The Monkey's Voyage

by Alan de Queiroz

  81“Patterns of geographic distributions . . . ”: Croizat (1962), 712.

  81Even to the ancient Greeks: Mayr (1982), who noted that Hippocrates, Aristotle, Theophrastus, and others attributed some discontinuous distributions, such as elephants occurring in India and Africa, to former connections.

  82Not even worth studying: Croizat (1962), 213, for example.

  82“Earth and life evolve together”: Croizat (1962), 604.

  82The tracks . . . run all over the place: For New Zealand, Page (1989); Jordan (2001); Winkworth et al. (2002); Wallis and Trewick (2009); Trewick and Gibb (2010). For Hawaii, Baldwin and Wagner (2010); Gillespie et al. (2012). Of these studies, only Page (1989) actually used the track method; however, the other studies imply the existence of diverse tracks for the two areas mentioned.

  82New Caledonia is an amalgamation: Heads (2008).

  82To collectively produce a clear pattern: The notion that chance dispersal can give rise to general patterns and, therefore, that tracks shared by different taxa are not evidence of a single (presumably vicariant) event is given in Ball (1975).

  83Had hardly been cited at all: For the fact that Croizat was widely known among botanists but not zoologists until the mid-1970s, Schmid (1986).

  83“Conspiracy of silence”: Colacino and Grehan (2003), 10.

  83“Totally unscientific style and methodology” and “a member of the lunatic fringe”: Nelson (1977), 452 and 451, respectively.

  83“Pondered for a time”: Email from Nelson to the author, April 20, 2010.

  83“Not wholly sound” and “blazing sermon”: Brundin (1966), 61.

  84An overlooked visionary: Hull (1988) describes Nelson’s championing of Croizat and the interactions between the two at length. The paper in which Nelson described Croizat’s work enthusiastically is Nelson (1973).

  84Should collaborate on a paper: The history of the Croizat, Nelson, and Rosen collaboration is discussed in Hull (1988). The resulting paper is Croizat et al. (1974).

  85“Is to be understood first . . . ”: Croizat et al. (1974), 269.

  85“Having failed to dissect these concepts . . . ”: Croizat et al. (1974), 276.

  85“A world of make-believe and pretense” and “No one well informed . . . ”: Croizat et al. (1974), 277.

  85A “hardening” of vicariance biogeography: Gould (1986).

  86“A science of the improbable . . . ”: Nelson (1978a), 289.

  86Cannot be refuted: The notion that dispersal hypotheses are untestable and/or unfalsifiable is found in Ball (1975); Rosen (1978); Craw (1979); Nelson and Platnick (1981).

  86We know long-distance dispersal happens: McDowall (1978).

  87Simply too young to have been influenced: For Mayr’s claim that most living groups of mammals, birds, and flowering plants are too young to have been affected by the opening of the Atlantic, Mayr (1952).

  88Assumed a strict molecular clock: The molecular clock and its use in biogeography are more fully discussed in Chapters Five and Six. An early demonstration of the inconstant nature of the clock is found in Goodman et al. (1971).

  88Vicariance scientists used this . . . to completely discount: Heads (2005); Nelson and Ladiges (2009); Parenti and Ebach (2009, 2013).

  90“Yep”: Email from Nelson to the author, October 23, 2010. Nelson also intimated that Homo sapiens might be much older than generally believed in Nelson (1978c).

  91“Offends a critical mind”: Brundin (1966), 51.

  91“Will have powerful influence . . . ”: Croizat (1962), 708.

  91“To formulate explicit methods . . . ”: Croizat et al. (1974), 277.

  91“Non-equilibrium thermodynamics theory”: Brooks and Wiley (1988).

  93Upland Sandpipers: McAtee (1914). The quotation, “I used to count the number . . . ” is from p. 404 of that article.

  Chapter Four: New Zealand Stirrings

  96That tuatara’s name is Henry: Marks (2009).

  97Contains just the one species: Tuatara from North Brother Island have been considered a separate species, Sphenodon guntheri, but a recent genetic study suggests these animals should be lumped with S. punctatus. See Hay et al. (2010).

  97Split from each other some 250 million years ago: This estimate is from Shedlock and Edwards (2009).

  97Tuatara . . . are anatomically distinct: For tuatara anatomy, Pough et al. (1998).

  97Sphenodontids were never a large group: For the fossil record of tuatara and other sphenodontids, Jones et al. (2009).

  97By about 83 million years ago: For the geologic history of New Zealand, Campbell and Hutching (2007).

  99Some seven hundred years ago: Higham et al. (1999).

  99The rats ate tuatara eggs: For the impact of rat and other mammal introductions on tuatara, Towns and Daugherty (1994).

  99Left some Sphenodon isolated: Hay et al. (2010).

  99Tuatara eating the giant, cricket-like weta: Angier (2010).

  100“With regard to general problems . . . ”: Nelson (1975) 494.

  100Joseph Hooker placed it: Gibbs (2006). For Darwin, Matthew, and Darlington arguing for dispersal origins of New Zealand’s biota, Darwin (1859); Matthew (1915); Darlington (1965). Pole (1994) gives a brief summary of the history of ideas about the origins of New Zealand’s biota.

  100“Stranded upon the shores of New Zealand . . . ”: Nelson (1975), 494.

  101I asked several New Zealand biologists: Email correspondence with the author from Mike Pole, November 1, 2010; Dallas Mildenhall, December 12, 2010; Steve Trewick, December 13, 2010.

  101“By the middle of the Cretaceous . . . ”: Pole (1994), 625, quoting Enting and Molloy (1982).

  102The moa record peters out: For the fossil records of moa and kiwi, Tennyson et al. (2010); Tennyson (2010). On possible kiwi fossil footprint, Fleming (1975). For Miocene tuatara, Jones et al. (2009). For New Zealand vertebrate fossil record in general, Tennyson (2010).

  102A handful of dinosaurs: For New Zealand vertebrate fossils from the Late Cretaceous, around the time of the separation of Zealandia from Antarctica/Australia, Tennyson (2010).

  102“Much of the present lowland flora . . . ”: Raven and Axelrod (1972), 1382.

  103Pollen is tough stuff: For general information on pollen and its analysis, Moore et al. (1991).

  103A history of taxa in constant flux: Fleming (1975); Mildenhall (1980); Pole (1993, 1994); Lee et al. (2001).

  103A 2001 survey: Lee et al. (2001).

  104A Field Guide to the Alpine Plants of New Zealand: Salmon (1992). For fossil records of plants we identified at Arthur’s Pass, Lee et al. (2001), except for Drosera, which is from Raine et al. (2008).

  106A paleontologist named Charles Fleming: Fleming (1962, 1975).

  106“There was a disconnect between paleontologists and biologists . . . ”: Email from Dallas Mildenhall to the author, December 12, 2010.

  106He published a paper making that point: Mildenhall (1980). For the citation history of Mildenhall’s 1980 paper, Web of Science citation database, accessed in March 2010 (http://thomsonreuters.com/web-of-science/).

  106“Do Araucarias have double trunks?”: Email from Pole to the author, November 1, 2010. For biographical information about Mike Pole, emails from Pole to the author, November 1, 2010; December 3, 2010; March 23, 2011.

  107That botanist was Michael Heads: Email from Heads to the author, April 5, 2011.

  107Pole compared the past floras: Pole (1993).

  108Pole fleshed out the case: Pole (1994).

  109Mike Pole spends much of his time: Email from Pole to the author, November 1, 2010.

  110He believes that explaining the origins: Email from Pole to the author, November 1, 2010.

  111Pole ment
ioned two sets of studies: For molecular clock studies of southern beeches and ratites, respectively, Martin and Dowd (1988); Sibley and Ahlquist (1987); and references in both.

  112A natural floating island: Powers (1911).

  Chapter Five: The DNA Explosion

  115Estimates of the age of the universe: Simanek and Holden (2001); Overbye (2013). The Simanek and Holden book is “science humor,” but the age estimates it provides are from real studies.

  116Selection for increased brain size: Shultz et al. (2012).

  117Whose focus was on cladograms: For the focus on cladograms or tracks and lack of use of evidence for the ages of groups, Croizat et al. (1974); Cracraft (1975); Rosen (1978); Nelson and Platnick (1981); Wiley (1988); and Humphries and Parenti (1989), among many others. Croizat et al. (1974) and Nelson and Platnick (1981) explicitly criticized the use of fossils to place ages on groups.

  117Both Hallam and Briggs wrote books: Hallam (1973, 1994); Briggs (1987, 1995). The ichthyologist John Lundberg, although a diehard cladist, was (and is) similar to Hallam and Briggs in that he believed that the fossil record was very informative. In an important paper, Lundberg (1993) used fossil evidence to challenge continental drift as a general explanation for freshwater fish distributions.

  118“Chicken scratchings”: Donoghue, telephone conversation with the author, September 3, 2010.

  119“Degree of divergence is a guide neither . . . ”: Heads (2005), 71.

  119“Does not solve biogeographical problems . . . ”: Heads (2005), 72.

  119“Molecular dating game”: Nelson and Ladiges (2009).

  119The idea of the molecular clock itself: The first presentation of the molecular clock is in Zuckerkandl and Pauling (1962). For the early history of the molecular clock idea, see Morgan (1998).

  120Darwin became a confirmed believer: The development of Darwin’s belief in evolution is from Browne (1995) and Quammen (2006), although those authors would not necessarily agree with my interpretation.

  120It was an unseasonably warm night: For Mullis’s invention of PCR and his other exploits, Mullis (1998); Wade (1998).

  124In 1985 the description of PCR had been published: The original paper describing PCR, with Mullis as the fourth of seven authors is Saiki et al. (1985). A later, more complete description of the method is in Mullis and Faloona (1987).

  126Examining that tree now: The first, fairly pathetic garter-snake sequencing study was de Queiroz and Lawson (1994). The later, much better one is de Queiroz et al. (2002). Incidentally, this later paper also presents a scenario for the vicariant origins of some highland garter snakes through fragmentation of woodland environments because of a drying climate.

  126The clock didn’t tick at a constant rate: Some relatively early studies on the inconstancy of the molecular clock are Goodman et al. (1971); Britten (1986); Vawter and Brown (1986).

  127A house made almost entirely of old bottles: For the history of the bottle house, Gildart and Gildart (2005).

  128Mathematical models to describe evolution: For a summary of many models of DNA change including pre-PCR examples such as the Jukes-Cantor and Kimura two-­parameter models, Felsenstein (2003).

  129The estimates are getting better and better: For a recent validation of complex over very simple models of evolution, Huelsenbeck et al. (2011). Also see Felsenstein (2003).

  131Rizal Shahputra and Melawati: For Rizal Shahputra, Fernandez (2005); Jones (2005). For Melawati, Associated Press (2005).

  Chapter Six: Believe the Forest

  133A molecular clock analysis using tapeworm DNA: Hoberg et al. (2001).

  134“I’ve been involved in a bunch of dating . . . ”: This and subsequent quotes from Michael Donoghue, Donoghue, telephone conversation with the author, September 3, 2010.

  135Their dismissal of this evidence: For pointed critiques of molecular dating from vicariance scientists, Heads (2005); Parenti (2006); Nelson and Ladiges (2009).

  136Certain apes: Benton et al. (2009).

  136The actual age will almost always be older: For the problem of first fossil occurrences being misleading for calibrating molecular clocks, Heads (2005); Nelson and Ladiges (2009).

  136The first fossil hummingbirds: Mayr (2003).

  137Use only especially good calibrations: For the notion of using especially good fossil calibration points and justification for many specific points, including the bird-crocodile split, Benton et al. (2009).

  137Incorporating uncertainty: For specific methods for taking into account uncertainty in calibration ages, Kumar et al. (2005); Drummond et al. (2006). Ho and Phillips (2009) and Hedges and Kumar (2009b) give reviews of the subject of uncertainty in calibrations.

  138Which ones were out of synch: For comparisons among multiple calibration points, Douzery et al. (2003); Near and Sanderson (2004).

  139The clock is pretty variable: Bousquet et al. (1992); Martin and Palumbi (1993); Rodríguez-­Trelles et al. (2004); and Thomas et al. (2006), among many others. Mammal and shark rates are from Marshall et al. (1994); Martin and Palumbi (1993).

  139Reasons for the inconstancy of the clock: Bromham (2009).

  140Relaxed clock methods: Welch and Bromham (2005); Hedges and Kumar (2009b).

  140Tested using computer programs: Kishino et al. (2001); Kumar et al. (2005); and Battistuzzi et al. (2010), among others.

  140A 2011 study: Meredith et al. (2011b). John Gatesy’s statement about the drastic effects of using calibrations from different groups is from a telephone conversation between Gatesy and the author, August 2011.

  141The two most convincing studies: Vidal et al. (2009); Pyron and Burbrink (2011). Many comparisons of timetree studies for individual taxa are in Hedges and Kumar (2009a), the book resulting from the Timetree of Life project.

  144Molecular age estimates match the fossil-based ones: Hedges and Kumar (2009b).

  144Molecular estimates are consistently older: For discussion of the discrepancies between molecular and fossil-based ages for branching points over 400 million years old and for the early radiations of birds and mammals, Cooper and Fortey (1999); Smith and Peterson (2002). Note, however, that the discrepancies between the fossil record and molecular age estimates may be lessening for the bird and mammal cases with the discovery of new fossils (Clarke et al. 2005) and the use of more sophisticated molecular dating approaches (Meredith et al. 2011b).

  148Three estuarine crocodiles: Campbell et al. (2010). On fossils indicating multiple crocodile oceanic dispersals, Brochu (2001). For the molecular genetic study indicating crocodile transatlantic dispersal, Meredith et al. (2011a).

  Box: The Molecular Clock and the Pitfalls of Extremism

  142Fossil-calibrated clock of cichlid fishes: Azuma et al. (2008).

  142A 2004 study on amphisbaenians: Macey et al. (2004). On amphisbaenians not being an early branch in the lizard evolutionary tree, Vidal and Hedges (2009). On the oldest lizard fossils being less than 200 million years old, Evans (2003).

  143Fragmentation events should be used as calibration points: Heads (2005, 2011). On the tenrec example using assumed vicariance for calibration, Heads (2005). On the oldest placental mammal fossils, O’Leary et al. (2013). Heads has suggested equally implausible calibration points for several other groups. One involving primates (Heads 2010) would push the origin of that order back to 180 million years ago, some 115 million years before the earliest known placental mammal fossil. For a rebuttal of this primate case, see Goswami and Upchurch (2010).

  Chapter Seven: The Green Web

  151Monolithic remnants of a sandstone plateau: On the geological history of tepuis, Briceño et al. (1990). On the environment on tepui summits and the possibility of being stranded on them, Jackson (1985).

  152Areas populated by relicts: Malatesta (1996).

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p; 152“Remnants of an ancient biota . . . ”: Funk and McDiarmid (1988), 48.

  152“They are like a place where time stopped”: Handwerk (2004).

  152Carnivorous plants . . . are a dime a dozen: On the connection between carnivorous tepui plants and nutrient-poor soil, Butschi (1989). On the protozoan-trapping plant, Barthlott et al. (1998).

  153Their seeds don’t float: For the facts that Drosera seeds do not float and are killed by saltwater and the suggestion that Drosera might have dispersed from Australia to South America as seeds stuck to the feet of a bird, email from Andreas Fleischmann to the author, January 19, 2010.

  153Related species tend to occur near each other: For the “geographic structure” for Drosera and the placement of some North American species with a South American group, Rivadavia et al. (2003).

  153The weirdest exception to the rule: For the study of Drosera meristocaulis, including both the DNA and anatomical work, Rivadavia et al. (2012).

  155“I grew up all over the West . . . ” and Matt Lavin’s personal and professional background: Lavin, telephone conversation with the author, September 16, 2009.

  157For a group called the dalbergioid legumes: Lavin et al. (2000). The quotation “relatively few instances where over-water . . . ” is from Lavin et al. (2000), 461.

  157“Oh definitely, definitely” and “Man these things have to be old . . . ”: Lavin, telephone conversation with the author, September 16, 2009.

  157, 158“We tried to bias ’em . . . ” and “ . . . We could hardly make them old . . . ”: Lavin, telephone conversation with the author, September 16, 2009.

  158An extensive molecular dating study: Lavin et al. (2004).

  158“A long slow death”: Lavin, telephone conversation with the author, September 16, 2009. Lavin also discussed the informal talk on Araucariaceae in this conversation.

  159A massive flood of evidence: Some recent papers (mostly review articles) collectively indicating hundreds of instances of oceanic dispersal by plants are Renner (2004a, b); Pennington et al. (2004); Pennington and Dick (2004); Yoder and Nowak (2006); Sanmartín et al. (2007); Crisp et al. (2009); Wallis and Trewick (2009); Christenhusz and Chase (2013). For the Cucurbitaceae study, Schaefer et al. (2009).