Similar plumage, but different songs: How many subspecies of Willow Flycatcher are there?

Acoustic analyses support the recognition of a distinct southwestern subspecies.

Classifying birds into species and subspecies can be a tricky exercise. Different criteria – such as morphology, genetics or behavior – can result in drastically different taxonomic arrangements. The incongruence between these criteria is expected when you understand that speciation is a gradual process. As two populations follow their own evolutionary trajectories, different traits will evolve at different rates. For example, populations might become genetically distinct while they do not develop morphological differences (or vice versa). When it comes to tyrannid flycatchers (genus Empidonax), song and plumage are evolving at contrasting speeds. These small songbirds show very little differentiation in plumage patterns, but tend to sing distinct songs. But how to classify these birds? A recent study in the Journal of Avian Biology took a closer look at one species: the Willow Flycatcher (Empidonax traillii).

Unsupervised Clustering

Despite the lack of clear plumage differences, the Willow Flycatcher has been divided into four subspecies that can be found in different parts of the USA: trailii in the east, brewsteri in the northwest, adastus in the interior west and extimus in the southwest. The studies underlying this subdivision have been criticized because they lacked rigorous statistical analyses, had small sample sizes and used wild birds that were released and could thus not be re-analyzed (see this paper for an overview of the critique). In a recent study, Sean Mahoney and his colleagues addressed these shortcomings by measuring museum specimens and analyzing publicly available song recordings. Moreover, they used unsupervised clustering algorithms that do not take into account the current taxonomic arrangement and are thus more objective.

Distribution of the four Willow Flycatcher subspecies across the USA. From: Mahoney et al. (2020) Journal of Avian Biology.

Song Groups

The clustering based on plumage coloration suggested two main groups that did not follow the subspecies classification. This result highlights the lack of plumage differentiation in these flycatchers. The song analyses, however, did align with the taxonomy of the Willow Flycatcher. The algorithm pointed to two clusters that correspond to the subspecies extimus and the remaining three subspecies (trailii, brewsteri, and adastus). Hence, the authors conclude that “our song data support the recognition of the southwestern population as a distinct subspecies.” This finding is relevant for the conservation of the Willow Flycatchers, because this subspecies is currently listed as endangered by the US Fish and Wildlife Service. Uncertainty around its taxonomic status would have complicated its protection.

Unsupervised clustering of song characteristics suggested two main groups, corresponding to the subspecies extimus (in black) and the other three subspecies (in grey). From: Mahoney et al. (2020) Journal of Avian Biology.

References

Mahoney, S. M., Reudink, M. W., Pasch, B., & Theimer, T. C. (2020). Song but not plumage varies geographically among willow flycatcher Empidonax traillii subspecies. Journal of Avian Biology, 51(12).

Featured image: Willow Flycatcher (Empidonax traillii) © VJ Anderson | Wikimedia Commons

Are there still ‘pure’ Javan Pied Starlings?

Historical samples inform conservation efforts to prevent extinction.

The “Javan Pied Starling” is extinct in the wild. This particular population, formerly located on the island Java, is part of the Asian Pied Starling (Gracupica contra) species complex and has been considered a distinct species by some ornithologists. Currently, it is treated as a subspecies (jalla), alongside four other subspecies (contra, sordida, superciliaris, and floweri). Regardless of its taxonomic status, the IUCN Specialist Group for Asian Songbird Trade considered it one of the top 10 taxa warranting immediate conservation action to prevent its extinction. Captive populations of the Javan Pied Starling could be the starting point for a breeding program. There is, however, an issue with these captive birds: jalla individuals are often crossed with other subspecies (especially floweri from Thailand). This raises the question whether there are still “pure” Javan Pied Starlings around. A recent study in the journal Evolutionary Applications tried to solve this mystery by returning to the situation before hybridization in captivity.

Genetic Groups

Before we can assess the degree of hybridization in captivity, we need to know whether the Javan Pied Starling is a separate taxon. It might look different from the other taxa – with its extensive deep-orange skin around the eye – but is it also genetically distinct? Pratibha Baveja and her colleagues sequenced the DNA of several historical samples (ranging from 1878 to 1983) and compared the genetic make-up of the different subspecies. Their analyses revealed three distinct genetic groups: the taxa contra and superciliaris clustered together whereas jalla and floweri formed their own clusters (samples for sordida were not included). This arrangement was further supported by mitochondrial DNA, showing each subspecies as a separate evolutionary line. The most relevant finding for this blog post is that the Javan Pied Starling is indeed a distinct taxon. The authors even propose to treat it as a separate species.

The genetic analyses uncovered three distinct clusters: contra + superciliaris (blue), floweri (green) and jalla (red). From: Baveja et al. (2021) Evolutionary Applications.

Captive Samples

But what about the captive birds? To figure out whether there are still “pure” Javan Pied Starlings in captivity, the researchers compared the DNA of several individuals from the Bali Bird Park (Indonesia) and the Jurong Bird Park (Singapore) with the historical samples. The captive individuals showed the same genomic profile as the historical samples, suggesting a lack of admixture from other other subspecies. These birds can thus be used to start a breeding program to save this species from extinction. There is still hope for the Javan Pied Starling.

References

Baveja, P., Garg, K. M., Chattopadhyay, B., Sadanandan, K. R., Prawiradilaga, D. M., Yuda, P., Lee, J. G. H. & Rheindt, F. E. (2021). Using historical genome‐wide DNA to unravel the confused taxonomy in a songbird lineage that is extinct in the wild. Evolutionary applications, 14(3), 698-709.

Featured image: Asian Pied Starling (Gracupica contra) © Sai Adikarla | Wikimedia Commons

Genomic islands of differentiation in seedeaters are mainly the outcome of selective sweeps

New statistical methods point to several soft sweeps that acted on standing genetic variation.

When you compare the genomes of two related species, you will observe a heterogenous distribution of genetic differentiation. Some genomic regions will be very similar, while other are drastically different. In recent years, evolutionary biologists have tried to unravel the evolutionary processes underlying these differentiated genomic regions – also known as “islands of differentiation” (I have covered a few of these studies on birds, including wood-warblers, white-eyes and hummingbirds). Two main explanations are currently under debate. One model suggests that these genomic islands contain loci that contribute to reproductive isolation. When two species interbreed, these barrier loci are expected to be immune to introgression. Hence, they will diverge while the remainder of the genome is homogenized by introgression. Alternatively, local peaks in genetic differentiation might be the result of species-specific selective sweeps. To discriminate between these two explanations, the majority of studies resorted to population genetic summary statistics (e.g., Fst, Dxy, etc.). A recent study in the journal PNAS took a different approach and applied some newly developed statistical methods to this conundrum.

Ancestral Recombination Graph

In 2017, Leonardo Campagna and his colleagues compared the genomes of several Capuchino seedeaters (genus Sporophila). Their analyses uncovered 25 genomic islands of differentiation, containing genes involved in plumage pigmentation. It remained to be determined whether these genomic islands arose because of they contribute to reproductive isolation or because they were the target of species-specific selection. In the new study (led by Hussein Hejase), the researchers revisited these genomic islands with novel statistical tools.

The first method is the ancestral recombination graph (ARG), which describes both the genealogical relationships as well as the changes in those relationships along the genome due to historical recombination events. This approach was recently used to detect introgression between archaic humans, Neanderthals and Denisovans. With regard to the debate of barrier loci vs. selective sweeps, the ARG-approach can be applied to test a particular prediction involving the TMRCA. This abbreviation stands for “time to most recent common ancestor” and concerns the timepoint where two genetic samples find their common ancestor (or in jargon, when they coalesce). Recent selective sweeps are expected to reduce the TMRCA, because the genetic variants that survived the selection process can probably trace their common ancestor back to that event. Based on this reasoning, the researchers developed a statistical test to detect these species-specific selective sweeps. They found that 23 of the 25 genomic islands showed signs of recent selective sweeps in at least one seedeater species.

Example of a selective sweep involving the gene SLC45A2. The selection event results in a reduction in the TMRCA which is visible in the gene tree as a group of samples with short branches (topright figure). The topleft figure shows the situation for a neutral genomic region. From: Hejase et al. (2020) PNAS.

Machine Learning

Next, the researchers turned to machine learning. They trained a machine learning algorithm with simulated data to discriminate between selective sweeps and neutral evolution. Using this approach, they “identified large numbers of apparent species-specific sweeps, many of which coincided with Fst peaks or otherwise occurred nearby genes involved in the regulation of melanogenesis.” One important caveat is that this method is sensitive to biases in the choice of parameters for simulations. The authors have tried to cope with this potential bias by simulating various evolutionary scenarios and validating the outcomes with independent methods. Indeed, the observation that both the ancestral recombination graph and the machine learning analyses point to a preponderance of selective sweeps is certainly a good sign. All in all, it seems likely that most genomic islands of differentiation can be explained by recent, species-specific selective sweeps. However, this conclusion does not rule out the involvement of barrier loci. The authors put it nicely in the discussion.

Thus, both models likely contributed to differentiation in the regulatory sequence of this gene, but at different times and in different species. Notably, the distinction between the two paradigmatic models may not be absolute, since loci that experienced early barriers to gene flow could later undergo selective sweeps, and loci that underwent species-specific sweeps could lead to reduced hybrid fitness resulting in barriers to gene flow.

References

Hejase, H. A., Salman-Minkov, A., Campagna, L., Hubisz, M. J., Lovette, I. J., Gronau, I., & Siepel, A. (2020). Genomic islands of differentiation in a rapid avian radiation have been driven by recent selective sweeps. Proceedings of the National Academy of Sciences, 117(48), 30554-30565.

Featured image: Tawny-bellied Seedeater (Sporophila hypoxantha) © Hector Bottai | Wikimedia Commons

What is so special about Darwin’s Finches?

Evolutionary analyses attempt to pinpoint the success of this adaptive radiation.

When I write Galapagos Islands, you might think about Darwin’s Finches. Indeed, this group of birds has become an iconic example of an adaptive radiation on these islands. However, several other bird species reached this archipelago, but never diversified in terms of species numbers or morphology. Think of the Yellow Warbler (Setophaga petechia) or the Little Vermillion Flycatcher (Pyrocephalus nanus). Or what about the Galapagos mockingbirds that are represented by just four species with little morphological differences. The contrast between these species and the more extensive radiation of the Darwin’s Finches raises an intriguing question: what is so special about these finches? A recent study in the journal Ecology and Evolution took the first steps in solving this mystery.

Diversification Rates

Ashley Reaney and his colleagues collected morphological data on 349 species from the Thraupidae family (to which the Darwin’s Finches belong). Next, they ran the Bayesian Analysis of Macroevolutionary Mixtures (BAMM) program to detect changes in evolutionary rates along the phylogeny of this bird group. These analyses revealed that the majority of Thraupidae experienced an early burst in diversification, followed by decreasing rates until the present. There were, however, two exceptions: the Darwin’s Finches and the seedeaters (genus Sporophila). These sections of the evolutionary tree experienced a recent increase in diversification rate – 6 million years ago for the Darwin’s Finches and 21 million years ago for the seedeaters. This dramatic contrast is nicely illustrated in the figure below where the rapid diversification (in red) stands out against the decreasing rates in the overall phylogeny (in blue).

Overall, the Thraupidae phylogeny shows an early burst in diversification, followed by a decreasing rate. Two notable exceptions are the Darwin’s Finches (Co.) and the seedeaters (Sp.). From: Reaney et al. (2020) Ecology and Evolution.

Evolvability

These findings highlight the unique radiation of the Darwin’s Finches, but still leave our original question unanswered: what is so special about these birds? Additional analyses revealed that these finches occupy a far larger area of the beak morphospace compared to the other species (including the seedeaters). In other words, the Darwin’s Finches show a greater variety of beak shapes, allowing them to enter more ecological niches and diversify into several species. And although ecological opportunities and biogeographic factors certainly played a role in the radiation of Darwin’s Finches, the researchers suspect that the unique developmental and genetic features of these birds were equally (or perhaps even more) important.

It is possible that the ancestor of the Darwin’s Finches that arrived on the islands was “already endowed with the genetic propensity to produce the high levels of beak variation needed to explore new dietary niches.” This propensity for diversification – also known as evolvability – concerns several intrinsic factors that allow certain species to rapidly adapt to new environments. These factors might be related to genetics (e.g., certain mutations or gene flow from other populations) or particular developmental programs. Previous research demonstrated that the cranium of Darwin’s Finches is highly modular, allowing different beak traits to evolve independently from one another. Another possibility – which might seem contradictory – involves the integration of the entire cranium through developmental and genetic connections between the different beak traits. The interplay between modular change and integration might explain the impressive evolvability of the Darwin’s Finches.

Darwin’s Finches (in red) occupy a larger section of the beak morphospace compared to all other members of the Thraupidae family. From: Reaney et al. (2020) Ecology and Evolution.

Evo-devo

The researchers conclude that these hypotheses will need to be tested in other adaptive radiations, such as the Hawaiian honeycreepers or the Malagasy vangas. Moreover, future research should focus on the evolution of developmental genetic programs, including those underlying beak morphology (which I covered in this blog post). If we want to understand the diversification of life on our planet, we will have to combine evolutionary analyses with detailed developmental studies. Time for some evo-devo.

References

Reaney, A. M., Bouchenak‐Khelladi, Y., Tobias, J. A., & Abzhanov, A. (2020). Ecological and morphological determinants of evolutionary diversification in Darwin’s finches and their relatives. Ecology and Evolution, 10(24), 14020-14032.

Featured image: a collage of different Darwin’s Finches (Geospiza magnirostris, Geospiza fortis, Certhidea fusca, Camarhynchus parvulus) © Kiwi Rex | Wikimedia Commons

Searching for a hybrid zone between two Andean warblers

Extensive phenotypic variation across a transect between Ecuador and Colombia.

From the 1930s into 1950s, John Zimmer published numerous extensive monographs about “Studies on Peruvian Birds”. In number 54 of the series, he focused on the bird families Catamblyrhynchidae (now part of the Thraupidae) and Parulidae. While describing specimens of the genus Myioborus, he commented on some “puzzling specimens” that showed characteristics of two subspecies of the Golden-fronted Redstart (M. ornatus chrysops) and the Spectacled Redstart (M. melanocephalus ruficoronatus).

The extreme characters of ruficoronatus strongly suggest those of the ornatus group, and an occasional specimen of o. chrysops shows a noticeable patch of rufous in the center of the crown, strongly suggesting ruficoronatus. It is not impossible, therefore, that the puzzling specimens of one sort and another may represent intergrades or even hybrids between the two groups, but much more material will be necessary before an adequate solution is reached.

Several researchers followed the advice of Zimmer and collected more material on these birds. A recent study in the journal Ornithology reported on their findings. Is there a hybrid zone or not?

Two Subspecies

Before we delve into the possibility of a hybrid zone, we need to clarify the distribution of the M. ornatus–M. melanocephalus species complex. First, the Spectacled Redstart (M. melanocephalus) is divided into five subspecies that replace each other when you travel along the Andes from Bolivia to Ecuador (see dots in the map below). The southern subspecies (malaris, melanocephalus and bolivianus) lack a rufous crown, which is present in the two northern subspecies (griseonuchus and ruficoronatus). Second, the Golden-fronted Redstart (M. ornatus) comprises two subspecies (ornatus and chrysops) that occur in different cordilleras in Colombia and Venezuela (see triangles in the map below). The putative hybrid zone concerns interactions between the most northern subspecies of the Spectacled Redstart (ruficoronatus) and the western subspecies of the Golden-fronted Redstart (chrysops). Laura Céspedes-Arias and her colleagues collected samples of these subspecies across a transect running from Ecuador into Colombia.

(A) Map showing the distribution of the subspecies in the M. ornatus-M. melanocephalus species complex. (B) Overview of the sampling transect in the study. From: Céspedes-Arias et al. (2021) Ornithology.

Clinal Patterns

Plumage analyses of over 300 specimens revealed a wide variety of phenotypes, representing different trait combination of both subspecies. It quickly became clear that individuals with intermediate phenotypes were most common along the transect. Some traits, such as head and chest coloration, showed a clear clinal transition from one subspecies into the other (see this blog post for more information on cline theory). All in all, these morphological patterns pointed to a roughly 200 kilometer wide hybrid zone, confirming the suspicion of John Zimmer.

Next, the researchers turned to genetic data by sequencing the mitochondrial gene ND2. In contrast to the plumage traits, this gene did not show a smooth transition. Instead the researchers found extensive haplotype sharing between the subspecies. This pattern can be explained by the recent origin of these subspecies (i.e. incomplete lineage sorting) or by extensive introgression due to hybridization. Genomic analyses will be needed to discriminate between these possibilities. Nonetheless, the most likely scenario seems to entail allopatric divergence leading to differences in plumage traits, followed by secondary contact and extensive hybridization. Another exciting avian hybrid zone to study in more detail.

A sample of the diversity of plumage phenotypes across the hybrid zone, from a typical chrysops (top) over intermediates to a typical ruficoronatus (bottom). From: Céspedes-Arias et al. (2021) Ornithology.

References

Céspedes-Arias, L. N., Cuervo, A. M., Bonaccorso, E., Castro-Farias, M., Mendoza-Santacruz, A., Pérez-Emán, J. L., Witt, C. C. & Cadena, C. D. (2021). Extensive hybridization between two Andean warbler species with shallow divergence in mtDNA. Ornithology, 138(1), ukaa065.

Featured image: Spectacled Redstart (Myioborus melanocephalus) © Francesco Veronesi | Wikimedia Commons

Bioacoustics support the decision to split the Elegant Pitta into three species

Playback experiments corroborate acoustic analyses.

An integrative approach to taxonomy is becoming more common. On this blog, I have covered several studies that used multiple lines of evidence to support a taxonomic decision (see for instance this lark species complex or the Gentoo Penguin). Combining multiple datatypes protects some taxonomists from their eagerness to split taxa into multiple species based on a few minor differences. For example, a morphological study on the bean goose complex found that it was possible to discriminate between the taxa fabalis and rossicus using just two measurements: the number of “teeth” in the upper mandible and the maximum height of the lower mandible. Some ornithologists argued that these differences were sufficient to elevate both taxa to species status. But how biologically relevant are these traits? Do they represent a plastic phenotype that is shaped by certain environmental conditions? Or are they heritable adaptations to a particular ecological lifestyle? Such questions need to be addressed before one can properly assess their taxonomic level. Similar reasoning can be applied to the songs and sounds produced by different taxa. Just because two birds sound different does not necessarily mean that they are different species (just think of all the dialects sung by certain songbirds). The biological relevance of bioacoustic differences needs to be investigated in more detail, such as conducting playback experiments. A recent study in the journal Avian Research did just that to evaluate the taxonomy of the Elegant Pitta (Pitta elegans) species complex.

Territorial Calls

Currently, the Elegant Pitta is classified into five subspecies (concinna, maria, vigorsii, elegans, and virginalis). Arya Yue and her colleagues took a closer look at these subspecies to see whether some might represent distinct species. An analysis of territorial calls revealed striking differences between the subspecies. Here is the succinct summary from the results section:

The widespread taxon concinna, resident from Lombok to Alor with the exception of Sumba, exhibited a distinct two-element motif. In contrast, most other taxa, including nominate elegans centered around Timor, maria and virginalis utter a three-element motif in which the first two elements are given in quick succession. The only taxon displaying variability in this trait was the far-eastern vigorsii, centered around the Tanimbar and Kai Islands, in which both two-element and three-element motifs were detected. However, neither of them resembled those given by the other taxa.

The bioacoustic differences were also apparent in the principal component analysis (PCA) where elegans, virginalis and maria formed one cluster distinct from the two other subspecies (concinna and vigorsii).

Principal component analysis plot for territorial calls in the Elegant Pitta species complex. From: Yue et al. (2020) Avian Research.

Playback Trials

However, as I explained at the beginning of this blog post, just because two taxa sound different does not necessarily mean that they are different species. So, how biologically relevant are these differences in territorial calls? One of the co-authors (James Eaton) performed playback experiments over multiple years to see how the different taxa respond to one another. These experiments revealed that the three subspecies from the PCA-cluster (elegans, virginalis and maria) responded aggressively to each others calls, whereas they ignored the calls of the other subspecies (concinna and vigorsii). It would take me too long to describe all the species combinations, so you can check the table below for the results. In essence, the playback trials corroborated the bioacoustic analyses.

An overview of the playback experiments involving different members of the Elegant Pitta species complex. From: Yue et al. (2020) Avian Research.

Three Species

Based on these bioacoustic findings – and additional analyses of plumage patterns and morphology – the authors suggest to split the Elegant Pitta into three species:

• Temminck’s Elegant Pitta (P. elegans) with subspecies elegans, virginalis and maria
• Wallace’s Elegant Pitta (P. concinna)
• Banda Elegant Pitta (P. vigorsii)

However, this classification remains to be confirmed with genetic analyses. If the genetic patterns follow the bioacoustic results, it would indicate that the territorial calls contribute to reproductive isolation between the different taxa. Then they could undoubtedly be considered a biologically relevant and taxonomically informative markers.

References

Yue, A. Y., Ng, E. Y., Eaton, J. A., & Rheindt, F. E. (2020). Species limits in the Elegant Pitta (Pitta elegans) complex from Wallacea based on bioacoustic and morphometric analysis. Avian Research, 11(1), 1-12.

Featured image: Elegant Pitta (Pitta elegans) © Abdul Azis Gizan | Wikimedia Commons

Before the invasion: Quantifying the level of pre-introduction selection on two Weaver species

Captured birds go through several selective filters before escaping into the wild.

A few months ago, I published a review paper on hybridization in the Anthropocene. Part of this study quantified the most common mechanisms underlying human-induced hybridization events. It turned out that almost half of the studies I looked at reported hybrids due to the introduction of non-native species (34% intentional and 19% unintentional). These numbers indicate that the invasions of exotic species can have substantial consequences. It is no surprise that many biologists have tried to identify the factors contributing to a successful invasion. However, most of these studies focused on the later stages of biological invasions, such as establishment of escaped individuals or population expansions. The very early stages of the invasion have been largely ignored, even though there might be biases in the capture and transport of exotic species. A recent paper in the journal Evolutionary Applications addressed this knowledge gap by focusing on two avian invaders: the Black-headed Weaver (Ploceus melanocephalus) and the Yellow-crowned Bishop (Euplectes afer).

Selection Filters

At the start of the study, Adrián Baños‐Villalba and his colleagues accompanied several professional bird trappers in Senegal. After catching the birds with traditional clap nets, the researchers took several morphological and behavioral measurements and marked each bird with a unique set of numbered rings. This allowed them to follow the individual birds through the different steps from capture to sale, and determine any selection pressures along the way. After spending about one week in traditional storage cages, the birds were transported over 350 kilometers to a bird-trading company in Dakar. According to this company, the birds were typically kept there for one to three months before export. So, the researchers quantified survival rates thirty days after arrival in Dakar. By comparing the morphological and behavioral traits of the surviving individuals at these different stages, it was possible to estimate the strength of selection on certain traits.

An overview of potential selective filters acting during the pre-introduction stages of an invasion process. From: Baños‐Villalba et al. (2021) Evolutionary Applications.

Micro-evolutionary Changes

The analyses revealed significant changes in several morphological and behavioral traits. During the capture stage, for instance, individuals with a smaller head volume (and perhaps smaller brains) were more likely to be caught. This might reflect some variation in cognitive features and the ability to escape. Later on, however, selection seemed to favor larger brains, possibly because these birds could cope better with novel situations. This example nicely illustrates how pre-introduction selection shapes the captive population and can potentially affect the future establishment success of escaped birds. The authors highlight the relevance of this finding at the end of the discussion:

However, as our results suggest, introduced populations may have already undergone micro-evolutionary changes (assuming traits are heritable) through selective filters (even when these are artificial and human-induced) before reaching the establishment stage, and this likely affects all subsequent changes involved in the adaptation to a new non-native area in the subsequent stages.

These insights can be used to better understand the mechanisms behind successful invasions, and to take appropriate management measures. And this study is also very relevant from a hybridization perspective (the main topic of this blog). While working on this blog post, I came across this paper on mussels: “Pre-introduction introgression contributes to parallel differentiation and contrasting hybridization outcomes between invasive and native marine mussels”. The unchartered territory of pre-introduction selection is waiting to be explored.

References

Baños‐Villalba, A., Carrete, M., Tella, J. L., Blas, J., Potti, J., Camacho, C., Diop, M. S., Marchant, T. A. & Edelaar, P. (2021). Selection on individuals of introduced species starts before the actual introduction. Evolutionary Applications, 14(3), 781-793.

Featured image: Black-headed Weaver (Ploceus melanocephalus) © Francesco Veronesi | Wikimedia Commons

How convincing is the evidence to split the Gentoo Penguin into four species?

A critical look at the genetic and morphological data supporting this taxonomic proposal.

Taxonomy is often in flux. As new data are collected or novel methods are being developed, the classification of certain sections on the Tree of Life might change. For example, a recent study in the journal Ecology and Evolution presented morphometric and genetic evidence to split the Gentoo Penguin (Pygoscelis papua) into four distinct species. Last year, this study attracted some media attention (including the BBC and the Oceanographic Magazine), but I remained somewhat skeptical about this taxonomic revision. I added the paper to my writing-list where it gathered dust from several months (there were so many other interesting papers to cover on the blog). Now, it has finally resurfaced and we can assess the evidence. How strong is the case for four species of Gentoo Penguin?

Genetic Lineages

In recent years, taxonomy has become more pluralistic, combining several lines of evidence to support taxonomic decisions (see for example this blog post on larks). The researchers in the penguin study also took an integrative approach and collected genetic and morphological data. The genetic analyses – based on more than 10,000 markers – pointed to four clearly distinct lineages, corresponding to populations from several islands (i.e. Falklands, South Georgia Island, South Shetland Islands + Western Antarctic Peninsula, and Kerguelen). In addition, species delimitation analyses supported a model that considers these four lineages as distinct species. However, as I have discussed in other blog posts (see here and here), genetic population structure does not necessarily coincide with species boundaries. Other data types are needed to validate the delimited species.

Genetic analyses revealed four distinct lineages. But do they represent different species? From: Tyler et al. (2020) Ecology and Evolution.

Morphological Overlap

Next, the researchers performed several statistical analyses on a set of morphological traits. A MANOVA test indicated that “all genetically distinct populations are significantly distinct from each other overall.” However, a closer look at the results of this MANOVA test shows that the p-values are just below the significance threshold of 0.05. For example, the p-value separating the Falklands from Kerguelen is 0.0446. Statistically significant, yes. But is this difference biologically relevant?

My skepticism towards the morphological patterns was reinforced by the output of the linear discriminant analysis where the authors reported that “a small number of specimens occupying positions closer to other lineages.” Moreover, assigning individuals to the genetic lineages using the morphological data resulted in an error rate of 10% (i.e. one individual out of ten was assigned to the wrong lineage). Clearly, the morphological differences are not absolute.

Linear Discriminant Analysis of the morphological data. Circles represent individual specimens with triangles showing the lineage mean. Notice the overlap between SGI (pink) and FALK (blue). Tyler et al. (2020) Ecology and Evolution.

Verdict

So, how convincing is the evidence to recognize four species of Gentoo Penguin? There appears to be some conflict between the genetic and morphometric results. We can recognize four distinct genetic lineages, but they overlap morphologically. And that is a logical finding when you keep in mind that speciation is a gradual process in which different traits evolve at different rates (more details in this blog post). In this case, the Gentoo Penguin populations have become genetically distinct, but the morphological separation might still be under way (or it might stabilize in the current situation). In my opinion, these penguins are in a “taxonomic grey zone”. One could make a case to treat them as subspecies. Or one could argue that the morphological differences are large enough to classify them as distinct species.

An additional argument to recognize four distinct species concerns their conservation status. In the press release, the researchers say that “regarding the four populations as separate species, gives conservationists a better chance of protecting their diversity because if there’s a decline in one of them it will change the threat status as defined by the IUCN Red List”. This is not a biological reason for a taxonomic revision, but a political one. And that is no problem. In light of the current biodiversity crisis it is important to protect as many species as possible. We could have endless academic discussions whether to classify these penguins as species or subspecies, but that won’t safeguard their future. Let’s focus on what matters.

References

Tyler, J., Bonfitto, M. T., Clucas, G. V., Reddy, S., & Younger, J. L. (2020). Morphometric and genetic evidence for four species of gentoo penguin. Ecology and Evolution, 10(24), 13836-13846.

Featured image: Gentoo Penguin (Pygoscelis papua) © Ben Tubby | Wikimedia Commons

Hybrids between Zebra Finch subspecies provide evidence for a weak meiotic driver

Subtle deviations from Mendelian expectations point to a meiotic driver in the Timor subspecies.

Every biology student has worked his or her way through the pea-experiments of Gregor Mendel, creating Punnett squares with recessive and dominant alleles. One of the most important insights from these pivotal experiments was the observation that every allele at a genetic locus has an equal probability of being transmitted to the next generation (ultimately giving rise to the predictable ratios of dominant and recessive traits). However, some alleles show clear deviations from these expected patterns. These genetic elements are known as meiotic drivers, because they “drive” the meiotic cell division process in such as way that they have a higher chance of ending up in the gametes (i.e. eggs or sperm cells).

During meiosis, the chromosomes are sorted into four daughter cells. In birds, one daughter cell develops into the mature egg, while the other three develop into polar bodies. The spindle apparatus attaches to the centromeres of the chromosomes and drags them into the different daughter cells. Meiotic drivers are often found close to centromeres, because this allows them to influence the spindle fibers and ensure that they end up in the daughter cell that becomes the mature egg. Indeed, previous research in chickens reported a meiotic driver at the centromere of chromosome 1.

An schematic representation of the meiotic process. Meiotic drivers influence the sorting of chromosomes so that they are transmitted to the next generation. From: Wikipedia.

Subspecies

Meiotic drivers can be difficult to detect, because they tend to be transient phenomena. In some cases, the meiotic drivers lead to deleterious effects and are quickly suppressed by other genetic elements that restore proper Mendelian segregation. Alternatively, meiotic drivers are so successful that they rapidly spread through a population and become fixed (i.e. all individuals have the same genetic variant). One way to identify such cryptic meiotic drivers is to cross individuals from divergent populations. If a meiotic driver evolved in one population but not the other, it will become visible in the hybrids. A recent study in the journal Ecology and Evolution used this approach to look for meiotic drivers in the Zebra Finch (Taeniopygia guttata). The researchers crossed two subspecies – Australian (castanotis) and Timor (guttata) Zebra Finches – and traced the genetic ancestry of several molecular markers. Did some deviate from the expected Mendelian patterns?

An overview of the extensive breeding scheme in this study. From: Knief et al. (2020) Ecology and Evolution.

Backcrosses

The experiments revealed “no clear evidence for any active meiotic driver in a cross between Australian and Timor Zebra Finches.” However, there was a significant deviation from Mendelian segregation in females of the first backcrossed generation. This finding suggests that there might be a weak meiotic driver which allows Timor centromeres to outcompete Australian variants in the race for the oocyte. It took numerous hybridization and backcrossing events to detect this subtle signal, indicating that weak meiotic drivers might be more common than we think. Another example of how avian hybrids can lead to exciting discoveries and new insights.

Segregation patterns in different hybrids and backcrosses between Australian an Timor Zebra Finches. Notice the slight deviation from the expected pattern (dotted line) in the female backcrosses (BC1). From: Knief et al. (2020) Ecology and Evolution.

References

Knief, U., Forstmeier, W., Pei, Y., Wolf, J., & Kempenaers, B. (2020). A test for meiotic drive in hybrids between Australian and Timor zebra finches. Ecology and evolution, 10(23), 13464-13475.

Featured image: Zebra Finch (Taeniopygia guttata) © Peripitus | Wikimedia Commons