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Fringillidae (2 Viewers)

Diaz Mendez, Sheylda N., Taylor Hains, Stacy Pirro, John Bates, and Shannon Hackett (2024) The complete genome sequence of Chlorophonia sclateri (Fringillidae, Passeriformes), the Puerto Rican Euphonia. Biodiversity Genomes.
The Complete Genome Sequence of Chlorophonia sclateri (Fringillidae, Passeriformes), the Puerto Rican Euphonia | Published in Biodiversity Genomes

Abstract
The Puerto Rican Euphonia (Chlorophonia sclateri) was recognized as an endemic species in 2023 based solely on morphological differences. A brightly plumaged finch that inhabits a variety of habitats, including lowland dry, scrub forests and shade-coffee plantations (Carlo et. al 2004). To provide molecular evidence for the genetic comparison of Antillean Euphonias, we present the whole genome sequence of Chlorophonia sclateri. Illumina paired-end reads were assembled by a de novo method followed by a finishing step. The raw and assembled data are publicly available via GenBank: Sequence Read Archive (SRR28963854) and assembled genome (JBFPDU000000000).
 
The Dutch taxonomic committee has ruled to hold on for the various redpolls for now.
I bet some of you won't be surprised, but to give you an idea of how the article that caused the lumps can also be interpreted, I've copied and pasted the reasoning:
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The AOS (Chesser et al 2024) has included Arctic Redpoll Acanthis hornemanni and Lesser Redpoll A cabaret in A flammea and recommended treatment of this group as a single species A flammea (Redpoll). The rationale for this change was that these taxa show ‘genomic homogeneity, continuous phenotypic variation, overlapping suitable habitat, and a lack of evidence supporting prolonged isolation among these three taxa (Mason & Taylor 2015, Funk et al 2021).’
We regard this lump as premature because 1 the two genomic studies (Mason & Taylor 2015, Funk et al 2021) lacked samples of A f rostrata; as a consequence, the genomic pattern of variation between A f rostrata and A h hornemanni has not been investigated; and 2 there is a lack of detailed quantitative studies of assortative mating in the areas where A f rostrata and A h hornemanni breed sympatrically, and where A f flammea and A h exilipes breed sympatrically. In addition, part of the case for conspecificity may be based on selective interpretation of the available genomic data – an interpretation that is inconsistent with other case studies of the genomics of speciation in birds.

During the past decade, several well-documented case studies have demonstrated that some taxa that are widely considered as valid species differ only in one or a few very small parts of the genome (‘islands of differentiation’). Examples include the parapatric Carrion Crow Corvus corone and Hooded Crow C cornix in Europe (Poelstra et al 2014), the parapatric Blue-winged Warbler Vermivora cyanoptera and Golden-winged Warbler V chrysoptera in North America (Toews et al 2016), the sympatric Iberá Seedeater Sporophila iberaensis and Tawny-bellied Seedeater S hypoxantha in South America (Turbek et al 2021), and the sympatric Plumbeous Seedeater S plumbea and Tropeiro Seedeater S beltoni in South America (Nguyen et al 2024).

In these pairs of species, very large parts of the genome of one species are almost entirely undifferentiated from the other species. Consequently, these pairs are characterised by very low genetic divergence (genome-wide Fst) values. Nevertheless, in each of these cases close examination of the genomic data showed that there is one relatively small part, or a few relatively small parts, in the genome that shows (nearly) complete genetic divergence between the species, and which contains genes coding for plumage differences, and sometimes other relevant differences (Poelstra et al 2014, Toews et al 2016, Turbek et al 2021, Nguyen et al 2024).

These case studies are highly relevant for species-level taxonomy, including that of the redpolls, because they demonstrate that: 1 valid species may show very low genome-wide divergence (ie, very low genome-wide divergence on its own is not evidence for conspecificity); 2 differences between species may be located on only one or a few islands of differentiation (ie, taxonomists should not conclude that two taxa ‘do not differ in their genomes’ if only (small) parts of the genomes have been sequenced, such as with ddRADseq or UCE sequencing); 3 sympatric populations with very low genomic divergence are not necessarily morphs of a single species; and 4 the case of Iberá Seedeater and Tawny-bellied Seedeater, which show strong assortative mating in sympatry and hence strongly reduced gene flow, further shows that very low genomic divergence does not necessarily mean extensive gene flow or lack of reproductive isolation, unless there is positive evidence for widespread hybridisation.

The pattern of genomic divergence among redpolls is similar to that of the four cases mentioned before. Funk et al (2021) demonstrated that differences between exilipes and flammea/cabaret are largely found on a relatively small part of the genome (a chromosomal inversion involving 55 million base pairs) and that this part includes candidate genes related to melanogenesis, carotenoid colouration, and bill shape. We see no reason to interpret the case of the redpolls as fundamentally different from the aforementioned cases.

The four aspects listed by Chesser et al (2024) in support of lumping the redpolls also apply to some or all well-studied cases cited above: genomic homogeneity in most of the genome (all four cases), continuous phenotypic variation (Corvus, Vermivora), overlapping suitable habitat (all except S plumbea/S beltoni), and a lack of evidence supporting prolonged isolation among taxa (all except S plumbea/S beltoni). Thus, the aspects listed in support of lumping are not convincing (see also Knox et al 2024).

We recommend that: 1 A hornemanni, A flammea and A cabaret are best retained as species pending the outcome of field studies; 2 field studies are conducted to assess levels of assortative mating between A h hornemanni and A f rostrata, between A h exilipes and A f flammea, and between A flammea and A cabaret; and 3 levels of song divergence between the three species (five taxa) are adequately studied (preferably where taxa are in contact).
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The Dutch taxonomic committee has ruled to hold on for the various redpolls for now.
I bet some of you won't be surprised, but to give you an idea of how the article that caused the lumps can also be interpreted, I've copied and pasted the reasoning:
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(...)

To me this reads like a rebuttal similar to those of NACC or SACC: "We don't like the result, therefore we nitpick the studies so that we can continue with the status quo." While I, and surely many others, will sorely miss the different Redpolls as their own species, the evidence for their lump seems quite good to me. More information is always encouraged, but if we always wait for more information, no corrections would ever happen. While I can't really comment on the Seedeaters, there's ample evidence for lumping the Crows or Warblers, which hybridise a lot. All taxa involved are highly distinct (unlike most of the redpolls), so that lumping them feels very counterintuitive, but the birds don't seem to discriminate that much. The hybrid zone of the crows is quite broad, in Germany it's around 80 km wide. Keeping the two as distinct species relies on a very nuanced interpretation of BSC. Therefore, I feel like the decision of the Dutch, while not factually wrong is based more on personal preferences than on actual data.
 
Funny, for me a hybrid zone of 80 km for a bird the size of a crow feels really narrow.
Niels
I know what you mean, I could have been clearer. The 80 km-hybrid zone stretches for several hundred, probably thousands of kilometers through much of central Europe, meaning that the number of hybrids will always number several thousands. The fitness of hybrids may be somewhat reduced in terms of total offspring, but I see crow pairs including hybrids all over the place here in northern Germany. If the birds differed in beak or wing measurements instead of feather colouration or if they lived in South America, I'd be sure they'd be treated as subspecies and not as species. To return to the topic of this thread, what I mean to say, is that the provided examples of "good species" are among the weakest recognised "good species" out there.
If all major checklists decided to lump these species (not completely unlikely), would the Dutch follow suit with the Redpolls or would they find other reasons not to?
 
Funny, for me a hybrid zone of 80 km for a bird the size of a crow feels really narrow.
Niels
yeah....this is a big issue with most species concepts. at some level they require parsing of continuous (how morphologically different something is, frequency of hybridization, size of hybrid zones) that are at the end of the day fairly subjective. To me the question to ask is: Is the degree of hybridization extensive enough that both populations are on track to merge into one species in the future? If not, I would say they would be best treated as species.
 
The pattern of genomic divergence among redpolls is similar to that of the four cases mentioned before. Funk et al (2021) demonstrated that differences between exilipes and flammea/cabaret are largely found on a relatively small part of the genome (a chromosomal inversion involving 55 million base pairs) and that this part includes candidate genes related to melanogenesis, carotenoid colouration, and bill shape. We see no reason to interpret the case of the redpolls as fundamentally different from the aforementioned cases.

The four aspects listed by Chesser et al (2024) in support of lumping the redpolls also apply to some or all well-studied cases cited above: genomic homogeneity in most of the genome (all four cases), continuous phenotypic variation (Corvus, Vermivora), overlapping suitable habitat (all except S plumbea/S beltoni), and a lack of evidence supporting prolonged isolation among taxa (all except S plumbea/S beltoni). Thus, the aspects listed in support of lumping are not convincing (see also Knox et al 2024).
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This almost seems disingenuous - when the other examples have such clear discreet plumage differences and the redpoll phenotypes grade into one another - at best this objection is lacking some explanation. There are tons of reasons to consider redpolls as different from these four (ahem) "cherry-picked" cases. Lets split Ruff while we're at it, then?

Also, I think it would be surprising if the genetics of the Greenland populations conflict much with the other genetic studies, which show that the taxa freely trade all their other genes aside from the on/off switch that is the supergene. How do they propose that this gene flow "mirrors" one another between Arctic/Common taxa so closely without coming into contact? And I know its old but didn't Seutin et al. (1995) sample hornmanni/rostrata and found no difference?
 
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These arguments in favor of keeping redpoll phenotypes as separate species are much more applicable to Homo sapiens. Under this approach it should be split into dozens of species. H. sapiens even includes populations that remain genetically and phenotypically distinctive after many centuries of full sympatry.
 
These arguments in favor of keeping redpoll phenotypes as separate species are much more applicable to Homo sapiens. Under this approach it should be split into dozens of species. H. sapiens even includes populations that remain genetically and phenotypically distinctive after many centuries of full sympatry.

Its not just this. If we step way back and take a look at the human species, we will notice that there are two very clear groups with gradational but distinct phenotypic differences. Either because of those differences or because of associated differences, but most likely because of a blending of the two factors - the two groups will often separate themselves behaviorally or even spatially - at lunch tables, nights out, bathrooms, social circles, etc. We commonly refer to these phenotypes as "male" and "female." Much like the redpolls, the two phenotypes share nearly all of their genome - with one major exception... a supergene. We call that gene the sex chromosomes and it codes for a suite of consistent and important characteristics. But it does not make us different species!!!!

Obviously, there is some facetiousness here, and the comparison to redpolls is not a neat fit... although the same can be said about Carrion Crows. But it illustrates that it takes more than an "island of differentiation" (as the committee put it), to be a species. The statement that "some taxa that are widely considered as valid species differ only in one or a few very small parts of the genome" is false - each example differs in all sorts of other ways that pertain to speciation, and in other cases they leave unmentioned (e.g. the Ruff, White-throated Sparrow, domestic pigeon, probably loads of others) that island of differentiation does not pertain.

I'm all for critical investigation of species limits in the redpolls - they are fascinating and unique in ways that raise questions and if they weren't we wouldn't be discussing them. But pointing to other species will bring so many points and counterpoints... so many caveats... that it is unhelpful.
 
Biologists have spent almost three centuries trying to make taxonomy less subjective. No reason to give up now :)
As for crows, yes, carrion/hooded crows are not separate species, they are just racist: they base their mating preferences on a single-allele difference in color that's not even skin-deep.
 
Biologists have spent almost three centuries trying to make taxonomy less subjective. No reason to give up now :)
As for crows, yes, carrion/hooded crows are not separate species, they are just racist: they base their mating preferences on a single-allele difference in color that's not even skin-deep.

He's out of line, but he's right.


 
He's out of line, but he's right.


Sounds very simplistic when we know that hybrids exist and show a number of intermediate phenotypes. It this was truly a switch, then no intermediate plumage birds would be expected.
Niels
 
Sounds very simplistic when we know that hybrids exist and show a number of intermediate phenotypes. It this was truly a switch, then no intermediate plumage birds would be expected.
Niels
Sometimes a switch is more of a control dial, but I see what you're saying.

I agree that the wording choice in the "interview" could be better and clearer, but the graphics showing the limitation of genetic differences to those three spots, and one major one in particular - sure is interesting.
 

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