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Western Flycatcher (1 Viewer)

Richard Klim

Douglas Futuyma, NYSbirds, 21 Nov 2015...
Western Flycatcher: two species or one?

Having enjoyed viewing the "Western" Flycatcher in Central Park today, I thought it might be useful to read the most relevant information on the question of whether or not the "Pacific-slope" and "Cordilleran" Flycatchers are distinct species. Some birders who have seen (or, hopefully, will soon see) this bird may be interested.

First, regarding identification, the account by Lowther in Birds of North America notes that "the commonly heard call, especially from migrant or overwintering birds, is a sharp seet! that is NOT DIAGNOSTIC for either species." [Emphasis added.] And, "identification by call of migrants and vagrants outside the known breeding range is problematic." Lowther discusses discrimination by measurements of flight feathers at some length, and notes that there is much overlap: only about 60% of individuals of KNOWN identity (by breeding location) can be discriminated.

The split of Western Flycatcher (Empidonax difficilis) into two species was recognized by the AOU in 1989, on the basis of a paper by Johnson and Marten in 1988. Since then there has been controversy about their "species'" status, based on phenotypically intermediate birds, especially in interior southern Canada (British Columbia and Alberta), where the ranges of the two forms come into contact. Johnson and Marten reported data from a contact zone in California, but not the Canadian zone.

In 2002, Johnson and Cicero reported that the two forms had different mitochondrial DNA (mtDNA) sequences. I should note that mtDNA is probably the DNA data one should LEAST rely on for discriminating species, because it is not at all representative of most of the genome, for several reasons.

The only subsequent DNA-based study -- and it is a good one-- is by A.C. Rush et al. 2009, Analysis of multilocus DNA reveals hybridization in a contact zone between Empidonax flycatchers, Journal of Avian Biology 40:612-624. They analyzed both mtDNA and chromosomal DNA for 48 specimens, including birds from 8 sites in the Canadian contact zone, plus "pure" Pacific-slope and Cordilleran populations from California and the Rocky Mountains in the U.S. The chromosomal DNA was not gene sequences, but a much cruder kind of data (AFLP), based on a method that reveals single small changes within any of a number of very short DNA sequences scattered throughout the chromosomes.

Their first important finding is that none of the chromosomal DNA markers completely separates Pacific-Slope from Cordilleran Flycatchers, even those distant from the contact zone. The "species" differ only in the percentages of different versions of each marker (like different proportions of people with different eye colors). Second, they found that birds from the contact zone have the same mtDNA as Pacific-slope Flycatchers. However, the chromosomal DNA markers showed a broad band of hybridization: over a span of 400 kilometers, birds show evidence of mixed ancestry.

Their data conform to a scenario in which an ancestral flycatcher was divided into two populations, presumably in the Pacific and Rocky Mountain regions, for a long time. They became somewhat genetically different, mostly by a process of random genetic change known as genetic drift, in which most of the genetic changes have absolutely no effect on the characteristics of the birds (plumage, voice, behavior, ecology). Any two separated populations will undergo this process of random genetic divergence -- all it needs is time. In this scenario, the two populations expanded their ranges northward and came into contact recently, perhaps less than 10,000 years ago, after the most recent glaciation receded. They have been freely interbreeding in southern Canada, and the Pacific-slope mtDNA (the authors suggest) has been spreading into the contact zone faster than the chromosomal DNA because the density of Pacific-slope Flycatcher populations is higher (so they flood the zone) and because they arrive earlier in the spring, so they may get more mates and father more hybrid offspring.

The bottom line: there is extensive hybridization and gene flow between these forms. The authors comment about the AOU decision to split: "We now wonder whether, given the present evidence, the decision to formally split..would have been made." If it were up to me to hand down AOU decisions, these forms would be retired, and we would go back to a single species, Western Flycatcher. I hope the AOU ultimately comes around to that view.

Doug Futuyma
Stony Brok, NY
Andrew Rush, NBHC ID-FRONTIERS, 22 Nov 2015...
Re: Western Flycatcher: two species or one?

Hello all,

Because I am the primary author on the most recent genetic analysis of these species (mentioned in the post by Douglas Futuyma cited by Peter Post), I thought that I could add a little to this discussion. I recently finished my dissertation research, most of which focused on these two species. While it is true that the two species are admixed in their DNA over a large part of the West, the Pacific-slope populations west of the crest of the Sierra, Cascades, and Coast Ranges (i.e., the Pacific Slope) remain genetically and phenotypically distinct. We know that gene flow from interior populations to the west slope Pacific-slope populations occurs to some extent, but it does not result in widespread genetic mixing like it does on the east slope. So, it is a little more complicated than two species just merging (back) into one. Pacific-slope seems to be merging more into Cordilleran than Cordilleran is merging into Pacific-slope. I’m not sure taxonomists will take this nuance into consideration when deciding what to do with these species, but from an evolutionary perspective, it is interesting. I will have at least a couple of more papers on this out soon.

As soon as you cross the crest of the Pacific Slope to the east side, you encounter mostly genetically intermediate birds with intermediate songs or calls. There is some proportion of admixed birds in populations all the way to the Black Hills and to northern Utah and Colorado. On the other hand, you almost never encounter birds with intermediate songs or calls on the west side and almost no birds are mixed in their DNA…and these are limited to areas like Mt. Shasta in California, which is very close to admixed populations.

So, if you have seen a Cordilleran Flycatcher in southern Colorado, New Mexico, or Arizona, you are probably safe…in terms of listing. If your Cordilleran Flycatcher is from Alberta, Idaho, Montana, Wyoming, or the eastern parts of the coastal states, you have a higher likelihood of having seen an admixed bird.

One last thing in terms of identifying these species. I have not formally analyzed the position notes yet (i.e., ‘pee-o-weet’ and ‘weet-seet’) but it seems that these change in a slightly different way than the songs geographically. I.e., you can encounter birds whose position note is more purely Cordilleran that has a more intermediate song type and a more intermediate genotype.

I hope this is interesting to some of you.

Andrew Rush
Farnsworth & Lebbin 2004 (HBW 9):
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Richard Klim

Channel Islands Flycatcher

Alvaro Jaramillo, NBHC ID-FRONTIERS, 25 Nov 2015...
Re: Western Flycatcher: two species or one?

Thanks for that! A great post to read. I would add a wrinkle in this Western Fly scenerio. That is the Channel Islands population of the Western Fly is apparently vocally the most distinct, and perhaps the one that deserves to be split, while the other two are lumped! The part I never understood about Johnson and Martin was why they chose to split Cordilleran and Pac Slope and not the island bird? Here is a bit out of Birds of North America online:

Although not presently recognized as a separate species by Am. Ornithol. Union (1998), birds breeding on Channel Is. off s. California genetically distinct. These populations, currently regarded as a subspecies under Pacific-slope Flycatcher (E. d. insulicola), exhibit substantial differences from mainland Pacific-slope Flycatchers in morphology, coloration, voice, and habitat preference; this population shows extremely reduced gene exchange with mainland populations of Pacific-slope Flycatcher, with which insulicola is otherwise most closely related (Johnson and Martin 1988).

E. d. insulicola Oberholser 1897: Possibly speci-fically distinct but further study needed (Johnson 1980). Breeds on Channel Is. off s. California; winter range unknown. Overall larger than both mainland subspecies; relatively long bill; medium wing length (though relatively long-winged when compared with nearby mainland E. d. difficilis); unusually long tarsus plus middle toe; very bright breast; male Position Note tends to emphasize steeply rising portion of call and have subdued introductory portion (zweep ! versus more wavering upslurred su-weep! of mainland subspecies) but some over-lap; ratio of exposed culmen length to wing length small (0.15-0.19); wing-bars buffy (Juvenal plumage) to white (Basic plumage). Genetic distinction of this race shown by Johnson and Martin (1988) and Barrowclough and Johnson (1988). Male wing range 64-70 mm (n = 10).

Alvaro Jaramillo
alvaro AT alvarosadventures.com
Andrew Rush, NBHC ID-FRONTIERS, 25 Nov 2015...
I have never observed insulicola (the Channel Islands Pacific-slope), but I have analyzed recordings. It is true that it is distinct from the coastal birds in its mitochondrial DNA. We are currently analyzing the nuclear DNA. The song type is more of a variety of the Pacific-slope type. It is much more similar to the coastal birds than to Cordilleran birds. It differs from coastal Pacific-slopes mainly in the frequency (pitch) of certain song elements. I can’t remember how the position note varies. Apparently insulicola occupies habitats that are pretty distinct from coastal birds as well.
Andrew Rush, NBHC ID-FRONTIERS, 25 Nov 2015...
Our analysis of these species has extended to Mexico. I have done a fair bit of fieldwork in Mexico and Guatemala focusing on these species and on Yellowish Flycatchers…including recording dozens of songs from populations for which there were no recordings. I can’t say too much about it at the moment, but the situation south of the US/Mexico border is complicated and interesting. I’m not trying to be coy…it just isn’t all my research, so I am not at liberty to disclose what we have found. If you hear Mexican Cordilleran Flycatcher songs or position notes, you probably will not notice any difference from US Cordilleran Flycatchers. They seem to hear differences though.

Southern Baja California birds are a distinct population. Northern Baja birds are not different from other Pacific-slope populations.

One interesting thing to note…almost no recordings of songs existed before I went to record them. Over much of the western US and Mexico, Cordillerans sing for about 15–25 minutes pre-dawn, and that’s it for the rest of the day (position notes are given throughout the day). They are often the second singer after the local Turdus. So, I think most observers (including Ned Johnson) missed their songs by just not being out early enough. I think there is probably a relatively short period early in the breeding season when these species sing later into the morning, but I have always done my fieldwork in these populations a bit later in the breeding season to try to minimize the presence of migrants. Pacific-slope Flycatchers sing much later into the morning for a longer part of the breeding season here on the coast (I live in SF).
Channel Islands Flycatcher Empidonax (difficilis) insulicola is also identified as a possible species by Monroe & Sibley 1993, Farnsworth & Lebbin 2004 (HBW 9) and H&M4.

[San Lucas Flycatcher E d cineritius was also once treated as a distinct species by AOU.]
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laurent raty
The birds in this complex that have the most divergent barcodes in the BOLD database are (by far) two E. occidentalis, presumably of the nominate race, collected in May in the highlands of Jalisco...
- Pacific-slope + US Cordilleran (hellmayri): [here]
- Jalisco Cordilleran (occidentalis): [here]
The distance between these two clusters is 2.73%; that between continental Pacific-slope and US Cordilleran is below 1%.

(Johnson & Cicero 2002 [pdf] found Yellowish Flycatcher Empidonax flavescens in a position similar to that of nominate occidentalis. I'd be curious to see how the BOLD Jalisco occidentalis mtDNA would compare to that of flavescens.)

(For what it's worth: Johnson & Cicero sequenced cox1 as well, but a fragment of the gene that is not the same as the one used for barcodes. There is an overlap between the two fragments, but it is only 75bp-long. These 75bp of the Jalisco sequences are in any case not identical, nor near-identical, to the the homologous 75bp in J&C's flavescens sequences. But 75bp, obviously, is really short.)
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Well-known member

Kirk Roth

Well-known member
New work on Cordilleran/Pacific-Slope Flycatchers:

Ethan Linck, Kevin Epperly, Paul van Els, Garth M. Spellman, Robert W. Bryson Jr., Ricardo Canales-del-Castillo, John E. McCormack, John Klicka. Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex. bioRxiv preprint: https://www.biorxiv.org/content/early/2018/12/10/491688

Twitter summary thread: https://twitter.com/ethanblinck/status/1072164261927936001

and the paper: https://www.biorxiv.org/content/early/2018/12/10/491688.full.pdf+html

Taxonomic recommendations are either a split between a lumped "Western" and Sierra del Madre flycatchers or separation into Pacific-slope, U.S. Cordilleran, Mexican Cordilleran, and Sierra Madre del Sur flycatchers, depending on species philosophy.

And they include this teaser for "proposal-worthy" recommendation:
"We recognize that a pragmatic approach to species delimitation for end users (e.g., field naturalists, conservationists, and ecologists) needs to incorporate diagnostic phenotypic characters, whether in range, ecology, behavior, song or morphology. A detailed analysis of these data will be presented elsewhere."

Peter Kovalik

Well-known member
Ethan Linck, Kevin Epperly, Paul van Els, Garth M Spellman, Robert W Bryson Jr, John E McCormack, Ricardo Canales-del-Castillo, John Klicka, Dense geographic and genomic sampling reveals paraphyly and a cryptic lineage in a classic sibling species complex, Systematic Biology, , syz027, https://doi.org/10.1093/sysbio/syz027


Incomplete or geographically biased sampling poses significant problems for research in phylogeography, population genetics, phylogenetics, and species delimitation. Despite the power of using genome-wide genetic markers in systematics and related fields, approaches such as the multispecies coalescent remain unable to easily account for unsampled lineages. The Empidonax difficilis/E. occidentalis complex of small tyrannid flycatchers (Aves: Tyrannidae) is a classic example of widely-distributed species with limited phenotypic geographic variation that was broken into two largely cryptic (or “sibling”) lineages following extensive study. Though the group is well-characterized north of the U.S. Mexico border, the evolutionary distinctiveness and phylogenetic relationships of southern populations remain obscure. In this paper, we use dense genomic and geographic sampling across the majority of the range of the E. difficilis/E . occidentalis complex to assess whether current taxonomy and species limits reflect underlying evolutionary patterns, or whether they are an artifact of historically biased or incomplete sampling. We find that additional samples from Mexico render the widely recognized species-level lineage E. occidentalis paraphyletic, though it retains support in the best-fit species delimitation model from clustering analyses. We further identify a highly divergent unrecognized lineage in a previously unsampled portion of the group’s range, which a cline analysis suggests is more reproductively isolated than the currently recognized species E. difficilis and E. occidentalis. Our phylogeny supports a southern origin of these taxa. Our results highlight the pervasive impacts of biased geographic sampling, even in well-studied vertebrate groups like birds, and illustrate what is a common problem when attempting to define species in the face of recent divergence and reticulate evolution.


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Opus Editor
Does not seem to be easily available online. Can someone with access please tell us more about that southern lineage?


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