What causes taxonomic disagreement between bird checklists?

Study identifies a combination of research bias and differences in divergence rates.

Why can’t we all just get along? This question often comes to my mind when I follow the heated debates between taxonomists. Personally, I find the quest to pigeonhole the immense biodiversity into species and subspecies not that interesting. I prefer to focus on the ecological and evolutionary processes that gave rise to all this diversity. For conservationists and policy makers, however, a reliable overview of the species in an area can be crucial. It is thus certainly important to continue with the correct classification of life.

But what is the correct way to classify organisms? The species problem has been haunting biologists for centuries. Charles Darwin already indicated that “No one definition has satisfied all naturalists; yet every naturalist knows vaguely what he means when he speaks of a species.” And the struggle continues to this day (see this blog post). Taxonomists often disagree about the species status of a certain population. A first step in solving these taxonomic disputes is to understand what factors cause the disagreements. And that is exactly what Montague Neate-Clegg and his colleagues did. They scoured four bird checklists for taxonomic disagreements and tried to identify the underlying causes. Their findings recently appeared in the journal Global Ecology and Biogeography.

Research Bias

The researchers examined four commonly used checklists for the world’s avifauna:

• Howard and Moore Checklist of the Birds of the World
• eBird/Clements Checklist of Birds of the World
• Birdlife International Digital Checklist of Birds of the World
• International Ornithological Community (IOC) World Bird List

This extensive comparison culminated in 11,389 extant species names of which 9,894 were recognized by the four checklists. Some simple math reveals 1,495 problematic cases. A minority of these (18 cases) were newly discovered species, whereas the rest were genuine taxonomic disagreements, such as the redpolls (genus Acanthis) and the crossbills (genus Loxia).

A detailed look at the disputed taxa showed a clear geographical research bias. The researchers noted that “taxonomic agreement was lowest for species in Southeast Asia/Australasia and the Southern Ocean, understudied regions where islands have driven high levels of cryptic diversification. In contrast, agreement was highest in the temperate Northern Hemisphere where diversity is lower and research is more extensive.” Luckily, ornithologists are working hard to stabilize the taxonomy in Southeast Asia and Australasia (see for example here and here).

Taxonomic agreement in birds across regions of the world for (a) all checklists and (b) excluding Howard & Moore (which has not been updated since 2014). From: Neate‐Clegg et al. (2021).

Ecological Reasons

Apart from the research bias, the analyses also pointed to several ecological traits. First, bigger species – especially with a body mass over 500 grams – were less likely to be in dispute. Obviously, big species are easier to observe and study. But there are also ecological reasons: larger body size is often associated with longer lifespans, smaller clutch sizes and larger home ranges. Together, these factors might lead to lower diversification rates, and consequently less diversity which is easier to classify.

Second, taxonomic agreement was higher in open-habitat species and migratory species. These traits tend to result in high levels of dispersal, resulting in gene flow between populations. The homogenizing exchange of genetic material prevents the formation of new species, resulting in clearly delineated species. This situation contrasts with altitudinal migrants that are partly depended on forest habitats. Here, the researchers found more taxonomic disagreements which they explained as follows:

Our results may, therefore, support the theory that intermediate dispersal ability leads to higher rates of diversification whereby sufficient dispersal capability is required to colonise new areas but not so much dispersal ability that gene flow prevents speciation. The greatest potential for cryptic lineage differentiation may, therefore, occur in lineages with intermediate forest dependence and intermediate mobility.

Ecological predictors of taxonomic agreement for the world’s birds for all checklists (in black) and excluding Howard & Moore (in grey, which has not been updated since 2014). From: Neate‐Clegg et al. (2021).

Species Concepts

The ecological traits discussed above could push some taxa into the “grey zone” of the speciation process where different species concepts support different taxonomic decisions. This conflict between species concepts is apparent when comparing certain check lists. Birdlife, Clements and Howard and Moore follow the Biological Species Concept (focusing in reproductive isolation) whereas the IOC adheres to the Evolutionary Species Concept (focusing on lineage differentiation, an approach that I also prefer). The reliance on and application of these different species concepts partly explains some taxonomic disagreements.

Hence, aligning the bird checklists will thus involve finding a consensus on the “best” species concept. It seems that we are right back from where we started. Those dreaded species concepts…

References

Neate‐Clegg, M. H., Blount, J. D., & Şekercioğlu, Ç. H. (2021). Ecological and biogeographical predictors of taxonomic discord across the world’s birds. Global Ecology and Biogeography, 30(6), 1258-1270.

Featured image: Common Redpoll (Acanthis flammea) © Jyrki Salmi | Wikimedia Commons

Hubbs Principle: Loneliness can lead to hybridization

The genetic consequences of unbalanced species numbers.

Imagine that you are a Hawaiian Goose (Branta sandviciensis) in a Dutch waterfowl collection. One day, your owner is not paying attention and forgets to lock the door to your cage. You sneak out and disappear into the spacious fields of the Netherlands. When the breeding season starts, you look for a potential mate. Unfortunately, there are no other Hawaiian Geese around. In the end, you become so desperate that you settle for another species, pairing up with a – perhaps slightly confused – Barnacle Goose (B. leucopsis). A few months later, Dutch birdwatchers report a peculiar hybrid goose (see picture above).

This short story illustrates the so-called “Desperation Hypothesis”. An individual cannot find a conspecific partner and eventually mates with another species. This scenario was first described in fish by Carl L. Hubbs. He noted that “Great scarcity of one species coupled with the abundance of another often leads to hybridization: the individuals of the sparse species seem to have difficulty in finding their proper mates.” This phenomenon – now known as Hubbs Principle – does not only apply to fish. It has also been observed in birds.

Disproportionate Ducks

The scenario of the lonely Hawaiian Goose is an extreme case. Hubbs Principle also applies when one species is much more abundant than another. On the Falkland Islands, for example, Speckled Teal (Anas flavirostris) outnumber Yellow-billed Pintails (A. georgica) by about ten to one. This numerical imbalance resulted in hybridization between these two duck species. Given the preponderance of Speckled Teals in the area, hybrids are more likely to backcross with this species. Genes are thus expected to flow from the Yellow-billed Pintail into the Speckled Teal. And indeed, genetic analyses by Kevin McCracken and Robert Wilson confirmed this pattern of gene flow. The genetic signature of Hubbs Principle in action.

A first-generation hybrids between Speckled Teal and Yellow-billed Pintail. From: McCracken & Wilson (2011).

Invasion Genetics

It becomes even more interesting when we consider the expansion of one species into the distribution of another one. During such an invasion scenario, the numerical imbalance between the species shifts, resulting in some peculiar genetic patterns. Let’s walk through the scenario step by step. In the beginning, the expanding species is outnumbered and is thus more likely to hybridize with members from the local population. As the expansion proceeds, the resident species and previously produced hybrids are engulfed by the expanding species, thereby overturning the numerical imbalance. Consequently, hybrids have a higher chance of backcrossing with members of the expanding species, resulting in gene flow from the resident into the expanding species.

A literature survey by Mathias Currat and his colleagues showed that these patterns regularly occur in nature. They found 44 studies that quantified gene flow during a species invasion. In 36 cases (82%), gene flow was highly asymmetrical from the local into the invading species (as expected). Only seven cases (16%) reported gene flow in the reverse direction. Exceptions to this general pattern provide exciting avenues for further research. Genes that are going against the flow might confer an advantage to their carriers. The invasion scenario assumes neutral genetic variation, but sometimes you need to invoke selection. But I will leave that topic – adaptive introgression – for another blog post.

References

Currat, M., Ruedi, M., Petit, R. J., & Excoffier, L. (2008). The hidden side of invasions: massive introgression by local genes. Evolution, 62(8), 1908-1920.

Hubbs, C. L. (1955). Hybridization between fish species in nature. Systematic Zoology, 4(1), 1-20.

McCracken, K. G., & Wilson, R. E. (2011). Gene flow and hybridization between numerically imbalanced populations of two duck species in the Falkland Islands. PLoS One, 6(8), e23173.

Featured image: Hawaiian Goose (Branta sandviciensis) x Barnacle Goose (B. leucopsis) © Luc Bekaert | Waarneming.nl

When 1 + 1 = 3: Hybrid speciation in birds

Exploring the origin of hybrid bird species.

Whenever an interesting hybrid combination is reported, people ask the question: Will this hybrid evolve into a new species? The answer is almost always a resounding no. The origin of a new species through hybridization – hybrid speciation – requires very specific conditions. First of all, you need several hybrid individuals that can breed with each other. In some cases, hybridization is too rare to sustain a population of hybrids. And the hybrids should be reproductively isolated from their parental species, allowing the hybrids to carve out their own independent evolutionary trajectory. But despite these restrictions, hybrid speciation does occur. Hybrid life finds a way.

Three Criteria

How to recognize a hybrid species? In 2014, Molly Schumer and her colleagues put forward three criteria to show that a species is of hybrid origin, namely (1) reproductive isolation of hybrid lineages from the parental species, (2) evidence of hybridization in the genome, and (3) evidence that this reproductive isolation is a consequence of hybridization. A survey of the literature revealed that only four species (three sunflowers and one butterfly) fulfilled all three criteria. The main bottleneck was the third criterion. The first two criteria make intuitive sense, but the third one does seem too strict. Why should hybridization directly lead to reproductive isolation before we can talk about a hybrid species? Other evolutionary mechanisms could lead to reproductive isolation between the hybrids and their parental species.

Several researchers indicated that the third criterion was too strict, leading to the exclusion of potentially interesting cases of hybrid speciation. In 2018, I proposed a possible solution to this clash of criteria by discriminating between two types of hybrid speciation: type I where reproductive isolation is a direct consequence of hybridization and type II where it is the by-product of other processes. Applying this approach to birds revealed that the majority of putative hybrid species belongs to the type II group. Specifically, reproductive isolation often evolved when the hybrid population became geographically isolated from the parental species. A combination of hybrid speciation and classic allopatric speciation.

An overview of how many putative hybrid species follow the three criteria of Schumer et al. (2014).

Italian Insights

This academic debate about criteria sounds rather abstract. Let’s explore an actual case to make it more tangible: the Italian Sparrow (Passer italiae). Morphologically, this small passerine resembles a cross between House Sparrow (P. domesticus) and Spanish Sparrow (P. hispaniolensis). Indeed, Jo Hermansen and his colleagues noted that:

Male Italian sparrows have a chestnut-coloured crown and nape, and white cheeks similar to the Spanish sparrow (house sparrows have a broad, grey band on the crown and nape, and grey cheeks), but a small bib and a brown-streaked back similar to the house sparrow (Spanish sparrows have a large black bib that extends all along the body flanks and a black- and yellow-streaked back). Interestingly, male F1-hybrids between house sparrows and Spanish sparrows resemble Italian sparrows.

The morphological intermediacy of the Italian Sparrow was confirmed by genetic analyses. As expected, the genome of the Italian Sparrow is a mixture of the House Sparrow (ca. 60%) and the Spanish Sparrow (ca. 40%). The hybrid speciation event probably occurred less than 10,000 years ago when House Sparrows expanded across Europe and came into contact with the Spanish Sparrow. The resulting hybrid population became geographically isolated on the Italian peninsula and adjacent islands, eventually evolving into the Italian Sparrow. A nice example of a type II hybrid species.

Genomic analyses of the Italian Sparrow revealed that it is a mixture of House Sparrow (blue) and Spanish Sparrow (red). The origin of this hybrid species probably involved geographical isolation on the Italian Peninsula and neighboring islands. From: Elgvin et al. (2017).

Big Bird

A scenario of hybrid speciation with an allopatric phase is not only limited to the Italian Sparrow. Another example concerns the Audubon’s Warbler (Setophaga auduboni), a hybrid between Myrtle Warbler (S. coronata) and Black-fronted Warbler (S. nigrifrons). And there is the Golden-crowned Manakin (Lepidothrix vilasboasi), a hybrid between Opal-crowned Manakin (L. iris) and Snow-capped Manakin (L. nattereri). Does this mean that all hybrid bird species belong to the type II group? Well, there is always an exception that proves the rule.

A beautiful example of a type I hybrid bird species – where reproductive isolation is directly caused by hybridization – is the so-called “Big Bird” on the Galapagos Islands. In 1981, a large Cactus Finch (Geospiza conirostris) arrived on the island Daphne Major and mated with a female Medium Ground Finch (G. fortis). The resulting offspring only bred with each other and as such established a new hybrid lineage on the island. The hybrids have an intermediate beak morphology and produce a distinctive song. These traits contribute to reproductive isolation from at least one parental species (G. fortis) because of differences in song and beak morphology. Reproductive isolation is thus directly due to hybridization.

The extensive pedigree of the hybrid lineage on the island Daphne Major. Hybridization between a female Medium Ground Finch (green) and a male Cactus Finch (blue) gave rise to a population of hybrids that only mated among themselves. From: Lamichhaney et al. (2018).

Extreme Hybrids

The hybrid species discussed above show intermediate morphology. The Italian Sparrow has plumage patterns of both parental species, and the “Big Bird” lineage sports an intermediate beak. In some cases, however, hybrids exhibit extreme phenotypes that surpass the range of the parental species. Think of the excessive size the hybrid ligers compared to their parents, lions and tigers.

Some researchers have used this phenomenon – known as transgressive segregation – to pinpoint potential hybrid species. Two intriguing examples concern the Steller’s Eider (Polysticta stelleri) and the Red-breasted Goose (Branta ruficollis). Both species have exceptional plumage patterns and show signs of past hybridization with other species. The Steller’s Eider shares genetic variation with Long-tailed Ducks (Clangula hyemalis) and several eider species. And the Red-breasted Goose might have originated through hybridization between Brent Goose (Branta bernicla) and the ancestor of the white-cheeked geese (a group which includes among others, the Canada Goose, B. canadensis).

There is, however, an alternative explanation for the genetic make-up of the Steller’s Eider and the Red-breasted Goose. These birds might have hybridized with several species at different times during their evolutionary history, picking up genetic variants in each of these hybridization events. The resulting mixture looks like a hybrid species, but developed along a different evolutionary path (see figure below). Discriminating between successive hybridization events and hybrid speciation requires more detailed genetic analyses. Clearly, we need more that a handful of criteria to identify a hybrid species.

The difference between hybrid speciation and successive hybridization events can be difficult to tease apart. In the right figure, hybridization repeatedly occurs between species A and B, but more species might be involved. From: Ottenburghs (2018).

References

Elgvin, T. O., Trier, C. N., Tørresen, O. K., Hagen, I. J., Lien, S., Nederbragt, A. J., Ravinet, M., Jensen, H. & Sætre, G. P. (2017). The genomic mosaicism of hybrid speciation. Science advances, 3(6), e1602996.

Hermansen, J. S., Sæther, S. A., Elgvin, T. O., Borge, T., Hjelle, E., & Sætre, G. P. (2011). Hybrid speciation in sparrows I: phenotypic intermediacy, genetic admixture and barriers to gene flow. Molecular Ecology, 20(18), 3812-3822.

Lamichhaney, S., Han, F., Webster, M. T., Andersson, L., Grant, B. R., & Grant, P. R. (2018). Rapid hybrid speciation in Darwin’s finches. Science, 359(6372), 224-228.

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

Nieto Feliner, G., Álvarez, I., Fuertes-Aguilar, J., Heuertz, M., Marques, I., Moharrek, F., Piñeiro, R., Riina, R., Rosselló, J. A., Soltis, P. S. & Villa-Machío, I. (2017). Is homoploid hybrid speciation that rare? An empiricist’s view.

Ottenburghs, J., Megens, H. J., Kraus, R. H., Van Hooft, P., van Wieren, S. E., Crooijmans, R. P., Ydenberg, R. C., Groenen, M. A. M. & Prins, H. H. (2017). A history of hybrids? Genomic patterns of introgression in the True Geese. BMC Evolutionary Biology, 17(1), 1-14.

Ottenburghs, J. (2018). Exploring the hybrid speciation continuum in birds. Ecology and Evolution, 8(24), 13027-13034.

Schumer, M., Rosenthal, G. G., & Andolfatto, P. (2014). How common is homoploid hybrid speciation?. Evolution, 68(6), 1553-1560.

Featured image: Italian Sparrow (Passer italiae) © Omar Bariffi | Wikimedia Commons

What is the most diverged avian hybrid?

Genetic analysis of a putative hybrid between species that diverged 65 million years ago.

In 1956, the Brazilian ornithologist Augusto Ruschi acquired a peculiar bird: a putative hybrid between Helmeted Guineafowl (Numida meleagris) and Rusty-margined Guan (Penelope superciliaris). These species belong to different bird families – Numididae and Cracidae, respectively – and diverged about 65 million years ago, making this cross the most divergent hybrid ever documented.

Early Skepticism

At a conference in South Africa, Dean Amadon – Chairman of the Department of Ornithology at the American Museum of Natural History in New York City – shared this case with his colleagues, generating some controversy. Especially, the French ornithologist Jacques Berlioz was skeptical and noted that “owing to differences in the structure of the cloacas, it is anatomically impossible for guans and guineafowl to mate – it would be almost equivalent to crossing a fowl and a duck.”

After Ruschi sent the preserved skin to the American Museum of Natural History, Amadon reconsidered his opinion, suggesting that it might be a hybrid between Helmeted Guineafowl and Chicken (Gallus gallus). Nonetheless, this hybrid combination still circulates in the scientific literature, such as the Handbook of Avian Hybrids of the World (which contains some other dubious records). How reliable is this hybrid record?

Photograph of the specimen by Peter Capainolo. © American Museum of Natural History.

Whole Genome Sequence

Solely relying on morphology to identify hybrids can be challenging. Genetic analyses are often needed to validate a particular hybrid combination (as I argued before). That is why James Alfieri and his colleagues decided to sequence the complete genome of the specimen that Dean Amadon received from Augusto Ruschi. Comparing the DNA sequences of the specimen with other species revealed that most genomic segments mapped to Helmeted Guineafowl and Chicken. Moreover, the mitochondrial DNA matched with the Helmeted Guineafowl, indicating that this species was the mother (mtDNA is passed down through the maternal line). Hence, the researchers concluded that “the parents of the hybrid were the frequently observed, yet still extremely diverged species pair, G. gallus (sire) and N. meleagris (dam).” Mystery solved.

Genomic segments of the specimen mostly mapped to Helmeted Guineafowl (Numida meleagris) and Chicken (Gallus gallus). From: Alfieri et al. (2023).

Golden Standard

Although the hybrid is not the outcome of mating between Helmeted Guineafowl and Rusty-margined Guan, it is still the most diverged avian hybrid to date. Helmeted Guineafowl and Chicken diverged about 47 million years ago. More importantly, this study highlights the danger of only using phenotypic data to determine the parental species that produced the hybrid. In their paper, the authors rightfully remark that “genetic approaches, such as whole-genome sequencing, remain the gold standard for validating hybridization events.” Amen to that.

References

Alfieri, J. M., Johnson, T., Linderholm, A., Blackmon, H., & Athrey, G. N. (2023). Genomic investigation refutes record of most diverged avian hybrid. Ecology and Evolution, 13(1): e9689.

Ruschi, A., & Amadon, D. (1959). A supposed hybrid between the families Numididae and Cracidae. Ostrich, 30(S1): 440-442.

Featured image: Rusty-margined Guan (Penelope superciliaris) © Luan Faitanin Volpato | Wikimedia Commons

The evolution of multi-copy genes on the W-chromosome

Is this avian sex-chromosome comparable to the mammalian Y-chromosome?

The Y-chromosome looks pretty pathetic in comparison with the much bigger X-chromosomes. In mammals, this male sex-chromosome went its separate evolutionary way when it acquired a sex-determining gene and stopped recombining with other chromosomes. The result is a decaying chromosome that harbors few functional genes. Interestingly, many of these remaining genes have experienced massive amplification, resulting in several multi-copy gene families. The exact trigger for this increase in gene copy numbers remains a matter of debate, but could be related to strong selection in males for sperm competition. More expressed Y-linked genes might improve sperm mobility (see for example this study).

The study of multi-copy genes on sex-chromosomes has mainly focused on the Y-chromosome (in mammals and Drosophila). What about the W-chromosome in birds? This small sex-chromosome is female-specific and not susceptible to sperm competition. We might thus expect different evolutionary dynamics on the W-chromosome. That is why Thea Rogers and her colleagues decided to take a closer look at multi-copy genes on this chromosome. Is it comparable to or drastically different from the Y-chromosome?

Counting Genes

The researchers quantified the variation in copy number of 26 W-linked genes in several duck breeds. Using a special molecular technique – NanoString nCounter assay – they found that most of these genes were present in single copies. Only the genes HINTW (18 copies) and KCMF1W (2 or 3 copies) have undergone amplification in ducks. This pattern contrasts with the situation on the Y-chromosome where massive gene amplification took place. What could explain the difference between these chromosomes?

The researchers offer several possibilities, such as the role of genetic drift and meiotic drive dynamics. In this blog post, however, I would like to focus on the explanation I introduced above: sperm competition. The W-chromosome is not affected by this competition where multiple gene copies might improve sperm success. Because there is no similar selection pressure on female fertility, having multiple versions of the same gene is not a suitable strategy. There is, however, an exception: the gene HINTW.

Variation in copy number for the gene HINTW in duck breeds (A) and chicken breeds (B). These patterns suggest selection for female fertility in the chicken breeds.

Egg Production

As mentioned in the previous section, the gene HINTW has 18 copies in the duck breeds. In chicken breeds, however, we observe some striking variation, ranging from 7 copies in the wild Red Junglefowl to 17 copies in the Black Minorca breed. Interestingly, the number of gene copies seems to be related to selection for egg production:

We find a general trend that breeds which have been selected for egg production via artificial female-specific selection, had on the average higher number of copies relative to breeds that have been bred for male fighting and plumage and subject to relaxed female-specific selection.

So, similar to the effects of male sperm competition on the Y-chromosome, artificial selection for female egg production can impact the number of gene copies on the W-chromosome. These sex-chromosomes might not be that different after all.

References

Rogers, T. F., Pizzari, T., & Wright, A. E. (2021). Multi-copy gene family evolution on the avian W chromosome. Journal of Heredity, 112(3), 250-259.

Featured image: Runner ducks © Bjoern Clauss | Wikimedia Commons

Applying the Biological Species Concept to Bacteria

Introgression is not limited to Eukaryotes.

Over the years, I have written several blog posts about species concepts (see for example here and here). I argued that most biologists currently follow the General Lineage Concept or the Evolutionary Species Concept, which both regard species as independently evolving lineages. Laypeople are probably most familiar with the Biological Species Concept (or BSC), defining species as “a group of organisms that can successfully interbreed and produce fertile offspring.” However, this concept can be difficult to apply in certain situations, such when populations are geographically isolated and will never meet. Another common criticism is that the BSC cannot be applied to Bacteria because they do not reproduce sexually. You can imagine my surprise when I came across a recent paper in the journal Genome Biology where researchers applied the BSC to Bacteria:

Some bacteria can engage in gene flow via homologous recombination and this observation has led a growing number of researchers to suggest that bacterial species and speciation might be best defined using the same evolutionary theory developed for sexual organisms; the biological species concept (BSC).

Introgression and Recombination

Awa Diop and her colleagues studied more than 30,000 bacterial genomes. First, they classified these genomes into species by using a cut-off value of 94% genetic similarity in a set of core genes. This arbitrary threshold is commonly applied to delineate bacterial “species”. In this study, however, it mainly allowed the researchers to create a set of “species” for further analyses. To determine whether there has been introgression between these different bacterial “species”, the researchers calculated the ratio between homoplasmic (h) and non-homoplasic (m) alleles. A homoplasmic allele is a genetic variant that is not the result of inheritance from parent to offspring (i.e. vertical inheritance). Instead, such an allele can be the outcome of introgression between bacterial species (i.e. horizontal transfer) or convergent evolution (i.e. bacteria that independently acquire the same mutation). Clonal species – that reproduce asexually – are expected to have few homoplasmic alleles and thus a low h/m ratio. Introgression will result in an increased h/m ratio due to the accumulation of homoplasmic alleles.

In addition, introgression will be accompanied by recombination, the exchange of homologous sections of chromosomes. This process leads to the breakdown of linkage between certain alleles – also known as linkage disequilibrium (LD) – across chromosomes. Clonal species don’t engage in recombination and will thus show no reduction in linkage disequilibrium.

The researchers simulated bacterial genomes without gene flow and compared these patterns – in terms of h/m ratio and LD – with the actual data. These analyses revealed that most bacterial “species” showed signs of introgression and only 2.6% were truly clonal. Some kind of sexual reproduction among Bacteria seems to be more common than we expected.

Genomic analyses pointed to high levels of gene flow (or introgression) between bacterial species. From: Diop et al. (2022).

MEPS

Although the level of introgression among bacterial “species” varied extensively (see figure above), it correlated nicely with sequence similarity. The more similar two species are on a genetic level, the higher the level of introgression uncovered in this study. This pattern can be explained by the observation that homologous recombination requires nearly identical stretches of DNA (also known as MEPS, Minimal Efficient Processing Segments). As genomes diverge, the density of these MEPS decreases and recombination becomes less likely. The relationship reported in this study shows a rapid reduction in introgression between 2% and 10% of sequence divergence. This result explains why an arbitrary threshold to define species of about 95% has been so useful in the past. However, introgression occurred between species that were 90% to 98% divergent. The exact threshold for bacterial species boundaries will thus depend on the study system. There is no silver bullet.

The relationship between sequence identify and level of introgression shows a sharp turn at ca. 90% sequence divergence. From: Diop et al. (2022).

From Bacteria to Birds

You might be wondering why I am covering a paper about bacterial species on a blog dedicated to birds. There are two main reasons: (1) I have a broad interest and don’t want to limit myself to literature on avian hybridization, and (2) you can learn a lot from other study systems. In this case, I noticed an interesting parallel between the arbitrary species threshold in birds (ca. 2% divergence in mitochondrial genes) and in Bacteria (ca. 95% divergence in core genes). These thresholds can be useful as a starting point, but are not always reliable (see for example this blog post). Moreover, this study confirmed a growing consensus among biologists studying speciation: introgression is more common than we previously thought. It doesn’t matter whether we are talking about Bacteria or birds.

References

Diop, A., Torrance, E. L., Stott, C. M., & Bobay, L. M. (2022). Gene flow and introgression are pervasive forces shaping the evolution of bacterial species. Genome Biology, 23(1), 1-19.

Featured image: Neisseria gonorrhoeae © Dr. Norman Jacobs | Wikimedia Commons

What determines range shifts up and down tropical mountains?

Exploring the impact of different ecological traits.

Some bird species might be on an “escalator to extinction.” As the climate changes and the suitable habitat shifts upslope, the birds have no choice but to move along. At some point, however, the mountain stops and the species might go extinct. This scenario makes intuitive sense, but is obviously too simple. Several other factors play a role in elevational range shifts and not all species will move up the mountain. Indeed, several studies reported that between a third and a fifth of species actually shift downslope.

In a recent Frontiers in Ecology and Evolution paper, Montague Neate-Clegg and his colleagues compiled a dataset of elevational range shifts for 421 bird species. They found that the species tend to move upslope with an average speed of 1.6 meter per year. However, this speed is only an average which does not capture the variation in underlying range shifts. These shifts are influenced by several ecological traits. Let’s head up this mountain of data and explore.

Species Traits

The dataset contained information from eight study sites across the tropics, from Peru to New Guinea. Detailed statistical analyses revealed that “elevational shift rates are associated with species’ traits, particularly body size, dispersal ability and territoriality.” The finding that dispersal ability plays a role in range shifts is not that surprising. Birds that disperse farther are more likely to explore new locations outside of their current distribution. Similarly, the influence of territoriality is also logical. Birds that do not hold territories are more free to move around and colonize new areas. Finally, the relationship between body size and elevational shifts can be explained within the context of life history theory. Small-bodies species shifted their ranges faster. Smaller species tend to have faster life histories, allowing them to rapidly respond to changing environments. Hence, we have three factors – dispersal ability, territoriality, and body size – that make ecological sense.

The analyses showed that body mass and territoriality have an effect on elevational shifts in tropical birds. These graphs illustrate the relationships with mean elevation (A and B), lower limit (C) and upper limit (D) of the distribution. From: Neate-Clegg et al. (2021).

Downhill

As mentioned above, not all bird species move upslope. And indeed, this study also found that a third of the shifts were downslope. What could explain this reversed movement? The authors offer two main ideas: (1) competitor release and (2) tracking of ecological requirements. The first explanation entails the scenario that a competitor goes extinct downhill, allowing another species to extend its distribution into the freely available niche and extend its range downslope. The second explanation is quite intuitive: species move where there is food. If your favorite food source happens to be down the mountain, that is where you will go there.

In the end, this study provides several ecological features to understand the movement of tropical bird species up and down mountains. However, they did not explicitly consider large-scale factors, such as the topography of the landscape and the configuration of the vegetation. A nice opportunity for further research into elevational range shifts. Much remains to be discovered, so I guess it is not all downhill from here.

The percentage of species that shifted downslope. The different shared of grey correspond to mean elevation, upper limit and lower limit. From: Neate-Clegg et al. (2021).

References

Neate-Clegg, M. H., Jones, S. E., Tobias, J. A., Newmark, W. D., & Şekercioǧlu, Ç. H. (2021). Ecological correlates of elevational range shifts in tropical birds. Frontiers in Ecology and Evolution, 9, 621749.

Featured image: Andean Motmot (Momotus aequatorialis) © Alejandro Bayer Tamayo | Wikimedia Commons

What is a species anyway?

Seeing “species as individuals” helps to understand taxonomic disagreements.

More than ten million years. It has been more than ten million years since the Rose-breasted Grosbeak (Pheucticus ludovicianus) and the Scarlet Tanager (Piranga olivacea) diverged. Despite this significant evolutionary gap, these species still managed to produce a hybrid (see this paper for the complete description). This unusual hybrid attracted some media attention – including this piece in National Geographic – prompting some Twitter-accounts to ask the age-old question: what is a species?

Most people still think about the Biological Species Concept, defining species as “a group of organisms that can successfully interbreed and produce fertile offspring.” A very strict application of this species concept will merge any two species that produce the occasional fertile hybrid. If the cross between the Rose-breasted Grosbeak and the Scarlet Tanager turns out to be fertile, should we consider these drastically different birds as members of the same species? No, because the reality is more nuanced and complicated than blindly following the Biological Species Concept.

As I have explained in a previous blog post, most biologists adhere to the General Lineage Concept or the Evolutionary Species Concept. Both of these concepts emphasize the independent evolutionary trajectory of a species. The General Lineage Concept talks about “separately evolving metapopulation lineages”, whereas the Evolutionary Species Concept mentions “the independent evolutionary fate and historical tendencies” of a species. An occasional hybrid – such as the one described above – will not impact the evolutionary trajectory of both species and we should thus not worry about the species status of the Rose-breasted Grosbeak or the Scarlet Tanager. But what about species that regularly hybridize?

Photographs of the hybrid from (a-c) and the putative parental species: Rose-breasted Grosbeak (d) and Scarlet Tanager (e). From: Toews et al. (2022).

Species as Individuals

The situation becomes more complicated when we consider species that regularly interbreed. Think of the Golden-winged Warbler (Vermivora chrysoptera) and the Blue-winged Warbler (V. cyanoptera) in North America, or the Hooded Crow (Corvus [c.] cornix) and the Carion Crow (C. [c.] corone) in Europe. Does the production of hybrids influence the evolutionary trajectories of these lineages? Here, it is important to consider that the origin of species (or speciation) is a gradual process. Before the development of “separately evolving metapopulation lineages”, these lineages might engaged in a complicated and intricate dance of merging and diverging. Due to the continuous nature of the speciation process, it can thus be difficult to establish clear species boundaries.

To understand this issue, I have always found it useful to consider species as individuals (a philosophical perspective introduced by David Hull). An evolutionary lineage can be regarded as an individual that is born (i.e. start of the speciation process) and will die (i.e. extinction). Some individuals will reach adulthood (i.e. become species) while others will not. However, at what point does an individual become an adult? When I look at the children of my nieces, I am confident that they are not adults yet. And when I meet my uncle or aunt at a family gathering, they are clearly adults. But somewhere between the transition from child to adult, there is a gray zone. Just ask any cashier that needs to check the age of her costumers when they buy alcohol.

Seeing species as individuals. But where do you draw the line between child and adult?

Species Criteria

What characteristics would you use to define an adult? You could focus on particular morphological features, such as secondary sexual traits (e.g., the development of a beard in men or breasts in women). Or you could pay attention to particular behaviors that you consider typical for adults. You could even devise a genetic test to measure the length of telomeres. But when you apply these criteria to a group of people – aged 16 to 25, for example – you will probably come to drastically different conclusions depending on the features you focus on. Different traits – whether morphological, behavioral or genetic – will develop at different rates in different people.

The same reasoning applies to species: during the speciation process, different criteria will evolve at different times in the speciation process. The order in which these criteria evolve will be contingent upon the speciation process. In some cases, morphological differences might emerge before genetic differentiation (see for example Redpolls). In other cases, lineages might be genetically distinct despite little morphological change (i.e. cryptic species, such as in the Warbling Vireo). The result is a taxonomic grey zone where different species criteria lead to different conclusions.

This simplified diagram represents a single lineage splitting into two independently evolving lineages (or species). The horizontal lines represent the times at which the lineages acquire different species criteria. This results in a taxonomic grey zone where alternative species criteria come into conflict. Adapted from De Queiroz (2007) Systematic Biology.

Labeling Life

From the perspective of “species as individuals”, it becomes clear where most taxonomic disputes come from. Lineages that are still in the process of speciation – or even subject to reverse speciation, such as American crows and bean geese – end up in a taxonomic grey zone where species criteria come into conflict. Classifying the inhabitants of this grey zone can be extremely difficult because personal preferences of certain taxonomists and political issues (e.g., protection of endangered species) come into play. This will inevitably lead to some man-made “species” that are not strongly supported by biological data. And the ensuing debate can become heated and unfriendly.

Personally, I prefer to acknowledge the fact that some lineages cannot be easily divided into distinct species. It might be better to just refer to them as taxa – not trying to label them as “species” or “subspecies” – and focus on understanding their ecology and evolution. These resulting insights will be more interesting and fulfilling compared to putting an arbitrary label on an individual.

References

Hull, D. L. (1976). Are species really individuals?. Systematic zoology, 25(2), 174-191.

Ottenburghs, J. (2019). Avian species concepts in the light of genomics. In Avian Genomics in Ecology and Evolution (pp. 211-235). Springer, Cham.

Toews, D. P., Rhinehart, T. A., Mulvihill, R., Galen, S., Gosser, S. M., Johnson, T., … & Latta, S. C. (2022). Genetic confirmation of a hybrid between two highly divergent cardinalid species: A rose‐breasted grosbeak (Pheucticus ludovicianus) and a scarlet tanager (Piranga olivacea). Ecology and Evolution, 12(8), e9152.

Featured image: Birds of North America infographic © Pop Chart | Trendhunter

Should we save the Kākāpō?

A philosophical perspective on nature conservation.

At the moment, there are only 252 adult Kākāpōs (Strigops habroptilus) left on this planet. This species almost went extinct after the introduction of non-native predators, such as cats and rats, to New Zealand during the British colonization. Without the extensive efforts of the Kakapo Recovery Program, we would have probably lost this iconic owl parrot forever. The extinction of a species sounds disastrous, but is that really the case? Recently, I read the book “Plastic Panda’s” by the Dutch philosopher Bas Haring in which he argues that the disappearing of species is not always a problem. We can survive with less species, less biodiversity. A provocative statement that requires more thought than Haring gave it in his book. The book – already published in 2011 – was terribly bad, mainly a collection of irrelevant anecdotes and a cherry-picking of scientific studies, written in a childish way that disrespects the intellect of the reader. However, it did force me to think about the rationale behind nature conservation. Do we need to save all species, such as the Kākāpō?

Ecosystem Services

Currently, the world is driven by economics. It is thus no surprise that scientists have tried to quantify the “economic value” of species in terms of the services that they provide. Some species might be important because they can be used as food sources and other species might play an important role in nutrient cycles. Although I am not a big fan of the concept of ecosystem services, it could be that this perspective contributes convincing evidence for protecting certain species. So, which ecosystem services does the Kākāpō provide? A quick search on Google Scholar revealed no clear studies that addressed this question. At first glance, it seems that the Kākāpō has little to offer in terms of ecosystem services.

There was, however, one PNAS-paper that mentioned how an endemic plant in New Zealand (the Wood Rose, Dactylanthus taylorii) probably relied on the Kākāpō for seed dispersal. Hence, even though the Kākāpō might not be useful for humans (within the context of ecosystem services), other organisms might rely on it. This observation brings me to another argument for nature conservation: ecosystem stability. The extinction of one species might trigger a cascade of negative effects, resulting in the collapse of entire ecosystems. This effect will be most severe when keystone species disappear. Such species tend to have little functional redundancy, meaning that no other species would be able to fill its ecological niche and stabilize the ecosystem. However, not all species are keystone species and the extinction of some species might have little to no effect on the entire ecosystem. It seems reasonable to assume that the Kākāpō does not play a central role in the New Zealand ecosystem. Its extinction would probably have few consequences for ecosystem stability.

Wood roses from the Whanganui Regional Museum. These plants probably relied on the Kākāpō for seed dispersal. Source: Wikimedia Commons.

Intrinsic Value

So far, we have not found any good arguments for preventing the Kākāpō from going extinct. However, the previous paragraphs mainly explored direct advantages of species in terms of ecosystem services. Perhaps the Kākāpō is just valuable in itself. Indeed, a common argument for conserving a species is that each species has intrinsic value: “the value that an entity has in itself, for what it is, or as an end”. In his book, however, Haring argues that species do not have intrinsic value. He states that nothing is valuable in itself, including species. Is that it? The Kākāpō has no value and its extinction is no big problem.

Not so fast. Here, Bas Haring show some philosophical shortcomings. He fails to discriminate between objective and subjective intrinsic value (see here for more information about these concepts). His argument relies on the objective intrinsic value, which is not conferred by humans. And indeed, if humans were to disappear from this planet, the Kākāpō will most likely not have any intrinsic value. But we should not forget about subjective intrinsic value, which is “created by valuers through their evaluative attitudes or judgments.” You only need one person to care about the Kākāpō to give it value. And luckily many people care about this beautiful species.

The Importance of Science

In this blog post, I have tried to follow the rational arguments for saving certain species. And although I am a strong advocate for the power of rationality, it should not blind us. Emotion is an important aspect of nature conservation. Some species might not provide clear ecosystem services or might play a minor role in stabilizing an ecosystem, but that does not mean they have no value. As long as biologists care about a species, it is valuable. And this appreciation for certain species often arises from studying them. Discovering the beauty of species through understanding its ecology and evolution. That is why science is so crucial for nature conservation, and why I will continue to write about the amazing diversity of the natural world.

References

Haring, B. (2011) Plastic Panda’s. Nijgh & Van Ditmar, Amsterdam.

Featured image: Kākāpō (Strigops habroptilus) © Dianne Mason | Wikimedia Commons

What is the difference between hard and soft selection?

An interesting perspective on the nature of natural selection.

You might be surprised to read that my employer – Wageningen University – houses several creationists. Their scientific work generally focuses on non-evolutionary topics, such as nitrogen deposition, but that does not prevent some colleagues from commenting on evolutionary biology. One professor, for example, said the following in an interview: “Humans not only share 96 percent of their DNA with monkeys, but also 88 percent with mice, while according to the theory of evolution humans are not descended from mice.” This statement clearly shows that he has no clue how evolution works. Humans are not directly descended from monkeys or mice, but share a common ancestor with both. And because the common ancestor of humans and monkeys is more recent than the one of humans and mice, we share more genetic material with monkeys. This “critique” on evolution actually contains supporting evidence for the fact that all life on our planet evolved. Unfortunately, this professor is blinded by religious dogma and cannot approach evolutionary questions unbiased. Any discussion is thus useless (see for example this blog post).

Another common creationist argument is that “random mutations and natural selection” are insufficient to explain the diversity of life. However, evolution is so much more than “random mutations and natural selection” (otherwise, evolutionary textbooks would be quite short). There are several other evolutionary processes, such as genetic drift and sexual selection, to consider. In addition, the term natural selection covers a whole range of possible selective mechanisms, such as directional selection or balancing selection. In fact, I recently came across an Ecology Letters paper on the concepts of hard and soft selection. An interesting framework that I had not thought about yet. So, in this blog post, I will try to explain the difference between these two types of selection.

Population Genetic Paradox

The concepts of hard and soft selection were introduced by Bruce Wallace to resolve an apparent paradox in population genetics. In the 1960s, evolutionary biologists assumed that any given environment has one optimal genotype. Any other genotypes in the population would thus have a lower fitness compared to this optimal genetic combination. This reasoning implies that populations with high levels of genetic variation will have a low mean fitness. When researchers were able to quantify genetic diversity in wild populations, they were surprised to find high levels of variation (see for example Hubby and Lewontin 1966). These observations were at odds with the proposed relationship between genetic variation and mean fitness. To resolve this paradox, Wallace introduced the concept of soft selection where the fitness of an individual is not quantified relative to an optimal genotype, but against the fitness of its conspecifics.

Bears and Hares

The theoretical explanation might make your head spin, so let’s use an example to clarify these concepts. Imagine a population of bears that are competing for a certain number of caves for hibernation. The bears are either aggressive or submissive. And obviously, aggressive bears will outcompete the submissive ones. When there are enough caves for all bears, there will be no selection. However, once there are more bears than caves, selection will occur. Now, the selection dynamics will depend on the behavioral composition of the population. In a situation with few aggressive bears, some submissive bears will be able to secure a cave and will have a higher relative fitness. But when there are more aggressive bears, the submissive bears will be outcompeted and will have a lower relative fitness. The fitness of the submissive bears thus depends on the amount of aggressive bears in the population. This is soft selection.

To understand how hard selection is different, consider another example: predation on snowshoe hares. The risk of predation depends on the coat color of the individual. Better camouflaged hares will survive better. The relative fitness of the different coat colors does not depend on the composition of the population. Badly camouflaged individuals – such as a white hare in a brownish landscape – will have a lower chance of survival regardless of the number of well-camouflaged conspecifics. This situation would result in hard selection.

Two examples to illustrate soft and hard selection. In the bear example, the fitness of the submissive individuals depends on the behavioral composition of the population. In the hare example, however, the fitness of badly camouflages (white) snowshoe hares is independent of the number of well-camouflaged individuals. From: Bell et al. (2021) Ecology Letters.

Slushy Selection

These two examples only scratch the surface when it comes to hard and soft selection. Bruce Wallace developed a population genetic model to explore the strength of selection in different scenarios. And numerous authors have expanded on these ideas. Some have argued that hard and soft selection are just two extremes on a continuum, while others have suggested that both types of selection might operate on the same traits (i.e. slushy selection). Diving into these details and exploring the ecological and evolutionary impacts of hard versus soft selection would takes us too far down the rabbit (or hare?) hole.

My goal was to introduce these concepts and show that evolution is more complex than “random mutations and natural selection”. If creationists would take to the time to really understand the intricacies of the evolutionary process, they would quickly realize how silly some of their arguments are. More importantly, they might discover how interesting and exciting evolutionary biology is.

References

Bell, D. A., Kovach, R. P., Robinson, Z. L., Whiteley, A. R., & Reed, T. E. (2021). The ecological causes and consequences of hard and soft selection. Ecology Letters, 24(7), 1505-1521.

Wallace, B. (1975). Hard and soft selection revisited. Evolution, 465-473.

Featured image: Grizzly Bear (Ursus arctos) © Gregory “Slobirdr” Smith | Wikimedia Commons