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

Rapid morphological evolution in the Silvereye: random processes or selection?

A clever combination of morphological and genomic analyses provide the answer.

Evolution is often depicted as a slow and gradual process that we cannot observe during our lifetime. However, evolutionary changes can happen relatively fast. When a few individuals colonize a new area, they get exposed to novel selective pressures and the population might show rapid morphological changes. In addition, the random sampling effect during the founding event can also speed up evolution. The newly arrived members might be a biased sample from the source population. For example, bigger birds might be more likely to reach an isolated island. It is, however, often extremely difficult to determine whether natural selection or random processes are driving the rapid morphological changes.

One approach is to study a recent colonization event and calculate the Ne* statistic, which was introduced by Lande (1976). This statistic can be applied to a morphological trait and indicates the effective population size that is required to explain morphological shifts by random processes alone. Next, the resulting Ne* can be compared with the actual effective population size (Ne). If this actual population size is larger than the Ne*, then drift is insufficient to explain the morphological changes and selection needs to be invoked.

French Polynesia

Calculating a statistic is relatively straightforward, but where can we find a recent colonization event? In 1937, the aviculturist Eastham Guild introduced the silvereye (Zosterops lateralis) to the island of Tahiti in French Polynesia. The introduced population persisted in low numbers until the late 1950s after which they expanded into all habitat types on the island, and later even dispersed to ten other islands in the archipelago. A recent study in the journal Heredity took advantage of this situation and closely studied morphological evolution of these silvereye populations.

Ashley Sendell-Price and his colleagues measured several morphological traits for almost 200 silvereyes. For each trait, they calculated Lande’s statistic Ne* and compared it with the actual effective population size. These analyses showed that most rapid morphological shifts could be explained by random processes alone. There were, however, some exceptions, such as the morphology of the bill. These exceptions were supported by additional genomic analyses.

Colonisation history of the silvereye across islands of French Polynesia. From Sendell-Price et al. (2020) Heredity.

Candidate Genes

Apart from the morphological analyses, the researchers performed a genomic scan to detect genes under positive selection. This exercise led to a list of 12 candidate genes. Here are the most relevant ones that have been found in other bird species:

• VPS50: associated with bill length in Berthelot’s pipit (Anthus berthelotii)
• VPS13B: under directional selection between species of Darwin’s finches
• NFIA: associated with bill length in the house sparrow (Passer domesticus)
• PTDSSI: under directional selection in birds of paradise
• OSR2: experimentally demonstrated to play a role in beak development in birds

The remaining candidate genes (E2F4, FREM2, PBX3, RALGPS1, TMC6 and ZMYND11) are all associated with craniofacial disorders in several non-avian species. Taken together, the morphological and genomic results indicate that the observed morphological shifts within the French Polynesian population of silvereyes are due to a combination of random and selective processes.

Overview of candidate genes under positive selection in different silvereye populations across French Polynesia. From Sendell-Price et al. (2020) Heredity.

References

Sendell-Price, A. T., Ruegg, K. C., & Clegg, S. M. (2020). Rapid morphological divergence following a human-mediated introduction: The role of drift and directional selection. Heredity, 124(4), 535-549.

Featured image: Silvereye (Zosterops lateralis) © Bernard Spragg | Wikimedia Commons

The evolution of the genomic landscape in Silvereyes does not follow theoretical predictions

The accumulation of genetic differences is unrelated to the development of genomic islands.

Imagine going for a walk through a mountainous region. You work your way up steep slopes, venture into valleys and stroll across expansive plateaus. You don’t even have to go outdoors to explore such heterogenous landscapes, just sequence a few genomes and compare the level of genetic differentiation of two species along these seemingly endless stretches of A, T, C and Gs. Indeed, numerous studies have described a heterogenous genomic landscape with highly divergent mountains and undifferentiated valleys. I have made my modest contribution to this field of research by exploring the genomic landscape of two goose taxa (you can read the whole story here).

The mechanisms responsible for these heterogenous genomic landscapes are still a matter of debate. The most often invoked verbal model goes as follows. At the onset of speciation, genetic differentiation is restricted to a few genomic regions that are under strong selection, resulting in peaks of divergence (the so-called “genomic islands”). As the speciation process continues and the diverging populations go their separate evolutionary ways, these genomic islands are predicted to expand through the linkage with neutral and weakly selected loci. This process – known as genetic hitchhiking – can be influenced by gene flow. The exchange of DNA between the diverging populations can homogenize certain genomic regions and slow down the expansion of genomic islands.

Testing Predictions

These theoretical predictions make intuitive sense but remains to be tested in different study systems. One possible approach is to compare diverging populations at different stages of the speciation process. A recent study in the journal G3: Genes|Genomes|Genetics applied this approach to the Silvereye (Zosterops lateralis), comparing population pairs that varied in their divergence timeframes (early stage:,150 years, mid stage: 3,000-4,000 years, and late stage: 100,000s years) and their mode of divergence (with gene flow or without gene flow).

In contrast to the predictions outlines above, the researchers did not find support for the genetic hitchhiking model. They write that “Genomic islands were rarely associated with SNPs putatively under selection and genomic islands did not widen as expected under the divergence hitchhiking model of speciation.” It seemed that the build-up of genetic divergence mostly occurred outside genomic islands. In addition, simulations suggested that the transition from localized divergence to genome-wide divergence can proceed without selection. All in all, these results question the theoretical model of genetic hitchhiking.

In contrast to the predictions of the genetic hitchhiking model, the genomic islands of differentiation did not expand with increasing divergence times. From: Sendell-Price et al. (2020) G3: Genes|Genomes|Genetics.

Theory and Practice

The authors concluded that “Genome-wide divergence in silvereyes does not hinge on the formation and growth of genomic islands.” Does this mean that we should discard the genetic hitchhiking model of speciation? Not necessarily, because the current study focused on recently diverged populations (with a late stage of ca. 100,000 years). Perhaps genetic hitchhiking becomes more apparent at larger times scales, such as millions of years. Comparisons between more diverged Zosterops species are needed to confirm this.

This study nicely illustrates the interplay between theory and practice. The genetic hitchhiking model is based on solid, theoretical thinking and provides several testable predictions (as a good model should). Results that are not in line with these predictions will help to improve the theoretical model (or discard it if too many incongruent observations start piling up). Hence, with rigorous analyses and the fine-tuning of our thinking, we slowly expand our knowledge on the genomic mechanisms underlying the origin of new species. This quote from Yogi Berra seems like fitting end to this blog post: “In theory there is no difference between theory and practice. In practice there is.”

References

Sendell-Price, A. T., Ruegg, K. C., Anderson, E. C., Quilodrán, C. S., Van Doren, B. M., Underwood, V. L., Coulson, T. & Clegg, S. M. (2020). The genomic landscape of divergence across the speciation continuum in island-colonising silvereyes (Zosterops lateralis). G3: Genes|Genomes|Genetics, 10(9), 3147-3163.

Featured image: Silvereye (Zosterops lateralis) © Bernard Spragg | Wikimedia Commons

The constrained evolutionary trajectories of White-eyes on the African mainland and its islands

The patterns of constrained evolution suggest a non-adaptive radiation.

There is more to evolution than adaptation. This message was conveyed by Stephen Jay Gould and Richard Lewontin in their 1979 paper with the wonderful title “The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.” In this paper, they argued that evolutionary thought has been dominated by the idea that organisms can be broken up into separate traits that are driven to an optimum by natural selection. Researchers would tell an “evolutionary story” to describe the most likely trajectory for a particular adaptation. Gould and Lewontin criticized this approach and proposed an alternative perspective that focuses on non-adaptive processes. Organisms should be analyzed as integrated wholes, with a bauplan that is constrained by phylogenetic history, developmental pathways, and general architecture. Some traits are not the optimal outcome of natural selection, but rather the byproduct of constrained, non-adaptive processes.

 

White-eyes

A similar discussion can be applied to the evolution of species-rich groups, such as island radiations. An often-heard explanation is that an ancestral population arrived on the island and diversified into several species that each adapted to a particular ecological niche. A well-studied case that immediately comes to mind is the Darwin’s Finches, a textbook example of an adaptive radiation. But this reasoning cannot automatically be applied to other radiations on islands on or the mainland. There might also be examples of non-adaptive radiations.

A recent study in the Journal of Biogeography took a closer look at the White-eyes (genus Zosterops). These small songbirds have been called “the Great Speciator” because they have diversified into more than 100 species in the last two million years. But are they also an example of an adaptive radiation? To answer this question, Julia Day and her colleagues performed a morphological analysis of 120 Afrotropical species.

The evolutionary tree of the White-eyes shows an early burst in diversification (warm colors) followed by a slowdown later on (cold colors). From: Day et al. (2020) Journal of Biogeography.

 

Exploring Morphospace

The analyses revealed a striking difference between mainland and island species. On the mainland, morphological evolution seems to be constrained, leading to convergence on certain phenotypes. In particular, White-eyes repeatedly evolve into highland or lowland forms. This pattern suggests that mainland White-eyes are “stuck” in an adaptive landscape with two optima. This constrained evolution can be due to the general morphology of these birds which does not allow for the evolutionary exploration of other phenotypes, or the lack of available niches due to competition with other species.

The situation on islands is slightly different. Here, different White-eye species have evolved novel phenotypes. The authors suspect that the evolution of different morphologies in island species might be due to less interspecific competition, allowing the birds to explore new ecological niches. However, the expansion of morphospace is still limited around the general bauplan of a typical White-eye, indicating that certain phylogenetic or developmental constraints might be at play here. Based on these patterns, the researchers concluded that “Given the apparent lack of ecological diversification, and limited insular diversification in Zosterops, the general pattern observed in this group may be explained by geographical speciation involving non-adaptive radiation.”

Figures a and b: Morphospace occupation of mainland species from the highland (green) and lowland (khaki). Figures c and d: Morphospace occupation of island radiations. Notice the overlap in mainland species and the separation in island species. From: Day et al. (2020) Journal of Biogeography.

 

References

Day, J. J., Martins, F. C., Tobias, J. A., & Murrell, D. J. (2020). Contrasting trajectories of morphological diversification on continents and islands in the Afrotropical white‐eye radiation. Journal of Biogeography, 47(10), 2235-2247.

Featured image: Cape white-eye (Zosterops pallidus) © Lip Kee | Wikimedia Commons

Solving the paradox of the great speciator on the Solomon Islands

Rapid loss of dispersal might be key to explain rapid speciation on islands. 

Charles Darwin called the origin of new species “that mystery of mysteries”. And despite decades of intensive evolutionary research, there are still several unsolved questions on speciation. One of my personal favorites is “the paradox of the great speciators”. This conundrum – which would make a great movie title – refers to avian species complexes that occur on islands with different levels of geographic isolation: from narrowly separated to very remote islands. Each island has its own endemic and genetically differentiated population (sometimes considered distinct species or subspecies). This situation raises the question of how some species complexes can disperse over a wide area, often coming into secondary contact and experiencing consequent gene flow, and still rapidly give rise to new species. To solve this paradox, ornithologists have often turned to the White-eyes (family Zosteropidae). This group of birds can be found across the Old World, but also on the archipelagos of the Pacific Ocean where they diversified into numerous (sub)species. A recent study in the journal Evolution focused on White-eyes of the Solomon Islands to find an answer to the paradox of this great speciator.

An overview of the different Zosterops populations on the Solomon Islands. From: Manthey et al. (2020) Evolution.

 

Gene Flow Patterns

To understand how new White-eye species evolve on these islands, we need to know how isolated the different islands populations are from one another. Therefore, Joseph Manthey and his colleagues collected DNA samples across the Solomon Islands to reconstruct patterns of gene flow. Using the software TreeMix, the researchers were able to reconstruct the historical relationships between the island populations and pinpoint gene flow events (indicated with red arrows in the figure below). The findings from TreeMix were supported by other statistical tests, such as D-statistics.

Interestingly, these analyses suggested gene flow between distant populations, but not between nearby islands. For example, there has been gene flow between Grey-throated White-eye (Zosterops ugiensis) and Yellow-throated White-eye (Z. metcalfii) that are separated by at least 50 kilometers of deep waters. In contrast, species in the New Georgia Group, such as Vella Lavella White-eye (Z. vellalavella) and Ranongga White-eye (Z. splendidus), are only a few kilometers apart but do not exchange genetic material. Moreover, the populations on neighboring islands are genetically and morphologically distinct, indicating rapid evolution.

The TreeMix analysis shows the historical relationships between the island populations with several gene flow events (indicated with red arrows). From. Manthey et al. (2020) Evolution.

 

Loss of Dispersal

What can explain these peculiar patterns?  The researchers offer two explanations for the lack of gene flow between neighboring islands: (1) these species do not venture across the narrow straits, or (2) they do visit neighboring islands but they do not mix with the resident species due to differences in plumage or song which evolve rapidly. Because species from distant islands can still interbreed, the researchers argue that the first explanation (a loss in dispersal) is the most likely explanation for the gene flow patterns at nearby islands. After a highly dispersive phase of island colonization, the newly established populations would immediately experience strong selection for reduced dispersal.

I would add another aspect to this scenario. Perhaps the selection for reduced dispersal is related to reproductive isolation between different islands (explanation 2). Early in this process, dispersing individuals end up on neighboring islands and occasionally manage to interbreed with the resident species. However, the resulting hybrids fail to reproduce because their intermediate phenotype prevents them from finding a suitable mate. Over time, this selection against hybrids could strengthen reproductive isolation between the parental species (i.e. a process known as reinforcement). Later on, dispersing birds stop interbreeding with their neighbors, increasing selection against dispersing individuals. Whether this idea makes sense remains to be tested. But slowly we are getting closer to understanding rapid speciation on islands and solving the paradox of the great speciator.

 

References

Manthey, J. D., Oliveros, C. H., Andersen, M. J., Filardi, C. E., & Moyle, R. G. (2020). Gene flow and rapid differentiation characterize a rapid insular radiation in the southwest Pacific (Aves: Zosterops). Evolution, 74(8), 1788-1803.

Featured image: Warbling White-eye (Zosterops japonicus) © Obubu Interns

 

This paper has been added to the Zosteropidae page.

The Great Speciator strikes again: Discovery of a Mangrove White-eye in Saudi Arabia

A mangrove population of White-eyes is morphologically distinct from other subspecies of the Abyssinian White-eye.

The constant interplay between speciation and extinction gives rise to the phylogenetic tree of life that evolutionary biologists are trying to reconstruct. Some branches on this tree used to be diverse, but have dwindled down to a few lonely twigs. Think of the Coelacanth (Latimeria chalumnae) or the Hoatzin (Opisthocomus hoazin) that each represent an entire order (check out this video by SciShow about these and other “evolutionary loners”). Other branches, however, are in full bloom, sprouting new species at record-breaking speed – evolutionary speaking. One example concerns the bird family Zosteropidae or white-eyes with over 100 species that originated in the last two million years, earning this group of birds the honorary title of “Great Speciator”. In a recent Journal of Ornithology paper, researchers present what could be the newest addition to this species-rich family.

 

Subspecies

The biggest diversity of white-eyes can be found on tropical islands, although an analysis of African taxa revealed numerous undescribed species. Another uncharted territory is the Middle East where you can find the Abyssinian White-eye (Zosterops abyssinicus). This small songbird has been split into four subspecies:

• abyssinicus in eastern Sudan, Eritrea, and northern and central Ethiopia
• omoensis in western Ethiopia and possibly eastern South Sudan
• socotranus on the island of Socotra (Yemen), and in coastal northern Somalia
• arabs in southwest Saudi Arabia, Yemen, and southwest Oman

An expedition in 1994 discovered a population of White-eyes in a mangrove, located in southwest Saudi Arabia between the villages of Shuqaiq and Amaq. This location suggests that they belong to the subspecies arabs, but the researchers were surprised by the small size and brighter plumage of these birds. Could they belong to a new subspecies?

Left: A montane Abyssinian White-eye (Zosterops abyssinicus arabs) from the Asir Province in Saudi Arabia. Right: A “Mangrove White-eye” (Zosterops sp. indet.) from the Jazan Province in Saudi Arabia. From: Babbington et al. (2020) Journal of Ornithology

 

Morphological Differences

During new expeditions (in 2015-2016) four individuals of this newly discovered “Mangrove White-eye” were caught. Morphological analyses revealed that these birds were significantly smaller than the montane subspecies arabs. Moreover, plumage patterns were clearly different, concisely described in the study.

First, the ‘Mangrove White-eye’ was noticeably more brightly coloured, with much more yellow-green in the head and upperparts. Second, the bright yellowish outer webs to all flight feathers of the ‘Mangrove White-eye’ gave it a prominent yellowish wing panel that was not obvious on Abyssinian White-eye Z. a. arabs. Third, the underparts of ‘Mangrove White-eye’ were slightly buffer than Abyssinian White-eye Z. a. arabs, and the former had more obvious yellow undertail-coverts.

From a morphological point of view, the “Mangrove White-eyes” are thus distinct from the other subspecies. What about genetics?

Morphological analyses clearly show that “Mangrove White-eyes” (green) are smaller than Abyssinian White-eyes (blue). From: Babbington et al. (2020) Journal of Ornithology

 

Matching Mitochondria

The researchers sequenced the mitochondrial gene cytochrome b for the “Mangrove White-eyes” and compared it to members of the Abyssinian White-eye subspecies arabs. The four mangrove specimens had identical DNA sequences, exactly the same as that of one Abyssinian White-eye individual. The other Abyssinian DNA sequences differed by just one or two nucleotides. From a genetic perspective, the Mangrove White-eyes are thus indistinguishable from the subspecies arabs. However, this conclusion is based on only one mitochondrial gene, there might be significant differences elsewhere in the genomes of these birds.

Based on the present data, the researchers suspect that the “Mangrove White-eyes” are the result of a recent colonization of mangrove habitats followed by rapid morphological evolution. Over time, this population might diverge genetically and could eventually give rise to a new (sub)species of White-eye. The Great Speciator keeps speciating…

The DNA sequences of ‘Mangrove White-eyes’ (green) are identical to one Abyssinian specimen (red). The others differ by a few nucleotides. From: Babbington et al. (2020) Journal of Ornithology

 

References

Babbington, J., Boland, C. R., Kirwan, G. M., & Schweizer, M. (2020). Morphological differences between ‘Mangrove White-eye’and montane Abyssinian White-eye (Zosterops abyssinicus arabs) in Arabia despite no differentiation in mitochondrial DNA: incipient speciation via niche divergence?. Journal of Ornithology, 1-10.