Primate Origins & Classification

Hi, Card-carrying Mammalogists. Is this reference as about as good as it gets for primate genealogy & systematics?

Abstract Phylogenetic relationships, divergence times, and patterns of biogeographic descent among primate species are both complex and contentious. Here, we generate a robust molecular phylogeny for 70 primate genera and 367 primate species based on a concatenation of 69 nuclear gene segments and ten mitochondrial gene sequences, most of which were extracted from GenBank. Relaxed clock analyses of divergence times with 14 fossil-calibrated nodes suggest that living Primates last shared a common ancestor 71–63 Ma, and that divergences within both Strepsirrhini and Haplorhini are entirely post-Cretaceous. These results are consistent with the hypothesis that the Cretaceous-Paleogene mass extinction of non-avian dinosaurs played an important role in the diversification of placental mammals. Previous queries into primate historical biogeography have suggested Africa, Asia, Europe, or North America as the ancestral area of crown primates, but were based on methods that were coopted from phylogeny reconstruction. By contrast, we analyzed our molecular phylogeny with two methods that were developed explicitly for ancestral area reconstruction, and find support for the hypothesis that the most recent common ancestor of living Primates resided in Asia. Analyses of primate macroevolutionary dynamics provide support for a diversification rate increase in the late Miocene, possibly in response to elevated global mean temperatures, and are consistent with the fossil record. By contrast, diversification analyses failed to detect evidence for rate-shift changes near the Eocene-Oligocene boundary even though the fossil record provides clear evidence for a major turnover event (‘‘Grande Coupure’’) at this time. Our results highlight the power and limitations of inferring diversification dynamics from molecular phylogenies, as well as the sensitivity of diversification analyses to different species concepts.

Citation: Springer MS, Meredith RW, Gatesy J, Emerling CA, Park J, et al. (2012) Macroevolutionary Dynamics and Historical Biogeography of Primate Diversification Inferred from a Species Supermatrix. PLoS ONE 7(11): e49521. doi:10.1371/journal.pone.0049521 Editor: Roscoe Stanyon, University of Florence, Italy Received May 17, 2012; Accepted October 9, 2012; Published November 16, 2012 Copyright: ß 2012 Springer et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by NSF (EF0629860 to MSS and JG; EF0629849 to WJM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: mark.springer@ucr.edu (MS); wmurphy@cvm.tamu.edu (WJM)

Karura Mammal List (draft)

Thanks to all corresponding mammal experts for help in ID-ing the Karura mammal photos. Below is a composite list a variation of which we would like to use to caption the photos in our Facebook Mammals album. Work in progress. The Primates are, of course, a bit of a muddle, and was not sure which authority to follow: this one or this one? Or something else?

Can someone help with species of bush squirrel and epauletted bat?   Many thanks.

Class: Mammalia — Mammals

Order: Primates

Superfamily: Cercopithecoidea (Old World Monkeys)       

Subfamily: Cercopithecinae

Olive Baboon, Papio anubis (only two occasional sightings in five years — non-residents)

Family: Cercopithecidae (Cheek-pouched monkeys)

Subfamily: Cercopithecinae

Syke’s Monkey (=Kolb's monkey), Cercopithecus mitis kolbi

          Subfamily: Colobinae

Colobus Monkey (= Guereza Colobus, = Black and White Colobus), Colobus guereza kikuyuensis

      Family: Galagonidae

Kikuyu Small-eared Galago (= Bushbaby), Otolemur garnettii kikuyuensis

 Order: Eulipotyphla — Misc. Insectivores 

   Family: Erinaceidae

White-bellied Hedgehog, Atelerix albiventris 

Order: Chiroptera — Bats

Family: Pteropodidae

Subfamily: Epomophorinae

Angolan Collared Fruit Bat, Myonycteris angolensis

[Wahlberg's] Epauletted Fruit Bat, Epomophorus [wahlbergi] <== can anyone confirm?

Order: Lagomorpha — Hares

Family: Leporidae

Cape Hare, Lepus capensis

Order: Rotentia — Rodents

Family: Sciuridae

Bush Squirrel, Paraxerus sp.

Family: Hystricidae

North African Crested Porcupine, Hystrix cristata

Family: Nesomyidae

Subfamily: Cricetomyinae

Giant Pouched Rat, Cricetomys gambianus

Order: Carnivora — Carnivores

Family: Mustelidae

      Subfamily: Mellivorinae

Ratel (= Honey Badger) Mellivora capensis

Family: Viverridae

Subfamily: Viverrinae

African Civet, Civettictis civetta

Large-spotted Genet (= Blotched, = Rusty-spotted), Genetta maculata

   Family: Nandiniidae

African Palm Civet (= Two-spotted Palm Civet),  Nandinia biotata arborea

Family: Herpestidae

    Subfamily: Herpestinae

Egyptian Mongoose, Herpestes ichneumon

Slender Mongoose, Herpestes sanguineus

White-tailed Mongoose, Ichneumia albicauda

Family: Mustelidae

    Subfamily: Lutrinae

African Clawless Otter, Aonyx capensis

Family: Canidae

Side-striped Jackal, Lupulella adusta (ex. Canis adustus)

[check recent name change here https://www.inaturalist.org/taxon_changes/89697]

Order: Artiodactyla — Even-toed Ungulates

Family: Suidae

Bush Pig, Potamochoerus larvatus

Family: Bovidae

Subfamily: Bovinae

Bushbuck, Tragelaphus scriptus

Subfamily: Cephalophinae

Harvey’s Duiker, Cephalophus harveyi

Subfamily: Neotraginae

Suni, Neotragus moschatus

Suni (?) Skull

Spotted by Peter Njui, Friends of Karura G4S Security and Infrastructure Manager, with Chantal Mariotte, FKF Board Member, near Junction 16 (you can see the Karura Map here).

Measurements (obviously approx. given condition of skull):

     Length:               110 mm

     Zygomatic width:  56mm

     Rostrum:              45mm

     Horn:                    45mm

Horns tip to (remaining) tip for scale: 44mm

Will get the skull to Simon Musila at NMK as soon as we can.

Leopard print?

Since we are bringing email thread together, let me pull in another one from last year that centred around a photo taken by Matthew Ling in Karura 25 September 2012. We'd love to get some more views. Here's the photo:

I put marks on his hand and sent the photo back to him for measurements to try to get an estimate of the size of the pug mark by ratio and proportions.  Matthew sent back the measurements (you can see them in the table below, under HAND).

There were a few other informal exchanges among a small group of Friends of Karura. I held off any Facebook announcement, fearing that we might put the wind up visitors, perhaps for a false alarm.

We then brought Zarek Cockar into the conversation. He trained with Mark Stavrakis, a 'Track & Sign Specialist Evaluator' under the Cybertracker Evaluation and Training System (http://www.cybertracker.org/tracking/evaluations), and sent me another tracking references that allowed me to get a range of leopard track estimates. So, we then had: Clive Walker (1992), Signs of the Wild and C & T Stuart (2000), A Field Guide to the Tracks and Signs of Southern and East African Wildlife, plus from Zarek, Louis Liebenberg's tracking cards (Liebenberg wrote The Art of Tracking: The Origin of Science. His website.

On 28 Aug 2014, at 17:34, Harvey Croze <hcroze@karurafriends.org> wrote to Zarek (a bit of waffle and then I get to the track):

And thanks for the links and fascinating references. Your material is certainly an improvement over Walker and the Stuarts. If you look at our FB discussion beast, the slender mongoose, Walker misses out the ‘heel’ detail entirely and the Stuarts’ little sketch could be anything.

I went, of course, to the cybertracker.org site, and found it most interesting. I downloaded Liebenberg’s 'The Art…' but haven’t read it yet. I note with relief from his introduction that he is personally against ’sport’ hunting. So look forward to how he develops the tracking-as-the-root-of-science thesis. 

I also downloaded the pdf of his track sketches in the hopes that it was a searchable version. His work, though basically excellent, suffers from not being indexed and the PDF not searchable. So I ran Adobe Acrobat X’s OCR routine on it, and now at least you can search for ‘slender’ and get to the right sketch. I’ll attach the OCR’d version, in case you’re interested.

The *.jpg cards with Liebenberg’s sketches and Ian Thomas’ field notes are also a great resource. The resolution on the ones you sent was a bit too low to generate a useful PDF binder. I wonder if we could scan the ones of Karura beasts a a higher resolution and make them available to visitors? As you can see from the bottom of our Ecology page on the website (http://www.friendsofkarura.org/the-karura-forest-researve/ecology-climate-soils-plants-animals/) we started hinting at the fascination of ID-ing tracks.

Finally, let me get your views on a track that a colleague from the World Conservation Monitoring Centre captured almost two years ago.

Here’s the photo with Matt Ling’s hand for scale. 

I put a series of reference points on his hand and sent the image back to him to measure the distances to get an estimate of the size of the print by ratios & proportions.

Here are the resultant numbers from the exercise earlier this year… [with a rough and ready new additions from Liebenberg’s sketches]

        HAND         PHOTO

AE = 85mm          77

BF = 95mm          91.5

CG = 83mm          85

CI = 95mm          106

AC = 45mm          42

EG = 45mm          48

HG = 70mm          76

HI = 65mm            69

                                             Clive Walker         Stuarts' Fnt     Stuarts’ Hind     Lieb’s Fnt  Lieb’s Hind
Pug L =  100.4       100             90                          70-90              80-100           75-100         90-95

Pug W = 77.5          80              65                         70-90               60-80             80-105        65-85

Photo Calculated Pug Ls = 110.4, 103.8, 97.6, 89.6; mean 100.4 (max range = 20.8)

Photo Calculated Pug Ws = 85.7, 75, 73.7, 75.7; mean 77.5       (max range = 12.0)

+++++++++++++

The sample is of course tiny, but even with the considerable range esp. for length (Matt, you sure about CG and CI?) the estimates are well within the leopard specs and well outside the specs for other wildlife candidates. A large dog is ruled out, we feel, by the complete absence of claw marks on what is a very clear print.

Now, given the uncertainty and variability in both the numbers as well as variation in nature of both individuals and substates, plus the fact that we don’t want to put the wind up visitors unnecessarily, we have kept the analysis to a very small group of people. I hope you will keep it to yourself for now. But please do give us your view on the owner of the print.

On 29 Aug 2014, at 08:55, Zarek Cockar <zarekcockar@gmail.com> wrote:

Onto the tracks in the photos.... 

 - The first track (with the full hand showing) looks like quite a young female leopard to me.  Elongated oval toes pressed closely together, with no claw marks. I can't really see the back pad to see if there are the characteristic feline 3 lobes, but that's basically irrelevant with all the other evidence presented. Shape and size are wrong for a large Civet.  Toe shape and lack of claws is wrong for a dog or a hyena.  There really are no other predators with a track that size.  I would probably still stare at this for a few minutes, second-guessing myself, but I'm quite confident this is a leopard track.

- The second track from Chantal's email (with just the finger showing) looks to me more like a domestic dog.  The toes are a little more sickle-shaped like a hyena, but the whole track is quite symmetrical, unlike a hyena.  I also do see what I believe to be stubby claw marks.  I once got very excited right outside the sports club gate when I found some massive predator prints in the red dust on the road.  No claw marks because the surface was too hard and the murram grains too large.  I then looked up to see a woman walking her Great Dane 100m down the road.  I followed the tracks just be sure.  Sadly it was just the dog.  

I have long suspected that there are leopards in Karurua.  There's really no reason there wouldn't be.  There are enough gulleys and valleys away from the pathways and roads where they can take refuge during the day.  And I would think there's enough prey for them in the forest as well.  There may only be a couple of leopard.  Possibly only two, and they're both probably quite small, as you can see from that first track.  They'd be feeding on duikers, rats, mice, and maybe the odd bush-buck every once in a while, so they would never grow very large (their size is also affected by their habitat).  One track obviously isn't exactly 'conclusive evidence', but as you say, this is not the first one you've seen. 

The best time to start tracking is early morning before the walkers and dogs have had a chance to obscure things.  In the deeper forest you might need a torch to help show track definition better that early in the morning, before the sun is on the ground.  And your best bet for finding leopard tracks I suspect would be in the river valleys and on less-used game trails in thick bush.

All this has made me very excited.  I'll have to plan the schlep across town from Karen one day early in the morning to do some tracking.

Washington Wachira on Bats, Colobus, Suni...

From: Washington Wachira <washingtonwachira@gmail.com>

Subject: Fwd: FW: Karura Mammals 4

Date: 10 September 2015 15:24:14 GMT+3

Dear Harvey and all,

Great to see the long discussion on Karura. I have been visiting the forest for many trips since 2011.

Just to add some more mammals. I recorded the Angolan Collared Fruit Bat (Myonycteris angolensis) from the forest caves. Shared photos.

I was there for a Crowned Eagle nesting study a week ago and will be most likely revisiting many more times to continue the study. I have found Harvey's Duikers on almost every visit, but with the new discussion I need to recheck all the greyer antelopes next time. I have not been so keen but have always thought there are Grimm's Duiker in the forest.

I also found a family of Colobus feeding together with the Syke's/Kolbi monkeys along River Gitathuru, which I found interesting (near point 3).

I have also attached two Suni pics from other Nairobi forests to show that pronounced preorbital gland (close-up photo). May support the highland spp.

Kind regards.

Rathbun on Camera Traps Again

From: Galen Rathbun <grathbun@gmail.com>

Subject: Camera Traps Again

Date: 10 September 2015 00:20:35 GMT+3

Hi Harvey,

Camera trap methods are really taking off.  Not my expertise, although my trap does capture lions and bears ETC behind our house here in Calif.  Anyway, here is another paper just published.  Hope some of this might be applied to your project.

Cheers, Galen

-- 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Galen B. Rathbun, Ph.D.
Department of Ornithology and Mammalogy
California Academy of Sciences (San Francisco)
c/o P.O. Box 202, Cambria, CA 93428, USA
Office/Home Phone: +1.805.927.3059
Emails: grathbun@calacademy.org or grathbun@gmail.com
www.rathbunX2.com
www.afrotheria.net
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Click to get to a dropbox folder with Parsons et al. Mark-Resight Assumptions, The Journal of Wildlife Management 79(7):1163–1172; 2015; DOI: 10.1002/jwmg.931

Butynski on Hyrax calls again...

From: TButynski@aol.com

Subject: Re: Hyrax call

Date: 10 September 2015 10:33:33 GMT+3

 

Hi Andy,

 

Here is a link for the loud calls of 4 species of hyrax.  If you have a problem opening this, then perhaps Yvonne can help.

 

http://www.wildsolutions.nl/vocal-profiles/hyrax-vocalizations/

 

For Ugalla, try:

 

 http://ugallaprimateproject.com/projects/bioacoustics

 

Otherwise, go to the main page and then to the hyrax download.

 

Cheers, Tom