Comps prep: visualizing tectonic plate interactions

Since I don’t have a blank map handy, I was playing around with a different way to visualize tectonic plate interactions so I can remember them more easily.  This sketch shows which plates touch other plates, but doesn’t go so far as to describe the direction of movement or the type of each boundary.  

 

Under this model (which is all sixteen of the plates shown in the textbook I’m using), there are 34 specific plate-plate interactions.  Luckily I don’t have to explicitly remember them as a list: just knowing what a few plates are doing makes it pretty simple to hypothesize the movement of everything else (in theory, at least).

Comps prep: Unionoida evolutionary relationships

Introduction

Note: This post is a work in progress that can and will change over the next few days.  I'm making it available for critique, so comment away!  MBK 2012-08-07 1629

With an oral exam coming up in a week, it's nose to the books time!  One of my committee members has posed a certain question relating to soon-to-be-published research on the phylogeny of Order Unionoida (Class Bivalvia1).  This post is an effort to figure out just what has been going on regarding the relative positions of the families in this order.  Were it a simple factual question, I might have more luck, but it happened to be one of those darn "describe the implications of…" inquiries.

According to Bogan and Roe (2008), below is the general arrangement of superfamilies and families within Unionoida.  There are other arrangements that have been made, however, notably placing Family Hyriidae in Superfamily Unionoidea (e.g., Roe and Hoeh, 2003; Walker et al., 2006) according to Simpson's (1900) original classification (Figure 1).

(Figure 1): Historical trees presented by Roe and Hoeh (2003).  Note that the Family Etheriidae is missing from these evolutionary hypotheses: where does it fit in?

  • Order Unionoida
    • Superfamily Unionoidea
      • Family Margaritifera
      • Family Unionidae
    • Superfamily Etherioidea
      • Family Etheriidae
      • Family Iridinidae
      • Family Mycetopodidae
      • Family Hyriidae 

Although the order and the families are relatively solid (according to the work so far), the contents of each superfamily (indeed, the number of superfamilies) is highly debatable.  The families themselves are not all entirely monophyletic, which leads to additional questions: what relationship do the ragged edges (those genera that belong to a different branch of the tree than the rest of the family) actually have to the families they are assigned?  Is it a poor selection of characters, or bad phylogenetic analysis, or wrong identification, or what?  

I'm digressing here, but I think it's important to point out again that the way we group taxa in order to keep things organized may not reflect the actual evolutionary relationships among those taxa.  For example, using the name "Unionidae" for a certain branch of the tree minus genus Psuedomulleria as in Figure 3 of Hoeh et al. (2009) might make sense from a classification standpoint but not from an evolutionary standpoint (Figure 2)2.  Ideally (and I can't think of a counterargument to this), classification systems would follow evolutionary relationships.


(Figure 2): One of three trees from Hoeh et al. (2009).  So what's up with Pseudomulleria?  Turns out Coelatura works better in another position (see Whelan et al., 2011).

Previous Discussion

Returning to the point of this exercise, what are the evolutionary relationships among the six families in Order Unionoida?  (Ordered as above for consistency.)  Interestingly enough as a paleontologist, the characters used for phylogenetic analyses at the family level are all soft-part anatomy and life history (some of which are listed below) rather than hard-part shell morphology.  Although shell morphology in Order Unionida is suspect due to convergence at both the evolutionary and ontogenetic levels, I'm not sure how much thought has been given to the rate at which this morphology evolves in comparison to soft-part anatomy (I spoke too soon).

Superfamily Unionoidea
Lack of "mantle fusion that results in incurrent and excurrent apertures" (Bogan and Roe, 2008).

Family Margaritiferidae
Considered to be monophyletic.  Soft-part morphology 'primitive' or basal to the rest of Order Unionoida; molecular analysis places as sister to Family Unionidae to form Superfamily Unionoidea (Graf and Cummings, 2006).  Skawina and Dzik (2011) support the basal ("least derived") hypothesis based on morphological similarity to Neotrigonia.  
Glochidial larvae.  
Brood in all four demibranchs.
Northern hemisphere (widespread) (Bogan and Roe, 2008).

Family Unionidae
Considered by different studies to be both monophyletic and paraphyletic.  Most recently, Whelan et al., 2011 claim a monophyletic Unionidae very similar to the Linnean classification produced by Bieler et al. (2010) but do not examine relationships with other families.  
Glochidial larvae.  
Brood in all four demibranchs or just outer pair.
Northern hemisphere (widespread) (Bogan and Roe, 2008).

Superfamily Etherioidea
"Some degree of fusion that results in, at least, a completely fused excurrent siphon and, often, a completely fused incurrent siphon" (Bogan and Roe, 2008).

Family Hyriidae
Monophyletic according to all studies so far.  Soft-part morphology places this family as sister to "anything with a lasidium" (Superfamily Etherioidea as listed at the top of this post), but mtDNA analysis breaks the Hyriidae out entirely and places it as sister of and basal to all other families in Order Unionoida (Graf and Cummings, 2006; Bogan and Roe, 2008).  This disagreement comes down to methods, which means it matters with whom you're speaking at the moment.  
Glochidial larvae.  

Brood in inner demibranchs.
Southern hemisphere (South America and Australasia) (Bogan and Roe, 2008).

Family Mycetopodidae
Lasidial larvae.  
Brood in inner demibranchs.
Southern hemisphere (South America) (Bogan and Roe, 2008).

Family Iridinidae
Lasidial larvae.  
Brood in inner demibranchs.
Southern hemisphere (Africa) (Bogan and Roe, 2008).

Family Etheriidae
Lasidial larvae.  
Brood in inner demibranchs.
Southern hemisphere (Africa) (Bogan and Roe, 2008).

Walker et al., 2006 summarizes the possible familial relationships as follows (although there may be others):

  • basal Margaritiferidae, paraphyletic Unionidae, derived Hyriidae+Mycetopodidae+Iridinidae.  "Analyses of morphological characters presented by Graf (2000) and Hoeh et al. (2001) both return the Margaritiferidae as the basal unionoid lineage, a paraphyletic Unionidae, and the Hyriidae + Mycetopodidae + Iridinidae as a derived lineage." 
  • basal Hyriidae, paraphyletic Unionidae. "In contrast, both the molecular (i.e., cox1 DNA sequences) and the combined analysis of morphological and molecular data presented by Hoeh et al. (1998a, 2001) (Fig. 1C) place the Hyriidae as the basal unionoid lineage, with the Unionidae returned as paraphyletic." 
  • basal Margaritiferidae, monophyletic Unionidae, sister Hyriidae+Iridinidae+Mycetopodidae. "Yet another combined analysis of morphological and molecular (i.e., cox1 DNA sequences) characters (Roe & Hoeh, 2003; Fig. 1D), this time using binary coding of the morphological data and a posteriori character weighting, returns the Margaritiferidae as basal and a monophyletic Unionidae as sister to a Hyriidae + Iridinidae + Mycetopodidae clade."  It is pointed out by Graf and Cummings, 2006 that the binary coding of characters resulted in the unforseen weighting of certain character pairs, i.e., coding "1" for one character necessitated coding "0" for another.

If we consider the methods used in each case to be equally plausible, each of these three scenarios supports the close relationship between Iridinidae and Mycetopodidae (Etheriidae, being represented by a single(?) genus, seems to be left out, but I believe is generally considered to be closely related to these two families as well).  This leaves Unionidae (paraphyletic or not), Hyriidae, and Margaritiferidae (the latter two of which are considered by different character sets as both basal and derived).  While you think on this, check out Figure 3.

(Figure 3):  Graf's interpretation of some relationships within Order Unionoida.

As a final thought on past work, click here to see what Graf and others have come up with for solutions, and a summary figure for the last several papers on this subject.  Confusing, isn't it?

 

New Discussion

I think I will wait a month or so before I finish this section up.  Some new information should be coming down the pipeline.

Works Cited

Many of the publications cited have been linked to in the text, often to a page on an academic social network.  By following these links, you are letting the authors know you are interested in their work.  Publications that have no official online presence are listed here.

Roe, K. J. and Hoeh, W. R. (2003). Systematics of freshwater mussels (bivalvia: Unionoida). In Lydeard, C. and Lindberg, D. R., editors, Molecular systematics and phylogeography of mollusks, chapter 4, pages p. 91–122. Smithsonian Books.

 

 

 

 

 

1 Why Bivalvia and not Pelecypoda?  Bivalvia has nomenclatural priority, unfortunately, so as cool as studying "hatchet-footed" animals is, we don't get to call them that in polite company.
2 This has supposedly been resolved by Whelan et al. (2011) by improving the position of Coelatura.

 

Quick idea for keeping track of file name abbreviations

I like to keep my file names short for several reasons: to make it easier to see the whole name at a glance, to make saving new files simpler, to allow room for additional characters when exporting new versions from different applications, and to (yes, still) deal with applications that have a set limit on the number of characters they will read or write from a file name.  

This leads me to abbreviate, and since I often end up with a few dozen files in the same folder with a bunch of different abbreviation combinations, I’ve come up with this trick to make sure I don’t forget things: add a few empy folders (or files, if you wish) as a key at the top of your directory.  In OS X, you can put a space at the beginning of the file name to force it to the top; in Windows I think you need to use an underscore.  So finally, in an image that is worth more than all the words I’ve just put down, here is an example.

 

List of GPlates rotation files

My dissertation is on BIOgeography, I swear!  I’ve had a hard time finding plate tectonic reconstructions (rotation files, .rot or .grot) to use in GPlates (hopefully a post on that sometime soon), so I will try to add to this list as I learn more.

Global rotation files:

  • First, the main GPlates Download page.  Scroll down to the “Download GPlates-compatible data” section, which contains some of what is listed here.
  • GPlates official sample data was commented on here.
  • Earthbyte rotations go back to 140 Ma.
  • CalTech rotations (which may or may not be different from EarthByte) go back to 140 Ma. 
  • Seton et al. (2012) rotations go back to 200 Ma.
  • Golonka (2007) has global rotation data in the supporting online material for the Late Triassic-Early Jurassic.
  • Supporting data for Williams et al. (2012), available from an FTP link in the text, has a rotation file from 1100 Ma to 530 Ma based on “the model of all Rodinia described by Li et al. (2008)” (SupplementaryTutorial2.pdf, p. 5).

Regional rotation files:

  • Australia
    • A rotation file for Australia (~1100 Ma – 530 Ma) by Giles et al. (2003) is included in the Williams et al. (2012) supporting data, above. 
    • A rotation file for Australia (~1100 Ma – 530 Ma) by Henson et al. (2011) is included in the Williams et al. (2012) supporting data, above.
    • A rotation file for Australia (~1100 Ma – 530 Ma) by Li and Evans (2011) is included in the Williams et al. (2012) supporting data, above.

 

Discussion in Other Places: Expanding Grand Forks

Relating to one of the interchange ideas recently published in the Herald, there is an ongoing discussion in the comments section for that article that is fairly interesting.  A little bit of local history, a little bit of speculation, and at least a few people thinking about where the city is headed.

OUR OPINION: Which comes first, the exit or the mall? (comments)

UPDATE:  Minutes after I posted, this article came out that summarizes some more things: http://www.grandforksherald.com/event/article/id/240410/

Exporting from Panorama Sheets

I just started playing with Panorama Sheets, which is a cheaper (and lower-power) version of Panorama, but which does exactly what I want: combines a spreadsheet interface with database-querying capabilities. At the moment, I don’t need the other functions of the full version of Panorama, so I may purchase this software after my trial runs out. I’ve seen a few glitches so far, one of them being that while in the Export Wizard (File->Export Text…), clicking on the “Export Text” button results in an “Error resolving alias.” error. Luckily, this can be solved by selecting the Export->Export to Text File… menu item. An additional problem I ran into is that the encoding is weird when trying to open this file in OpenOffice Calc, so it was easiest to open the text file, copy the contents, and paste into Calc, which will bring up a dialog box you can use to select your delimiter, etc.

 

South Washington Street Corridor – Bicycles in the Updated Plan

A while back fellow streets enthusiast and cycling commuter A.K. forwarded me a link to the new South Washington Street Corridor draft plan (which is listed as “final” now).  This post will cover some of my thoughts on the cycling aspects of the plan.

Figure 7.28, from The Forks MPO

The plan as stated will set aside multiple sections of bicycle “route” (I am using “route” as an indeterminate word for “places designed for cyclists to be”).  They are (from south to north)

  1. The existing shared-use path on the west side of South Washington Street, from 55th Avenue South to a point even with Hammerling Avenue, with the hopeful widening or addition of a shared-use path from this point for one block north to 14th Avenue South (Figure 7.28, top pane).
  2. 14th Street South, from 14th Avenue South to DeMers Avenue (Figure 7.28, top and middle panes).
  3. A section that will cross DeMers Ave and the railyard (Figure 7.28, middle pane):
    1. A new shared-use path on the south side of DeMers Avenue, between 14th Street South and South Washington Street.
    2. The existing shared-use path on the west side of DeMers Avenue, between DeMers Avenue and 1st Avenue North.  This is the railyard underpass itself, and modifying this stretch of road is discussed elsewhere in the report.
    3. 1st Avenue North, between North Washington Street and 14th Street North.
  4. 14th Street North, from 1st Avenue North to 8th Avenue North (Figure 7.28, bottom pane).
    1. The push-button crossing at 15th Street North would be moved to 14th Street North to help kids cross.  This is a great idea.
  5. The existing shared-use path on the west side of North Washington Street, from 8th Avenue North to Gateway Drive.

Frankly, I’m excited about this plan.  It would create a for-sure, straightforward, north-south bicycle route along one of the busiest corridors in the city.  It would be around 4.6 miles long, probably the longest straight stretch of cycling “route” that we have outside of the Greenway (which, of course, is not straight).  There are a few details that remain to be worked out, however.

  • It is granted, in general, that routing cyclists through controlled crossings is desired, however it should be understood that regular commuters will be utilizing routes that do not force them to stop and wait to cross streets at controlled intersections.  This should be kept in mind by the planners.
  • Section 1, above, has half a block of traffic (from Hammerling Avenue to 14th Avenue South) to deal with in the form of curb cuts for the businesses along that stretch.  I think this is in order to move cyclists through the controlled crossing at 17th Avenue South, rather than force riders to wait for traffic to cross 17th Avenue South at at 14th Street South.  It would seem better to route people along 15th Street South instead of 14th Street South.  Even though this leaves a relict half-block section of shared-use path to the north, it would minimize the potential interactions with vehicles turning into businesses along that stretch.
    • Most riders who know what they are doing will probably cross 17th Avenue South at 14th Street South and not at the light.
  • Section 3.1, above, routes cyclists through an apparently new shared-use path where the Hertz rental store is now.  Are they going to go for this?  Is there space for such a route?  The DeMers crossing is long and dangerous, and it is hoped that pedestrian/cycle signals will be given greater priority.
    • Again, most regular commuters will probably cross DeMers Avenue at 15th or 17th Avenue South while heading to or coming from the shared-use path on the north side of Demers Avenue.
  • Section 3.3, above, routes cyclists (coming from the south) from the existing shared-use path onto 1st Avenue North.  This intersection is heavily used by motor vehicles and they are not used to looking for cyclists who are not in the street.  It is suggested that an engineering solution to the grade problems at Dyke Avenue or the alley between Dyke Avenue and 1st Avenue North would alleviate the congestion issue at this intersection, at least for cyclists who are continuing north rather than crossing North Washington Street at 1st Avenue North.
  • Finally, I hope these improvements utilize some good signage, and that the bicycle signage in general is improved.  Clear “Bicycle Route” signs would be especially beneficial along 14th Street South and where the route turns.  Sharrows (I am not certain whether they are explicitly planned) would be an excellent addition to 14th Street and, although it is outside the scope of this plan, 17th Street South and other roads that we would like to encourage bicycle commuting along.
    • One comment from A.K. on this: ”
      I think the best way to implement the shared road on 14th, is to bring this concept to others. Otherwise it just becomes another 1-time deal in the city making drivers (and bikers alot) more confused.  Whatever signage/markings they do to 14th should also be done to other N/S streets such as 34th, 20th, 17th, 14th, etc. “

So that’s what I think, what about you?  If any of this is confusing, I will do my best to make additional concept maps available so we can all be on the same page.  Like I said at the top: it’s exciting that Grand Forks is putting this much thought into cycling facilities.  If you want to get involved, the MPO has just release the “MPO Citizen’s Guide For Participating In The Transportation Planning Process,” which has information on how to be notified about upcoming meetings, how the process works, and how much of an expert you need to be (I’m kidding, they want everyone’s input).