows how different environmental conditions affect the evolutionary trajectory of a population. The relatively stable climate of the Chinese mountains resulted in a stable population of Common Pheasants, making further diversification of this lineage (elegans) unlikely. Other populations ended up in regions with more pronounced climatic cycles that led to diversification into several separate lineages. Ultimately, the researchers could discriminate between eight distinct lineages.

Taxonomic-minded readers might be wondering if all these lineages should be elevated to species rank. At the moment, the researchers argue that the diversity within the Common Pheasant can be captured in three species: the Yunnan Pheasant (P. elegans), the Chinese Pheasant (P. vlangallii which includes the torquatus, strauchi–vlangallii and formosanus lineages) and the Turkestan Pheasant (P. colchicus which includes the tarimensis, principalis–chrysomelas, mongolicus and colchicus lineages). However, more research is needed to justify this classification.

References

Liu et al. (2020) Regional drivers of diversification in the late Quaternary in a widely distributed generalist species, the common pheasant Phasianus colchicus. Journal of Biogeography47(12), 2714-2727.

Featured image: Common Pheasant (Phasianus colchicus) © David Croad | Wikimedia Commons

You only need one genome to unravel the demographic history of the Chinese Grouse

Genomic analyses reveal population fluctuations during the Pleistocene.

A few weeks ago, scientists announced that they almost completed a sequence of the human genome. This might come as a surprise: did we not sequence the human genome in 2003 when the results from the Human Genome Project were published? That genome sequence was actually incomplete, about 15% was missing (especially stretches of repetitive DNA are difficult to assemble). Similarly, many avian genome assemblies contain significant gaps (see this blog post for more details). However, scientists can still extract a lot of information from incomplete genome assemblies. For instance, you can reconstruct the demographic history of a species from one genome using a pairwise sequentially Markovian coalescent (PSMC) analysis. This technique – developed by Heng Li and Richard Durbin – is nicely explained by David Reich in his book Who We Are and How We Got Here:

A 2011 paper by Heng Li and Richard Durbin showed that the idea that a single person’s genome contains information about a multitude of ancestors was not just a theoretical possibility, but a reality. To decipher the deep history of a population from a single person’s DNA, Li and Durbin leveraged the fact that any single person actually carries not one but two genomes: one from his or her father and one from his or her mother. Thus it is possible to count the number of mutations separating the genome a person receives from his or her mother and the genome the person receives from his or her father to determine when they shared a common ancestor at each location. By examining the range of dates when these ancestors lived—plotting the ages of one hundred thousand Adams and Eves—Li and Durbin established the size of the ancestral population at different times. In a small population, there is a substantial chance that two randomly chosen genome sequences derive from the same parent genome sequence, because the individuals who carry them share a parent. However, in a large population the chance is far lower. Thus, the times in the past when the population size was low can be identified based on the periods in the past when a disproportionate fraction of lineages have evidence of sharing common ancestors.

Population Fluctuations

A recent study in the journal BMC Genomics applied this PSMC analysis to the genome of a Chinese Grouse (Tetrastes sewerzowi). This forest-dwelling species can be found in the mountains east of the Qinghai-Tibet Plateau. It is currently considered “Near Threatened” because of population declines due to ongoing deforestation and fragmentation of its habitat.

The genomic analyses revealed that the population size of the Chinese Grouse has fluctuated over time. Populations decreased during early to middle Pleistocene but showed an expansion during late Pleistocene (between 30,000 and 40,000 years ago), followed by a sharp decline during the last glacial maximum (about 20,000 years ago). Similar patterns have been found in other bird species, highlighting the influence of the climatic cycles during the Pleistocene (see for example this study by Krystyna Nadachowska-Brzyska and her colleagues).

The PSMC analysis showed population fluctuations of the Chinese Grouse during the Pleistocene. From: Song et al. (2020) BMC Biology.

Coniferous Forests

Next, the researchers focused on the underlying mechanisms of these population fluctuations. Why did the number of Chinese Grouse wax and wane during the Pleistocene? To answer this question, the researchers turned to Ecological Niche Modelling and reconstructed the distribution of the Chinese Grouse throughout the Pleistocene. This exercise showed that the population expansion during the late Pleistocene (30,000–40,000 years ago, also known as the Greatest Lake Period) can be explained by the warmer weather which allowed conifer forests, the primary habitat for Chinese Grouse, to reach their greatest extent. Later on, during colder periods, the coniferous habitat shrunk and the Chinese Grouse populations moved westwards into higher altitudes.

These findings indicate that the distribution of the Chinese Grouse is strongly dependent on the coniferous forest cover. It is thus essential to protect these fragmented forests and safeguard the future of this beautiful bird.

Ecological Niche Modelling showed how the suitable habitat for Chinese Grouse increased during the late Pleistocene (figure a), followed by extensive loss of habitat later on (figure b). The current distribution is depicted in figure c. From: Song et al. (2020) BMC Genomics.

References

Song, K., Gao, B., Halvarsson, P., Fang, Y., Jiang, Y. X., Sun, Y. H., & Höglund, J. (2020). Genomic analysis of demographic history and ecological niche modeling in the endangered Chinese Grouse Tetrastes sewerzowiBMC genomics21(1), 1-9.

Featured image: A drawing of Chinese Grouse (Tetrastes sewerzowi) © Ornithological Miscellany. Volume 2 | Wikimedia Commons

Bad news for the Brown Eared Pheasant?

Genomic study finds low genetic diversity and high levels of inbreeding in this vulnerable species.

Small populations are often at risk. They can get sucked in a negative feedback loop of genetic and demographic decline that culminates in their extinction (the so-called extinction vortex, which I covered in this blog post). In general, small populations are more vulnerable to genetic drift and inbreeding, leading to a loss of genetic diversity. This lower level of genetic diversity might prevent small populations from adapting to changing environments. However, it is not all misery and mayhem for small populations. One potential benefit of a small population size is genetic purging, the process in which deleterious variants appear more often due to inbreeding and get purged from the population because individuals carrying these variants fail to survive or reproduce. The result is a genetically healthier population, despite low levels of genetic diversity.

A recent study in the journal Molecular Biology and Evolution examined the situation of the brown eared pheasant (Crossoptilon mantchuricum), a vulnerable bird species that is declining across its range in China due to human activities, such as deforestation and hunting. Is this species heading for extinction or does it reap the benefits of genetic purging?

Genetic Purging?

Based on the genomes of 40 individuals, the researchers identified three distinct populations corresponding to locations in Shaanxi (Western), Shanxi (Central), and Hebei & Beijing (Eastern). The genetic diversity across these three populations was extremely low. In fact, it was the lowest genome-wide estimate for any bird species to date. But, as explained above, this low level of genetic diversity might result in genetic purging when deleterious alleles are filtered out by purifying selection.

The action of genetic purging can be tested with the population genetic statistic Tajima’s D. I have explained the rationale behind the statistic in another blog post, but for this story you only need to understand the main interpretation. In general, a negative Tajima’s D points to a selective sweep (and thus genetic purging), while a positive Tajima’s D suggests balancing selection. In the three brown eared pheasant populations, Tajima’s D was highly positive. There is thus no evidence for genetic purging. And that is bad news…

The brown eared pheasant shows very low levels of genetic diversity (left figure). The positive values of Tajima’s D suggest that there is little purifying selection across the genome of this species (right figure). Blue refers to the blue eared pheasant, Brown-W, Brown-C and Brown-E refer to three populations of the brown eared pheasant. Adapted from Wang et al. (2021) Molecular Biology and Evolution.

Genetic Load

Low genetic diversity is often the outcome of inbreeding. When related individuals mate, their offspring will mostly receive the same genetic variants from both parents. This results in large genomic regions with little genetic variation, also known as runs of homozygosity (ROHs). The brown eared pheasant did indeed show more ROHs compared to its sister species, the blue eared pheasant (C. auritum), that is of little conservation concern.

A closer look at these genomic regions revealed that some brown eared pheasant populations have accumulated missense and loss-of-function mutations. Missense mutations occur when a change in the DNA results in the wrong amino acid being incorporated into a protein. And loss-of-function mutations lead to functional problems in the activity of a protein. Clearly, the brown eared pheasant is suffering from inbreeding depression. Moreover, because natural selection seems unable to eliminate deleterious mutations, this species is accumulating a high genetic load. Unless conservation actions are implemented – such as a genetic rescue program – the brown eared pheasant might be heading for extinction.

The brown eared pheasant populations show more runs of homozygosity (ROHs) compared to the blue eared pheasant, suggesting high levels of inbreeding. From: Wang et al. (2021) Molecular Biology and Evolution.

References

Wang et al. (2021). Genomic Consequences of Long-Term Population Decline in Brown Eared Pheasant. Molecular Biology and Evolution38(1), 263-273.

Featured image: Brown eared pheasant (Crossoptilon mantchuricum) © Josh More | Flickr