Aphelocoma jays (1 Viewer)

Richard Klim · Mar 23, 2014

Sumichrast's Scrub Jay

Richard Klim said:
McCormack, Heled, Delaney, Peterson & Knowles 2010. Calibrating divergence times on species trees versus gene trees: implications for speciation history of Aphelocoma jays. Evolution: in press.

McCormack et al 2010. Evolution 65(1): 184–202. [pdf]

Gowen, Maley, Cicero, Peterson, Faircloth, Warr & McCormack (MS). Speciation in Western Scrub-Jays, Haldane's Rule and genetic clines in secondary contact.

IOC World Bird List:
www.worldbirdnames.org/updates/update-diary/
www.worldbirdnames.org/updates/proposed-splits/

2014 Mar 23: Post proposed Sumichrast's Scrub Jay split on Updates/PS
... Gowen et al 2014

Richard Klim · Jun 18, 2014

Gowen et al

Richard Klim said:
Gowen, Maley, Cicero, Peterson, Faircloth, Warr & McCormack (MS). Speciation in Western Scrub-Jays, Haldane's Rule and genetic clines in secondary contact.

Gowen, Maley, Cicero, Peterson, Faircloth, Warr & McCormack (in press). Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact. BMC Evol Biol 14(135). [abstract] [pdf]

A. californica, including subspecies californica, oocleptica, caurina, obscura, hypoleuca, superciliosa, immanis, and cactophila

A. sumicrasti [sic], including subspecies sumicrasti and remota

A. woodhouseii including subspecies texana, woodhouseii, nevadae, grisea, and cyanotis

Nutcracker · Jun 18, 2014

Be interesting to see if this finally persuades AOU to catch up with IOC in accepting Woodhouse's Scrub Jay.

Just wish they'd get rid of that ghastly hyphen-followed-by-capital; either Scrub Jay or Scrub-jay is fine, but having "Scrub-Jay" is plain bad grammar.

Mysticete · Jun 18, 2014

We'll see if a new proposal is released next year. James Maley is second author, and his clapper rail splits seem to have been accepted, plus the proposal addresses the big concern from the last proposal...what is happening at the contact zones between the interior and coastal forms.

Kratter · Jun 18, 2014

Nutcracker said:
Be interesting to see if this finally persuades AOU to catch up with IOC in accepting Woodhouse's Scrub Jay..

Finally? This paper, which gets to the meat and potatoes of what is happening in the contact zone, is in-press. Prior papers hinted at species level differences and possible reproductive isolation, but the AOU NACC was waiting for better evidence, which we knew was in the pipeline (third author Carla Cicero is on the NACC). I would say that the those who already split these jays were jumping the gun. I am not sure that the IOC has ever seen a proposed split that it did not like. A recent paper on Anas ducks (Peters et al. 2014), shows that mtDNA is often not showing a very good picture of what is happening in contact zones. Many splits advocated by the more split-happy taxomnomic groups have relied on mtDNA data.

JEFFREY L. PETERS, KEVIN WINKER, KENDRA C. MILLAM, PHILIP LAVRETSKY, IRINA KULIKOVA ROBERT E. WILSON, YURI N. ZHURAVLEV and KEVIN G.MCCRACKEN. Mito-nuclear discord in six congeneric lineages of
Holarctic ducks (genus Anas).
Molecular Ecology (2014) 23, 2961–2974

Andy

Nutcracker · Jun 18, 2014

Kratter said:
I am not sure that the IOC has ever seen a proposed split that it did not like.

A couple straight off the top of my head: Lesser Redpoll Acanthis [flammea] cabaret, and Greenland Whitefront Anser [albifrons] flavirostris; IOC rejected both of those. Another they've rejected: the various proposed Fox Sparrow Passerella iliaca splits. I'd guess there's plenty more.

Methinks you're being very unfair and demeaning to IOC.

Kratter · Jun 19, 2014

Yes, I was a little over the top. It's thankless work, for the most part

Andy

njlarsen · Jun 19, 2014

Andy,
I am one of those who sometimes voice discontent with particular things (decisions, statements). To make sure that the other side is also heard: I am personally happy with the work that you and the rest of the two AOU committees do, even if I am a critical observer. I would love for the NACC to change the process to more closely mimic what the SACC does, but even so, both committees show some openness about the proposals they look at, which is much better than some other committees I could mention.

Thank you
Niels

Mysticete · Jun 19, 2014

Yeah...I have to say working on any bird checklist committee is pretty thankless work. Sure people love it when you split things, but heaven forbid you alter traditional taxonomy/change a common name/lump a taxon/split something that is cryptic and difficult to identify in the field.

Anyway...I actually think the bird community is overall pretty reasonable in their deliberation of taxonomy. unlike say CNAH/SSAR, which will split practically anything on the basis of one paper, regardless of the quality of the data or intensity of the sampling. And usually those splits will be made within weeks of the paper being published.

Kirk Roth · Jun 19, 2014

Mysticete said:
Yeah...I have to say working on any bird checklist committee is pretty thankless work. Sure people love it when you split things, but heaven forbid you alter traditional taxonomy/change a common name/lump a taxon/split something that is cryptic and difficult to identify in the field.

Anyway...I actually think the bird community is overall pretty reasonable in their deliberation of taxonomy. unlike say CNAH/SSAR, which will split practically anything on the basis of one paper, regardless of the quality of the data or intensity of the sampling. And usually those splits will be made within weeks of the paper being published.

While we're spinning off topic, is there any moderately accepted alternative to CNAH? I like that they are responsive, but agree that there is not one ornithological listing committee that could be called trigger-happy in comparison.

Getting back to the jays, I noticed the discussion of the .87 probability node between the Edwards Plateau birds and the rest of the Woodhouse's group. But what about that .94 node deeper in the phylogeny? Where are those birds? Maybe I didn't read carefully enough, but can someone help me out?

-Kirk

Mysticete · Jun 19, 2014

The SSAR checklist would be the equivalent to the AOU checklist, however really they are not any more conservative than CNAH, they just don't update as regularly. I have noticed that in the last couple of years CNAH has reverted a lot of their more controversial decisions to be inline with SSAR (Ratsnake taxonomy, etc). I suspect this might have to do with Joseph T. Collin's recent death, who founded the CNAH and was the director of it for 19 years.

I find the SSAR checklist to be way harder to use than CNAH, so I generally follow CNAH.

On a related note...birders are really really spoiled. the last official mammal checklist for mammals of North America was 2003. We have at least 3-4 regional checklists and 2 world checklists that update yearly. That's pretty amazing when you think about it.

Nutcracker · Jun 19, 2014

Mysticete said:
... unlike say CNAH/SSAR, ....

Sorry, you've lost me there :h?: what are CNAH and SSAR please?

Mysticete said:
On a related note...birders are really really spoiled. the last official mammal checklist for mammals of North America was 2003. We have at least 3-4 regional checklists and 2 world checklists that update yearly. That's pretty amazing when you think about it.

For most plant groups, there's no official checklists at all.

Richard Klim · Jun 19, 2014

Kirk Roth said:
Getting back to the jays, I noticed the discussion of the .87 probability node between the Edwards Plateau birds and the rest of the Woodhouse's group. But what about that .94 node deeper in the phylogeny? Where are those birds? Maybe I didn't read carefully enough, but can someone help me out?

Table 2 (locality information) isn't correlated with Figure 4 (BEAST consensus tree). But it should be possible to determine the Figure 4 groupings via the FMNH Birds Collection Database. Volunteers...?

Kratter · Jun 19, 2014

Kirk Roth said:
Getting back to the jays, I noticed the discussion of the .87 probability node between the Edwards Plateau birds and the rest of the Woodhouse's group. But what about that .94 node deeper in the phylogeny? Where are those birds? Maybe I didn't read carefully enough, but can someone help me out?

-Kirk

I think the nodes in figure 4 may be mislabeled. According to the results, the split between the Edward's Plateau (the clade that includes the sample indicated with the arrow in Fig 4) and rest of woodhousei should be 0.87 PP, but is labelled 0.94 . The next deeper node (100% PP) splits A. sumichrasti from A. woodhousei. The node labelled 0.87 PP, is a polytomy and thus not 0.87 PP.

Andy

Mysticete · Jun 19, 2014

CNAH and SSAR are academic Reptile/Amphibian related organizations active in North America. CNAH is Center for North American Herpetology, while I can't remember and am too lazy to look up SSAR

Nutcracker · Jun 20, 2014

Mysticete said:
CNAH and SSAR are academic Reptile/Amphibian related organizations active in North America. CNAH is Center for North American Herpetology, while I can't remember and am too lazy to look up SSAR

Thanks! I don't do reptiles or amphibians, so no surprise I'd not heard of them!

l_raty · Jun 20, 2014

Richard Klim said:
Table 2 (locality information) isn't correlated with Figure 4 (BEAST consensus tree). But it should be possible to determine the Figure 4 groupings via the FMNH Birds Collection Database. Volunteers...?

The data are now accessible in Dryad http://datadryad.org/resource/doi:10.5061/dryad.57f48. (I think they were not yesterday.)

In the order in which they appear in the tree (Fig.4), "Interior US and northern Mexico (proposed A. woodhouseii)" clade:

- FMNH334230 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA
- FMNH334109 nevadae Toiyabe Mts., 10 mi S, 4 mi W Austin, Lander Co., Nevada, USA
- FMNH334102 nevadae 6.5 mi N Mt. Charleston, Clark Co., Nevada, USA
- FMNH333981 superciliosa x nevadae Pine Nut Mts, 4 km S, 7 km E Hot Springs Mt, Douglas Co., Nevada, USA
- FMNH334083 nevadae 6.5 mi N Mt. Charleston, Clark Co., Nevada, USA
- FMNH334226 woodhouseii left fork Antelope Canyon, 13 mi S, 6 mi E Duchesne, Duschesne Co., Utah, USA
- FMNH333982 superciliosa x nevadae Pine Nut Mts, 4 km S, 7 km E Hot Springs Mt, Douglas Co., Nevada, USA
- FMNH333996 superciliosa x nevadae Gardnerville, 10 mi SE, Douglas Co., Nevada, USA
- FMNH333989 superciliosa x nevadae Pine Nut Mts., Brunswick Canyon, 4.3 mi S Carson River, Douglas Co., Nevada, USA

- FMNH343467 grisea Villa Ocampo, Durango, Mexico (according to doi:10.1111/j.1558-5646.2010.01097.x ; lacking in the .xlsx file)
- FMNH343478 cyanotis El Diamante Pass, 12 km E, 6 km S Saltillo, Coahuila, Mexico
- FMNH343481 cyanotis El Diamante Pass, 12 km E, 6 km S Saltillo, Coahuila, Mexico
- FMNH393698 cyanotis Bledos, 2 km N, 3 km W, San Luis Potosi, Mexico
- FMNH343488 cyanotis Bledos, 5 km N, 5 km E, Sierra de Bledos, , San Luis Potosi, Mexico
- FMNH343452 grisea Rancho Santa Rita, 9 km N Lago de Moreno, Jalisco, Mexico
- FMNH393609 grisea Lagos de Moreno, 9 km N, Jalisco, Mexico
- FMNH334157 woodhouseii Fort Davis, 14 mi W, Jeff Davis Co., Texas, USA
- FMNH393610 grisea Sombrerete, 11 km WNW, Zacatecas, Mexico

- FMNH334215 woodhouseii Gardner, 7 mi N, 3 mi E, Huerfano Co., Colorado, USA
- FMNH334183 woodhouseii Manzano, 7 mi W, Valencia Co., New Mexico, USA
- FMNH393711 grisea Villa Ocampo, 3 km N, 2 km E, Durango, Mexico
- FMNH334068 nevadae Drake, 8 mi ESE, Yavapai Co., Arizona, USA
- FMNH334212 woodhouseii Gardner, 7 mi N, 3 mi E, Huerfano Co., Colorado, USA
- FMNH334181 woodhouseii Manzano, 7 mi W, Valencia Co., New Mexico, USA

- FMNH334235 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334248 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334250 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334231 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA
- FMNH334252 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334232 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA
- FMNH334240 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334253 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334244 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334246 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334242 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334234 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334237 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334239 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334256 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334254 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334243 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334245 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334255 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334241 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334247 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334238 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334249 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334229 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA
- FMNH334251 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334236 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA
- FMNH334233 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

Richard Klim · Jun 20, 2014

l_raty said:
The data are now accessible in Dryad http://datadryad.org/resource/doi:10.5061/dryad.57f48. (I think they were not yesterday.)
In the order in which they appear in the tree (Fig.4), "Interior US and northern Mexico (proposed A. woodhouseii)" clade:...

Thanks, Laurent!

It's notable that AOU 1910 (Check-list 3rd Ed) treated A cyanotis 'Blue-eared Jay' (incl grisea?) and A texana 'Texas Jay' as distinct from A woodhouseii 'Woodhouse's Jay': darwiniana.org/zoo/AOUd.htm#Jays

Kirk Roth · Jun 20, 2014

l_raty said:
The data are now accessible in Dryad http://datadryad.org/resource/doi:10.5061/dryad.57f48. (I think they were not yesterday.)

In the order in which they appear in the tree (Fig.4), "Interior US and northern Mexico (proposed A. woodhouseii)" clade:

FMNH334230 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA

FMNH334109 nevadae Toiyabe Mts., 10 mi S, 4 mi W Austin, Lander Co., Nevada, USA

FMNH334102 nevadae 6.5 mi N Mt. Charleston, Clark Co., Nevada, USA

FMNH333981 superciliosa x nevadae Pine Nut Mts, 4 km S, 7 km E Hot Springs Mt, Douglas Co., Nevada, USA

FMNH334083 nevadae 6.5 mi N Mt. Charleston, Clark Co., Nevada, USA

FMNH334226 woodhouseii left fork Antelope Canyon, 13 mi S, 6 mi E Duchesne, Duschesne Co., Utah, USA

FMNH333982 superciliosa x nevadae Pine Nut Mts, 4 km S, 7 km E Hot Springs Mt, Douglas Co., Nevada, USA

FMNH333996 superciliosa x nevadae Gardnerville, 10 mi SE, Douglas Co., Nevada, USA

FMNH333989 superciliosa x nevadae Pine Nut Mts., Brunswick Canyon, 4.3 mi S Carson River, Douglas Co., Nevada, USA

FMNH343467 grisea Villa Ocampo, Durango, Mexico (according to doi:10.1111/j.1558-5646.2010.01097.x ; lacking in the .xlsx file)

FMNH343478 cyanotis El Diamante Pass, 12 km E, 6 km S Saltillo, Coahuila, Mexico

FMNH343481 cyanotis El Diamante Pass, 12 km E, 6 km S Saltillo, Coahuila, Mexico

FMNH393698 cyanotis Bledos, 2 km N, 3 km W, San Luis Potosi, Mexico

FMNH343488 cyanotis Bledos, 5 km N, 5 km E, Sierra de Bledos, , San Luis Potosi, Mexico

FMNH343452 grisea Rancho Santa Rita, 9 km N Lago de Moreno, Jalisco, Mexico

FMNH393609 grisea Lagos de Moreno, 9 km N, Jalisco, Mexico

FMNH334157 woodhouseii Fort Davis, 14 mi W, Jeff Davis Co., Texas, USA

FMNH393610 grisea Sombrerete, 11 km WNW, Zacatecas, Mexico

FMNH334215 woodhouseii Gardner, 7 mi N, 3 mi E, Huerfano Co., Colorado, USA

FMNH334183 woodhouseii Manzano, 7 mi W, Valencia Co., New Mexico, USA

FMNH393711 grisea Villa Ocampo, 3 km N, 2 km E, Durango, Mexico

FMNH334068 nevadae Drake, 8 mi ESE, Yavapai Co., Arizona, USA

FMNH334212 woodhouseii Gardner, 7 mi N, 3 mi E, Huerfano Co., Colorado, USA

FMNH334181 woodhouseii Manzano, 7 mi W, Valencia Co., New Mexico, USA

FMNH334235 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334248 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334250 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334231 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA

FMNH334252 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334232 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA

FMNH334240 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334253 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334244 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334246 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334242 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334234 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334237 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334239 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334256 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334254 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334243 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334245 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334255 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334241 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334247 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334238 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334249 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334229 texana Carta Valley, 2 mi W, Edwards Co., Texas, USA

FMNH334251 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334236 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

FMNH334233 texana Carta Valley, 3 mi N, Edwards Co., Texas, USA

Thank you, Laurent - I tip my hat to your effort!

Two things strike me immediately after inspecting this for a few minutes. All the Edwards Plateau birds seem to be within the same valley - within a couple miles of each other? If all these samples derive from a few family groups, it would be no wonder that they would cluster together so tightly and distinctly from the other samples.

With the exception of one Edwards Plateau jay, the nevadae ssp. (group) seems interesting. With the caveat that I'm no pro at reading phylogenies, it seems to me that there is a fairly deep split between the Nevada/Utah populations and the rest of the Woodhouse's complex. Its not sumichrasti deep, but comparable. Given my limited understanding of the data, a Great Basin Scrub Jay seems more compelling than a potential Edwards Plateau Scrub Jay. Would be curious about behavioral differences in these taxa.

Thanks,
Kirk

Mysticete · Jun 21, 2014

Keep in mind, just because there are subclades within the Interior form with somewhat strongish support, doesn't mean these clades = new species. My understanding is that the big morphological differences in Scrub-Jays largely occur between California, Woodhouse's, and Sumichrast's. I am skeptical Woodhouse's will ever be subdivided into smaller units.

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