Social bonds and migratory behavior determine the likelihood of hybridization in birds

What behavioral mechanisms underlie these associations?

Sometimes the title of a paper says it all: “Sociality and migration predict hybridization across birds.” In a recent study in the Proceedings of the Royal Society B, Gavin Leighton and his colleagues correlated the incidence of hybridization across birds with several life history traits. These analyses revealed that bird species with long-lasting social bonds are less likely to hybridize. In addition, a migratory lifestyle increases the likelihood of hybridization. Some interesting findings that require more exploration. What behavioral mechanisms could be driving these associations between sociality, migration and hybridization?

Pair Bonds and Migration

Species with no pair bonds will look for a new partner every year, increasing the opportunities for making the “wrong” choice and hybridize. Species with long-lasting social bonds, on the other hand, will often pair for several mating seasons. This reproductive strategy can lead to substantial fitness costs if an individual mates with the “wrong” species. The resulting hybrids might be sterile or unviable, culminating in a significant waste of reproductive effort. Such maladaptive hybridization can lead to increased selection for proper species recognition. An interesting exception to this result – which might prove the rule – concerns my own study system: geese. Most goose species tend to form long-lasting pair bonds, but still engage in regular hybridization. The production of hybrids has been attributed to several behavioral mechanisms, such as forced extra-pair copulations, interspecific brood parasitism and vagrant individuals (see this paper for an overview).

The last mechanism related to goose hybridization – vagrant individuals – leads into the next main finding of the study: migratory species are more likely to hybridize. To again focus geese, migratory goose species might have a higher chance of reaching new habitats where they interbreed with local species. For example, North American Snow Geese (Anser caerulescens) are occasionally observed in Europe during migration and hybrids between Snow Goose and several European species have indeed been reported. An additional explanation relates to mate choice in sedentary species: these birds might have extended periods of mate searching and pair formation, lowering the probability of choosing a partner from another species.

Phylogenetic distribution of hybridization (grey, inner circle), social bond length (green, middle circle), and migratory status (blue/yellow, outer circle). From: Leighton et al. (2021).

Future Research

Clearly, there are multiple mechanisms to explain the associations uncovered in this study. The details might differ across the avian phylogeny, but the broad-scale importance of sociality and migration seems justified. This macroevolutionary perspective opens new exciting avenues for further research, disentangling how these life history traits (and probably many other factors) interact to determine the probability of hybridization.

A final note on the dataset. The researchers assembled a dataset of bird hybrids using the Handbook of Avian Hybrids of the World, indicating that they took “a liberal approach and included any reported hybridization where an individual was identified by sight as a putative hybrid.” I completely understand this pragmatic choice as it is nearly impossible to assess the reliability of each hybrid combination mentioned in the Handbook of Avian Hybrids of the World. However, I have become more skeptical about the list of bird hybrids that Eugene McCarthy has produced (see for example this blog post). I do not think that the inclusion of less reliable hybrids has affected the analyses in the present study, but I do encourage ornithologists to be careful in using this book in their future work. Always check the original source before including a dubious hybrid record.

References

Leighton, G. M., Lu, L. J., Holop, E., Dobler, J., & Ligon, R. A. (2021). Sociality and migration predict hybridization across birds. Proceedings of the Royal Society B, 288(1947), 20201946.

Featured image: Greylag Goose (Anser anser) x Canada Goose (Branta canadensis) © Dirk Ottenburghs

Mismatches between mtDNA, nuclear markers and morphology in the Canada Jay

Extensive hybridization in contact zones leads to mitonuclear discordance.

Different genes tend to tell different stories. This phenomenon – known as gene tree discordance – can be particularly obvious when comparing mitochondrial DNA with nuclear markers. Mismatches between these molecular markers can be the outcome of different processes, such as hybridization, incomplete lineage sorting, sex-biased dispersal or natural selection. Regardless of the underlying mechanism, mitonuclear discordance can be problematic in species delimitation, especially when morphological information is insufficient to delineate species. How can you discriminate between two or more species when different molecular markers give you different answers? This issue is relevant for the Canada Jay (Perisoreus canadensis) which consists of three morphotypes that might even interbreed. A recent study in the Biological Journal of the Linnean Society attempted to unravel this complex situation.

Crown Patch

The most widespread morphotype of the Canada Jay – the Boreal morphotype – can be found from Alaska to Newfoundland. The other two morphotypes are more restricted: the Pacific form resides along the coast from California to British Columbia, and the Rocky Mountains form occurs at high elevation in the Rocky Mountains from New Mexico to British Columbia. Apart from their distinct – but overlapping – distributions, these morphotypes show variation in their plumage patterns. Specifically, the Pacific birds have a darker crown patch compared to the Boreal birds, whereas the Rocky Mountain birds have a conspicuous white head. Despite these subtle differences, some intermediate birds have been observed, suggesting the occurrence of hybridization.

An overview of morphological differences between the three morphotypes: (a,d) Pacific, (c,e) Rocky Mountains, and (c,f) Boreal. And their distribution in the west of North America. From: Graham et al. (2021).

Mitonuclear Discordance

Between 1990 and 2018, Brendan Graham and his colleagues collected blood samples from over 600 individuals. Based on several morphological traits, each of these individuals was assigned to one morph. However, 15 individuals showed traits of at least two morphotypes and were classified as intermediates. Next, the researchers took a closer look at the genetic make-up of all birds, using 12 microsatellites and the mitochondrial control region. Both marker types were reasonable successful in discriminating between the three morphotypes. The geographic distribution of the morphotypes was mirrored by the mitochondrial lineages, although some populations contained individuals from multiple lineages. And analyses of the nuclear data pointed to three distinct clusters, corresponding to the three morphotypes. However, in regions of overlap, a large number of individuals (27%) were assigned to a genetic cluster that did not match their morphology.

Moreover, no less than 222 individuals showed mismatches between the mitochondrial and nuclear assignments. Mitonuclear discordance was most prominent in sympatric areas, such as southern British Columbia and northern Washington, Wyoming and Utah. The most likely explanation for these patterns seems extensive hybridization after a period of isolation.

Distribution of mtDNA, microsatellite genetic cluster and combined mtDNA and microsatellite genotypes among the three morphotypes and intermediate morphotypes. The first four categories (Pacific, Intermountain West-IMW, Boreal and Southeast) represent individuals that showed congruent patterns between mtDNA and microsatellites. The fifth category (Cyto-ND) represents individuals that exhibited mitonuclear discordance. For each of the main morphotypes, the expected genetic group is marked with an asterisk. From: Graham et al. (2021).

Plumage Genes

The mismatches between morphology and the genetic markers in this study suggest that the plumage patterns in the morphotypes are controlled by a few genetic loci. Similar patterns have been uncovered in several other bird groups, such as wagtails, woodpeckers and warblers. The authors note that “analysis with next generation sequencing techniques may help uncover the genes associated with plumage variation in Canada Jays.” And when they manage to perform these analyses, you will definitely read about it on the Avian Hybrids blog.

References

Graham, B. A., Cicero, C., Strickland, D., Woods, J. G., Coneybeare, H., Dohms, K. M., Szabo, I. & Burg, T. M. (2021). Cryptic genetic diversity and cytonuclear discordance characterize contact among Canada jay (Perisoreus canadensis) morphotypes in western North America. Biological Journal of the Linnean Society, 132(4), 725-740.

Featured image: Canada Jay (Perisoreus canadensis) © Mdf | Wikimedia Commons

Chromosomal evolution in sandpipers

Dynamic reshuffling of chromosomes across the Charadriiformes phylogeny.

In general, birds have a very stable number of chromosomes. Most species house 40 pairs of chromosomes – so, 80 in total – in their cells (commonly noted down as 2n = 80). These chromosomes can be divided into a few huge macrochromosomes and several tiny microchromosomes. However, not all species adhere to this “2n = 80 rule” in birds. In biology, there are always some exceptions. Falcons, for example, show chromosomal numbers of only 2n = 40 to 2n = 52. These atypical counts are probably the outcome of fusions between microchromosomes into macrochromosomes (see this blog post for more about the peculiar genomes of falcons). The order Charadriiformes – waders, gulls and allies – exhibit a wide range of karyotypes, ranging from 2n = 42 in the Eurasian Thick-knee (Burhinus oedicnemus) to 2n = 98 in the Common Snipe (Gallinago gallinago). To gain more insights into the patterns of chromosomal evolution in this bird group, researchers took a closer look at the karyotype of the Spotted Sandpiper (Actitis macularius). Their findings appeared in the journal BMC Ecology and Evolution.

Fissions

The Spotted Sandpiper has 92 chromosomes of which 14 pairs are macrochromosomes. To reconstruct the chromosomal evolution of this species, the researchers “painted” the chromosomes of the Spotted Sandpiper onto the karyotype of the Eurasian Thick-knee. This molecular technique revealed how different chromosomes were rearranged in the two species. It turns out that in the Spotted Sandpiper several chromosomes have been split into two or more smaller chromosomes. For instance, the second chromosome pair in the Eurasian Thick-knee (denoted as BOE2) split into four new pairs in the Spotted Sandpaper (namely AMA3, AMA11, AMA12 and AMA13). Similarly, BOE3 was divided into AMA4, AMA14 and AMA15. The figure below provides a nice overview of this karyotypic puzzle.

An overview of the chromosomal rearrangements between the Eurasian Thick-knee (BOE) and the Spotted Sandpiper (AMA). From: Pinheiro et al. (2021).

Phylogeny

By combining the chromosomal information of the Eurasian Thick-knee and the Spotted Sandpiper with karyotypic knowledge of other bird species, the researchers managed to reconstruct the evolutionary history of chromosome numbers in the order Charadriiformes. Most fissions occurred quite early in the evolution of these birds, namely after the gulls (family Laridae) split from the other families. An additional fission probably took place at the base of the sandpiper family Scolopacidae. Interestingly, rearrangements in the opposite direction – fusion of several chromosomes – happened within the Jacanidae family, giving rise to an ancestral-like karyotype of 2n = 82.

Seeing all these chromosomal reshuffling, I cannot help but wonder whether these changes were adaptive. Did the birds benefit from having more or less chromosomes in their cells? Or are these just non-adaptive rearrangements without much impact on individual fitness? Exciting questions that will hopefully be addressed in a future blog post.

Chromosomal changes across the phylogeny of the Charadriiformes. The karyotypes at the bottom depict the putative ancestral karyotype (PAK) of birds and the PAK of Scolopaci (SPAK).

References

Pinheiro, M. L. S., Nagamachi, C. Y., Ribas, T. F. A., Diniz, C. G., Ferguson-Smith, M. A., Yang, F., & Pieczarka, J. C. (2021). Chromosomal painting of the sandpiper (Actitis macularius) detects several fissions for the Scolopacidae family (Charadriiformes). BMC Ecology and Evolution, 21(1), 1-10.

Featured image: Spotted Sandpiper (Actitis macularius) © Mike Baird | Wikimedia Commons

The benefits and drawbacks of living on an island

If you were a bird, would you want to live on an island?

Island populations have played a key role in the development of evolutionary theory. I guess everyone is familiar with the scientific work on Darwin’s Finches – including groundbreaking work by Charles Darwin himself, David Lack, and more recently Peter and Rosemary Grant. Other examples include convergent evolution of anole lizards on tropical islands and the adaptive radiation of honeycreepers on Hawaii. Evolution on islands can take surprising turns. Just think of the extinct giant swan (Cygnus falconeri) on Sicily and Malta or the flightless Kakapo (Strigops habroptilus) of New Zealand. Studying evolution on islands is certainly worthwhile, but what about actually living on island? Do organisms that colonize island environments do better or worse than their mainland counterparts? The answer to that question depends on the aspect you focus on, as nicely illustrated by some recent studies in Biology Letters and Current Biology.

Adult Survival

Let’s start by looking at the individual level. Using a dataset of no less than 697 bird species, Guy Beauchamp investigated whether adult birds survive better on islands. He first needed to correct for certain confounding factors. Birds with a larger body size tend to have higher survival rates. And due to the well-known trade-off between reproduction and survival, a lower clutch size is often associated with better survival. Finally, species with a cooperative breeding system survive better as adults. After controlling for these factors, Beauchamp still found that “birds living on islands showed higher apparent survival than their mainland counterparts.” The exact mechanisms behind the higher survival rate on islands remain to be determined but might be related to the absence of predators and parasites on islands. So, from an individual perspective, it would be a good idea to settle on an island.

Apparent survival of adult birds is higher on islands (blue lines) compared to the mainland (red line). This pattern holds across latitudes and on both hemispheres. From: Beauchamp (2021).

Slightly Deleterious Mutations

Adult survival is thus higher on islands. But the situation is quite different on a population level. Thibault Leroy and his colleagues compared the effective population size (Ne) – a measure of genetic diversity – between songbirds on islands and on the mainland. Based on whole-genome sequences of almost 300 individuals, representing 25 species, they found that “island species exhibit significantly lower mean Ne than continental species over the last one million years.” This reduction in effective population size has serious consequences for evolutionary dynamics on islands. According to the nearly neutral theory of molecular evolution, small populations will accumulate slightly deleterious mutations due to the stronger effect of genetic drift. And indeed, the researchers found more slightly deleterious mutations in island species compared to mainland species. Hence, on a population level, island birds are genetically less healthy than their mainland relatives.

Island species (filled circles) have smaller effective population sizes and more slightly deleterious alleles (estimated by the π_N/π_S ratio) compared to their mainland counterparts. From: Leroy et al. (2021).

Paradox

These two studies appear to contradict each other. How can island birds live longer when the populations accumulate slightly deleterious mutations? The answer to this paradox is probably related to the interaction between the deleterious mutations and the island environment. As you might have guessed from the term, these mutations are only slightly deleterious. Individuals might experience some inconvenience from these mutations, but they are not deadly and they often do not impact individual survival rates that much. In addition, the absence of certain predators and parasites on islands leads to weaker selective pressures, potentially allowing island birds to live longer.

However, a sudden change in the environment or the introduction of a predator can quickly increase selective pressures on the island population. The lower level of genetic diversity and the higher mutational load of island populations might then prevent rapid adaptation, potentially resulting in extinction. Indeed, numerous island species have perished in recent times. You could say that life on an island is great until the environment changes. And unfortunately, the environment is currently changing rapidly due to human activities.

References

Beauchamp, G. (2021). Do avian species survive better on islands?. Biology Letters, 17(1), 20200643.

Leroy, T., Rousselle, M., Tilak, M. K., Caizergues, A. E., Scornavacca, C., Recuerda, M., … & Nabholz, B. (2021). Island songbirds as windows into evolution in small populations. Current Biology, 31(6), 1303-1310.

Featured image: Blue Chaffinch (Fringilla teydea) © Bartkauz | Wikimedia Commons

Isolated in Iberia: Unraveling the origin of an Iberian Rook population

Is it an ancestral population or the result of a recent expansion?

During my postdoc in the Swedish city Uppsala, I would regularly visit a colony of Rooks (Corvus frugilegus) close to the city center. Their heavy, greyish beaks always fascinated me and I enjoyed observing their social interactions. If you want to find Rooks, you do not have to travel specifically to Sweden. This corvid species has a wide distribution, stretching from western Europe into eastern Siberia. Interestingly, there is a small, isolated population of Rooks on the Iberian peninsula (i.e. Spain and Portugal). The origin of this population is still largely unknown. In general, there are two possible explanations. Perhaps the Iberian birds are the descendants from a larger population that survived in the south of Europe during the glacial cycles of the Pleistocene. As Europe was covered by thick ice sheets, Iberia functioned as a glacial refugium. When the ice retreated, Rooks recolonized Europe from this refugium. Another possibility is unrelated to the ice ages, but entails habitat fragmentation from a much wider distribution. The Iberian population might have been split off from a bigger population in Europe. A recent study in the Journal of Avian Biology relied on genetic data to discriminate between these scenarios.

Predictions

Both explanations – glacial refugium or fragmented population – lead to specific predictions about the expected genetic patterns. From a phylogenetic point of view, the glacial refugium scenario would give rise to a star-like phylogeny with the Iberian individuals in the center. Rook populations in western Europe would then represent subsamples from the ancestral population that expanded out of Iberia, giving rise to different rays of the star-like pattern. In addition, the European Rook populations would show genetic signatures of recent population expansion (which can be captured with several statistical tests). Finally, genetic diversity should decrease from south to north, as each expansion involves a genetic bottleneck. The expectations for the fragmented population scenario are drastically different. On a phylogenetic tree, the Iberian individuals would represent a small cluster within a larger European clade. There would be no signs of population expansion in Europe, and a significant decrease in genetic diversity in the Iberian population.

The wide distribution of Rooks, including the isolated population in Iberia. From: Salinas et al. (2021).

Population Expansion

Pablo Salinas and his colleagues tested these predictions using mtDNA and several nuclear markers. Let’s have a look at the patterns that emerged from their analyses. First, the haplotype network of the mitochondrial markers consisted of a central core of Iberian samples, surrounded by several rare haplotypes from European populations. This star-like pattern points to population expansions from an ancestral population in Iberia. This interpretation was supported by Fu’s and Tajima’s neutrality test, which was consistent with a recent population expansion. To remove all doubt, explicit scenario testing with coalescent modelling also indicated that the European population diverged from an ancestral Iberian population. Hence, the glacial refugium scenario seems most likely.

Haplotype networks of the two mitochondrial markers (B = ND2 and C = control region) show a clear star-like pattern with the Iberian samples (dark purple) in the center. From: Salinas et al. (2021).

Genetic Gradient

However, the pattern of genetic diversity did not fit with the glacial refugium scenario. In this scenario, we expected that the level of genetic diversity would decrease from south to north, but in reality there was no such gradient. This result can be explained by the isolated nature of the Iberian population and the vastness of the European populations. Indeed, the authors indicate that “Isolated populations are also expected to have low genetic diversity because of limited gene flow with other populations, as previously argued for the small breeding rook population in the Iberian Peninsula. This is in contrast to the widespread populations in northern Europe, which have been able to maintain large effective population sizes and thus increase genetic diversity through the persistence of recent mutations.”

All in all, we now have several lines of genetic evidence to argue that the Iberian population represents the remnant of an ancient ancestral population. Moreover, the glacial refugium scenario is further supported by fossil data. Paleontologists have found Rook fossils in early Pleistocene rocks from Iberia, indicating that this species was present there before the last glacial maximum. Isn’t it wonderful when everything converges upon the same explanation?

References

Salinas, P., Morinha, F., Literak, I., García, J., Milá, B., & Blanco, G. (2021). Genetic diversity, differentiation and historical origin of the isolated population of rooks Corvus frugilegus in Iberia. Journal of Avian Biology, 52(3).

Featured image: rook (Corvus frugilegus) © Hobbyfotowiki | Wikimedia Commons

Recent and ancient hybridization among sea duck species, including a potential hybrid species

Genomic analyses point to several bouts of past gene flow.

Waterfowl hybridize like there is no tomorrow. Between 30% and 40% of ducks, geese and swans are known to interbreed. For some species combinations, hybrids are regularly observed because they are easy to recognize and occur close to humans. A nice example concerns Greylag Goose (Anser anser) x Canada Goose (Branta canadensis) hybrids in the Netherlands. The aberrant morphology of these crosses allows for easy identification and they reside around several Dutch cities (see this paper for more details). But what about sea ducks? This group of waterfowl – classified in the tribe Mergini – spend most of their lives at sea, making them difficult to observe. Some hybrids have been reported, such as Barrow’s Goldeneye (Bucephala islandica) x Common Goldeneye (B. clangula). However, the incidence of hybridization among the 15 species in this tribe remains largely unknown. A recent study in the journal Molecular Phylogenetics and Evolution addressed this knowledge gap with genomic data. Sampling more than 350 individuals, the researchers searched for genetic signatures of hybridization.

Recent Hybrids

Before starting their quest for sea duck hybrids, the researchers needed to be sure that they could confidently discriminate between all species. A principal component analysis pointed to three main groups: (1) Harlequin Ducks (Histronicus histronicus), (2) eider species and Long-tailed Ducks (Clangula hyemalis), and (3) Bufflehead (Bucephala albeola), scoters, mergansers, and goldeneyes. Within these three groups, population assignment analyses (using ADMIXTURE) could identify the different species and even provided some insights into more fine-scale population structure within certain species.

Now, we can explore the dataset for possible hybrids. The ADMIXTURE results indicated a first-generation hybrid between Barrow’s Goldeneye and Common Goldeneye. Moreover, there were 18 individuals with signs of ancestry from several species, suggesting possible backcrosses. The ADMIXTURE analyses had too low resolution to pinpoint the species involved, so the researchers turned to a more powerful co-ancestry analysis (using fineRADstructure). Here is an overview of the uncovered hybrids with number of individuals between parentheses:

• Barrow’s Goldeneye x Common Goldeneye (1)
• Barrow’s Goldeneye backcrossed with Bufflehead (1)
• Bufflehead backcrossed with White-winged Scoter (3)
• Common Eider backcrossed with Common Goldeneye (1)
• Common Eider backcrossed with Harlequin Duck (3)
• Harlequin Duck backcrossed with Common Merganser and Bufflehead (2)
• King Eider backcrossed with Surf Scoter (1)
• Long-tailed Duck backcrossed with Black Scoter (1)
• Long-tailed Duck backcrossed with Bufflehead (2)
• Long-tailed Duck backcrossed with Harlequin Duck and a scoter species (1)
• Long-tailed Duck backcrossed with eider species (1)
• Red-breasted Merganser backcrossed with King or Spectacled Eider (1)

A principal component analyses uncovered three main groups among the sea duck species (described in the text). From: Lavretsky et al. (2021).

Ancient Gene Flow

The results described above nicely fit with general hybridization patterns in birds: rare on an individual basis (only 18 out of 363 individuals), but common at a species level (just count the number of species in the list). But the sea duck story does not end here. Next, the researchers explored the genomes of the sea duck species for signs of ancient introgression. These analyses suggested gene flow between the ancestors of scoters and mergansers, and between the ancestors of scoters and goldeneyes. However, it is difficult to pinpoint the exact species involved in these ancient introgression events. It could entail hybridization between the ancestors of extant species, or between extinct lineages that left their genetic signature in present-day species (i.e. ghost introgression). Regardless of the details, introgression clearly played a pivotal role in the evolutionary history of sea ducks.

A phylogenetic tree of sea ducks. However, their evolutionary history might be better represented as a network given the signatures of ancient introgression. From: Lavretsky et al. (2021).

A Hybrid Species?

And then there is the Steller’s Eider (Polysticta stelleri). The genetic analyses indicated that this species contains genetic ancestry from Long-tailed Ducks and several eider species. Specifically, 94-98% of genetic variation in the Steller’s Eider came from three other eider species, while the remaining 2-6% was assigned to Long-tailed Ducks. These patterns raise the possibility that the Steller’s Eider is a hybrid species. If that is the case, its unique plumage might be the result of transgressive segregation (i.e. hybrids showing extreme phenotypes). However, the hybrid species hypothesis remains to be tested with more detailed analyses. There is still the possibility that the genetic make-up of the Steller’s Eider is the outcome of several, independent hybridization events (similar to the situation in Red-breasted Goose, Branta ruficollis). Indeed, the researchers indicate that “while we cannot definitively identify the source of the shared genetic variation, we provide strong evidence for a complex evolutionary history of shared variation between true Eiders, long-tailed ducks, and Steller’s eider that will require additional sampling of individuals and genomes to fully understand.” To be continued.

References

Lavretsky, P., Wilson, R. E., Talbot, S. L., & Sonsthagen, S. A. (2021). Phylogenomics reveals ancient and contemporary gene flow contributing to the evolutionary history of sea ducks (Tribe Mergini). Molecular Phylogenetics and Evolution, 161, 107164.

Featured image: Steller’s Eider (Polysticta stelleri) © Ron Knight | Wikimedia Commons

Quantitative genetic analyses of Song Sparrows reveal the dark side of gene flow

Genetic variation from immigrant birds contributes to lower juvenile survival.

Gene flow is always good, right? The influx of individuals from neighboring regions leads to more genetic diversity, allowing the population to cope better with environmental changes. It sounds wonderful. The reality, however, is not that straightforward. Gene flow can also have negative effects, as nicely shown by a recent paper in the journal Evolution Letters. The researchers took a quantitative genetic approach to study juvenile survival in a population of Song Sparrows (Melospiza melodia). Before we delve into the findings of this paper, we need a crash course in the mathematics behind quantitative genetics. Take a deep breath and continue reading.

Quantitative Genetics

Most phenotypic traits show a range of variation. With regard to juvenile survival, for example, some individuals will die quickly while others make it into adulthood. This phenotypic variation (V_P) is determined by genetic factors (V_G), environmental factors (V_E) and the interaction between genetics and environment (V_EG). Or if we put into a formula:

V_P = V_G + V_E + V_EG

Next, let’s focus on the genetic component (V_G). This part of the equation can be divided into three terms. The first term – additive genetic variance (V_A) – captures the effect of an allele on a particular phenotype, causing it to deviate from the population mean. For example, imagine that a gene occurs in two variants: A and B. Individuals with variant A might show survival rates above the mean, while individuals with variant B survive lower than average. This variation can be captured in the term V_A. The other two terms concern interactions between alternative alleles or different genes. The term V_D focuses on dominance effects, such as variant X being dominant over variant Y. And the term V_I captures interactions between different genes. These terms are less important for this blog post, but I mention them to provide the entire picture. Putting it all together gives this formula:

V_G = V_A + V_D + V_I

Splitting it up

Now that we have covered the basics of quantitative genetics, we can explore the findings of this study. The researchers focused on the additive genetic variance (V_A) of juvenile survival. The value of V_A can provide insights into the average fitness in a population. High values suggest plenty of genetic variation available for adaptation, while low values point to possible constraints. Scientists can calculate V_A for particular phenotypes using mathematical “animal models”. I will not go into the details of these models, but you can check this paper for more information. Most models calculate V_A for the entire population without taking into account potential population structure. Here, the new study comes into play. Jane Reid and her colleagues decided to split V_A into two parts: the genetic variance in the local population (a_i) and the genetic variance from immigrant birds (q_i). To quantify the genetic difference between local birds and several immigrant populations, the researchers added a factor g to the mix. To put it into a formula (the last one, I promise):

V_A = a_i + g.q_i

Migration-Selection Balance

With all the ingredients in place, we can finally look at the results from the analyses. When focusing on the local population, the breeding value for juvenile survival (a_i) increased over time (between 1993 and 2018). In other words, juveniles with local parents had a higher chance of surviving into adulthood. The situation was drastically different from the immigrants. The contribution of immigrant genes lead to decreased breeding values (q_i) over the years. This means that juveniles with an immigrant parent had a lower chance of reaching adulthood. The two effects – from the local population and from immigration – counteracted each other, resulting in a stable value for the total additive genetic variance (V_A). This situation can be seen as a migration-selection balance where alleles from other populations are removed from the population through the low survival of juveniles.

The breeding values for the local population increase over time (figure A), while the values from immigrants decrease (figure C). Both effects balance each other out in the total additive genetic variance (figure E). Red dots indicate the arrival immigrant birds. From: Reid et al. (2021).

Overestimation

This study nicely shows the potential negative consequences of gene flow. Genetic variation from immigrant birds leads to lower juvenile survival. This effect would not have been apparent if the researchers had not discriminated between local birds and immigrants. Indeed, analyses without the immigrant effect resulted in an overestimation (by 47%) of the additive genetic variance for juvenile survival. The exact mechanisms behind the immigrant effect remain to be determined, but could be related to local adaptation or the dispersal of low-quality individuals. Regardless of the underlying mechanism, these findings highlight the importance of taking population structure into account when running animals models. More accurate fitness estimates will help us better understand the evolutionary changes in wild bird populations.

References

Reid, J. M., Arcese, P., Nietlisbach, P., Wolak, M. E., Muff, S., Dickel, L., & Keller, L. F. (2021). Immigration counter‐acts local micro‐evolution of a major fitness component: Migration‐selection balance in free‐living song sparrows. Evolution Letters, 5(1), 48-60.

Featured image: Song Sparrows (Melospiza melodia) © Frank Schulenburg | Wikimedia Commons

Using evolution in conservation: Genomic vulnerability of the Little Greenbul

Taking into account future climatic changes.

You are probably familiar with the words of Theodosius Dobzhansky: “Nothing in biology makes sense except in the light of evolution.” The statement has been applied to many different disciplines, including conservation biology. If we want to prevent species from going extinct, we need to understand how they evolve. This knowledge is especially relevant in the context of current climate change where species are forced to adapt, move or die. By studying how certain species coped with past climatic changes, we can gain insights into possible future responses and take appropriate conservation measures. A recent study in the journal Evolutionary Applications focused on the Little Greenbul (Andropadus virens) in Central Africa. How will this passerine deal with future environmental changes?

Genomic Vulnerability

The researchers tried to estimate the “genomic vulnerability” of the Little Greenbul. This concept refers to the mismatch between current and predicted genomic variation based on current relationships between genotypes and environmental variables. If this sounds like jibber jabber to you, let me walk you through the different steps. First, the researchers captured the genetic variation across populations of the Little Greenbul (using RADseq). Next, they correlated the uncovered genetic variants with environmental variables, such as temperature and precipitation. The resulting correlations give an indication which genotypes are associated with particular environmental conditions. For example, a genetic variant (or SNP) on chromosome 11 might correlate strongly with local rainfall, suggesting it is involved in local adaptation to wet or dry conditions. Finally, the researchers modelled future climatic changes (in 2080) and other disturbances, such as logging and mining, and correlated the current genomic variation with these future conditions. The degree of mismatch in genotype-environment correlations for the current and the future situation gives an indication of the genomic vulnerability of a species. If a correlation remains similar, there is no problem. But if a correlation weakens or disappears in the future, the Little Greenbul is in trouble.

Rapid Evolution Required

The analyses revealed that populations in coastal and central areas of Cameroon will require large changes in genomic variation, while populations in forest-savannah transitions are relatively safe. The situation is nicely illustrated in the map below where green areas correspond to low genomic vulnerability and red areas to high genomic vulnerability. The authors note that “in the most genomically vulnerable areas of Cameroon, they will need to evolve at a rate faster than they have done since the LGM [i.e. last glacial maximum] – a magnitude of change in 50 years likely beyond the limits of biological reality.” That is bad news for the Little Greenbul.

A map of Cameroon showing the genomic vulnerability of the Little Greenbul based on the genomic mismatch between current and future conditions. From: Smith et al. (2021).

Future Distributions

This study nicely shows how we can use evolutionary information in conservation research. In particular, these results highlight that we should not only focus on the current distributions of endangered species, but also take into account future range shifts. Conservation often gives the impression of preserving a static situation, but the reality is that the world is constantly and rapidly changing. And we have to keep up.

References

Smith, T. B., Fuller, T. L., Zhen, Y., Zaunbrecher, V., Thomassen, H. A., Njabo, K., … & Harrigan, R. J. (2021). Genomic vulnerability and socio‐economic threats under climate change in an African rainforest bird. Evolutionary Applications, 14(5), 1239-1247.

Featured image: Little Greenbul (Andropadus virens) © Francesco Veronesi | Wikimedia Commons

Resolving the White-eye phylogeny

Genetic analyses detect three main clades in Indo-Africa, Asia and Australasia.

It only took the genus Zosterops – or white-eyes – about 3 million years to diversify into more than 100 species. Indeed, Jared Diamond referred to these birds as “great speciators”. On this blog, I have covered a few studies on the evolution of particular species (see for example here and here). However, the large-scale phylogeny of the white-eyes remains largely unresolved. Many species are morphologically indistinguishable, making it difficult to determine evolutionary relationships. Moreover, several species of white-eye are known to hybridize, potentially complicating phylogenetic analyses. Resolving the white-eye phylogeny is thus a challenging endeavor. But that did not scare off Chyi Yin Gwee, Kritika Garg, Balaji Chattopadhyay and their colleagues from taking a genomic approach. Their findings recently appeared in the journal eLife.

Three Clades

The researchers extracted DNA from historical and recent samples, representing 33 species from the southern hemisphere. Using specific RNA-probes, they sequenced more than 800 loci across the genome. A variety of phylogenetic methods converged on the same evolutionary tree, showing three main clades that correspond to Indo-Africa, Asia and Australasia. However, the phylogenetic relationships between these three clades could not be resolved confidently. This lack of resolution at the base of the phylogeny can be explained by a rapid succession of speciation events or ancient hybridization. More detailed analyses are needed to untangle this complex web. 

Phylogenetic analyses uncovered three main clades that are centered in Indo-Africa (yellow), Asia (red) and Australasia (blue). The arrows in the phylogenetic tree indicate introgression between certain species. From: Gwee et al. (2020).

Introgression and Conservation

In the figure above, you might have noticed two species without a color: Black-capped White-eye (Z. atricapilla) and Hume’s White-eye (Z. auriventer). The phylogenetic position of these species – which can be found on the Sunda Islands – could not be determined as different methods gave different results. Additional analyses pointed to introgression with other species. Specifically, the sharing of genetic variation between the Sundaic species and two Australasian species – the Sangkar White-eye (Z. melanurus) and the Shy-bellied White-eye (Z. citrinella) – suggests ancient introgression between the ancestors of these species. In other words, it’s complicated. These results also question whether the evolutionary history of white-eyes can be captured in a bifurcating tree. A network approach might be more suitable.

Finally, the researchers noted that all three main clades overlap in the Indonesian archipelago, indicating that this area is an evolutionary hotspot for the diversification of the genus Zosterops. This finding has important consequences for conservation.

The identification of areas in western Indonesia as a major center of modern phylogenetic diversity not only contributes to their recognition as an arena of important evolutionary processes, but also elevates their status as a region of global conservation relevance.

References

Gwee, C. Y., Garg, K. M., Chattopadhyay, B., Sadanandan, K. R., Prawiradilaga, D. M., Irestedt, M., … & Rheindt, F. E. (2020). Phylogenomics of white-eyes, a ‘great speciator’, reveals Indonesian archipelago as the center of lineage diversity. Elife, 9, e62765.

Featured image: Black-capped White-eye (Zosterops atricapilla) © Lip Kee | Wikimedia Commons