Colonization and diversification: towards a phylogeographic synthesis for the Canary Islands

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         Colonization and diversification:
       towards a phylogeographic synthesis
              for the Canary Islands
       Carlos Juan, Brent C. Emerson, Pedro Oromí and Godfrey M. Hewitt

                                                                                                      Biogeography and ecology

      T
            he Canary Islands are his-                  Recently, the Canary Islands have become
            torically and biologically                   a focus for studies of the colonization and  The Canary Islands have a sub-
            of particular interest. Pliny                the diversification of different organisms.  tropical climate; temperatures
      the Elder heard about ‘Canaria,                     Some authors have considered Canarian       are warm and show little seasonal
      so called from the multitude of                      endemisms as relicts of Tertiary origin,   variation. The climate is strongly
      dogs (canes) of great size’,                      but new molecular data suggest a general      influenced by the humid trade
      through an expedition (c. 40 BC)                 pattern of continental dispersion followed by  winds from the northeast, which,
      to the islands by Juba II, King                   in situ speciation. Recent phylogeographic    in combination with the altitude of
      of Mauritania. The island of                      studies are revealing variants of the simple  the volcanoes and the drier north-
      El Hierro was chosen by Ptolemy                     stepping-stone colonization model that      west winds blowing at higher lev-
      as the prime meridian of longi-                    seems to hold for many Hawaiian groups.      els, produce an inversion zone
      tude because it was the most                          Many factors can generate deviations      and marked vegetational zones
      westerly place known in his                             from such a pattern: the stochastic     (Box 2). Some of the most pecu-
      time. The aboriginal inhabitants                        nature of colonization, competitive     liar and interesting habitats in the
      of the Canary Islands were the                       exclusion, phylogenetic constraints on     Canary Islands are those pro-
      Guanches, probably of Berber                             adaptive evolution and extinction.     duced by the volcanic terrains,
      origin1,2, who were conquered by                    An understanding of island colonization     which are inhabited by special-
      the Spanish in the 15th century.                   and diversification can best be developed    ized animals9 (Box 3).
      Following this, the Canaries be-                      from an ecosystem level synthesis as          The Canarian fauna and flora,
      came an important base for sea                      more data for the Canarian archipelago      which is related to that of Madeira
      journeys to the Americas and                                       come to hand.                and, to some extent, to that of the
      Christopher Columbus replen-                                                                    Azores and the Cape Verde Is-
      ished all four of his westbound                                                                 lands, has affinities with the Medi-
      fleets at the islands.                     Carlos Juan is at the Departamento de Biologia,      terranean region, although some
                                                          Universitat de les Illes Balears,           elements are related to more re-
                                                         07071 Palma de Mallorca, Spain
      The Canary archipelago                                  (dbacjc8@clust.uib.es);
                                                                                                      mote regions [Ceropegia (Asclepi-
      The Canary Islands are situated in          Brent Emerson and Godfrey Hewitt are at the         adaceae) and Sideroxylon (Sapo-
      the northeast Atlantic ocean be-                    School of Biological Sciences,              taceae) to East Africa; Apollonias
      tween 278379 and 298259N, and              University of East Anglia, Norwich, UK NR4 7TJ       (Lauraceae) to India; Bystropogon
      138209 and 188109W (Box 1). The           (b.emerson@uea.ac.uk, g.hewitt@uea.ac.uk); and        (Lamiaceae) to South America;
      nearest island (Fuerteventura) to          Pedro Oromí is at the Departamento de Biología       Picconia (Oleaceae) to Australia;
      the continent lies approximately Animal, Facultad de Biología, Universidad de La Laguna, Vanessa indica (Nymphalidae) and
      110 km off the northwest African                      38205 La Laguna, Tenerife,                Cyclyrius webbianus (Lycaenidae)
      mainland (Cape Juby) and the                             Spain (poromi@ull.es).                 to Asia; Danaus spp. (Nymphali-
      most distant island (La Palma)                                                                  dae) to America and Ethiopian
      lies 460 km off the mainland. The                                                               Africa, etc.]. Given the prevailing
      archipelago has seven islets, and                                                               winds and the sea currents, two
      seven main islands aligned from east to west: Lanzarote, plausible sources of colonizers are neighbouring North
      Fuerteventura, Gran Canaria, Tenerife, La Gomera, La Palma Africa and the Iberian Peninsula. Endemism is high in the
      and El Hierro.                                                        archipelago: about 27% of the approximately 1000 native
          All the islands were formed in the past 20 million years vascular plant species and 50% of the terrestrial inverte-
      (Ma) by volcanic eruptions. The central and western brate fauna (c. 6500 species) are endemic. Amphibians were
      islands exceed 1400 m at the highest volcanoes, with Teide absent from the original fauna; only one snake has been
      on Tenerife rising to 3718 m. The geological history of the recorded (already extinct), and apart from bats only five
      islands is well documented3–6 (Box 1), providing a known mammals were present – two shrews and three rodents
      temporal sequence for the origin of the islands and thus for (although rodents are now extinct).
      their availability for colonization by diverse biota. The                   Some notable invertebrate families that occur on the
      Pacific Hawaiian Islands and the Atlantic Canaries have mainland are absent, for example, from the order Coleop-
      similarities, but also have distinctive differences, with the tera (Lucanidae, Geotrupidae and Lampyridae) and from
      Atlantic Canaries having longer life, more complex vol- the order Hemiptera (Cicadidae, Naucoridae and Nepidae).
      canic evolution and close proximity to the continent. In some instances complete orders are absent, such as the
      Island formation is controversial; the two main competing Plecoptera and Phasmoptera. Other orders were originally
      theories being a ‘hot spot’ origin and ‘propagating fracture’ absent but have been introduced, such as Scorpiones,
      from the Atlas mountains7,8 (Box 1).                                  Symphyla and Embioptera.

104    0169-5347/00/$ – see front matter © 2000 Elsevier Science Ltd. All rights reserved.   PII: S0169-5347(99)01776-0   TREE vol. 15, no. 3 March 2000
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    Examples of diversifi-
cation within the archipelago                                     Box 1. Volcanism and the age of the islands
can also be found among             The Canary archipelago originated from volcanic activity that began during the Oligocene [24.6–38 million years
vertebrates, notably geckos         (Ma)]; the islands began to emerge during the past 21 Ma (Ref. 5).
(Tarentola), lizards (Gallotia)
and skinks (Chalcides). Incipi-
ent speciation processes (sub-                                                                                           Lanzarote (15.5)
species divergence) are oc-         La Palma (2)
curring in some birds, such
as finches (Fringilla coelebs)                                        Tenerife (11.6)
and blue tits (Parus caeruleus).
But, by far the most striking
cases of diversification are                                                             Gran Canaria (14–16)
among invertebrates, because            La Gomera (10)
of either geographic isolation
or adaptation to diverse                                                                                                         Fuerteventura (20)
niches. Some of the groups                         El Hierro (1)
(number of endemic species
in parenthesis) are: Gastro-                                                                                                   Trends in Ecology & Evolution
poda10 – Napaeus (50) and
                                                                                                                                               (Online: Fig. I)
Hemicycla (35); Araneae11
(M.A. Arnedo, PhD thesis,           The ages of subaerial shields (shown in parentheses) decrease from east to west from 20 Ma for Fuerteventura
Universitat de Barcelona,           to less than 1 Ma for El Hierro. Scale bar 5 100 km. It has been proposed that the archipelago is due to a mantle
1998) – Spermophorides (22),        plume or hot spot with a slow plate motion, giving the longer life of Atlantic volcanoes compared with the Pacific
                                    ones8. An alternative explanation relates the island formation to a fracture propagating from the Atlas mountains
Dysdera (44) and Oecobius           with irregular velocity7. Another less supported theory is that of the uplifted blocks, based on the presence of
(34); Isopoda – Porcellio (18);     mixed plutonic rocks and pillow lavas at as much as 1000 m above sea level6. Several periods of volcanic activ-
Diplopoda12 – Dolichoiulus          ity and quiescence have occurred in the past 20 Ma on each island, with the exception of La Gomera4 – the only
(46); Collembola13 – Pholso-        island in the archipelago without major activity for the past 4 Ma (although the last residual activity could be as
mides (16); Hemiptera14 –           recent as 2 Ma).
Cyphopterum (24) and Erythro-
neura (23); Coleoptera15,16 –
Calathus (24), Cardiophorus (31), Attalus (51), Tarphius (30),
Hegeter (23), Nesotes (20), Laparocerus (66) and Acalles (18).                                 Box 2. Vegetational zones
                                                                                 The central (Gran Canaria and Tenerife) and western (La Gomera, La Palma
Colonization pathways and the stepping-stone                                     and El Hierro) islands have high volcanoes that for most of the year have
model                                                                            cloud banks at around 1000 m on the windward slopes. These clouds are
DNA data are better suited for a phylogenetic tree than                          caused by the upper hot dry air and by the lower humid trade winds. As a
                                                                                 result, five vegetation zones can be distinguished: (1) arid subtropical scrub
morphology when interpreted in terms of dispersal (i.e.                          up to 250 m; (2) humid and semi-arid subtropical scrub, and woods from
colonization sequence)17. A morphological phylogenetic                           250 to 600 m altitude; (3) humid laurel forest in the cloud belt from
tree is constrained by the ecogenetic adaptation to current                      600–1000 m; (4) humid to dry temperate pine forest from 1000–2000 m;
and to recent selective pressures, but these are unlikely to                     and (5) dry subalpine scrub over 2000 m.
confound a DNA-based phylogeny. Recently, molecular
phylogenies have been obtained for Canarian lizards17–22,                                                       3700
skinks23, geckos24, beetles25–31, butterflies32, Drosophila33,34,
cockroaches (I. Izquierdo, PhD thesis, Universidad de La
Laguna, Tenerife, 1997), bees35–37, spiders (M.A. Arnedo, PhD                       SW                                                          NE
thesis)38, mites39 and plants40–47. Most of these studies have                                               Subalpine
made use of mitochondrial or chloroplast DNA sequences                                                         scrub
as a marker for inferring dispersal events between islands.                                      2200
In some of these taxa, the predominant pattern is similar to                                                                    2000
the one found for Hawaiian organisms; a stepwise coloniz-                                                       Pine
                                                                                                               forest                            Cloud layer
ation sequence from older to younger islands in the chain.
                                                                                                                                        1200
However, this simple pattern can be complicated by several                             1100
                                                                                                                        Laurel forest
factors. Back colonization, recent colonization, within-island
differentiation, adaptation and extinction are some of the                          600     Semiarid to humid woods                            600          Trade
                                                                                                                                                            winds
historical events that confound a simple ‘island colonized                                         Arid to semiarid scrub
                                                                                                                                                    300
as it emerges’ pattern.
    Thorpe et al.17 have proposed two ways of interpreting a                                                                           Trends in Ecology & Evolution
tree in terms of colonization sequence, taking into account
                                                                                                                                                        (Online: Fig. I)
biogeographical and genetic data. One method uses tree
topology and geography, based on the increased probability                          The eastern islands are influenced less by trade winds because of their
                                                                                 lower altitude and because rainfall is also scarcer owing to their geographic
of an island being colonized by founders from a closer island                    situation. An arid scrub with many xerophilous African plants dominates
than from a distant one. The other method of determining                         almost everywhere. Only on the top of a few mountains (Jandia in
the polarity of dispersal uses tree topology plus branch                         Fuerteventura and Famara in Lanzarote) can local hygrophilous endemisms
length. This method relies on the proposal that there is an                      be found. These are most probably the remains of more humid woods
                                                                                 occurring before the glaciations.
acceleration of divergence caused by a founder effect, thus
allowing discrimination between colonist and ancestor.

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                                                                                    model. Recent studies of Calathus31, a genus of ground
               Box 3. Lava flow and lava-tube habitat                               beetles, have also revealed a phylogeographic pattern
 The recent, barren lava flows are inhabited by ‘lavicolous’ species, which         that conflicts with a stepping-stone colonization model.
 are adapted to extreme conditions (drought, exposure to sun, temperature           Calathus has colonized the Canary Islands at least twice
 changes and no primary production)9. They feed on biological fall-out and          and probably three times (mtDNA COI and COII sequence
 are quickly replaced by competitors as soon as primary succession pro-             data). The most recent colonization from the mainland
 vides the lava with soil and plants (a few hundred years). The underground
 environment is also peculiar in volcanic, oceanic islands, where basaltic
                                                                                    has occurred on the oldest islands of Fuerteventura and
 flows prevail. The existing caves are lava tubes with the typical environ-         Lanzarote.
 mental conditions of caves (humidity, darkness and scarce food), but are
 highly different in other features49. Unlike karstic caves, lava tubes are shal-   Within-island phylogeography and volcanism
 low, with roots inside, little running water and few ponds. The formation is       Once an island has been colonized, within island differ-
 quick and succession usually takes place upwards instead of downwards,
 with troglobites moving closer to the surface as the lava ages and shallow         entiation is facilitated by vicariance events produced by
 passages become more isolated from the surface climate. This contrasts             lava flows and by local extinctions followed by recolo-
 with karstic caves where hypogean communities tend to extend deeper                nization. This has been documented in many Hawaiian
 down as time goes by. Succession in lava flows and volcanic caves is               biota48. Across the islands of Fuerteventura and Lanzarote,
 closely related. The timespan during which a lava tube provides a suitable
 environment for particular adapted life forms is longer than in lavas, but
                                                                                    subaerial volcanic activity has been almost continuous
 much shorter than in karstic caves. Collapsing and silting limit the tube          in the past 20–22 Ma (Ref. 5). The current top layers
 duration from 20 000 to 500 000 years. However, troglobites in the Canary          of the islands are the result of two distinct cycles, one
 Islands are not really fugitive species because the lava tubes are not their       ranging from 21 to 12 Ma, and another ranging from 6 Ma
 only habitat, they also occur in the cracks and voids of the bedrock and           to prehistoric and historic eruptions. This volcanic activ-
 in the mesocavernous shallow stratum, in medium and old volcanic ter-
 rains. The variety of underground habitats, geological history and under-          ity has resulted in a SSW (oldest) to NNE (youngest) age
 ground barriers has led to the evolution of a rich troglobitic fauna in most of    gradient for the surface terrains of Fuerteventura and
 the islands.                                                                       Lanzarote. This geological age gradient is consistent with
                                                                                    the mitochondrial genealogy (mtDNA COI sequence data)
                                                                                    found for the endemic Hegeter politus (Coleoptera, Tene-
             The phylogeographic hypothesis for the lizard of the                   brionidae)30. This can be explained by an ancestral popu-
         western Canary Islands, Gallotia galloti17–22, based upon                  lation in the south, which colonized in a northerly direction
         recent studies using different DNA markers, is compatible                  following the progressive northward cessation of volcanic
         with the time of emergence and the sequence of island for-                 activity.
         mation. Gallotia galloti appears to have dispersed from                         A repeated phylogeographic pattern is found in di-
         Tenerife along two independent pathways: one from north                    verse organisms on the island of Tenerife. Gallotia lizards,
         Tenerife to La Palma, and the other from south Tenerife                    Chalcides skinks, Pimelia, Calathus and Eutrichopus beetles,
         to La Gomera and to El Hierro. The sister group relation-                  Steganecarus mites, Dysdera spiders and Loboptera cock-
         ship of the western G. galloti lineage to either G. stehlini               roaches all possess vicariant sister taxa affiliated with the
         (Gran Canaria) or the eastern G. atlantica (Fuerteventura                  Anaga and Teno massifs. The level of divergence between
         and Lanzarote) is less robust21,22. Also compatible with the               these sister lineages varies considerably among the differ-
         stepping-stone model are the darkling beetles of the gen-                  ent taxa and molecular markers used, but, in all cases, this
         era Pimelia and Hegeter26–30. Both show colonization pat-                  pattern can be related to the disjunct volcanic evolution of
         terns that are essentially compatible with a stepwise dis-                 the island3. The relatively recent volcanic activity (less
         persal from older islands in the east to younger islands in                than 2 Ma) producing the Pico Viejo and Teide eruptions,
         the west. A back colonization probably occurred from                       generated massive lava flows that joined the previously
         Tenerife to Gran Canaria for Pimelia. The phylogenetic                     separate massifs of Anaga in the northeast and Teno in
         relationships of brimstone butterflies32 (genus Gonepteryx)                the northwest. These geologically old massifs (.4.5 Ma)
         point to a North African ancestry for the Canarian taxa                    have not been covered by recent lava flows (Box 4). The
         (three species) and subsequent within-archipelago disper-                  present-day distributions and phylogeographies of many
         sals from Tenerife to La Gomera and Tenerife to La Palma.                  organisms in Tenerife can be related to the recent connec-
         The colonization of the archipelago by Drosophila subob-                   tion of the massifs. For example, the beetle Pimelia shows
         scura is also consistent with a stepping-stone model of                    two distinct mtDNA and ITS (internal transcribed spacer)
         directional east–west migration33,34.                                      lineages associated with the west and the east of Tenerife,
             The phylogeography of the endemic skinks of the genus                  which probably originated on Teno and Anaga, respectively,
         Chalcides23 is only partially concordant with a stepping-                  and spread over the central regions after the connective
         stone colonization. A relatively recent dispersal from La                  eruptions28.
         Gomera to El Hierro is apparently the only colonization                         The Gran Canarian skink Chalcides sexlineatus shows
         following the ages of emergence of the islands. More                       considerable within-island morphological variation that
         ancient colonizations between La Gomera and Tenerife,                      is, in part, coincident with genetic differentiation23. Simi-
         and between Gran Canaria and Tenerife or La Gomera can                     lar morphological and genetic differentiation is present
         be deduced, but the relationship of those clades with the                  in Tarentola geckos from Gran Canaria24. These phylo-
         Fuerteventuran Chalcides simonyi lineage or with the North                 geographic patterns are probably related to vicariance
         African outgroups is unclear.                                              caused by the last volcanic cycle on the island approxi-
             For the genus Tarentola24 (Gekkonidae), mitochondrial                  mately 2.8 Ma. There is a distinct possibility of mass
         12S and cytochrome b sequences indicate several inde-                      extinctions about 3.4–4.5 Ma on Gran Canaria caused by
         pendent colonization events from the continent. The phy-                   the violent emission of volcanic agglomerates over a great
         logeny shows higher genetic divergences compared with                      part of the island. This could explain some of the back
         Gallotia and Chalcides. The greater age of the Tarentola                   and relatively recent colonizations of Gran Canaria shown
         group could have involved more extinction followed by                      by the phylogeographies of Dysdera, Calathus, Tarphius
         replacement, generating a contemporary phylogenetic pat-                   (B. Emerson, unpublished), and possibly Chalcides and
         tern that is not consistent with a simple stepping-stone                   Tarentola species.

106                                                                                                                 TREE vol. 15, no. 3 March 2000
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Radiations, habitat shifts and adaptations
Oceanic islands show considerable habitat diversity, pro-                           Box 4. Volcanic evolution of Tenerife
duced by topology and humidity gradients, which, com-                                                                          Anaga
bined with their isolation, produces lower competition
and empty ecological niches. This provides a template for                                                                      5.8 Ma
the evolution of species radiations. For example, the plant                                       370–650 ka
genus Argyranthemum has radiated into virtually all habi-                             170 ka
tats of the Atlantic islands42–47. In the Canarian archipelago,
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      its own characteristic fauna, general patterns among islands                    13 Fjellberg, A. (1993) Revision of European and North African
      are seldom apparent within individual genera. Stochastic-                          Folsomides Stach with special emphasis on the Canarian fauna
      ity must be seen as a primary factor in determining species                        (Collembola: Isotomidae). Entomol. Scand. 23, 453–473
      compositions on the islands – you cannot speciate if you                        14 Lindberg, H. (1953) Hemiptera Insularum Canariensium. Comm. Biol.
                                                                                         14, 1–304
      are not there. Even if colonization occurs, subsequent evo-
                                                                                      15 Dajoz, R. (1977) Faune de l’Europe et du bassin méditerranéen, 8.
      lution will be contingent upon the floral and faunal com-                          Coléoptères Colydiidae et Anommatidae Paléarctiques, pp. 1–275,
      position of the colonized island. All groups on the archi-                         Masson, Paris
      pelago have survived the turmoils of volcanism and have                         16 Lindberg, H. and Lindberg, H. (1958) Coleoptera Insularum
      responded in different ways to the presence of diverse                             canariensium. 1. Aglycyderidae und curculionidae. Comm. Biol. 17,
      habitats. This response would typically have depended on                           1–97
      the fundamental niche of a colonizing species (i.e. ecologi-                    17 Thorpe, R.S. et al. (1994) DNA evolution and colonization sequence of
      cal requirements) and the competitive presence of other                            island lizards in relation to geological history: mtDNA, RFLP,
      species within that niche. The potential for both rapid mor-                       cytochrome B, cytochrome oxidase, 12S rRNA and nuclear RAPD
      phological change and convergent evolution further com-                            analysis. Evolution 48, 230–240
      plicates the picture, particularly within some invertebrate                     18 Thorpe, R.S. et al. (1993) Population evolution of western Canary
                                                                                         Island lizards (Gallotia galloti): 4-base endonuclease restriction
      groups (e.g. the genus Nesotes; D. Rees, unpublished). How-
                                                                                         fragment length polymorphisms of mitochondrial DNA. Biol. J. Linn.
      ever, the relative effects of these variables can be truly as-                     Soc. 49, 219–227
      sessed only at the level of the ecosystem. Phylogenetic                         19 Thorpe, R.S. et al. (1996) Matrix correspondence tests on the DNA
      data from DNA studies now allow us to assess the process                           phylogeny of the Tenerife Lacertid elucidate both historical causes and
      of diversification within genera. Continued efforts to obtain                      morphological adaptation. Syst. Biol. 45, 335–343
      phylogenetic data across a diversity of taxa, from a diver-                     20 Thorpe, R.S. and Malhotra, A. (1998) Molecular and morphological
      sity of habitats, in conjunction with geological and ecological                    evolution within small islands. In Evolution on Islands (Grant, P.R.,
      data, would seem the best way to evaluate diversification                          ed.), pp. 67–82, Oxford University Press
      on the Canary Islands and on other island systems.                              21 González, P. et al. (1996) Phylogenetic relationships of the Canary
                                                                                         Islands endemic lizard genus Gallotia (Sauria: Lacertidae), inferred
                                                                                         from mitochondrial DNA sequences. Mol. Phylog. Evol. 6, 63–71
      Acknowledgements                                                                22 Rando, J.C. et al. (1997) Phylogenetic relationships of the Canary
      We wish to thank Pablo Oromí for producing the figure of                           Islands endemic lizard genus Gallotia inferred from mitochondrial
      volcanic evolution on Tenerife. We are also grateful for                           DNA sequences: incorporation of a new subspecies. Mol. Phylog. Evol.
      comments on this article by three anonymous referees. This                         8, 114–116
      work has been supported by NERC and EU grants (G.M.H.)                          23 Brown, R.P. and Pestano, J. (1998) Phylogeography of skinks
      and by the Spanish DGICYT PB 96/0090 (P.O.).                                       (Chalcides) in the Canary Islands inferred from mitochondrial DNA
                                                                                         sequences. Mol. Ecol. 7, 1183–1191
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                   Recreating ancestral proteins
                           Belinda S.W. Chang and Michael J. Donoghue

M
        olecular evolution leaves                                                            lysozyme should be evident in a
                                                 Tracing the history of molecular changes using
        behind a trail of amino acid               phylogenetic methods can provide powerful phylogeny of primate lysozyme
        substitutions potentially                insights into how and why molecules work thesequences, on the lineage leading
rich in information about mol-                                                               to colobine monkeys. By inferring
                                                    way they do. It is now possible to recreate
ecular function. Tracing changes                                                             and comparing ancestral lysozyme
                                                   inferred ancestral proteins in the laboratory
in protein structure along the                                                               sequences, Messier and Stewart1
                                                    and study the function of these molecules.
branches of a phylogenetic tree                                                              were able to demonstrate adap-
                                                   This provides a unique opportunity to study
can provide important insights                     the paths and the mechanisms of functionaltive change in this lineage. Specifi-
into molecular function, and the                       change during molecular evolution.    cally, they estimated the numbers
role of selection in shaping the                     What insights have already emerged from of nonsynonymous (dN) and syn-
relationship between molecular                         such phylogenetic studies of protein  onymous (dS) substitutions along
structure and function. Recreation                     evolution and function, what are the  each branch using Li’s method2,
of inferred ancestral proteins                      impediments to progress and what are the and found a dN/dS ratio much
using gene synthesis and protein                             prospects for the future?       greater than one in the lineage
expression methods, whose bio-                                                               leading to the colobine monkeys
chemical functions can then be                                                               (Fig. 1). This analysis also re-
directly measured in vitro, pro-          Belinda S.W. Chang and Michael J. Donoghue are     vealed a previously unsuspected
vides a powerful approach to this        at the Dept of Organismic and Evolutionary Biology, episode of positive selection in
                                           Harvard University Herbaria, 22 Divinity Avenue,
problem.                                             Cambridge, MA 02138, USA
                                                                                             the ancestral hominoid lineage.
                                                     (chang24@oeb.harvard.edu;                   Subsequently, Yang3 devel-
Phylogenies, molecular                             mdonoghue@oeb.harvard.edu).               oped a more rigorous statistical
function and natural selection                                                               approach to this problem, using
Phylogenies can be used in several                                                           a codon-based maximum likeli-
ways to infer the effects of natural                                                         hood model of evolution4 to de-
selection on molecular function.                                                             tect elevated dN/dS ratios along
Because directional selection is known to elevate the ratio lineages in a phylogeny. Yang’s method3 uses likelihood
of nonsynonymous to synonymous nucleotide substitu- ratio tests to compare the performance of different likeli-
tions, this ratio can be used as a tool to detect lineages in a hood models, and to determine if the dN/dS ratio for the lin-
molecular phylogeny along which selection has occurred. eage of interest is elevated compared with other lineages
Cows and langur monkeys convergently evolved foregut in the phylogeny. This approach avoids using reconstructed
fermentation as a mechanism to digest the large amounts ancestral states as if these were actual observations in the
of plant material in their diets; a key component of this calculations of nonsynonymous and synonymous substi-
involved the recruitment of the lysozyme enzyme to digest tution rates. When applied to the primate lysozyme data,
foregut bacteria. Selection for this specialized function of this method showed strong evidence for positive selection

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