Using iNat maps to illustrate Ensatina as a ring species

Your described method also works to find interesting outliers, which may be valid waifs, or (usually) a good candidate for quality control on observations–note the pink boxes in the Sierra Nevadas!

3 Likes

Yes. These types of maps can be a good way to spot outliers.

In the case of the pink spots in the Sierras, I believe these are a recognized population of Ensatina eschscholtzii ssp. xanthoptica (Yellow-eyed Ensatina). It is thought that in cooler, wetter conditions, the range of this subspecies stretched across the Central Valley, but that it has split into separate populations as the climate got warmer and drier: http://www.californiaherps.com/salamanders/pages/e.e.xanthoptica.html#description

3 Likes

Very interesting! I wonder if this points to a more recent continous wetland habitat that only recently closed up between SF Bay and that region.

Tulare Lake springs to mind, the northern border may be about right for this, it’d be interesting to do an overlay if possible.

2 Likes

I remember finding a member of that population - totally thought it would have been a different subspecies as xanthoptica is the subspecies in my county. Definitely interesting and cool they are found on both sides of the valley.

1 Like

There were some interesting conclusions from mitochondrial DNA research on Bay Area Ensatinas published in 2009 by Sean Kuchta and Duncan Parks in David Wake’s lab at Berkeley (reference below). They showed that that there was a surprisingly high level of genetic diversity and the evolutionary relationships are a lot more complex than was originally suspected.

The overall picture is a patchwork of many distinct lineages that rarely overlap:

The xanthoptica and eschscholtzii coastal clade

  • The ssp. xanthoptica and ssp. eschscholtzii populations form a “coastal clade” that is separate from the other Ensatina subspecies, which are all more closely related to each other than to the coastal clade.

  • Within xanthoptica there are actually two separate clades (identified as xanthoptica [1] and xanthoptica [2]).

  • The xanthoptica [1] clade has “a dark brown back, a vibrant orange belly, orange proximal limb
    segments, and a striking yellow eye patch [and] is thought to be Batesian mimetic of Pacific newts, genus Taricha … which are highly toxic and possess a similar aposematic coloration.” This clade occurs both in the Sierra Nevada and north and east of San Francisco Bay.

  • mtDNA analysis of xanthoptica [1] suggests there are three different basal lineages in the Sierra Nevada, whereas the East Bay xanthoptica [1] populations form a monophyletic clade. This is consistent with a scenario where xanthoptica [1] originated in the Sierra Nevada and later colonized the Coast Ranges. However, this determination did not exceed the 95% confidence threshold for statistical validation and it’s still possible that xanthoptica [1] originated on the coast.

  • The relatively weak level of divergence between Sierra Nevada and East Bay populations of xanthoptica [1] suggests that this “transvalley leak” was likely open during the Pleistocene (i.e. up until 11,700 years ago). Similar patterns of colonization from the Sierra to the Coast Range have been seen in other California salamanders and snakes.

  • The East Bay xanthoptica [1] lineage was apparently the source for the few xanthoptica [1] populations on the eastern edges of the San Francisco Peninsula.

  • The distinct xanthoptica [2] clade “has a less conspicuous coloration than xanthoptica [1], and was considered by Stebbins (1949) to be xanthoptica x oregonensis intergrades”. This clade occurs in the mountains around Santa Cruz in the southern part of the San Francisco Peninsula.

  • Two different lineages of ssp. eschscholtzii were identified, with the northern lineage stretching as far north as Monterey Bay where it comes within 7.8 km of the southernmost xanthoptica [2] population. Due to extensive farming of this area, it’s unlikely there remains much opportunity for these populations to hybridize.

Separate histories for two oregonensis clades in the Bay Area

Kuchta, Parks and Wade also found interesting results about the ssp. oregonensis populations:

  • There are two different ssp. oregonensis clades in the Bay Area (identified as oregonensis [1] and oregonensis [2]). “Both lineages possess a generalized camouflaged color pattern with a light brown back and a pale belly, and are very similar in appearance. In general, oregonensis [1] is particularly drab in color, while the limbs, tail, and torso of oregonensis [2] possess subdued yellow and orange elements, which is why Stebbins (1949) interpreted them as intergrades between oregonensis and xanthoptica

  • Despite their visual similarity, the two clades are genetically quite distant, with oregonensis [2] apparently more closely related to the picta, platensis, croeater and klauberi subspecies, plus various other ssp. oregonensis clades, than it is to the more basal oregonensis [1].)

  • The oregonensis [1] clade lives close to the coast. Kuchta, Parks and Wake mapped three lineages, one in Sonoma and Mendocino counties, a second in the southern part of the Point Reyes Peninsula and the third, south of San Francisco, along the coast of San Mateo and Santa Cruz counties. They hypothesize that during the Pleistocene, when sea levels were lower and the coastline was further west, these three lineages were part of a continuous population. As the sea level rose at the end of the Pleistocene, the three lineages became isolated from each other. Based on its current distribution the authors suggest that oregonensis [1] may be best suited to “low elevation terraces with a relatively cool, moist climate.”

  • The oregonensis [2] clade generally lives a little further inland. Kuchta, Parks and Wake mapped four Bay Area lineages, one on the San Francisco Peninsula (north of the oregonensis [1] and xanthoptica [2] lineages), a second in Sonoma and Napa counties (north of the North Bay xanthoptica [1] lineage), a third around the Russian River, west of Santa Rosa, and a fourth in southwest Sonoma County and Marin County (surrounding the Point Reyes Peninsula oregonensis [1] population). They noted a fifth oregonensis [2] lineage further north, outside their study area.

Bringing this back to mapping iNat observations, there’s both an opportunity and a challenge here. By adding a substantial number of geolocated Ensatina observations, iNat users can contribute to the knowledge of distribution for these different subspecies. But the cryptic nature of the lineages involved will still limit the conclusions that can be safely drawn. In particular, it seems unlikely that oregonensis [1] can be reliably distinguished from oregonensis [2] without DNA sequencing, so it would be difficult to draw conclusions from iNat observations about interbreeding between these clades.

As is the conclusion of many a research paper: “More study is required.”

Source: Shawn R. Kuchta, Duncan S. Parks, David B. Wake,
Pronounced phylogeographic structure on a small spatial scale: Geomorphological evolution and lineage history in the salamander ring species Ensatina eschscholtzii in central coastal California,
Molecular Phylogenetics and Evolution, Volume 50, Issue 2, 2009, Pages 240–255, ISSN 1055-7903, https://doi.org/10.1016/j.ympev.2008.10.019

5 Likes

Thank you, @rupertclayton . If you don’t mind, a couple of questions that are tangential to this interesting discussion:

  1. Are there instructions on how to use these tools? I’ve not come across that.
  2. looking at your Taxa Map, is there a way to put a calendar boundary on the observations?

Thank you.

1 Like

Very interesting! Both content and the used techniques. Many thanks!

1 Like

This is amazing, and a wonderful way to use these tools! Very cool and informative posts retracing one of the basics of amphibian genetics in iNat, I love it!

2 Likes

Hi @charlescrussell. I don’t believe there’s any official documentation for these mapping tools. I think both of them were mentioned by iNat staff in passing in various discussions on this forum. Here are some threads with info on the Taxa Map and/or the Compare tool:

Maybe there’s something more formal, but I’m not aware of it. Basically, for the Taxa Map, you can take the URL I listed above and substitute your own taxon IDs. For the compare tool there’s an actual interface, but you still need to add in your own search terms, which use the same syntax you’d see on the Explore and Identify pages.

As far as I know, it is possible to do this with the Compare tool but not the Taxa Map. You can use all the same search parameters that are available for Explore and Identify searches. For example, this first string below would map all the Ensatina eschscholtzii ssp. orgeonensis observations between April 1 and June 30 this year, and the second would map all observations in April, May or June of any year:

taxon_id=123959&d1=2020-04-01&d2=2020-06-30

taxon_id=123959&month=4,5,6

Are you looking for something like that?

2 Likes

Thank you - I will explore this further

1 Like

Great info, I was thinking about this while reading and thought similarly, it would make sense that the SN xanthoptica would colonize the coast and not vice versa since the xanthoptica lineage is unique on the coast but definitely not a closed question.

Lots of great info here, I’ll have to read through another time, I just wanted to check and see if Lake Corcoran was a better match as a barrier/bridge to/from the Sierra Nevada xanthoptica. It seems that it overlaps in epoch (Pleistocene), but maybe had drained before the time xanthoptica crossed over.

Something fascinating about all the large lakes (and their role in species dispersal) that used to exist across California in the distant and not-so-distant past!

2 Likes

Ring species are definitely fascinating. My favorite one is the Song Sparrow. For some reason, the sparrows do not breed in eastern California and southern Nevada. Starting from the southwestern-most subspecies and going clockwise, you have heermanni in western Cal and Central Valley being olive-brown with blackish streaking and gray fringes to the mantle. gouldii surrounding the San Francisco area who tend to be more reddish-olive. cleonensis in the northwestern corner of the state who is red overall with well defined streaking. montana from northeastern California to Utah with brownish-gray with clean white underparts with brownish-red streaking. Lastly, fallax in Arizona with redder streaking but pale brown-gray body.

heermanni and fallax overlap ranges in Coachella Valley, completing the ring. The research confirmed that out of 400 sampled birds, only 8 putative hybrids were found. The plumage characteristics are clear and consistent and they’re ecologically divergent with heermanni preferring coastal-type riparian while fallax liked desert scrub riparian.

I think the biggest problem with splitting the species is where do you draw the line of one species from the other. This isn’t the only evolutionary divergence in the Song Sparrow either. mtDNA results showed that Aleutian Island Song might be elevated to species status as they are reproductively isolated from the rest of the population and the two island subspecies are genetically more different than the other 22 subspecies combined!

3 Likes

Hi @yerbasanta. In that paper, Kuchta, Parks and Wake do mention (p. 240) the prehistory of the Central Valley as an inland sea connecting to the Pacific via the Monterey Bay plain. They note that the sea converted to a lake (i.e. Lake Corcoran) around 2 mya (million years ago) and then the drainage shifted to exit through the Golden Gate around 600,000 years ago. They also mention (pp. 241–242) that their earlier work had dated the coastal arm of the Ensatina complex to more than 2 mya, which raises the question of how Ensatinas could have spread down the coast before there was a continuous Coast Range in place.

In 1997, Wake proposed that around 5 mya Ensatinas colonized an island mass of Salinian terrane (i.e. the granite rocks that form land west of the San Andreas fault, such as the Santa Cruz Mountains, Point Reyes and Bodega Head) and that this was where ssps. xanthoptica and eschscholtzii originated. Under this theory, the island territory was reconnected to mainland California around 2 mya, allowing ssp. xanthoptica to spread north to meet ssp. oregonensis and ssp. eschscholtzii to spread south to meet ssp. klauberi. But this theory didn’t seem to be a good explanation for the high genetic distance (i.e. low relatedness) detected between nearby populations in coastal central California. Kuchta, Parks and Wake set out to examine the genetic makeup of these populations in more detail so as to better explain how they might have evolved.

My main takeaway from the paper is that the relationships are a lot more complex than was previously expected. Ssp. oregonensis is actually two distinct clades that are not very closely related, with oregonensis [1] having a fragmented coastal distribution that hints to it being stranded in several remnants of coastal plain following post-glacial sea level rise. Ssp. xanthoptica [1] probably orignated in the Sierra and colonized the coast quite recently (during the Pleistocene), but the reverse hypothesis cannot be totally ruled out. Ssp. xanthoptica [2] and the northern and southern lineages of ssp. eschscholtzii are all related to xanthoptica [1], but the paper doesn’t say much about how they arrived where they are now.

The same authors, along with a colleague, wrote another 2009 paper that seems more likely to provide answers to those questions. Maybe this is the one I need to read next!

Closing the ring: historical biogeography of the salamander ring species Ensatina eschscholtzii
Shawn R. Kuchta*, Duncan S. Parks, Rachel Lockridge Mueller and David B. Wake, Journal of Biogeography (2009) 36, 982–995

3 Likes

As I remember Larus isn’t considered a ring genus anymore. https://www.researchgate.net/publication/8454571_The_Herring_Gull_complex_is_not_a_ring_species

Fascinating, thank you for the explanation. I honestly feel as though I need an animation to put it all together in my head since there’s so many moving pieces, and I’m not used to thinking on geological time scale and thinking about multiple landmasses with species moving across them with highly dynamic barriers (like fresh and saltwater).

I’ll have to sit down and read the paper several times I think, since it’s just such a great example of how evolution can be so complex in space and time, along with being able to trace this through molecular phylogenetics!

In regard to how Ensatina may have spread down the coast without a contiguous mountain range, do you think it plausible that one or more were able to hitch a ride on a downed log? Given the fire and flood history in CA, I could imagine some living in/on a downed or live tree, being washed down a river by flooding, out to sea, and then washed inward on a current (possibly storm-driven). Maybe that’s too far-fetched, but I think more implausible things have been documented before!

2 Likes

I agree that animation has a great potential to convey hypothesized evolutionary histories for groups of organisms, especially when changes in sea-level, climate, habitat and even tectonic plates are involved. I wish I knew some good tools to use for that that didn’t require real animation skills.

Rafting is definitely how species have spread from time to time, such as the ancestors of the New World monkeys reaching South America from Africa. And while it’s very occasional over long distances, it’s much more plausible over short ones. I don’t know whether the UC Berkeley researchers have analyzed the likelihood of that explaining any Ensatina distribution patterns though.

1 Like

It’s been many, many years since I’ve done such, but PowerPoint had quite simple animation tools that could demonstrate a sequence of events overtime. FWIW… Microsoft tutorial for animation

2 Likes

I ran across this short nature documentary (from KQED) on Ensatina radiation in CA, it really helped me think about this in a different way. Though there are probably some omissions or slight mischaracterizations, I’d be really interested to hear what you think about it: Ensatina Salamanders Are Heading For a Family Split

1 Like

Yes @yerbasanta that’s a really nice video! Thanks for sharing it. And the close-up photography is wonderful. Also, the explanation on the aposematic coloring of xanthoptica and the camouflage coloring of platensis is nicely done.

In terms of genetic relationships it focuses on the classic “ring species” hypothesis, which still seems to have a lot of truth in it. The more recent messy details raised by phylogenetic analysis would make for a pretty complex story to convey in a four-minute video. At least two of the seven recognized Ensatina subspecies (oregonensis and platensis) have been shown to be polyphyletic, meaning they’re made up of different lineages, some of which are more closely related to other subspecies.

It’s broadly true that “coastal clade” of xanthoptica and eschscholtzii spread down the coast from north to south, while the “inland clade” of southern platensis, croceater and klauberi spread along the Sierra Nevada into southern California, but I’m pretty sure the animation in the video where the subspecies appear in their current locations progressively from north to south is a wild oversimplification. In reality, the species has been slowly dispersing, evolving, interbreeding and occasionally replacing other populations over a fairly long period. For much of that time, the forbears of today’s populations may not have been recognizable using today’s subspecies categories, and even if they were recognizable they would likely have had different distributions.

So we don’t (and possibly can’t) know enough to show where the subspecies originated except to say that the inland and coastal clades radiated separately from north to south where they met (and discovered that they can’t interbreed or don’t want to). Nevertheless the visualization is a good way to get the basic picture of a ring species.

BTW, the second Kuchta et al paper from 2009 gives a lot more detail on the interrelationships between the subspecies and clades.

Closing the ring: historical biogeography of the salamander ring species Ensatina eschscholtzii
Shawn R. Kuchta*, Duncan S. Parks, Rachel Lockridge Mueller and David B. Wake, Journal of Biogeography (2009) 36, 982–995

1 Like

This topic was automatically closed 60 days after the last reply. New replies are no longer allowed.