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

he Canary Islands are his- Recently, the Canary Islands have become Biogeography and ecology torically and biologically a focus for studies of the colonization and The Canary Islands have a sub- Tof 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 stepping-stone colonization model that west winds blowing at higher lev- as the 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- , 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 journeys to the Americas and come to hand. and, to some extent, to that of the Christopher Columbus replen- 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- The Canary archipelago 07071 Palma de Mallorca, Ceropegia ([email protected]); mote regions [ (Asclepi- The Canary Islands are situated in Brent Emerson and Godfrey Hewitt are at the adaceae) and Sideroxylon (Sapo- the northeast be- School of Biological Sciences, taceae) to East ; Apollonias tween 27Њ37Ј and 29Њ25ЈN, and University of East Anglia, Norwich, UK NR4 7TJ (Lauraceae) to India; Bystropogon 13Њ20Ј and 18Њ10ЈW (Box 1). The ([email protected], [email protected]); and (Lamiaceae) to South America; nearest island () to Pedro Oromí is at the Departamento de Biología Picconia (Oleaceae) to Australia; the continent lies approximately , Facultad de Biología, Universidad de La Laguna, Vanessa indica (Nymphalidae) and 110 km off the northwest African 38205 La Laguna, , Cyclyrius webbianus (Lycaenidae) mainland (Cape Juby) and the Spain ([email protected]). to Asia; Danaus spp. (Nymphali- most distant island () 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: , plausible sources of colonizers are neighbouring North Fuerteventura, , Tenerife, , 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.

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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 (14Ð16) 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 Hemicycla (35); Araneae11 (Online: Fig. I) (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 ϭ 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 8 Oecobius ones . An alternative explanation relates the island formation to a fracture propagating from the Atlas mountains (44) and 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 ation sequence from older to younger islands in the chain. forest Cloud layer 1200 However, this simple pattern can be complicated by several 1100 factors. Back colonization, recent colonization, within-island Laurel forest differentiation, adaptation and extinction are some of the 600 Semiarid to humid woods 600 Trade winds historical events that confound a simple ‘island colonized 300 Arid to semiarid scrub 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 biogeographical and genetic data. One method uses tree (Online: Fig. I) topology and , 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 acceleration of divergence caused by a founder effect, thus occurring before the glaciations. 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 (, 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 (Ͼ4.5 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.

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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 370Ð650 ka genus Argyranthemum has radiated into virtually all habi- 170 ka tats of the Atlantic islands42–47. In the Canarian archipelago, <2 Ma two major clades of this genus can be distinguished by DNA markers. One of the groupings is formed by the taxa La occurring in arid–subarid zones (high altitude desert, pine Orotava Güímar forest, arid lowland scrub and coastal desert), but the 7.4 Ma Teno other clade comprises species in zones influenced by the ? ka humid trade winds (laurel forest and humid lowland scrub). Las Cañadas Inter-island colonization of taxa pre-adapted to particular microhabitats, rather than to radiation within each island, <2 Ma <2 Ma seems to have been a significant factor in the evolution of 11.6 Argyranthemum and other Canarian plants. Roque Ma Recently, several plant genera have been studied using del Conde molecular markers, such as ITS and chloroplast sequences or RFLPs. The genera Sonchus40 (Asteraceae) and Echium41 (Boraginaceae) have experienced rapid radiations in the Trends in Ecology & Evolution Canaries following single colonization events in Gran Canaria or Tenerife in the late Miocene or early Pliocene. (Online: Fig. I) Colonization patterns for Argyranthemum (Asteraceae) are Shaded areas are the oldest terrains, which are considered independent less clear, but morphological, phytochemical and molecu- former islands, with a possible connection between Teno and Roque lar data suggest that some elements of the Canarian flora del Conde. After a period of quiescence, volcanic activity resumed approxi- are relictual42. Also, there is evidence of extensive inter- mately 2.0 Ma with the development of the central part of Tenerife. island dispersal between similar ecological zones, of hy- Approximately 1.0 Ma, the formation of the Cordillera Dorsal began, joining the older massifs that were not covered by the new lavas. bridization in the Macaronesian island flora and even of More recent investigations50 have demonstrated that huge landslides back-colonization to the continent by island taxa. ‘Insular have occurred in Tenerife owing to instability of steep volcanic massifs. woodiness’ has been identified in numerous angiosperm These landslides are shown (indicated by arrows) with the approximate families. The problem of ascertaining the polarity of per- ages (unknown for Güímar) deduced from the dating of the rocks lying on ennial woodiness of plants in the Macaronesian Islands the sea floor in front of each volcanic massif. Valley and Güímar has been examined in both Echium and Sonchus (ITS se- Valley remained as they were just after the landslides, but the Las Cañadas 40,41 landslide was partially refilled with lava from the Teide . These quences) . Both studies conclude that the most plaus- recent landslides would have further promoted the isolation between Teno ible explanation is a founding colonization of the Canary and Anaga for many species, helping to explain the absence of some Ana- Islands from a continental herbaceous ancestor followed gan species in Teno and vice versa. This is particularly true for the Las by intense speciation. Cañadas and the La Orotava landslides, which disrupted the humid forest Adaptation to hypogean life in the volcanic tubes is connection between Teno and Anaga along the northern slopes. exemplified by the spider genus Dysdera and the cock- roach genus Loboptera. Morphological and molecular data suggest two independent Dysdera colonizations from the In the Canarian Calathus ground beetles, there is no re- continent to the eastern islands, a third colonization re- lationship between the age of colonization and speciation31. sulting in a central–western islands lineage, and a possible For example, seven species occur in the small island of fourth colonization for D. unguimmanis (to be confirmed La Gomera, but only three occur in the topologically simi- when more data are available) (M.A. Arnedo, PhD thesis). lar, but much larger, island of Gran Canaria. Habitat de- Eight of the 43 species of Dysdera are found exclusively in struction on Gran Canaria could account, in part, for these lava tubes, most of them on the island of Tenerife38. These differences. However, genetic data point to recent diversi- troglomorphic taxa are not relictual species (with the poss- fication rather than the presence of relict species in Gran ible exception of D. unguimmanis, by far the most adapted Canaria. The ecological data available for this genus sup- species), they share the same ancestor with the epigean port the idea that recent speciation on La Gomera has been species, and switches to life in the caves have occurred promoted mainly by marginal isolation or niche specializ- periodically throughout the evolutionary history of the ation into laurel forest microhabitats from a generalist genus. Only two of the troglomorphic species, D. hernandezi ancestor. At the population level, morphological differenti- and D. esquiveli, are monophyletic. ation of the Tenerife and Gran Canarian skinks (Chalcides Different degrees of adaptation to life in caves are also viridanus and C. sexlineatus) is not consistent with vicari- present in the 11 known taxa of cockroaches of the genus ance or isolation-by-distance models exclusively23. The two Loboptera (I. Izquierdo, PhD thesis). These species occur in islands show similar mesic/xeric heterogeneity and the pat- Tenerife, La Palma and El Hierro, and show colonization tern of geographical variation in Chalcides is better ex- patterns strictly compatible with the sequential emer- plained by differential selection along an aridity gradient. gence of those islands. All but one of the Canarian species of the genus Loboptera show some degree of adaptation to Conclusion the hypogean habitat and most of them are strict troglo- As more and more DNA-based phylogeographic studies are bites. It appears that the colonization and radiation on the undertaken on the Canary Islands, a picture is emerging of an Canaries by epigean ancestors of the present-day Loboptera ecosystem that is perhaps best seen as a mosaic. Although was followed by local speciation underground49. the archipelago can be viewed as a delineable entity with

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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. are not there. Even if colonization occurs, subsequent evo- 14, 1–304 15 lution will be contingent upon the floral and faunal com- Dajoz, R. (1977) Faune de l’Europe et du bassin méditerranéen, 8. 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 groups (e.g. the genus Nesotes; D. Rees, unpublished). How- Island lizards (Gallotia galloti): 4-base endonuclease restriction ever, the relative effects of these variables can be truly as- fragment length polymorphisms of mitochondrial DNA. Biol. J. Linn. 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.). 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Recreating ancestral proteins Belinda S.W. Chang and Michael J. Donoghue

olecular evolution leaves Tracing the history of molecular changes using lysozyme should be evident in a behind a trail of amino acid phylogenetic methods can provide powerful phylogeny of primate lysozyme Msubstitutions potentially insights into how and why molecules work the sequences, on the lineage leading rich in information about mol- way they do. It is now possible to recreate to colobine monkeys. By inferring ecular function. Tracing changes inferred ancestral proteins in the laboratory and comparing ancestral lysozyme in protein structure along the and study the function of these molecules. sequences, Messier and Stewart1 branches of a phylogenetic tree This provides a unique opportunity to study were able to demonstrate adap- can provide important insights the paths and the mechanisms of functional tive 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. 3 ([email protected]; Subsequently, Yang devel- Phylogenies, molecular [email protected]). 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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