True's beaked whale.jpg

Western spotted skunk

Hooded skunk

Yellow-throated Marten


Archive for March, 2005

Crafty octopus

Thursday, March 24th, 2005

Have a look at this octopus. It camoflages itself while it walks around.

Two tiny species of tropical octopus have demonstrated a remarkable disappearing trick. They adopt a two-armed ‘walk’ that frees up their remaining six limbs to camouflage them as they slink away from trouble.

View movies below the fold.

Worst case sea level rise

Saturday, March 19th, 2005

From an interview with National Center for Atmospheric Research in Colorado’s Gerald Meehl discussing an NCAR paper in Science:

Experts say sea levels have risen 4 inches already over the past century and could rise between 4 and 40 inches more in the next century.

If completely melted, the Greenland ice sheet would add 25 feet to overall sea level and the West Antarctic Ice Sheet would raise it by 16 feet — enough to swamp most of Florida, Bangladesh and New York City’s Manhattan island.

So that’s the upper limit on sea level rise. And while the modelers predict a mm/year rate, ice sheets melt catastrophically and we’re getting into the range of losing some of them, so I’ll make a wild-ass guess that we’ll see a bad decade with a foot or so sea level rise this century.

(To digress, this reminds me of how bad the premise of Waterworld is. You know a movie’s science is bad when it makes you look fondly on the scientific plausibility of Planet of the Apes. Waterworld is a full point higher on the Scientfic Implausibility Richter scale.)

From the abstract of the paper, “The Climate Change Commitment”. Wigley, TML. (2005) Science 307:1766-9:

These constant-composition (CC) commitments and their uncertainties are quantified. Constant-emissions (CE) commitments are also considered. The CC warming commitment could exceed 1°C. The CE warming commitment is 2° to 6°C by the year 2400. For sea level rise, the CC commitment is 10 centimeters per century (extreme range approximately 1 to 30 centimeters per century) and the CE commitment is 25 centimeters per century (7 to 50 centimeters per century).

The CE senario predicts 2.5 mm/year rise, but emissions are rising so this is definitely an underestimate.

Bioinformatics books

Friday, March 18th, 2005

Notes on some bioinformatics books from two perspectives. Here’s what I’m looking for: 1) advanced discussion of computational and statistical methods for genomics, especially microarray analysis, and 2) suitability for an intro and survey bioinformatics course I teach.

edited by Giovanni Parmigiani, Elizabeth S Garrett, Rafael A Irizarry, Scott L Zeger
companion website
Great medium depth howto. Covers R, dChip, SAM, and packages that take more sophisticated approaches to analysis, clustering, and visualization.

Bioinformatics for Geneticists
Edited by Michael R. Barnes and Ian C. Gray
Published Online: 22 May 2003
Genomic orientation, but too light and introductory for my needs, too genomic focused for my course. Good starting point book for a geneticist.

Advances in Systems Biology
Series: Advances in Experimental Medicine and Biology, Vol. 547
Opresko, Lee K.; Gephart, Julie M.; Mann, Michaela B. (Eds.)
Pulled this book for A Systems Approach to Discovering Signaling and Regulatory Pathways—or how to digest large interaction networks into relevant pieces by Trey Ideker.

Microarray Gene Expression Data Analysis: A Beginners Guide
by Helen C. Causton , John Quackenbush , Alvis Brazma
What it says it is: design, image processing, normalization, basic stats, clustering.

Bioinformatics: Databases and Systems
Edited by Stan Letovsky
Kluwer Academic Press, Boston, 1999
A chapter a database. Covers the usual gang, plus chapters on WIT/WIT2, KEGG, BioWidgets (Java), and AceDB (overview).

Statistical Methods in Bioinformatics An Introduction
Series: Statistics for Biology and Health
Ewens, Warren J. and Grant, Gregory
2nd ed. , 2004, 588p
Heavy statistical treatment of sequence analysis. Starts with stats, then stat properties of one seq, multiple seq alignments, BLAST, Marlov chains, HMMs.

‘In Silico’ Simulation of Biological Processes
No. 247 Novartis Foundation Symposium
270 pages January 2003
Picked this up for the GO chapter. Also has a chapter on KEGG.

oarrays Methods and Applications: Nuts and Bolts

Edited by Gary Hardiman
Covers topics from basic MA howtos to more specialized applications. A mixed bag. One chapter on microarray scanner evaluation, another on C. elegans 50-mer oligos made by the Hardiman lab at UCSD. Chapter text and figures are online.

Microarray Quality Control

by Wei Zhang, Ilya Shmulevich and Jaakko Astola
136 pages February 2004
What the title says. Microarrays from a core facility perspective. Ends with normatization. Covers long oligo design.

Microarray Bioinformatics
by Dov Stekel
Cambridge University Press. 2003
Thorough and clear coverage of microarray design, construction, image proc, and normalization. What caught my eye was the chapter on oilgo design, but its all good. Best single book on microarrays I’ve seen.

Bioinformatics: Methods and Protocols
Edited by Stephen Misener, Stephen A. Krawetz
Humana Press; 1st edition 2000
Program based by chapter. Too program based for a course. Has good chpaters on Clustal and Phylip. A chapter on Trascription control regions using MatInspector/GenomeInspector, weight matrix based sequence scanning for single or paired binding sites.

Computational Molecular Biology: an Algorithmic Approach
by Pavel A. Pevzner
MIT Press, 2000
Takes a unique approach. Looks at interesting computational aspects of seqeunce-based biology, and sometimes takes an odd sideways view of problems, getting deep into the underlying mathematics. A great complement to a more straightforward survey book. The topic coverage isn’t broad enough for my course, and the topics get covered in more depth than I need. Runs thorugh algorithmics of restircition digests to microarrays including, of course, sequencing by hybridization. Covers algorithmics of genomic comparisons. Great source book for a serious comp bio student.

DNA Microarrays: A Practical Approach
Edited by Mark Schena
Oxford University Press, Oxford, UK, 1999
A book on microarray technology. From DNA spotted on glass to enzymatic oligo arrays to ink jets, to microelectronic arrays. Written early on when many different approaches were being explored. Great source for technical information.

Mathematics of Genome Analysis
by Jerome K. Percus
Cambridge University Press; 1st edition 2002
Not a genomics book, but a mathmatician’ s look at DNA sequence, from clone libraries through seq alignments.

Post-genome Informatics
by Minoru Kanehisa
Oxford University Press, Oxford, 2000
Cool cover! Written by the guy behind KEGG. An eclectic choice of topics, first databases, then sequence analysis basics, then network analysis. Had a few pages on comparing networks that I found useful.

Guide to Analysis of DNA Microarray Data
by Steen Knudsen
John Wiley and Sons, New York, 2002
A what-to-do book on microarray data analysis. Very short, too short to explain how to do things, but describes what to do, issues to consider, and what results will look like. Useful as a place to start, will show you what you don’t know. The linked site has example R and BioConductor code.

Methods of Microarray Data Analysis II
Edited by Simon M. Lin and Kimberly F. Johnson
Springer, 2002
Papers from CAMDA ‘01 Various array analysis, especially advanced clsutering methods. Particularly interesting are:

  • Biology-Driven Clustering of Microarray Data; K.R. Coombes, et al.
    GO-based clustering.
  • Analysis of Gene Expression Profiles and Drug Activity Patterns by Clustering and Bayesian Network Learning; Jeong-Ho Chang, et al.
  • Topomap and bayesian clustering

DNA Arrays: Technologies and Experimental Strategies
Edited by Elena V. Grigorenko
CRC Press, 2001
What caught my eye are the technology chapters, one on oligo arrays and another on electrochemical array detection.

DNA Arrays: Methods and Protocols
Edited by Jang B. Rampal
Humana Press, 2001
This is another array technology book. Great information on ink-jet and photolithographic oligo synthesis. There are several sequencing by hybridization articles. It starts with a chapter on the history of the field by Southern. Great book for a collection of articles!

Primate life spans

Monday, March 14th, 2005

Googling for AcePerl tutorials (there has to be a better way to use AcePerl than what I’ve been doing!) , I happened across a list of primate lifespans. List has 239 primates. The winners are the great apes, with some monkeys having lifespans nearly as long, at a guess not really different given the sparsity of the data. Would be interesting to plot lifespans on a phylogram.

The Life Spans of Nonhuman Primates

Species                                                   Life Span
Allenopithecus nigroviridis (Allen's Swamp Monkey)        28 yrs. (1)
Allocebus trichotis (Hairy-eared Dwarf Lemur)             NA
Alouatta belzebul (Red-handed Howler)                     NA
Alouatta caraya (Black-and-gold Howler)                   20 yrs. (2)
Alouatta coibensis (Coiba Island Howler)                  NA
Alouatta fusca (Brown Howler)                             NA
Alouatta palliata (Mantled Howler)                        20 yrs. (1)
Alouatta pigra (Black Howler)                             20 yrs. (1)
Alouatta sara (Bolivian Red Howler)                       NA
Alouatta seniculus (Red Howler)                           25 yrs. (1)
Aotus nigriceps (Southern Red-necked Night Monkey)        20 yrs. (1)
Aotus trivigratus (Northern Gray-necked Owl Monkey)       20 yrs. (1)
Arctocebus aureus (Golden Angwantibo)                     13 yrs. (3)
Arctocebus calabarensis (Angwantibo)                      11 yrs. (1)
Ateles belzebuth (White-bellied Spider Monkey)            20 yrs. (1)
Ateles chamek (Black-faced Spider Monkey)                 40 yrs. (3)
Ateles fusciceps (Brown-headed Spider Monkey)             24 yrs. (1)
Ateles geoffroyi (Black-handed Spider Monkey)             48 yrs. (3)
Ateles marginatus (White-whiskered Spider Monkey)         NA
Ateles paniscus (Black Spider Monkey)                     33 yrs. (1)
Avahi laniger (Woolly Lemur)                              NA
Brachyteles arachnoides (Woolly Spider Monkey or
    Muriqui)                                              30 yrs. (1)
Bunopithecus [Hylobates] hoolock (Hoolock                 42 yrs. (1)
    or White-browed Gibbo
Cacajao calvus (Bald Uacari)                              20.1 yrs. (1)
Cacajao melanocephalus (Black-headed Uacari)              18 yrs. (2)
Callicebus brunneus (Brown Titi Monkey)                   NA
Callicebus caligatus (Chestnut-bellied Titi Monkey)       NA
Callicebus cinerascens (Ashy Titi Monkey)                 NA
Callicebus cupreus (Red Titi Monkey)                      NA
Callicebus donacophilus (Bolivian Gray Titi Monkey)       NA
Callicebus dubius (Titi Monkey)                           NA
Callicebus hoffmannsi (Hoffman's Titi Monkey)             NA
Callicebus modestus (Titi Monkey)                         NA
Callicebus moloch (Dusky Titi Monkey)                     25 yrs. (2)
Callicebus oenanthe (Andean Titi Monkey)                  NA
Callicebus olallae (Beni Titi Monkey)                     NA
Callicebus personatus (Masked Titi Monkey)                NA
Callicebus torquatus (Collared Titi or Widow Monkey)      NA
Callimico goeldii (Goeldi's Monkey)                       17.9 yrs. (1)
Callithrix argentata (Bare-ear Marmoset)                  17 yrs. (2)
Callithrix aurita (Buffy Tufted-eared Marmoset)           NA
Callithrix flaviceps (Buffy-headed Marmoset)              NA
Callithrix geoffroyi (Geoffroy's Tufted-eared Marmoset)   NA
Callithrix humeralifer (Tassel-eared Marmoset)            15 yrs. (2)
Callithrix jacchus (Common Marmoset)                      11.7 yrs. (1)
Callithrix mauesi (Maues Marmoset)                        NA
Callithrix penicillata (Black Tufted-eared Marmoset)      NA
Callithrix pygmaea (Pygmy Marmoset)                       11.7 yrs. (1)
Callthrix kuhlii (Wied's Tufted-eared Marmoset)           NA
Callthrix nigriceps (Black-headed Marmoset)               NA
Cebus albifrons (White-fronted Capuchin)                  44 yrs. (1)
Cebus apella (Tufted or Brown Capuchin)                   40 yrs. (1)
Cebus capucinus (White-throated Capuchin)                 46.9 yrs. (1)
Cebus olivaceus (Weeper or Wedge-capped Capuchin)         NA
Cercocebus agilis (Agile Mangabey)                        NA
Cercocebus galeritus (Tana River Mangabey)                19 yrs. (1)
Cercocebus torquatus (White-collared Mangabey)            27 yrs. (1)
Cercocebus torquatus atys (Sooty Mangabey)                18 yrs. (1)
Cercopithecus campbelli (Campbell's Guenon)               25 yrs. (2)
Cercopithecus cephus (Mustached Guenon)                   22 yrs. (1)
Cercopithecus diana (Diana Monkey)                        34.8 yrs. (1)
Cercopithecus dryas (Dryas Guenon)                        NA
Cercopithecus erythrogaster (White-throated Guenon)       NA
Cercopithecus erythrotis (Red-eared Guenon)               NA
Cercopithecus hamlyni (Owl-faced Monkey)                  27 yrs. (2)
Cercopithecus lhoesti (L'Hoest's Monkey)                  NA
Cercopithecus mitis (Blue Monkey)                         20 yrs. (1)
Cercopithecus mona (Mona Monkey)                          22 yrs. (1)
Cercopithecus neglectus (De Brazza's Monkey)              22 yrs. (1)
Cercopithecus nictitans (Putty-nosed                      23 yrs. (2)
     or Greater Spot-nosed Guenon)
Cercopithecus petaurista (Lesser Spot-nosed Guenon)       19 yrs. (2)
Cercopithecus pogonias (Crowned Guenon)                   20 yrs. (1)
Cercopithecus preussi (Preuss's Monkey)                   NA
Cercopithecus sclateri (Sclater's Guenon)                 NA
Cercopithecus solatus (Sun-tailed Guenon)                 NA
Cercopithecus wolfi (Wolf's Guenon)                       NA
Cheirogaleus major (Greater Dwarf Lemur)                  8.8 yrs. (1)
Cheirogaleus medius (Fat-tailed Dwarf Lemur)              19 yrs. (2)
Chiropotes albinasus (White-nosed Bearded Saki)           12 yrs. (2)
Chiropotes satanas (Bearded Saki)                         15 yrs. (1)
Chlorocebus aethiops (Vervet, Grivet, or Green Monkey)    31 yrs. (1)
Colobus angolensis (Angolan Black-and-white Colobus)      NA
Colobus guereza (Abyssinian, Guereza, or
    Eastern Black-and-white Colobus)                      22.2 yrs. (1)
Colobus polykomos (King or Western Black-and-white
    Colobus)                                              30.5 yrs. (1)
Colobus satanas (Black Colobus)                           NA
Colobus vellerosus (Geoffroy's or White-thighed
    Black-and-white colobus)                              NA
Daubentonia madagascariensis (Aye-aye)                    24 yrs. (2)
Erythrocebus patas (Patas Monkey)                         21.6 yrs. (1)
Eulemur coronatus (Crowned Lemur)                         NA
Eulemur fulvus (Brown Lemur)                              30.8 yrs. (1)
Eulemur macaco (Black Lemur)                              27.1 yrs. (1)
Eulemur mongoz (Mongoose Lemur)                           <26 yrs.  (4)
Eulemur rubriventer (Red-bellied Lemur)                   NA
Euoticus elegantulus (Southern Needle-clawed Bush Baby)   NA
Euoticus pallidus (Northern Needle-clawed Bush Baby)      NA
Galago alleni (Allen's Bush Baby)                         12 yrs. (1)
Galago gallarum (Somali Bush Baby)                        NA
Galago matschiei (Matschie's Bush Baby)                   NA
Galago moholi (Southern Lesser Bush Baby)                 16 yrs. (1)
Galago senegalensis (Northern Lesser Bush Baby)           16 yrs. (1)
Galagoides demidoff (Demidoff's Bush Baby)                13 yrs. (1)
Galagoides thomasi (Thomas's Bush Baby)                   NA
Galagoides zanzibaricus (Zanzibar Bush Baby)              16.5 yrs. (3)
Gorilla gorilla beringei (Mountain Gorilla)               40-50 yrs. (1)
Gorilla gorilla gorilla (Western Lowland Gorilla)         50 yrs. (1)
Gorilla gorilla graueri (Eastern Lowland Gorilla)         NA
Hapalemur aureus (Golden Bamboo Lemur)                    NA
Hapalemur griseus (Lesser Bamboo Lemur)                   17 yrs. (2)
Hapalemur simus (Greater Bamboo Lemur)                    NA
Hylobates agilis (Dark-handed or Agile Gibbon)            32 yrs. (1)
Hylobates klossi  (Kloss's Gibbon)                        NA
Hylobates lar (White-handed Gibbon)                       44 yrs. (1)
Hylobates moloch (Silvery Javan Gibbon)                   35 yrs. (1)
Hylobates muelleri (Mueller's Bornean Gray Gibbon)        47 yrs. (1)
Hylobates pileatus (Pileated or Capped Gibbon)            39 yrs. (1)
Indri indri (Indri)                                       NA
Kasi [Trachypithecus] vetulus (Purple-faced Leaf Monkey)  8 yrs. (4)
Kasi [Trachypithecus] johnii (Nilgiri Langur)             NA
Lagothrix flavicauda (Yellow-tailed Woolly Monkey)        NA
Lagothrix lagotricha (Woolly Monkey)                      25.9 yrs. (1)
Lemur catta (Ring-tailed Lemur)                           27 yrs. (1)
Leontopithecus caissara (Black-faced Lion Tamarin)        NA
Leontopithecus chrysomelas (Golden-headed Lion Tamarin)   NA
Leontopithecus chrysopygus (Black Lion Tamarin)           NA
Leontopithecus rosalia (Golden Lion Tamarin)              24 yrs. (2)
Lepilemur dorsalis (Gray-backed Sportive Lemur)           NA
Lepilemur edwardsi (Milne-Edwards' Sportive Lemur)        NA
Lepilemur leucopus (White-footed Sportive Lemur)          NA
Lepilemur microdon (Small-toothed Sportive Lemur)         NA
Lepilemur mustelinus (Weasel Sportive Lemur)              NA
Lepilemur ruficaudatus (Red-tailed Sportive Lemur)        NA
Lepilemur septentrionalis (Northern Sportive Lemur)       NA
Lophocebus albigena (Gray-cheeked Mangabey)               32.6 yrs. (1)
Lophocebus aterrimus (Black Mangabey)                     32.7 yrs. (3)
Loris tardigradus (Slender Loris)                         15 yrs. (1)
Macaca arctoides (Stump-tailed Macaque)                   30 yrs. (1)
Macaca assamensis (Assamese Macaque)                      NA
Macaca cyclopis (Formosan Rock Macaque)                   NA
Macaca fascicularis (Long-tailed, Crab-eating or
    Cynomolgus Macaque)                                   37.1 yrs. (1)
Macaca fuscata (Japanese Macaque)                         33 yrs. (1)
Macaca maura (Celebes Moor Macaque)                       NA
Macaca mulatta (Rhesus Macaque)                           29 yrs. (1)
Macaca nemestrina (Pig-tailed Macaque)                    26.3 yrs. (1)
Macaca nigra (Celebes or Crested Black)                   18 yrs. (1)
Macaca ochreata (Booted Macaque)                          NA
Macaca radiata (Bonnet Macaque)                           30 yrs. (1)
Macaca silenus (Lion-tailed Macaque)                      38 yrs. (1)
Macaca sinica (Toque Macaque)                             30 yrs. (1)
Macaca sylvanus (Barbary Macaque)                         22 yrs. (1)
Macaca thibetana (Tibetan Macaque)                        20 yrs. (1)
Macaca tonkeana (Tonkean Macaque)                         NA
Mandrillus leucophaeus (Drill)                            46 yrs. (4)
Mandrillus sphinx (Mandrill)                              46.3 yrs. (1)
Microcebus coquereli (Coquerel's Dwarf Lemur)             15 yrs. (2)
Microcebus murinus (Gray Mouse Lemur)                     15.5 yrs. (1)
Microcebus myoxinus (Pygmy Mouse Lemur)                   NA
Microcebus rufus (Brown Mouse Lemur)                      NA
Miopithecus talapoin (Dwarf Guenon or Southern
    Talapoin Monkey)                                      27.7 yrs. (1)
Nasalis [Nasalis] larvatus (Proboscis Monkey)             21 yrs. (2)
Nomascus [Hylobates] leucogenys (Chinese
    White-cheeked Gibbon)                                 28 yrs. (1)
Nomascus [Hylobates] gabriellae (Golden-cheeked Gibbon)   46 yrs. (1)
Nycticebus coucang (Slow Loris)                           20 yrs. (1)
Nycticebus pygmaeus (Pygmy Loris)                         20 yrs. (1)
Otolemur crassicaudatus (Thick-tailed Greater Bush Baby)  15 yrs. (1)
Otolemur garnettii (Garnett's Greater Bush Baby)          15 yrs. (1)
Pan paniscus (Bonobo or Pygmy Chimpanzee)                 40 yrs. (1)
Pan troglodytes (Chimpanzee)                              53 yrs. (1)
Papio hamadryas anubis (Olive Baboon)                     30-45 yrs. (1)
Papio hamadryas cynocephalus (Yellow Baboon)              40 yrs. (1)
Papio hamadryas hamadryas (Hamadryas Baboon)              35.6 yrs. (1)
Papio hamadryas papio (Guinea Baboon)                     40 yrs. (1)
Papio hamadryas ursinus (Chacma Baboon)                   45 yrs. (1)
Perodicticus potto (Potto)                                26 yrs. (1)
Phaner furcifer (Fork-marked Lemur)                       12 yrs. (2)
Piliocolobus [Procolobus] pennantii (Pennant's Red
    Colobus)                                              NA
Piliocolobus [Procolobus] preussi (Preuss's Red Colobus)  NA
Piliocolobus [Procolobus] rufomitratus (Tana River
    Red Colobus)                                          NA
Piliocolobus [Procolobus] baduis (Western Red Colobus)    NA
Pithecia aequatorialis (Equatorial Saki)                  NA
Pithecia albicans (Buffy Saki)                            NA
Pithecia irrorata (Bald-faced Saki)                       NA
Pithecia monachus (Monk Saki)                             25 yrs. (2)
Pithecia pithecia (White-faced Saki)                      35 yrs. (3)
Pongo abelii (Sumatran Orangutan)                         >50 yrs. (1)
Pongo pygmaeus (Borneo Orangutan)                         59 yrs. (1)
Presbytis comata (Grizzled Leaf Monkey)                   NA
Presbytis femoralis (Banded Leaf Monkey)                  NA
Presbytis frontata (White-fronted Leaf Monkey)            NA
Presbytis hosei (Hose's Leaf Monkey)                      NA
Presbytis melalophos (Mitered Leaf Monkey)                16 yrs. (2)
Presbytis potenziani (Mentawai Island Leaf Monkey)        NA
Presbytis rubicunda (Maroon Leaf Monkey)                  NA
Presbytis thomasi (Thomas's Leaf Monkey)                  NA
Procolobus [Procolobus] verus (Olive Colobus)             NA
Propithecus diadema (Diademed Sifaka)                     20 yrs. (1)
Propithecus tattersalli (Golden-crowned Sifaka)           NA
Propithecus verreauxi (Verreaux's Sifaka)                 20 yrs. (2)
Pygathrix [Pygathrix] nemaeus (Red-shanked Douc Langur)   >30 yrs. (1)
Pygathrix [Pygathrix] nigripes (Black-shanked Douc
    Langur)                                               NA
Rhinopithecus [Pygathrix) roxellana
(Sichuan Golden Snub-nosed Monkey)                        NA
Rhinopithecus [Pygathrix] avunculus (Tonkin
    Snub-nosed Monkey)                                    NA
Rhinopithecus [Pygathrix] bieti (Black or Yunnan
    Snub-nosed Monkey)                                    NA
Rhinopithecus [Pygathrix] brelichi (Guizhou
    Snub-nosed Monkey)                                    NA
Saguinus bicolor (Bare-faced Tamarin)                     8 yrs. (1)
Saguinus fuscicollis (Saddleback Tamarin)                 24 yrs. (2)
Saguinus geoffroyi (Red-crested Tamarin)                  13 yrs. (1)
Saguinus imperator (Emperor Tamarin)                      17 yrs. (1)
Saguinus inustus (Mottled-face Tamarin)                   NA
Saguinus labiatus (Red-bellied Tamarin)                   NA
Saguinus leucopus (Silvery-brown Bare-faced Tamarin)      NA
Saguinus midas (Golden-handed Tamarin)                    13.2 yrs. (1)
Saguinus mystax (Mustached Tamarin)                       12-20 yrs. (1)
Saguinus nigricollis (Spix's Black-mantled Tamarin)       13.9 yrs. (1)
Saguinus oedipus (Cotton-top Tamarin)                     13.5 yrs. (1)
Saguinus tripartitus (Golden-mantled Saddleback Tamarin)  6 yrs. (1)
Saimiri boliviensis (Bolivian Squirrel Monkey)            NA
Saimiri oerstedii (Red-backed Squirrel Monkey)            NA
Saimiri sciureus (Common Squirrel Monkey)                 21 yrs. (1)
Saimiri ustus (Golden-backed Squirrel Monkey)             NA
Saimiri vanzolinii (Black Squirrel Monkey)                NA
Semnopithecus entellus (Hanuman Langur)                   20 yrs. (1)
Simias [Nasalis] concolor (Pig-tailed Langur)             NA
Symphalangus [Hylobates] syndactylus (Siamang)            35yrs. (1)
Tarsius bancanus (Western Tarsier)                        8-12 yrs. (1)
Tarsius pumilus (Pygmy Tarsier)                           NA
Tarsius spectrum (Spectral Tarsier)                       12 yrs. (1)
Tarsius syrichta (Phillippine Tarsier)                    13.5 yrs. (1)
Tarsius dianae (Dian's Tarsier)                           NA
Theropithecus gelada (Gelada Baboon)                      19.2 yrs. (1)
Trachypithecus [Trachypithecus] auratus (Ebony Langur)    NA
Trachypithecus [Trachypithecus] cristatus (Silvered
    Langur)                                               31 yrs. (3)
Trachypithecus [Trachypithecus] delacouri (Delacour's
    Langur)                                               NA
Trachypithecus [Trachypithecus] francoisi (Francois's
    Langur)                                               <20 yrs. (4)
Trachypithecus [Trachypithecus] geei (Golden Langur)      NA
Trachypithecus [Trachypithecus] obscurus (Dusky or
    Spectacled Leaf Monkey)                               NA
Trachypithecus [Trachypithecus] phayrei (Phayre's Leaf
    Monkey)                                               NA
Trachypithecus [Trachypithecus] pileatus (Capped Leaf
    Monkey)                                               NA
Varecia variegatus (Ruffed Lemur)                         19 yrs. (1)

Numbers in parenthesus following lifespans refer to the following references:

1. Rowe, Noel. The Pictorial Guide to Living Primates. Pogonias Press, East Hampton, New York, 1996.
2. Hakeem A., et al. Handbook of the Psychology of Aging. 4th ed. Birren, J.E., Schaie, K.W., Editors. San Diego:
Academic Press. 1996.
3. Nowak, R. Walker’s Primates of the World. Johns Hopkins University Press, Baltimore, Maryland, 1999.
4. American Association of Zoo Keepers Greater San Francisco Bay Area Chapter. Biological Values for Selected
Mammals. Topeka: AAZK. 1992. 3rd ed. Pgs: v, 481

*The data presented here is taken from the secondary sources listed above and users are advised to consult primary
sources before citing this information. According to Rowe (1996, p. 6), “Species life span is given in years and
measures the maximum amount of time between birth and death rather than an average.” However, life span
information varies, as might be expected, from source to source. Moreover, the information provided is drawn mainly
from reports on captive animals. While it is generally assumed that captive animals will live longer than animals in
the wild, because of the consistent care and support provided in laboratory or zoo settings, according to Hakeem
et al.:

“We have very little information on the longevity of primates in the wild,
because this requires sustained observations of wild populations for many
decades. One of our concerns in using life spans of captive animals was that
they might vary greatly from the species — maximum life span in the wild; one
might think that primates living in zoos would have longer maximum life spans
than those living in the wild. The few very long-term studies of primates
living under natural conditions indicate, however, that some individuals do live
into extreme old age in the wild. Long-term observational data suggest that
the maximum life spans for zoo-living and wild primates may be about the
same (p. 78-9).”

Anyone who would like to contribute verifiable information about nonhuman primate life spans — especially for those
where information is not provided (NA) — should contact Ray Hamel at

Information compiled by Derek Johnson.

Tasmanian Tiger

Friday, March 4th, 2005

Here’s a site with films of the tasmanian tiger, the thylacine (Thylacinus cynocephalus). It was driven to extinction in the 1930’s.

mounted thylacine

Thylacine films

There’s interest in sequencing the genome of the tasmanian devil with an eye toward eventual cloning. Reconstructing a genome of an extinct species is currently not technically feasible. So far they have been able to clone short DNA segments from preserved tissue.