Adaptive potential of the endangered Antioquia wren

Reduced genetic diversity in neutral and functional markers raises a red flag.

In a recent perspective paper, João Teixeira and Christian Huber argued that “neutral genetic diversity has only very limited relevance for conservation genetics.” They indicated that there is no simple general relationship between neutral genetic diversity and the risk of species extinction. We should thus be careful when using this metric to assess the long-term survival of a species. However, conservation biologists should not completely discard neutral genetic diversity in their work (as explained in this paper). Neutral variation certainly plays a role in adaptation (see for example this blog post) and can be a sign of past genetic drift and inbreeding due to a low effective population size. Nonetheless, it only covers a small section of the total genetic diversity in a species. It is thus advisable to also quantify functional genetic diversity.

One group of genetic markers that can be used to probe functional genetic diversity are immune genes. These genes are expected to experience strong selective pressures due a variety of pathogens. They might thus provide insights into the adaptive potential of a species and its capacity to deal with changing conditions. A recent study in the journal Conservation Genetics focused on one class of immune genes – the Toll-like Receptors (TLRs) – to assess the level of functional genetic diversity in the endangered Antioquia Wren (Thryophilus sernai). The researchers also looked at several neutral genetic markers – microsatellites and the mitochondrial control region – to cover the different aspects of genetic diversity in this species.

Genome-wide nucleotide diversity is a poor predictor of IUCN’s Red List status. From: Teixeira & Huber (2021) PNAS.

Low Genetic Diversity

The Antioquia Wren is a recently described species that can be found in the Cauca river Canyon in Colombia. In recent years, this small passerine species has lost nearly 90% of its habitat, leading to a drastic population contraction to less than 1000 individuals (probably even below 250). The declining population is further threatened by the construction of the Ituango Hydroelectric project which flooded a significant section of its habitat. Conservation efforts might be warranted and it is thus important to understand the adaptive potential of this species in terms of genetic diversity.

Danny Zapata and his colleagues sequenced three genetic markers (microsatellites, mitochondrial control region and TLRs) for 31 individuals. The genetic analyses revealed low levels of genetic diversity in all markers. Hence, the researchers concluded that “these results suggest current low evolutionary potential for the species, as its reduced genetic diversity is expected to increase extinction risk by limiting the ability to cope with environmental changes.” Bad news for the Antioquia Wren.

Genetic diversity for two TLR-markers and the mitochondrial control region is very low. Only a handful of haplotypes were found across the range of the Antioquia Wren. From: Zapata et al. (2020) Conservation Genetics.

Immune Genes

However, the low genetic diversity of the immune genes might not be a big problem. A previous study on variation in Toll-like Receptors of the endangered Pale-headed Brushfinch (Atlapetes pallidiceps) found that individuals with low genetic diversity at these immune genes had higher survival rates. This finding suggests that this low diversity might be adaptive for the selection regime in a restricted habitat where the birds are exposed to few pathogen species. The current diversity in Toll-like Receptors of the Antioquia Wren could thus be beneficial in its limited distribution.

However, this potential benefit will probably not hold in the long run. The low genetic diversity at these immune genes – and at the neutral markers – diminishes the adaptive potential of this species, making it extremely vulnerable to changing conditions (which can be expected due to further habitat loss and climate change). Conservation efforts will need to be implemented soon.

References

Zapata, D., Rivera-Gutierrez, H. F., Parra, J. L., & Gonzalez-Quevedo, C. (2020). Low adaptive and neutral genetic diversity in the endangered Antioquia wren (Thryophilus sernai). Conservation Genetics21(6), 1051-1065.

Featured image: Antioquia Wren (Thryophilus sernai) © Andres Cuervo | Wikimedia Commons

How strong is reproductive isolation between Golden-winged and Blue-winged warbler?

A summary of a recent debate in the journal Ecology and Evolution.

The future of the Golden-winged Warbler (Vermivora chrysoptera) is threatened by habitat loss. In addition, it runs the risk of being outcompeted and “out-hybridized” by the invading Blue-winged Warbler (V. cyanoptera). The interactions between these two closely related species have a long history of scientific research (summarized on the Parulidae page). However, it is still unclear how strong the level of reproductive isolation between these warblers is. Recent work by David Toews and his colleagues pointed to six genomic regions that are highly divergent between Golden-winged and Blue-winged Warblers, of which four are likely involved in feather development or pigmentation. These findings suggest that differences in plumage patterns could act as a strong reproductive barrier. The strength of this potential barrier can be tested by quantifying the frequency of mixed pairings between different plumage types, and following the reproductive success of hybrids (if there are any).

A recent study in the journal Ecology and Evolution performed these measurements and reported strong reproductive isolation between Golden-winged and Blue-winged Warblers. However, another team of researchers questioned these results and indicated potential pitfalls in the analyses, to which the original authors responded. In this blog post, I will try to summarize the main arguments in this interesting debate.

Strong Reproductive Isolation?

Let’s start with the first study. To determine the degree of reproductive isolation between Golden-winged Warbler and Blue-winged Warbler, John Confer and his colleagues aggregated data on social pairing from nine studies. Apart from the two pure phenotypes, the researchers also considered two hybrid phenotypes: the “Brewster’s Warbler” and the “Lawrence’s Warbler”. These phenotypes were initially described as distinct species before they were recognized as hybrids. According to the model of Kenneth Parkes (1951), “Brewster’s Warblers” are first-generation hybrids between genetically pure Golden-winged and Blue-winged Warblers, while the “Lawrence’s Warbler” can be produced by crossing two first-generation hybrids.

The analyses revealed a low level of hybridization. Only 14 out of 1680 (0.9%) Golden-winged Warblers and 14 out of 583 (2.4%) Blue-winged Warblers paired up with another phenotype. These patterns indicate high levels of behavioral isolation between the different plumage phenotypes. Next, the researchers turned to the breeding success of the hybrid phenotypes. The pairing success of “Brewster’s Warblers” (54%) was significantly smaller compared to the pure Golden-winged (83%) and Blue-winged Warblers (77%). These percentages suggest some degree of sexual selection against hybrids. Putting it all together, the researchers calculated a reproductive isolation score of 0.96. Given that a score of 1 corresponds to complete reproductive isolation, this number indicates strong reproductive isolation.

The different phenotypes considered in the study: Golden-winged Warbler (V. chrysoptera; GWWA), Blue-winged Warbler (V. cyanoptera; BWWA), “Brewster’s” Warbler (hybrid; BRWA) and “Lawrence’s” Warbler (hybrid LAWA). From: Confer et al. (2020) Ecology and Evolution.

Three Points of Critique

A few months later, David Toews and his colleagues published a critique on this conclusion of strong reproductive isolation, raising three main issues. First, the plumage classification scheme in the original study is not suitable to determine hybrid ancestry in these warblers. Recent genetic work by Marcella Baiz and her colleagues showed that none of the six “Brewster’s Warblers” that they analyzed were first-generation hybrids (see this blog post for the details). Moreover, many warblers that look like pure phenotypes might actually contain some genetic ancestry from past hybridization. The original study did not take these “cryptic hybrids” into account.

A second issue that was not considered in the analyses concerns extra-pair copulations in which birds mate with other individuals besides their social partner. This phenomenon has been well-documented in Vermivora warblers and could significantly contribute to hybridization between Golden-winged and Blue-winged Warblers.

Finally, Toews et al. (2021) pointed out that behavioral isolation is not always sufficient to maintain complete reproductive isolation. For example, recent simulations by Darren Irwin showed that assortative mating on its own cannot prevent populations from merging, some form of postzygotic isolation is needed (see this blog post for the whole story). Although “Brewster’s Warblers” have lower pairing success compared to pure phenotypes, their reproductive output might still be too high to prevent genetic exchange. Hence, the authors of the critique argue that “extensive mixing in areas of sympatry is more consistent with low levels of total reproductive isolation—that is, both low pre-and postmating isolation—and results in high gene flow.”

The range of Golden-winged (orange) and Blue-winged (blue) Warblers. Areas of overlap are highlighted in light blue. From: Toews et al. (2021).

Counterarguments

Recently, the authors of the original study – this time led by Cody Porter – replied to the critique by Toews et al. (2021). First, with regard to the unsuitability of the plumage classification scheme, they explain that the complex genetic ancestry of the warblers (including cryptic hybrids) is actually not that relevant for their question. The focus of their study concerns different plumage phenotypes, not the whole genomic context. They write: “In essence, our study could be viewed as testing whether the six major genomic differences between V. chrysoptera and V. cyanoptera (which largely correspond to plumage differences; Toews et al., 2016) promote reproductive isolation.”

Second, they argue that extra-pair copulations were unlikely to bias their results, referring to the findings of Vallender et al. (2007). This study found only 3 cases of extra-pair copulations (ca. 1.5%) between different phenotypes. In two cases a hybrid female mated with a Golden-winged Warbler and in one case a Golden-winged Warbler female mated with a hybrid.

The third point of critique focuses on the contribution of behavioral isolation to the level of reproductive isolation. You need some degree of postzygotic isolation to prevent species from merging. Toews et al. (2021) argued that the reproductive success of the hybrids is still too high, facilitating gene flow between the species. The authors counter this argument by highlighting the 26% reduction in the pairing success of phenotypic hybrids compared to both parental forms and the fact that only 1.2% of birds with a “pure” phenotype paired with an individual of the alternative phenotype. These numbers “appear to fall well within the parameters for a stable hybrid zone according to Irwin’s (2020) simulations.”

The Verdict

You might be wondering who won this debate? I don’t think this is the right question to ask here. Both groups of authors approached the scientific conundrum of reproductive isolation from a different perspective. The original study focused on behavioral isolation on the phenotypic level, whereas the critique used the genomic patterns of introgression as a starting point. At first sight, the strong reproductive isolation between plumage phenotypes seems incompatible with the largely homogeneous genomes of these warblers. However, reproductive isolation is not complete (remember the score of 0.96), which seems to allow for enough gene flow to homogenize the majority of the genome. Only the genomic regions containing “plumage genes” are able to withstand this homogenizing force.

Similar patterns have been described in other avian systems, such as Hooded Crow (Corvus cornix) and Carion Crow (C. corone) or Taiga Bean Goose (Anser fabalis) and Tundra Bean Goose (A. serrirostris). A few divergent genomic regions seem to be sufficient for a high level of reproductive isolation. We need more studies that quantify reproductive isolation at the phenotypic level and provide a link with the genomic underpinnings of the isolation barriers. Studying the evolution of reproductive isolation from different perspectives – behavioral, morphological and genetic – will fuel healthy debates and will provide more insights into the origin of species.

References

Confer, J. L., Porter, C., Aldinger, K. R., Canterbury, R. A., Larkin, J. L., & Mcneil Jr, D. J. (2020). Implications for evolutionary trends from the pairing frequencies among golden‐winged and blue‐winged warblers and their hybrids. Ecology and Evolution10(19), 10633-10644.

Toews, D. P., Baiz, M. D., Kramer, G. R., Lovette, I. J., Streby, H. M., & Taylor, S. A. (2021). Extensive historical and contemporary hybridization suggests premating isolation in Vermivora warblers is not strong: A reply to Confer et al. Ecology and Evolution.

Porter, C. K., Confer, J. L., Aldinger, K. R., Canterbury, R. A., Larkin, J. L., & McNeil Jr, D. J. (2021) Strong yet incomplete reproductive isolation in Vermivora is not contradicted by other lines of evidence: A reply to Toews et al. Ecology and Evolution.

Featured image: Golden-winged warbler (Vermivora chrysoptera) © Bettina Arrigoni | Wikimedia Commons

These papers have been added to the Parulidae page.

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

Genetic evidence for hybridization between Magellanic and Humboldt penguins

Several genetic markers are useful to identify hybrids and backcrosses.

A few months ago, I published a scoring scheme to assess the reliability of hybrid reports (see this blog post). In short, this scheme is based on three criteria: (1) the observation of a putative hybrid with photographic evidence or a detailed description, (2) thorough morphological analyses in which the putative hybrid is compared with potential parental species, and (3) genetic analyses of the putative hybrid with reference material from potential parental species. To express the varying levels of confidence that each of these criteria provide, I weighted them differently in the final score for a putative hybrid, namely one point for an observation, two for a morphological analysis, and three for a genetic test. The final tally of these three criteria (ranging from 0 to 6 points) will indicate the level of confidence for a particular hybrid combination. I applied this scheme to the tinamous (family Tinamidae), resulting in one well-documented case and three doubtful records that require further investigation.

The goal is to apply this approach to other bird families in order to provide a better overview of the incidence and reliability of bird hybrids. A recent study in the journal Genetica summarized the literature on penguin hybrids and indicated that most hybridization studies were “based solely on morphological or nesting observations, with no genetic confirmation of hybridization.” In the context of the scoring scheme, most cases of penguin hybrids would thus receive a reliability score between 0 and 3 points. Clearly, more genetic studies are needed to determine the incidence of penguin hybrids. And the study in Genetica delivers a nice example for hybrids between Magellanic Penguins (Spheniscus magellanicus) and Humboldt Penguins (Spheniscus humboldti).

Genetic Markers

Eric Hibbets, Katelyn Schumacher and their colleagues focused on six individuals that were sampled at three colonies from the Atlantic Ocean basin (Caleta Valdés, Punta Tombo, and Cabo Dos Bahías). These birds were initially noted down as Magellanic Penguins, but were later identified as putative hybrids based on the presence of mitochondrial variants (of the COI gene) that are characteristic for Humboldt Penguins. The researchers tested this conclusion with three additional genetic markers: a set of six microsatellites, the immune gene DRβ1 and the sex-linked gene CDH1. They sequenced these markers for several reference samples from both species. The analyses revealed that “three of the four markers (COI, microsatellites, and DRß1) were informative because they provided both Magellanic and Humboldt species-specific alleles or haplotypes that could be used to trace species ancestry in hybrid individuals.”

Distribution ranges of Magellanic (S. magellanicus; light gray stripes) and Humboldt (S. humboldti; dark gray) penguins during the breeding season. Reference populations of Magellanic penguins include samples from three colonies in the Atlantic Ocean (Caleta Valdés, Punta Tombo, and Cabo Dos Bahías). From: Hibbets et al. (2020) Genetica

Backcrosses

What about the six putative hybrids? It turned out that four individuals were backcrosses with some degree of genetic introgression from Humboldt Penguins. The remaining two individuals were actually Humboldt penguins instead of hybrids. These results highlight the value of genetic analyses in hybrid detection. Morphological characters or field observations are not always reliable.

Detailed analyses revealed more admixed individuals among the reference samples. Five out of 37 penguins showed some genetic signs of past hybridization events. Interestingly, all five samples come from the Puñihuil colony, which holds a significant number of intermixed nesting sites of Magellanic and Humboldt penguins. More expeditions will probably uncover more penguin hybrids. And not just between Magellanic and Humboldt Penguins. A recent genomic study reported gene flow between several other species (see this blog post for the details). Who know what penguin hybrids will be discovered with genetic data.

Structure analysis of microsatellite and MHC loci of Magellanic and Humboldt penguin samples. Vertical bars represent individuals with assignment probabilities (Q, y-axis) to the Magellanic (gray) and Humboldt (white) populations. The grey and white horizontal bars below the assignment probabilities represent corresponding species-specific mitochondrial haplotypes of those individuals as determined by COI sequences. Asterisks (*) indicate individuals of hybrid origin that were identified by this study. From: Hibbets et al. (2020) Genetica

References

Hibbets, E. M., Schumacher, K. I., Scheppler, H. B., Boersma, P. D., & Bouzat, J. L. (2020). Genetic evidence of hybridization between Magellanic (Sphensicus magellanicus) and Humboldt (Spheniscus humboldti) penguins in the wild. Genetica148(5), 215-228.

Featured image: Magellanic penguin (Spheniscus magellanicus) © David | Wikimedia Commons

This paper has been added to the Sphenisciformes page.

The Pleistocene Arc Hypothesis explains the evolution of the Rufous-fronted Thornbird

Genetic patterns in this species follow the distribution of dry forests around Amazonia.

The evolution of South American birds is a complicated story, to put it mildly. Different species have been affected by different environmental barriers, such as the open vegetation corridor between the Andes and Amazonia or the myriad of rivers that crisscross the Amazon rainforest. And don’t forget about the climatic fluctuations during the Pleistocene (between 2.5 million and 11,000 years ago) which impacted vegetation patterns across South America, and consequently shaped the distribution patterns of the avifauna inhabiting certain vegetation types. For example, the evolutionary history of the Variable Antshrike (Thamnophilus caerulescens) was mainly driven by the expansion and contraction of forest habitat (see this blog post for the details). The evolution of this species follows the so-called “Rainforest Refugia Hypothesis”, which proposes that the fragmentation of the rainforests during cold and dry periods resulted in allopatric speciation by separating birds into distinct rainforest “refugia” surrounded by open habitat.

The “Rainforest Refugia Hypothesis” mainly focuses on birds in the wet rainforest, but what about species that inhabit dry forests? Their evolution might adhere to a related scenario: the “Pleistocene Arc Hypothesis” which states that dry periods might have promoted the expansion of dry forests, culminating in a continuous arc around the southern half of Amazonia from Peru to Brazil. A recent study in the journal Molecular Ecology tested this hypothesis for the Rufous-fronted Thornbird (Phacellodomus rufifrons), a common dry forest bird species.

Past Connections

Eamon Corbett and his colleagues collected samples across the range of the Rufous-fronted Thornbird, which has been divided into several subspecies that follow the distribution of dry forests around Amazonia (see figure below). Genetic analyses of the different populations uncovered patterns that are in line with the “Pleistocene Arc Hypothesis”. Specifically, the researchers found evidence that certain populations in currently distinct patches of dry forest were connected in the recent past.

For example, even though the subspecies peruvianus and sincipitalis are separated by more than 1000 kilometers of lush rainforest, they share genetic variants and show signatures of recent divergence. The authors write that “the most likely scenario is that peruvianus and sincipitalis were connected through formerly suitable habitat in central and southern Peru in the recent past, and that the large modern-day disjunction between them is a recent phenomenon.” Similarly, the subspecies sincipitalis and rufifrons are currently isolated by 500 kilometers of unsuitable Cerrado habitat, but they nonetheless show low genetic differentiation. Interestingly, the genetic splits between the different subspecies did not occur in the same time period, suggesting that particular patches of dry forest along the Pleistocene Arc became isolated at different times.

Range and sampling localities of the Rufous-fronted Thornbird, showing a highly disjunct distribution that corresponds to the extent of the dry forest biome. From: Corbett et al. (2020) Molecular Ecology.

Putative Hybrid Zone

Apart from the recent divergence between geographically isolated subspecies, the authors uncovered the opposite pattern between two neighboring subspecies (rufifrons and specularis). Although these subspecies have overlapping distributions in eastern Brazil, the genetic analyses pointed to a relatively deep divergence compared to the other subspecies. The exact geographic barriers responsible for this genetic divergence remain to be determined. The São Francisco River seems like an unlikely candidate because several rufifrons individuals were found on the other side of the river (where specularis resides) when following it inland. Perhaps the ecological transition between the dry Caatinga and wet Cerrado habitats can explain this genetic pattern?

Moreover, despite the deep genetic divergence between rufifrons and specularis, the researchers reported evidence for recent gene flow. There might thus be a hybrid zone between these subspecies in Brazil. The authors nicely set the stage for future research: “Detailed vocal, morphological, and genetic data at a fine geographic scale will be needed to illuminate the evolutionary dynamics at work in this putative contact zone.” As I wrote at the beginning of this blog post: the evolution of South American birds is a complicated story, to put it mildly.

References

Corbett, E. C., Bravo, G. A., Schunck, F., Naka, L. N., Silveira, L. F., & Edwards, S. V. (2020). Evidence for the Pleistocene Arc Hypothesis from genome‐wide SNPs in a Neotropical dry forest specialist, the Rufous‐fronted Thornbird (Furnariidae: Phacellodomus rufifrons). Molecular Ecology29(22), 4457-4472.

Featured image: Rufous-fronted Thornbird (Phacellodomus rufifrons) © Hector Bottai | Wikimedia Commons

This paper has been added to the Furnariidae page.

The Herring Gull complex is not a ring species

The evolution of this species complex does not follow the strict definition of a ring species.

If you enjoy watching educational videos on YouTube, I can recommend the channel Crash Course. Over the years, they have produced numerous online courses, ranging from artificial intelligence to world history. Currently, conservationist and ecologist Rae Wynn-Grant is hosting an interesting course on Zoology. The latest episode on species concepts (see video below) included a discussion on ring species, using the Herring Gull complex (Larus argentatus) as an example. While watching this video, I remembered a paper in the Proceedings of the Royal Society B showing that the Herring Gull complex is not a ring species. But why?

The concept of a ring species developed from a speciation model involving isolation-by-distance in which the most distant populations differentiate despite a chain of interconnected populations that continue to exchange genes. A special case of this “speciation by distance” concerns ring species, in which the chain of populations is wrapped around a geographical barrier and the populations at the end meet without interbreeding. The Herring Gull complex was often presented as an example of a ring species around the Arctic circle.

Two Scenarios

In his book Systematics and the Origin of Species, Ernst Mayr described his version of the evolutionary history of the Herring Gull complex. He envisioned that ancestral populations in Europe extended in two directions: One group moved west across Scandinavia towards Britain and Iceland differentiating into dark-mantled lesser black-backed gulls (fuscus, intermedius and graellsii), while another group went east, giving rise to the progressively paler-mantled forms taimyrensis (Taimyr), birulai and vegae (eastern Siberia), and into North America (smithsonianus). Later on, the North American herring gulls crossed the North Atlantic and invaded Europe, giving rise to argentatus and argenteus, which now overlap with lesser black-backed gulls. This scenario depicted a circumpolar chain of populations connected by gene flow, resulting in the reproductively isolated herring gulls and the lesser black-backed gulls at the ends of the circle in Europe. A ring species. (Note that the Crash Course video does not accurately depict this scenario).

In 2004, Dorit Liebers and her colleagues tested this scenario with genetic data. Using mitochondrial DNA, they reconstructed the evolutionary history of the Herring Gull complex. Their analyses uncovered a more complicated picture compared to the ring species scenario described by Mayr. During the Ice Ages, two ancestral lineages originated in a North Atlantic refugium and a continental Eurasian refugium. From these locations, different gull populations spread across Eurasia and North America. These genetic patterns do not fit a model of speciation by distance. Indeed, the authors write that “not isolation by distance, but vicariance and subsequent range expansion […] were the processes that played the decisive role in the evolution of the herring gull complex.” The situation is even more complicated due to gene flow between several populations, as shown by a more recent genetic study.

Moreover, reproductive isolation in regions of overlap is not the outcome of isolation by distance, but is mainly due to genetic differentiation in allopatry. For example, marinus was probably isolated in northeastern North America before making secondary contact with smithsonianus in North America and with argentatus and fuscus in Europe.

Two hypotheses about the differentiation and colonization history of the herring gull complex based on (a) Mayr (1942) and (b) Liebers et al. (2004). Current ranges are shown in green (from an Atlantic refugium, green circle) and brown (Aralo-Caspian refugium, brown circle). The checkerboard pattern indicates areas of overlap.

Avian Examples?

So, the Herring Gull complex is not a ring species. Other avian examples of ring species have been shown to not adhere to the strict definition of a ring species (i.e. isolation by distance and reproductive isolation between the end points of the ring), such as the Great Tit (Parus major) in Eurasia and the Greenish Warbler (Phylloscopus trochiloides) in Asia. These findings suggest that ring species are probably a rare phenomenon, as nicely described in the paper on the Herring Gull complex.

In conclusion, although ring speciation is theoretically possible, the few well-studied examples suggest that it occurs infrequently, because the dynamics of species’ ranges are more likely to result in fragmentation, i.e. periods of allopatry, before the slow process of isolation by distance leads to sufficient divergence to allow for circular overlap.

References

Alcaide, M., Scordato, E. S., Price, T. D., & Irwin, D. E. (2014). Genomic divergence in a ring species complex. Nature511(7507), 83-85.

Kvist, L., Martens, J., Higuchi, H., Nazarenko, A. A., Valchuk, O. P., & Orell, M. (2003). Evolution and genetic structure of the great tit (Parus major) complex. Proceedings of the Royal Society of London. Series B: Biological Sciences270(1523), 1447-1454.

Liebers, D., De Knijff, P., & Helbig, A. J. (2004). The herring gull complex is not a ring species. Proceedings of the Royal Society of London. Series B: Biological Sciences271(1542), 893-901.

Martens, J., & Päckert, M. (2007). Ring species–do they exist in birds?. Zoologischer Anzeiger-A Journal of Comparative Zoology246(4), 315-324.

Sonsthagen, S. A., Wilson, R. E., Chesser, R. T., Pons, J. M., Crochet, P. A., Driskell, A., & Dove, C. (2016). Recurrent hybridization and recent origin obscure phylogenetic relationships within the ‘white-headed’gull (Larus sp.) complex. Molecular phylogenetics and evolution, 103, 41-54.

Featured image: Herring Gull (Larus argentatus) © Ввласенко | Wikimedia Commons

Studying the global conquest of the Common Starling with haplotype networks

Recent study compares the genetic diversity of three independent invasions.

If there is one species that deserves the adjective “common” in its name, it is definitely the Common Starling (Sturnus vulgaris). This noisy songbird can be found on every continent (except Antarctica). Starlings are native to the Palearctic but have been repeatedly introduced in other locations. In a previous blog post, I described how the Common Starling conquered Australia where it spread across the island after its release in the 1850s. Similar introductions occurred in North America as part of an American Acclimatization Society initiative to populate Central Park with the birds from Shakespeare’s plays. This initiative led to the release of 60 individuals in 1890 and an additional 40 in 1891. The introduction in South Africa was more modest with about 18 individuals being released around 1897. In each case, the starlings managed to get a foothold and establish stable populations. Their success has been attributed to their generalist diet and their ability to quickly change their migratory behavior.

These three independent introduction events (North America, Australia and South Africa) all started with small populations that quickly expanded. How has this impacted the genetic make-up of the current starling populations? A recent study in the journal Ecology and Evolution compared genetic diversity at the mitochondrial control region to answer this question.

Haplotypes

Before we dive into the results of this study, we need to understand the concept of a haplotype. This commonly used term refers to a DNA sequence of genetic variants that are inherited as a whole. By comparing different haplotypes and identifying particular mutations, we can construct a haplotype network that visualizes the connections between the haplotypes. Imagine that we sequenced a short DNA sequence in four individuals:

  • Individual 1: AAAA
  • Individual 2: AAAA
  • Individual 3: AATA
  • Individual 4: AATC

We can clearly see that individuals 1 and 2 have the same haplotype (AAAA) while individual 3 has one mutation (T instead of A) and individual 4 has two mutations (TC instead of AA). The relationships between these four individuals can be depicted by circles (representing the haplotypes) connected by lines. The size of the circles indicates the number of individuals with a particular haplotype and the length of the line signifies the number of mutations separating two haplotypes. Hence, the haplotype network for our example looks like this. The different colors indicate the sampling locations: individuals 1, 2 and 3 come from one area (in blue), whereas individual 4 was found somewhere else (in green).

An example of a haplotype network. See text for the explanation.

Source Populations

The researchers constructed a haplotype network using almost 1000 samples from North America, Australia, South Africa and the United Kingdom. They found a total of 64 unique haplotypes that revealed some interesting patterns. In the haplotype network, the South African samples form a separate cluster (in light gray) from the other locations. A more detailed look at the network shows that only one haplotype (H25) is shared by the other two non-native areas, namely North America and Australia. These results suggest that the different introduction events used Common Starlings from different parts of the United Kingdom. To pinpoint the exact source populations, more genetic data is needed.

A network of Common Starlings from the native-range (United Kingdom, black) and three invasive populations (North America, dark gray; Australia, white; South Africa, light gray) constructed using 928 bp of mitochondrial control region haplotypes. From: Bodt et al. (2020) Ecology and Evolution.

Population Expansion

Unsurprisingly, all three invasive populations showed a reduction in genetic diversity compared to the native populations from the UK, reflecting the genetic bottlenecks that occurred at the onset of the introductions. This finding indicates that a low level of genetic diversity of no insurmountable obstacle for the rapid spread of the Common Starling. However, not all invasive populations showed genetic signatures of this expansion. The researchers found genetic support for population expansion in both North America and Australia, but the analysis of South African data did not support a sudden expansion model. Possibly, the South African population is still in a lag-phase following the introduction. The population might be slowly expanding until it reaches a certain threshold that triggers a more explosive expansion. Or the spread of South African starlings is being slowed down by other processes, such as adverse climatic conditions or competition with native species. As always, more research is needed to figure this out. And while ornithologists keep studying these invasions, the Common Starlings will probably keep expanding.

The worldwide distribution of the Common Starling. From: Wikimedia Commons.

References

Bodt, L. H., Rollins, L. A., & Zichello, J. M. (2020). Contrasting mitochondrial diversity of European starlings (Sturnus vulgaris) across three invasive continental distributions. Ecology and Evolution10(18), 10186-10195.

Featured image: Common Starling (Sturnus vulgaris) © Pierre Selim | Wikimedia Commons

A mallard mystery: Unraveling the genetic basis of green egg color

A series of experiments narrows the mystery down to one candidate gene.

You might not think about it when you prepare eggs for breakfast, but the color of an egg is an important ecological trait. The eggshell color is mainly determined by a mixture of three types of pigments: protoporphyrin-IX, biliverdin-IX and biliverdin zinc chelate. These pigments provide protection against damaging solar radiation and play a role in thermoregulation, creating the ideal conditions for embryonic development. Moreover, egg color is often a crucial factor in brood parasites that mimic the egg color of their unsuspecting hosts. In some species, the color of eggs is even used as a signal for female quality (see for example this blog post on hoopoes).

Despite this variety of roles in ecological and evolutionary processes, the genetic basis of egg color remains largely unknown. A recent study in the journal Molecular Ecology focused on the green egg color of a Chinese domesticated duck breed (the Jinding duck). What genes underlie this peculiar green color?

Comparing Genomes

The researchers performed a series of clever experiments to determine the genetic basis of green egg color (similar to the case of the mosaic canary described in this blog post). First, they compared the genomes of reciprocal crosses between Pekin ducks (with white eggs) and mallards (with green eggs). The genome-wide search identified a broad target region on chromosome 4 that was significantly associated with egg color. This region was explored in greater detail by analyzing the genomes of seven indigenous duck populations that differ in the coloration of their eggshells. The divergence between green-shelled and white-shelled populations could be traced to a small section of the target region, containing two genes: PRKG2 and ABCG2. The second gene (ABCG2) codes for a membrane transporter that carries biliverdin, one of the pigments that contribute to egg shell coloration. Sounds like the perfect candidate gene.

The genome-wide association study (GWAS) pointed to a region on chromosome 4 that might contain the genes underlying green egg color. From: Liu et al. (2021) Molecular Ecology.

Gene Expression

The researchers did not stop at identifying the candidate gene. They performed more detailed analyses to understand how this gene contributes to the green egg color. Eggshell formation takes place in the uterus, so the researchers measured gene expression in uterine tissues from four populations. As expected, ABCG2 was expressed at a higher level in the green-shelled groups compared to the white-shelled groups. Moreover, the data revealed that ABCG2 produces five distinct isoforms (i.e. different proteins that derive from the same DNA sequence). This is achieved by combining different sections of the gene during protein translation. In the mallard case, the third isoform (ABCG2-X3) is expressed most.

Finally, the researchers took a closer look at the DNA sequence of ABCG2. Does it contain genetic differences that clearly separate green-shelled from white-shelled ducks? Using a collection of sophisticated analyses (including ATAC-sequencing and a luciferase assay), the search could be narrowed down to one genetic variant on nucleotide 47,418,074 of chromosome 4. This position is targeted by different transcription factors (ATF and c/EBPα) in white-shelled compared to green-shelled ducks: ATF binds the white-shelled variant, whereas c/EBPα binds the green-shelled variant. The green egg color of the Jinding duck can thus be explained by a regulatory change in the expression of a specific isoform of the ABCG2-gene. The resulting protein is active in the uterus where it transports the pigment biliverdin from the blood onto the developing egg shell. Mystery solved.

A specific isoform of the candidate gene (ABCG2-X3) shows the highest expression level in green-shelled ducks. From: Liu et al. (2021) Molecular Ecology.

References

Liu et al. (2021). A single nucleotide polymorphism variant located in the cis‐regulatory region of the ABCG2 gene is associated with mallard egg colour. Molecular Ecology30(6), 1477-1491.

Featured image: Green eggs in the nest of a duck © Smudge9000 | Flickr

The importance of taxonomy in saving the critically endangered Black-winged Myna

The taxonomic decision has important consequences for breeding programs.

The black-winged myna (Acridotheres melanopterus) is almost extinct in the wild. This species contains three subspecies: one subspecies (melanopterus) is practically extinct in the wild except for a small flock inside a Javan wildlife park, while the other two subspecies (tricolor and tertius) each number less than 200 individuals in the wild. Captive breeding programs have been established the safeguard the future of the black-winged myna. However, a recent taxonomic decision by the IUCN has complicated the conservation efforts of these breeding programs. Based on differences in plumage patterns and biometrics, the IUCN decided to elevate the three subspecies to species level. A decision that is not unanimously supported within the IUCN’s Asian Songbird Trade Specialist Group.

This taxonomic change has important implications for captive breeding strategies. The recognition of three species leads to a three small populations for breeding, increasing the risk of genetic inbreeding. Considering three subspecies opens the opportunity to a bigger breeding population (with the possibility of crossing subspecies), but might result in the loss of evolutionarily unique lineages due to hybridization. A recent study in the journal Scientific Reports tried to solve this dilemma with a genomic perspective on the black-winged myna complex.

Genomic Gradient

Keren Sadanandan and her colleagues sequenced thousands of genome-wide markers from 85 captive individuals across the morphological spectrum of the black-winged myna. The genetic analyses pointed to two population clusters: one cluster with melanopterus individuals from western Java and morphological hybrids (between melanopterus and tricolor), and a second containing tertius individuals from Bali. Moreover, the melanopterus individuals and hybrids were distributed along a gradient with varying levels of shared ancestry with the tertius cluster. These results thus show a smooth genomic cline from melanopterus in western Java to tertius in Bali. This clinal pattern does not support the IUCN’s decision to recognize three species (check out this paper for more on the dangers of clinal variation in taxonomy). The classification into three subspecies is further supported by low differentiation of the mitochondrial gene ND2 (less than 1.5%) which does not exceed the mitochondrial divergence threshold typically used for the species level (2-3%).

Genomic analyses uncovered a genomic cline from melanopterus to tertius individuals. From: Sadanandan et al. (2020) Scientific Reports.

Melanistic Introgression?

Additional analyses suggested ancient introgression between the Javan Myna (A. javanicus) and the tertius subspecies on Bali. It is possible that the genomic regions underlying black plumage introgressed from the dark Javan Myna into the most melanistic tertius subspecies. The researchers could not pinpoint the exact introgressed regions, so this hypothesis remains to be tested. Nonetheless, the findings of this study indicate that melanism (the degree of black plumage) does not reflect the genomic differentiation between the three subspecies and is thus not a reliable character for taxonomic decisions. This leads the researchers to the following conclusion:

Our study showed that the two geographically and morphologically terminal forms of BWM, melanopterus in the west and darker tertius in the east, are characterized by a mtDNA divergence below the species level. Variation in levels of melanism, recently used to separate BWMs into three species, is not reflected by deep genomic differentiation, arguing in favour of the traditional taxonomic arrangement that unites all three forms as subspecies rather than species.

What does this mean for the breeding programs? The researchers recommend “three separate breeding sub-programs under the umbrella of a single species-wide program without a strict separation.” This will hopefully preserve the range of morphological and genetic diversity within the black-winged myna.

References

Sadanandan, K. R., Low, G. W., Sridharan, S., Gwee, C. Y., Ng, E. Y., Yuda, P., Prawiradilaga, D. M., Lee, J. G. H., Tritto, A. & Rheindt, F. E. (2020). The conservation value of admixed phenotypes in a critically endangered species complex. Scientific reports10(1), 1-16.

Featured image: Black-winged Myna (Acridotheres melanopterus) © Doug Jasonjj | Wikimedia Commons

This paper has been added to the Sturnidae page.

The taxonomic story of the Stipplethroats

A recent phylogenetic study proposes nine distinct species.

Worldwide, there might be about 50 billion individual wild birds (according to this recent PNAS paper). Taxonomists classified all this diversity in about 10,000 species. Each species has been given a binomial name, consisting of genus and a species name. For example, the house sparrow is also known as Passer domesticus, ever since Linneaus named in 1758. The taxonomic position of the house sparrow has been stable for centuries, but other bird groups have been prone to more changes. Some have been promoted from subspecies to species rank (or the other way around), while others have received different genus names.

A nice example of this taxonomic instability concerns the stipplethroats of South America (currently in the genus Epinecrophylla). These small passerines were considered close relatives of the Myrmotherula antwrens and were classified in the same genus. Genetic studies revealed that the stipplethroats were actually more closely related to the bushbirds of the genera Neoctances and Clytotanctes. This finding resulted in the naming of a new genus for the group: Epinecrophylla. Since taxonomists have pinned down the genus name for the stipplethroats (at least for now), they turned to the species level. A recent study in the journal Molecular Phylogenetics and Evolution proposed to recognize nine distinct species. Let’s meet the stipplethroats!

Genetic Splits

The genus Epinecrophylla contains 21 recognized taxa, but their classification into species and subspecies is still a matter of debate. Using thousands of ultraconserved elements (UCEs), Oscar Johnson and his colleagues reconstructed the phylogenetic relationships between these taxa. At the base of the phylogeny, we find the checker-throated stipplethroat (E. fulviventris), followed by the ornate stipplethroat (E. ornata). The latter one showed deep genetic splits and clear population structure between three subspecies (meridionalis, hoffmannsi and atrogularis), suggesting that there might be multiple species hiding in this section of the phylogeny. However, the situation could be complicated by a potential hybrid zone between atrogularis and meridionalis in southern Peru. More research on the ornate stipplethroat is definitely warranted.

Next, the researchers reported a clear split between the rufous-tailed stipplethroat (E. erythrura) and the white-eyed stipplethroat (Epinecrophylla leucophthalma). These taxa are clearly distinct species, but the classification of subspecies within the white-eyed stipplethroat needs more work (currently containing leucophthalma, phaeonota, sordida and dissita).

Dated phylogenies for the genus Epinecrophylla based on (A) ultraconserved elements and (B) mitogenomes. From: Johnson et al. (2021) Molecular Phylogenetics and Evolution.

Short Branches

The classification of the first four species was rather straightforward, but now we arrive at the “Epinecrophylla haematonota group” which holds eight taxa that have undergone many taxonomic rearrangements. Apart from the position of the brown-bellied stipplethroat (E. gutturalis), the researchers found considerable disagreement between the phylogenetic methods regarding the relationships among the three other main clades in this group (see figure below). The rapid evolution of these birds probably resulted in very short branches between the clades, making it extremely difficult to uncover the exact branching order. More detailed analyses – perhaps using genomic data – might be necessary to solve this phylogenetic knot.

Despite this methodological issue, the researchers could identify four species that diverged at roughly the same time (about 2 to 3 million years ago): the rufous-backed stipplethroat (E. haematonota), the Rio Madeira stipplethroat (E. amazonica), the foothill stipplethroat (E. spodionota) and the Negro stipplethroat (E. pyrrhonota). The classification into genera and species seems to be quite stable, so now taxonomists can dive into the subspecies level.

Different phylogenetic methods lead to different outcomes. From: Johnson et al. (2021) Molecular Phylogenetics and Evolution.

References

Johnson, O., Howard, J. T., & Brumfield, R. T. (2021). Systematics of a Neotropical clade of dead-leaf-foraging antwrens (Aves: Thamnophilidae; Epinecrophylla). Molecular Phylogenetics and Evolution154, 106962.

Featured image: brown-bellied stipplethroat (E. gutturalis) © Hector Bottai | Wikimedia Commons

This paper has been added to the Thraupidae page.