- Email: [email protected]
Moving primate genomics beyond the chimpanzee genome
Review
TRENDS in Genetics Vol.21 No.9 September 2005
Moving primate genomics beyond the chimpanzee genome Morris Goodman1,2, Lawrence I. Grossman2 and Derek E. Wildman2,3 1
Department of Anatomy and Cell Biology, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, Michigan 48201 USA 2 Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 259 Mack Ave, Detroit, MI 48201, USA 3 Services in Support of the Perinatology Research Branch, National Institute of Child Health and Development/NIH/DHHS, Detroit, MI 48201, USA
The comparative DNA sequence data that already exist on individual genomic loci depict the phylogenetic relationships of nearly all extant primate genera. Such a phylogenetic representation of the primates, validated by many sequenced primate genomes, and encompassing the full adaptive diversity of the order, is a prerequisite for identifying the genetic basis of humankind, and for testing the proposed human uniqueness of these traits. Some of these traits have been discovered recently, particularly in genes encoding proteins that are important for brain function.
Introduction There is mounting DNA evidence that the living members of the great ape clade (see Glossary) are common and bonobo chimpanzees, humans, gorillas and orangutans, with chimpanzees being the sister group to humans, gorillas to the chimpanzee-human clade, and orangutans to the chimpanzee-human–gorilla clade [1–12]. The degree of genetic similarity among the members of this great ape clade is reflected in the predominantly noncoding orthologous DNA sequences, which from human and chimpanzee nuclear genomes are on average w98.9% identical, whereas with gorilla orthologs they are on average w98.5% identical and with orangutan orthologs w97.0% identical [3,6,11,12]. These values are based on multispecies alignments in which the human, chimpanzee, gorilla, orangutan and other primate DNA sequences were aligned against one another. Humans and chimpanzee are equally divergent from gorillas, and human, chimpanzees and gorillas are equally divergent from orangutans. The close genetic kinship between humans and chimpanzees is now being documented by large-scale DNA comparisons involving a draft sequence of the entire chimpanzee genome (www.nhgri.nih.gov/ 11509418). The proposal to sequence an entire chimpanzee genome was based on the premise that this genome sequence would be needed to search for the genetic basis of being human [13,14]. Supposedly, the search for the genetic basis could then be restricted to the small percentage of Corresponding author: Goodman, M. ([email protected]). Available online 11 July 2005
differing nucleotides between the human and chimpanzee genomes. However, that would be far too restrictive. Although uniquely human features have certainly emerged since the time of the last common ancestor (LCA) of humans and the common and bonobo chimpanzees, it is also true that many traits used to define Glossary Anthropoid: a primate clade that includes catarrhines and New World monkeys. The sister group of tarsiers. Ape: a primate clade that as a crown group includes humans, common and bonobo chimpanzees, gorillas, orangutans, gibbons and siamangs. The sister group of Old World monkeys. Catarrhine: a primate clade that includes Old World monkeys and apes. The sister group of New World monkeys. Clade: a group of organisms united by evolutionary descent from a common ancestor. The group includes a most recent common ancestor and all its descendants. A monophyletic group. Crown group: a group of organisms that includes the most recent common ancestor of a group plus all of its descendants. Family: a taxonomic rank above genus (e.g. Hominidae, Muridae). Genus (pl. genera): a taxonomic rank above species (e.g. Homo, Mus). Great Ape: a primate clade that as a crown group includes humans, common and bonobo chimpanzees, gorillas and orangutans. Haplorhine: a clade that includes tarsiers and anthropoids. The sister group of strepsirrhines. Monkey: a paraphyletic group that includes New World monkeys and Old World monkeys. Monophyletic group: a clade; all of the descendants of a most recent common ancestor (e.g. mammals). New World monkey: a primate clade that includes the families Cebidae, Pitheciidae and Atelidae; also called platyrrhines. The sister group of catarrhines. Old World monkey: a primate clade that includes the tribes Colobini (leafeating Old World monkeys) and Cercopithicini (cheek-pouched Old World monkeys). The sister group of apes. Order: a taxonomic rank above family (e.g. Primates, Rodentia). Paraphyletic group: some of the descendants of a most recent common ancestor (e.g. reptiles). Polyphyletic group: a group of organisms that share characters not related by descent (e.g. flying animals). Prosimian: a paraphyletic group that includes tarsiers and strepsirrhines. Strepsirrhine: a primate clade that includes the five living families of primates endemic to Madagascar (Lemuriformes), in addition to lorisiform members of the family Lorisidae (lorises, pottos, angwantibos) and Galagonidae (bush babies). The sister group of haplorhines. Tarsier: a primate clade endemic to Asia. The sister group of anthropoids. Taxon (pl. taxa): a formally named group of organisms. For example, a species or an order. Total group: a group of organisms that includes all members of the crown group plus any extinct taxa (e.g. a plesion) that are more closely related to the crown group than they are to any other crown group. The crown group plus its stem lineage. Tribe: a taxonomic rank between genus and family. This rank is not formally regulated like species, genera, families and orders.
www.sciencedirect.com 0168-9525/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.tig.2005.06.012
512
Review
TRENDS in Genetics Vol.21 No.9 September 2005
humanity have much deeper roots. For example, the intricate capabilities that humans possess to make and use tools have their origins in the prehensile and opposable grasping hands that are shared by all clades in the order Primates. Indeed, to identify the genetic roots of being human the comparative primate genomic data need to be enlarged and placed in a phylogenetic framework that encompasses the entire order Primates. Here we present a molecular view of primate phylogeny as revealed by the comparative primate genomic data that currently exist. An accurate phylogenetic framework should facilitate the genomic search for the genetic roots that shaped being human. To illustrate our viewpoint, we discuss how comparative genomic data can test the model that depicts probable adaptive evolution of those genes involved in the process of encephalization in primates. Primate phylogeny Of the O300 species of O60 genera that represent the extant members of the order Primates, complete or nearly complete DNA sequences are as yet available only for the human and common chimpanzee genomes. However, sequencing of the rhesus macaque genome, a representative of the Old World monkey branch of primates, is far advanced and an assembled version of this genome was publicly released in May 2005 (http://www.genome.gov/ 11008262; http://www.hgsc.bcm.tmc.edu/projects/rmacaque). Additionally, sequencing of the orangutan genome is likely to be accomplished in the next few years (http://www. genome.gov/12511858), and the common marmoset (a New World monkey) has recently also been slated for sequencing (http://www.genome.gov/13014443). DNA sequence data from many more primates are accumulating from expressed sequence tags (ESTs), cDNA sequencing projects, the ENCODE project [15] and for a variety of individual genomic loci. Figure 1 indicates the relative amounts of comparative primate DNA data that were accessible at the start of 2005. Phylogenetic analyses [3,7,9,16–24] have been undertaken on those genomic loci that are represented by a range of primate genera. The results, when pieced together, describe the cladistic relationships that exist among almost all genera of extant primates (Figure 2). The molecular view of primate phylogeny, such as depicted in Figure 2, provides a framework for reconstructing the genetic changes that occurred at crucial stages during primate evolution in the stems and terminal branches leading to the extant primate taxa. The reconstructions are certain to become more accurate and more detailed as the accumulating DNA sequence data encompass an increasing number of primate species, increasing numbers of individual genomic loci and entire primate genomes. The evidence on primate phylogeny from the present bodies of comparative DNA sequence data shows that the order Primates divides into the Strepsirrhini (e.g. lemurs, lorises), the Tarsiiformes (tarsiers) and the Anthropoidea. In turn, the Strepsirrhini divides into Lemuriformes and Lorisiformes, whereas the Anthropoidea divides into Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys, apes including humans). Lemuriformes, Lorisiformes, Platyrrhini and Catarrhini then divide into www.sciencedirect.com
lower ranking taxa, named at the familial and generic levels in Figure 2. The emerging genomic picture of primate phylogeny is resolving ambiguities and correcting outright errors in the traditional morphologically based picture. Clearly a glaring error in the traditional view was the closer grouping of chimpanzees and gorillas to orangutans rather than to humans. This error is perpetuated, even in genomic studies (e.g. see Ref. [25]), when the investigators assume that the group of great apes excludes humans, implying that chimpanzees and gorillas are more like orangutans than humans. In fact there is already compelling DNA evidence that not only are chimpanzees (Pan) and gorillas (Gorilla) more closely related to humans (Homo) than to orangutans (Pongo) but also chimpanzees and humans are more closely related to each other than either is to gorillas. There are several other examples (Box 1) of how our view of primate phylogeny is being clarified or corrected by the DNA evidence gathered so far. In turn, it is also evident that more extensive DNA sequence data are needed fully to resolve the phylogenetic relationships of the more than 60 primate genera. This is evident in Figure 2 at both family and generic levels. For example, the branching order of the three platyrrhine families (Pitheciidae, Atelidae, Cebidae) is not yet resolved. Similarly the branching order of the lemuriform clade consisting of the families Megaladapidae, Lemuridae, Indridae and Cheirogaleidae is not yet resolved. At the generic level the branching order of the four genera (Hylobates, Symphalangus, Nomascus, Bunopithecus) of smaller sized apes (e.g. gibbons, siamangs) is unresolved. Similarly among leaf-eating Old World monkeys, the branching order within the African genera (Colobus, Piliocolobus, Procolobus) and within the Asian genera (Semnopithecus, Trachypithecus, Presbytis, Pygathrix, Rhinopithecus, Nasalis, Simias) is not yet resolved (partially because of the scarcity of biomaterials available to laboratory researchers). A fully resolved primate phylogenetic tree, validated by many sequenced genomes (Box 2), will provide the framework needed to reveal the courses of genetic change during descent of the primate lineages. When the sequenced genomes adequately represent the adaptive diversity of the primates, a much more thorough analysis of the genetic basis of being human can be achieved. This analysis should be able to identify not only the coding but also the noncoding sequences of primate genomes showing accelerated evolution driven by darwinian positive selection. Moreover, those examples of accelerated evolution that are proposed to be unique for humans can be tested for their proposed human uniqueness by examining the lineages of many other primates. Among accelerated evolving genes in human ancestry that should be so examined are genes that encode proteins important for brain functions. Darwinian evolution Of the 20 000 to 25 000 genes in a human genome, relatively few as yet have sequenced orthologs from enough different primates to reflect the adaptive diversity
Review
TRENDS in Genetics Vol.21 No.9 September 2005
(a)
513
(b) Old World monkeys
Malagasy ‘lemurs’
Gibbons and siamangs
Lorises and galagos
Orangutans
Tarsiers
Gorilla
New World monkeys
Human
Old World monkeys
Bonobo chimpanzee
Apes
Common chimpanzee 70
60
50
40 30 20 Million years
10
0
30
(c) Apes
25
20 15 10 Million years
5
0
Old World monkeys
Homo Pan Pongo Gorilla Hylobatini
10.14 million records
69 000 records
New World monkeys
Strepsirrhines
Callithrix Aotus Ateles Saguinus Saimiri Alouatta Cebus Lagothrix Callicebus Leontopithecus Pithecia Callimico Chiropotes Brachyteles Cacajao
5400 records
3500 records
Macaca Chlorocebus Papio Colobus Trachypithecus Cercocebus Mandrillus Presbytis Cercopithecus Theropithecus Miopithecus Semnopithecus Lophocebus Allenopithecus Procolobus Microcebus Eulemur Otolemur Lepilemur Lemur Propithecus Hapalemur Varecia Galago Cheirogaleus Nycticebus Daubentonia Loris Avahi Perodicticus Galagoides Mirza Arctocebus Allocebus Phaner Indri Euoticus
Tarsius ~100 records TRENDS in Genetics
Figure 1. Primate phylogenetic studies. (a) Evolutionary timescale and phylogenetic relationships among major primate clades. Formal taxonomic names for these organisms are given in the text and in Figure 2. (b) Evolutionary timescale and phylogenetic relationships among the apes and their sister group, the Old World monkeys. Formal taxonomic names for these organisms are given in the text and in Figure 2. (c) The numbers of unique nucleotide sequence records found in the nonredundant (NR) GenBank database for each extant primate genus (tribal level figures are represented for the four gibbon genera). ESTs and complete genome sequences are not included in this database. Each genus is represented by a different color in the pie charts. We used our own primate classification scheme (i.e. that depicted in Figure 2) rather than the classification used by NCBI.
of the order. Nevertheless the results gathered so far indicate that darwinian evolution frequently occurred, more often in common ancestral lineages or in one or another terminal non-human lineage than in the terminal human lineage [9,26–30]. A case in point is provided by a gene (SEMG2) encoding semenogelin, the main protein of seminal fluid. Phylogenetic comparisons involving the human semenogelin gene and orthologs in other primates have demonstrated that positive selection acted more www.sciencedirect.com
strongly on the ancestral Old World monkey protein, and also on the chimpanzee protein, than on the human protein [30]. The gene signature of positive selection was a markedly elevated rate of nonsynonymous (i.e. amino acid-changing) nucleotide substitutions, which was evident in the stem lineage to Old World monkeys and in the lineage to chimpanzees but not in the lineage to humans. Dorus et al. [30] observed that the semenogelin gene evolves more rapidly in polyandrous primates such as
514
Review
TRENDS in Genetics Vol.21 No.9 September 2005
Homo Pan* Gorilla Pongo Apes Hylobates Symphalangus Nomascus Bunopithecus Papio Theropithecus* Lophocebus* Mandrillus* Cercocebus Macaca Allenopithecus Miopithecus Old World Cercopithecus monkeys Chlorocebus** Colobus Piliocolobus Procolobus Semnopithecus Trachypithecus Presbytis Pygathrix Rhinopithecus Nasalis Simias Alouatta Brachyteles Lagothrix Ateles Cebus Saimiri New World Aotus monkeys Saguinus Leontopithecus Callimico Callithrix Callicebus Pithecia Cacajao* Chiropotes Tarsius Tarsiers Galagoides Otolemur Galago Lorises and Euoticus Perodicticus galagos Arctocebus Loris Nycticebus Daubentonia Lepilemur Varecia Eulemur Lemur Malagasy Hapalemur Avahi ‘lemurs’ Propithecus Indri Phaner Cheirogaleus Allocebus Mirza Microcebus Dermoptera (Flying ‘Lemurs’) Scandentia (Treeshrews) Rodentia (Rodents) Lagomorpha (Rabbits and allies) TRENDS in Genetics
Figure 2. Genus level phylogeny of the primates. Phylogenetic relationships are depicted among O60 genera of living primates. Taxa traditionally recognized as genera but whose taxonomic rank is considered that of a subgenus in time-based phylogenetic classifications (e.g. Refs [9,18]) are indicated by an asterisk. Thirteen monophyletic families of extant primates are indicated as follows: apes, family Hominidae (red); Old World monkeys, family Cercopithecidae (light blue); New World monkeys, families Atelidae (green), Cebidae (pink) and Pitheciidae (gray); tarsiers, family Tarsiidae (medium blue); and seven strepsirrhine families, Lorisidae (lorises, peach), Galagonidae (galagos, purple); Daubentoniidae (aye-ayes, brown), Megaladapidae (sportive lemurs, lavender), Lemuridae (lemurs, orange), Indridae (sifakas, dark blue), and Cheirogaleidae (dwarf and mouse lemurs, light green). There have been no published molecular phylogenies that depict the placement of four of the primate genera (Euoticus, Piliocolobus, Procolobus and Simias). Dashed lines indicate phylogenetic ambiguity regarding these genera. In addition, the phylogenetic relationships within the leaf-eating Old World monkeys (Colobini) have not been well established by published molecular studies, although there is evidence for three monophyletic clades grouping within the tribe as follows: (African colobins (langurs, odd-nosed monkeys)). Phylogenetic relationships were taken from the following studies: apes [7,9,46]; Old World monkeys [19,24,47]; New World monkeys [16,17]; lorises and galagos [21]; and Malagasy ‘lemurs’ [21,22]. Molecular evidence supporting the grouping of tarsiers with anthropoids is ambiguous. Some studies support this grouping [18,20,48], whereas others reject this view and group the tarsiers with the strepsirrhines [49,50]. Hypotheses suggesting which mammalian order(s) is the sister group of Primates are contentious and poorly supported. The genus Cercopithecus (indicated by the double asterisk) is not monophyletic as traditionally constructed [24]. Instead, the genus Chlorocebus is now recognized to include the African green monkey, vervets and allies (C. aethiops), the patas monkey (C. patas) and the C. lhoesti species group. The genus Cercopithecus refers to the w20 species of arboreal guenons.
chimpanzees than in primates that have other types of mating behaviors. The authors also noted that the acceleration in semenogelin evolution correlates with increased testis size and increased level of postcopulatory sperm competition. There are several cases of darwinian evolution afforded by genes that encode brain-important proteins www.sciencedirect.com
[11,28,29,31–35]. These cases, unlike the semenogelin case, occurred at relatively high frequency on the anthropoid lineage that eventually gave rise to humans. This appears to correlate with the fact that encephalization progressed further in anthropoids, especially so in humans, than in other primates. Several representative cases might serve to illustrate the darwinian evolution
Review
TRENDS in Genetics Vol.21 No.9 September 2005
515
Box 1. Errors in traditional primate taxonomy
Box 2. The promise of comparative primate genomics
Errors in the traditional view of primate phylogeny involve Old World monkeys, New World monkeys and strepsirrhines. For example, among Old World monkeys, mandrills and drills (Mandrillus) traditionally group with baboons (e.g. Papio) whereas terrestrial (Cercocebus) and arboreal (Lophocebus) mangabeys group together. By contrast, DNA evidence groups the arboreal mangabeys (Lophocebus) with the baboons (Papio) whereas the terrestrial mangabeys (Cercocebus) group with the mandrills and drills (Mandrillus) [19,47,51]. Among New World monkeys, titi monkeys (Callicebus) traditionally group with owl monkeys (Aotus). By contrast, DNA evidence (Figure 2) groups titi monkeys (Callicebus) with the clade of bearded saki (Pithecia), uacari (Cacajao) and saki monkeys (Chiropotes), whereas owl monkeys (Aotus) are members of a clade in which the other members are squirrel monkeys (Saimiri), capuchin monkeys (Cebus) and callitrichines – tamarins (Saguinus), lion tamarins (Leontopithecus), marmosets (Callithrix) and Goeldi’s monkeys (Callimico) [16–18]. Among the strepsirrhines, are the aye-ayes (family Daubentoniidae) sister to all other members of Lemuriformes or all other strepsirrhines? The DNA evidence clearly places Daubentoniidae as sister to all other lemuriforms [21,22].
To understand fully the genetic basis of humankind it is important to obtain comparative genomic data from many primate clades. Admirably, projects such as the Encyclopedia of DNA Elements (ENCODE) are obtaining a large set of comparative data from strepsirrhines, New World monkeys, Old World monkeys and apes. Additional large-scale cDNA and BAC-end sequencing projects will greatly improve our understanding of primate genomics in the coming years. It is our hope that one day there will be a complete genome sequence for every genus of living primate and also comprehensive data on the expression patterns of its genes. At minimum, we would like to see all primate families, and in some cases subfamilies or tribes, so represented in order that the genomic correlates of the adaptive diversity of primates can be better assessed. Thus we suggest that sequencing projects should be initiated on the following species to supplement current sequencing efforts: (i) Apes: gorilla and gibbon. (ii) Old World monkeys: langur or colobus, green monkey or guenon. (iii) New World monkeys: seven genomes; one from each of the major clades – pitheciids (titi and saki monkeys), cebids (capuchin, squirrel and owl monkey) and atelids [i.e. Ateles (spider monkey) and Alouatta (howler monkey)]. (iv) Tarsiers: one species is necessary but two would be better. (v) Strepsirrhines: one species from each family. (vi) Outgroups: the sister group of primates has not yet been determined. Candidates include one, some or all of the following orders: Dermoptera, Scandentia, Lagomorpha and Rodentia. We need at least genomes from the three non-rodent candidate sister taxa.
that possibly is associated with the process of encephalization. These cases involve phylogenetic comparisons carried out for each of the following genes: ASPM (abnormal spindle-like microcephaly associated), MCPH1 (microcephalin) and COX8 (cytochrome c oxidase subunit 8). These genes are not brain-specific, although ASPM and MCPH1 are thought to have their largest phenotypic impact on brain anatomy. Because certain mutations in MCPH1 apparently cause severe reductions in brain size (microcephaly), Evans et al. [34] and Wang and Su [35] suggested that the molecular evolution of microcephalin could have contributed to the brain expansion. COX8 encodes one of the many protein components in the machinery for aerobic energy production. Cytochrome c oxidase itself contains 13 different protein subunits, nine of which show bursts of change within the Anthropoidea but are slow evolving in nonanthropoid lineages [29,36]. It has been suggested that darwinian evolution optimized the biochemical machinery required to satisfy the rapacious need anthropoid brains have for aerobically produced energy [28,36]. In addition to the evidence for positive selection, several recent studies have focused on differences and similarities in gene expression in the brains of primates (e.g. Refs [37,38]). The published phylogenetic comparisons of ASPM orthologs [11,31,33] as yet do not represent enough branches of the order Primates to determine whether or not accelerated nonsynonymous changes occurred in the anthropoid stem. However, the phylogenetic comparisons that have been published show marked acceleration in the human lineage and, in the study of Kouprina et al. [11], almost as much in the gorilla lineage, somewhat weaker acceleration in the chimpanzee lineage and in the stem of the African great ape (human, chimpanzee, gorilla) clade or, in the study of Evans et al. [33], the great ape (human, chimpanzee, gorilla, orangutan) clade. Kouprina et al. [11] suggested that the ASPM coding sequence changes were positively selected and that their phenotypic impact was originally on some as yet undiscovered feature of www.sciencedirect.com
embryonic neurogenesis shared by gorillas, humans and chimpanzees but not orangutans or other primates. MCPH1 presents a somewhat different pattern of darwinian evolution. Again, not enough primate branches were compared to determine whether the anthropoid stem lineage showed an accelerated rate of MCPH1 evolution [34,35]. However, accelerated rates are evident on the catarrhine, ape, gre at ape and chimpanzee–human stems, with the most elevated rate being on the ape stem. Other than these stems none of the remaining lineages, including the terminal human and terminal chimpanzee lineages, showed elevated rates. The signature of positive selection is clearly evident on the ape stem, where the rate of nonsynonymous substitutions was two-and-a-half times greater than the rate of synonymous (amino acidunchanging) substitutions [34] in earlier ape ancestors in the lineage leading eventually to humans and chimpanzees. Phylogenetic comparisons of COX8 coding sequences were carried out with orthologs from 17 primates and four non-primate eutherians [28]. Accelerated rates showing the signature of positive selection occurred on the anthropoid stem, the platyrrhine stem, the Old World monkey stem and in papionans, the ape stem, and the terminal human lineage. The COX8 Old World monkey lineage to Trachypithecus (a leaf-eating Old World monkey) did not show an elevated nonsynonymous rate in contrast to the marked elevation in the cheek-pouched Old World monkeys, whose diet is much more diverse than that of the leaf-eaters. Of possible significance, the Old World monkeys with the longest life spans and largest brains are cheek-pouched monkeys such as mandrills and baboons, and those with the shortest life spans and
516
Review
TRENDS in Genetics Vol.21 No.9 September 2005
smaller brains are the colobins (leaf-eating Old World monkeys). Similar results were found for COX6C and for a complex III protein of the electron transport chain (iron sulfur protein, ISP) [29,39]. It would be well worth finding out if the pattern of accelerated rates afforded by these three electron transport proteins exists more widely among genes that encode brain-important proteins. Comparative studies of brain evolution have already established that enlarged brains evolved independently in several clades but not in their sister clades. Thus it is feasible to explore in each such pair of closely related clades if the proteins important for brain function evolved faster in the clade showing the most encephalization. Outlook and conclusion The nearly complete human genome sequence (build 35) suggests that there are between 20 000 and 25 000 genes in our species [40]. Complete primate genome sequences will enable us to trace the evolution of all of these genes and their regulatory sequences. The upsurges in nonsynonymous substitutions, indicative of positive selection for protein sequence changes, should be readily detectable. In addition, via a variety of techniques including phylogenetic footprinting [41,42], phylogenetic shadowing [43,44] and differential phylogenetic footprinting [45], it should eventually be possible to tabulate virtually all the functionally important cis-acting noncoding elements. The data gathered should detect any probable positively selected bursts of nucleotide change within normally conserved elements and should also map any changes in the genomic locations of those annotated DNA sequences judged to be functionally important. These data along with those gathered on gene expression patterns during different developmental stages – both those patterns shared by different species and those that are speciesspecific – would permit a more probing analysis of the genetic changes responsible for shaping the uniqueness of each primate lineage. No doubt, thousands and thousands of positively selected genetic changes will be implicated in the evolutionary history of that primate lineage that ultimately led to humankind and shaped such features as bipedalism, enlarged brains, tool use, speech and complex social relationships. Evolutionary genetic changes that have occurred on other lineages will also provide valuable clues about the development and function of key organismal features. Different primate species possess disease resistance capabilities not shared with humans (e.g. chimpanzees are resistant to AIDS). Finding the genetic loci that enable disease resistance in non-human primates will provide candidate loci for human therapeutic interventions. Availability of a draft sequence of the common chimpanzee genome, together with the detailed sequence of the human genome, only marks the beginning of largescale primate comparative genomics. In this review, we have argued that a fully resolved primate phylogenetic tree, validated by many sequenced genomes, is a prerequisite for uncovering the genetic basis of being human, and for testing the supposed human uniqueness of these traits. Of course, the goal of understanding the www.sciencedirect.com
genetic basis of human uniqueness is central to comparative primate genomics, but that goal would be only partially achieved if we had a detailed list of all the structural and functional genomic differences between humans and chimpanzees. To understand fully why humans are humans, it is necessary to discover, for instance, why primates as a group are not rodents or ungulates, why monkeys are not lemurs and why the gorilla–chimpanzee–human phyletic group is separate from the orangutan. Perhaps the most remarkable aspect of the current status of comparative primate genomics is that answering such questions is becoming feasible. We confidently anticipate rapid progress and look forward to often being astonished by exciting discoveries. Update Nielsen et al. [52] have recently compared 13 731 annotated human genes with their chimpanzee orthologs and found that the strongest evidence of positive selection is afforded by genes involved in sensory perception or immune defenses, including tumor suppression and apoptosis as well as spermatogenesis. The design of these comparisons precluded investigating the evolutionary history of these genes showing evidence of more recently occurring positive selection in either humans or chimpanzees or both. Acknowledgements We thank Edwin McConkey, Jianzhi Zhang, Robert Shields and two anonymous reviewers for providing stimulating and thoughtful comments on this manuscript. We also acknowledge the generous support of the National Institutes of Health (DK-56927, GM-65580) and the National Science Foundation (BCS-0318375).
References 1 Miyamoto, M.M. et al. (1987) Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region. Science 238, 369–373 2 Sibley, C.G. and Ahlquist, J.E. (1987) DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J. Mol. Evol. 26, 99–121 3 Bailey, W.J. et al. (1992) Reexamination of the African hominoid trichotomy with additional sequences from the primate beta-globin gene cluster. Mol. Phylogenet. Evol. 1, 97–135 4 Horai, S. et al. (1995) Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. U. S. A. 92, 532–536 5 Arnason, U. et al. (1996) Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J. Mol. Evol. 43, 650–661 6 Chen, F.C. and Li, W.H. (2001) Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68, 444–456 7 Salem, A.H. et al. (2003) Alu elements and hominid phylogenetics. Proc. Natl. Acad. Sci. U. S. A. 100, 12787–12791 8 Shi, J. et al. (2003) Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units. Proc. Natl. Acad. Sci. U. S. A. 100, 8331–8336 9 Wildman, D.E. et al. (2003) Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo. Proc. Natl. Acad. Sci. U. S. A. 100, 7181–7188 10 Kitano, T. et al. (2004) Human-specific amino acid changes found in 103 protein-coding genes. Mol. Biol. Evol. 21, 936–944
Review
TRENDS in Genetics Vol.21 No.9 September 2005
11 Kouprina, N. et al. (2004) Accelerated evolution of the ASPN gene controlling brain size begins prior to human brain expansion. PLoS Biol. 2, e126. doi: 10.1371/journal.pbio.0020126 (http://www.plos.org) 12 Pavlicek, A. et al. (2004) Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. Hum. Mol. Genet. 13, 2737–2751 13 McConkey, E.H. and Goodman, M. (1997) A human genome evolution project is needed. Trends Genet. 13, 350–351 14 McConkey, E.H. et al. (2000) Proposal for a human genome evolution project. Mol. Phylogenet. Evol. 15, 1–4 15 Margulies, E.H. et al. (2005) An initial strategy for the systematic identification of functional elements in the human genome by lowredundancy comparative sequencing. Proc. Natl. Acad. Sci. U. S. A. 102, 4795–4800 16 Porter, C.A. et al. (1995) Evidence on primate phylogeny from epsilonglobin gene sequences and flanking regions. J. Mol. Evol. 40, 30–55 17 Porter, C.A. et al. (1997) Sequences of the primate epsilon-globin gene: implications for systematics of the marmosets and other New World primates. Gene 205, 59–71 18 Goodman, M. et al. (1998) Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 9, 585–598 19 Page, S.L. and Goodman, M. (2001) Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade. Mol. Phylogenet. Evol. 18, 14–25 20 Poux, C. and Douzery, E.J. (2004) Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP. Am. J. Phys. Anthropol. 124, 1–16 21 Roos, C. et al. (2004) Primate jumping genes elucidate strepsirrhine phylogeny. Proc. Natl. Acad. Sci. U. S. A. 101, 10650–10654 22 Yoder, A.D. and Yang, Z. (2004) Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol. Ecol. 13, 757–773 23 Ray, D.A. et al. (2005) Alu insertion loci and platyrrhine primate phylogeny. Mol. Phylogenet. Evol. 35, 117–126 24 Tosi, A.J. et al. (2004) Sex chromosome phylogenetics indicate a single transition to terrestriality in the guenons (tribe Cercopithecini). J. Hum. Evol. 46, 223–237 25 Gibbons, R. et al. (2004) Distinguishing humans from great apes with AluYb8 repeats. J. Mol. Biol. 339, 721–729 26 Messier, W. and Stewart, C.B. (1997) Episodic adaptive evolution of primate lysozymes. Nature 385, 151–154 27 Zhang, J. et al. (2002) Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30, 411–415 28 Goldberg, A. et al. (2003) Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates. Proc. Natl. Acad. Sci. U. S. A. 100, 5873–5878 29 Doan, J.W. et al. (2004) Coadaptive evolution in cytochrome c oxidase: 9 of 13 subunits show accelerated rates of nonsynonymous substitution in anthropoid primates. Mol. Phylogenet. Evol. 33, 944–950 30 Dorus, S. et al. (2004) Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity. Nat. Genet. 36, 1326–1329 31 Zhang, J. (2003) Evolution of the human ASPM gene, a major determinant of brain size. Genetics 165, 2063–2070
517
32 Dorus, S. et al. (2004) Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 119, 1027–1040 33 Evans, P.D. et al. (2004) Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans. Hum. Mol. Genet. 13, 489–494 34 Evans, P.D. et al. (2004) Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size. Hum. Mol. Genet. 13, 1139–1145 35 Wang, Y.Q. and Su, B. (2004) Molecular evolution of microcephalin, a gene determining human brain size. Hum. Mol. Genet. 13, 1131–1137 36 Grossman, L.I. et al. (2004) Accelerated evolution of the electron transport chain in anthropoid primates. Trends Genet. 20, 578–585 37 Uddin, M. et al. (2004) Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc. Natl. Acad. Sci. U. S. A. 101, 2957–2962 38 Caceres, M. et al. (2003) Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl. Acad. Sci. U. S. A. 100, 13030–13035 39 Doan, J.W. et al. (2005) Rapid nonsynonymous evolution of the iron sulfur protein in anthropoid primates. J. Bioenerg. Biomembr. 37, 35–41 40 Human Genome Sequencing Consortium. (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 41 Tagle, D.A. et al. (1988) Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203, 439–455 42 Gumucio, D.L. et al. (1992) Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes. Mol. Cell. Biol. 12, 4919–4929 43 Boffelli, D. et al. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391–1394 44 Berezikov, E. et al. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24 45 Gumucio, D.L. et al. (1994) Differential phylogenetic footprinting as a means to identify base changes responsible for recruitment of the anthropoid gamma gene to a fetal expression pattern. J. Biol. Chem. 269, 15371–15380 46 Roos, C. and Geissmann, T. (2001) Molecular phylogeny of the major hylobatid divisions. Mol. Phylogenet. Evol. 19, 486–494 47 Disotell, T.R. (1994) Generic level relationships of the Papionini (Cercopithecoidea). Am. J. Phys. Anthropol. 94, 47–57 48 Schmitz, J. et al. (2001) SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157, 777–784 49 Hasegawa, M. et al. (1990) Mitochondrial DNA evolution in primates: transition rate has been extremely low in the lemur. J. Mol. Evol. 31, 113–121 50 Murphy, W.J. et al. (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409, 614–618 51 Disotell, T.R. et al. (1992) Mitochondrial DNA phylogeny of the Old World monkey tribe Papionini. Mol. Biol. Evol. 9, 1–13 52 Nielsen, R. et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PloS Biol 3, e170. doi: 10.1371/ journal.pbio.0030170 (http://www.plos.org)
Elsevier.com – Dynamic New Site Links Scientists to New Research & Thinking Elsevier.com has had a makeover, inside and out. As a world-leading publisher of scientific, technical and health information, Elsevier is dedicated to linking researchers and professionals to the best thinking in their fields. We offer the widest and deepest coverage in a range of media types to enhance crosspollination of information, breakthroughs in research and discovery, and the sharing and preservation of knowledge. Visit us at Elsevier.com.
Elsevier. Building Insights. Breaking Boundaries www.sciencedirect.com
TRENDS in Genetics Vol.21 No.9 September 2005
Moving primate genomics beyond the chimpanzee genome Morris Goodman1,2, Lawrence I. Grossman2 and Derek E. Wildman2,3 1
Department of Anatomy and Cell Biology, Wayne State University School of Medicine, 540 E. Canfield Avenue, Detroit, Michigan 48201 USA 2 Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, 259 Mack Ave, Detroit, MI 48201, USA 3 Services in Support of the Perinatology Research Branch, National Institute of Child Health and Development/NIH/DHHS, Detroit, MI 48201, USA
The comparative DNA sequence data that already exist on individual genomic loci depict the phylogenetic relationships of nearly all extant primate genera. Such a phylogenetic representation of the primates, validated by many sequenced primate genomes, and encompassing the full adaptive diversity of the order, is a prerequisite for identifying the genetic basis of humankind, and for testing the proposed human uniqueness of these traits. Some of these traits have been discovered recently, particularly in genes encoding proteins that are important for brain function.
Introduction There is mounting DNA evidence that the living members of the great ape clade (see Glossary) are common and bonobo chimpanzees, humans, gorillas and orangutans, with chimpanzees being the sister group to humans, gorillas to the chimpanzee-human clade, and orangutans to the chimpanzee-human–gorilla clade [1–12]. The degree of genetic similarity among the members of this great ape clade is reflected in the predominantly noncoding orthologous DNA sequences, which from human and chimpanzee nuclear genomes are on average w98.9% identical, whereas with gorilla orthologs they are on average w98.5% identical and with orangutan orthologs w97.0% identical [3,6,11,12]. These values are based on multispecies alignments in which the human, chimpanzee, gorilla, orangutan and other primate DNA sequences were aligned against one another. Humans and chimpanzee are equally divergent from gorillas, and human, chimpanzees and gorillas are equally divergent from orangutans. The close genetic kinship between humans and chimpanzees is now being documented by large-scale DNA comparisons involving a draft sequence of the entire chimpanzee genome (www.nhgri.nih.gov/ 11509418). The proposal to sequence an entire chimpanzee genome was based on the premise that this genome sequence would be needed to search for the genetic basis of being human [13,14]. Supposedly, the search for the genetic basis could then be restricted to the small percentage of Corresponding author: Goodman, M. ([email protected]). Available online 11 July 2005
differing nucleotides between the human and chimpanzee genomes. However, that would be far too restrictive. Although uniquely human features have certainly emerged since the time of the last common ancestor (LCA) of humans and the common and bonobo chimpanzees, it is also true that many traits used to define Glossary Anthropoid: a primate clade that includes catarrhines and New World monkeys. The sister group of tarsiers. Ape: a primate clade that as a crown group includes humans, common and bonobo chimpanzees, gorillas, orangutans, gibbons and siamangs. The sister group of Old World monkeys. Catarrhine: a primate clade that includes Old World monkeys and apes. The sister group of New World monkeys. Clade: a group of organisms united by evolutionary descent from a common ancestor. The group includes a most recent common ancestor and all its descendants. A monophyletic group. Crown group: a group of organisms that includes the most recent common ancestor of a group plus all of its descendants. Family: a taxonomic rank above genus (e.g. Hominidae, Muridae). Genus (pl. genera): a taxonomic rank above species (e.g. Homo, Mus). Great Ape: a primate clade that as a crown group includes humans, common and bonobo chimpanzees, gorillas and orangutans. Haplorhine: a clade that includes tarsiers and anthropoids. The sister group of strepsirrhines. Monkey: a paraphyletic group that includes New World monkeys and Old World monkeys. Monophyletic group: a clade; all of the descendants of a most recent common ancestor (e.g. mammals). New World monkey: a primate clade that includes the families Cebidae, Pitheciidae and Atelidae; also called platyrrhines. The sister group of catarrhines. Old World monkey: a primate clade that includes the tribes Colobini (leafeating Old World monkeys) and Cercopithicini (cheek-pouched Old World monkeys). The sister group of apes. Order: a taxonomic rank above family (e.g. Primates, Rodentia). Paraphyletic group: some of the descendants of a most recent common ancestor (e.g. reptiles). Polyphyletic group: a group of organisms that share characters not related by descent (e.g. flying animals). Prosimian: a paraphyletic group that includes tarsiers and strepsirrhines. Strepsirrhine: a primate clade that includes the five living families of primates endemic to Madagascar (Lemuriformes), in addition to lorisiform members of the family Lorisidae (lorises, pottos, angwantibos) and Galagonidae (bush babies). The sister group of haplorhines. Tarsier: a primate clade endemic to Asia. The sister group of anthropoids. Taxon (pl. taxa): a formally named group of organisms. For example, a species or an order. Total group: a group of organisms that includes all members of the crown group plus any extinct taxa (e.g. a plesion) that are more closely related to the crown group than they are to any other crown group. The crown group plus its stem lineage. Tribe: a taxonomic rank between genus and family. This rank is not formally regulated like species, genera, families and orders.
www.sciencedirect.com 0168-9525/$ - see front matter Q 2005 Elsevier Ltd. All rights reserved. doi:10.1016/j.tig.2005.06.012
512
Review
TRENDS in Genetics Vol.21 No.9 September 2005
humanity have much deeper roots. For example, the intricate capabilities that humans possess to make and use tools have their origins in the prehensile and opposable grasping hands that are shared by all clades in the order Primates. Indeed, to identify the genetic roots of being human the comparative primate genomic data need to be enlarged and placed in a phylogenetic framework that encompasses the entire order Primates. Here we present a molecular view of primate phylogeny as revealed by the comparative primate genomic data that currently exist. An accurate phylogenetic framework should facilitate the genomic search for the genetic roots that shaped being human. To illustrate our viewpoint, we discuss how comparative genomic data can test the model that depicts probable adaptive evolution of those genes involved in the process of encephalization in primates. Primate phylogeny Of the O300 species of O60 genera that represent the extant members of the order Primates, complete or nearly complete DNA sequences are as yet available only for the human and common chimpanzee genomes. However, sequencing of the rhesus macaque genome, a representative of the Old World monkey branch of primates, is far advanced and an assembled version of this genome was publicly released in May 2005 (http://www.genome.gov/ 11008262; http://www.hgsc.bcm.tmc.edu/projects/rmacaque). Additionally, sequencing of the orangutan genome is likely to be accomplished in the next few years (http://www. genome.gov/12511858), and the common marmoset (a New World monkey) has recently also been slated for sequencing (http://www.genome.gov/13014443). DNA sequence data from many more primates are accumulating from expressed sequence tags (ESTs), cDNA sequencing projects, the ENCODE project [15] and for a variety of individual genomic loci. Figure 1 indicates the relative amounts of comparative primate DNA data that were accessible at the start of 2005. Phylogenetic analyses [3,7,9,16–24] have been undertaken on those genomic loci that are represented by a range of primate genera. The results, when pieced together, describe the cladistic relationships that exist among almost all genera of extant primates (Figure 2). The molecular view of primate phylogeny, such as depicted in Figure 2, provides a framework for reconstructing the genetic changes that occurred at crucial stages during primate evolution in the stems and terminal branches leading to the extant primate taxa. The reconstructions are certain to become more accurate and more detailed as the accumulating DNA sequence data encompass an increasing number of primate species, increasing numbers of individual genomic loci and entire primate genomes. The evidence on primate phylogeny from the present bodies of comparative DNA sequence data shows that the order Primates divides into the Strepsirrhini (e.g. lemurs, lorises), the Tarsiiformes (tarsiers) and the Anthropoidea. In turn, the Strepsirrhini divides into Lemuriformes and Lorisiformes, whereas the Anthropoidea divides into Platyrrhini (New World monkeys) and Catarrhini (Old World monkeys, apes including humans). Lemuriformes, Lorisiformes, Platyrrhini and Catarrhini then divide into www.sciencedirect.com
lower ranking taxa, named at the familial and generic levels in Figure 2. The emerging genomic picture of primate phylogeny is resolving ambiguities and correcting outright errors in the traditional morphologically based picture. Clearly a glaring error in the traditional view was the closer grouping of chimpanzees and gorillas to orangutans rather than to humans. This error is perpetuated, even in genomic studies (e.g. see Ref. [25]), when the investigators assume that the group of great apes excludes humans, implying that chimpanzees and gorillas are more like orangutans than humans. In fact there is already compelling DNA evidence that not only are chimpanzees (Pan) and gorillas (Gorilla) more closely related to humans (Homo) than to orangutans (Pongo) but also chimpanzees and humans are more closely related to each other than either is to gorillas. There are several other examples (Box 1) of how our view of primate phylogeny is being clarified or corrected by the DNA evidence gathered so far. In turn, it is also evident that more extensive DNA sequence data are needed fully to resolve the phylogenetic relationships of the more than 60 primate genera. This is evident in Figure 2 at both family and generic levels. For example, the branching order of the three platyrrhine families (Pitheciidae, Atelidae, Cebidae) is not yet resolved. Similarly the branching order of the lemuriform clade consisting of the families Megaladapidae, Lemuridae, Indridae and Cheirogaleidae is not yet resolved. At the generic level the branching order of the four genera (Hylobates, Symphalangus, Nomascus, Bunopithecus) of smaller sized apes (e.g. gibbons, siamangs) is unresolved. Similarly among leaf-eating Old World monkeys, the branching order within the African genera (Colobus, Piliocolobus, Procolobus) and within the Asian genera (Semnopithecus, Trachypithecus, Presbytis, Pygathrix, Rhinopithecus, Nasalis, Simias) is not yet resolved (partially because of the scarcity of biomaterials available to laboratory researchers). A fully resolved primate phylogenetic tree, validated by many sequenced genomes (Box 2), will provide the framework needed to reveal the courses of genetic change during descent of the primate lineages. When the sequenced genomes adequately represent the adaptive diversity of the primates, a much more thorough analysis of the genetic basis of being human can be achieved. This analysis should be able to identify not only the coding but also the noncoding sequences of primate genomes showing accelerated evolution driven by darwinian positive selection. Moreover, those examples of accelerated evolution that are proposed to be unique for humans can be tested for their proposed human uniqueness by examining the lineages of many other primates. Among accelerated evolving genes in human ancestry that should be so examined are genes that encode proteins important for brain functions. Darwinian evolution Of the 20 000 to 25 000 genes in a human genome, relatively few as yet have sequenced orthologs from enough different primates to reflect the adaptive diversity
Review
TRENDS in Genetics Vol.21 No.9 September 2005
(a)
513
(b) Old World monkeys
Malagasy ‘lemurs’
Gibbons and siamangs
Lorises and galagos
Orangutans
Tarsiers
Gorilla
New World monkeys
Human
Old World monkeys
Bonobo chimpanzee
Apes
Common chimpanzee 70
60
50
40 30 20 Million years
10
0
30
(c) Apes
25
20 15 10 Million years
5
0
Old World monkeys
Homo Pan Pongo Gorilla Hylobatini
10.14 million records
69 000 records
New World monkeys
Strepsirrhines
Callithrix Aotus Ateles Saguinus Saimiri Alouatta Cebus Lagothrix Callicebus Leontopithecus Pithecia Callimico Chiropotes Brachyteles Cacajao
5400 records
3500 records
Macaca Chlorocebus Papio Colobus Trachypithecus Cercocebus Mandrillus Presbytis Cercopithecus Theropithecus Miopithecus Semnopithecus Lophocebus Allenopithecus Procolobus Microcebus Eulemur Otolemur Lepilemur Lemur Propithecus Hapalemur Varecia Galago Cheirogaleus Nycticebus Daubentonia Loris Avahi Perodicticus Galagoides Mirza Arctocebus Allocebus Phaner Indri Euoticus
Tarsius ~100 records TRENDS in Genetics
Figure 1. Primate phylogenetic studies. (a) Evolutionary timescale and phylogenetic relationships among major primate clades. Formal taxonomic names for these organisms are given in the text and in Figure 2. (b) Evolutionary timescale and phylogenetic relationships among the apes and their sister group, the Old World monkeys. Formal taxonomic names for these organisms are given in the text and in Figure 2. (c) The numbers of unique nucleotide sequence records found in the nonredundant (NR) GenBank database for each extant primate genus (tribal level figures are represented for the four gibbon genera). ESTs and complete genome sequences are not included in this database. Each genus is represented by a different color in the pie charts. We used our own primate classification scheme (i.e. that depicted in Figure 2) rather than the classification used by NCBI.
of the order. Nevertheless the results gathered so far indicate that darwinian evolution frequently occurred, more often in common ancestral lineages or in one or another terminal non-human lineage than in the terminal human lineage [9,26–30]. A case in point is provided by a gene (SEMG2) encoding semenogelin, the main protein of seminal fluid. Phylogenetic comparisons involving the human semenogelin gene and orthologs in other primates have demonstrated that positive selection acted more www.sciencedirect.com
strongly on the ancestral Old World monkey protein, and also on the chimpanzee protein, than on the human protein [30]. The gene signature of positive selection was a markedly elevated rate of nonsynonymous (i.e. amino acid-changing) nucleotide substitutions, which was evident in the stem lineage to Old World monkeys and in the lineage to chimpanzees but not in the lineage to humans. Dorus et al. [30] observed that the semenogelin gene evolves more rapidly in polyandrous primates such as
514
Review
TRENDS in Genetics Vol.21 No.9 September 2005
Homo Pan* Gorilla Pongo Apes Hylobates Symphalangus Nomascus Bunopithecus Papio Theropithecus* Lophocebus* Mandrillus* Cercocebus Macaca Allenopithecus Miopithecus Old World Cercopithecus monkeys Chlorocebus** Colobus Piliocolobus Procolobus Semnopithecus Trachypithecus Presbytis Pygathrix Rhinopithecus Nasalis Simias Alouatta Brachyteles Lagothrix Ateles Cebus Saimiri New World Aotus monkeys Saguinus Leontopithecus Callimico Callithrix Callicebus Pithecia Cacajao* Chiropotes Tarsius Tarsiers Galagoides Otolemur Galago Lorises and Euoticus Perodicticus galagos Arctocebus Loris Nycticebus Daubentonia Lepilemur Varecia Eulemur Lemur Malagasy Hapalemur Avahi ‘lemurs’ Propithecus Indri Phaner Cheirogaleus Allocebus Mirza Microcebus Dermoptera (Flying ‘Lemurs’) Scandentia (Treeshrews) Rodentia (Rodents) Lagomorpha (Rabbits and allies) TRENDS in Genetics
Figure 2. Genus level phylogeny of the primates. Phylogenetic relationships are depicted among O60 genera of living primates. Taxa traditionally recognized as genera but whose taxonomic rank is considered that of a subgenus in time-based phylogenetic classifications (e.g. Refs [9,18]) are indicated by an asterisk. Thirteen monophyletic families of extant primates are indicated as follows: apes, family Hominidae (red); Old World monkeys, family Cercopithecidae (light blue); New World monkeys, families Atelidae (green), Cebidae (pink) and Pitheciidae (gray); tarsiers, family Tarsiidae (medium blue); and seven strepsirrhine families, Lorisidae (lorises, peach), Galagonidae (galagos, purple); Daubentoniidae (aye-ayes, brown), Megaladapidae (sportive lemurs, lavender), Lemuridae (lemurs, orange), Indridae (sifakas, dark blue), and Cheirogaleidae (dwarf and mouse lemurs, light green). There have been no published molecular phylogenies that depict the placement of four of the primate genera (Euoticus, Piliocolobus, Procolobus and Simias). Dashed lines indicate phylogenetic ambiguity regarding these genera. In addition, the phylogenetic relationships within the leaf-eating Old World monkeys (Colobini) have not been well established by published molecular studies, although there is evidence for three monophyletic clades grouping within the tribe as follows: (African colobins (langurs, odd-nosed monkeys)). Phylogenetic relationships were taken from the following studies: apes [7,9,46]; Old World monkeys [19,24,47]; New World monkeys [16,17]; lorises and galagos [21]; and Malagasy ‘lemurs’ [21,22]. Molecular evidence supporting the grouping of tarsiers with anthropoids is ambiguous. Some studies support this grouping [18,20,48], whereas others reject this view and group the tarsiers with the strepsirrhines [49,50]. Hypotheses suggesting which mammalian order(s) is the sister group of Primates are contentious and poorly supported. The genus Cercopithecus (indicated by the double asterisk) is not monophyletic as traditionally constructed [24]. Instead, the genus Chlorocebus is now recognized to include the African green monkey, vervets and allies (C. aethiops), the patas monkey (C. patas) and the C. lhoesti species group. The genus Cercopithecus refers to the w20 species of arboreal guenons.
chimpanzees than in primates that have other types of mating behaviors. The authors also noted that the acceleration in semenogelin evolution correlates with increased testis size and increased level of postcopulatory sperm competition. There are several cases of darwinian evolution afforded by genes that encode brain-important proteins www.sciencedirect.com
[11,28,29,31–35]. These cases, unlike the semenogelin case, occurred at relatively high frequency on the anthropoid lineage that eventually gave rise to humans. This appears to correlate with the fact that encephalization progressed further in anthropoids, especially so in humans, than in other primates. Several representative cases might serve to illustrate the darwinian evolution
Review
TRENDS in Genetics Vol.21 No.9 September 2005
515
Box 1. Errors in traditional primate taxonomy
Box 2. The promise of comparative primate genomics
Errors in the traditional view of primate phylogeny involve Old World monkeys, New World monkeys and strepsirrhines. For example, among Old World monkeys, mandrills and drills (Mandrillus) traditionally group with baboons (e.g. Papio) whereas terrestrial (Cercocebus) and arboreal (Lophocebus) mangabeys group together. By contrast, DNA evidence groups the arboreal mangabeys (Lophocebus) with the baboons (Papio) whereas the terrestrial mangabeys (Cercocebus) group with the mandrills and drills (Mandrillus) [19,47,51]. Among New World monkeys, titi monkeys (Callicebus) traditionally group with owl monkeys (Aotus). By contrast, DNA evidence (Figure 2) groups titi monkeys (Callicebus) with the clade of bearded saki (Pithecia), uacari (Cacajao) and saki monkeys (Chiropotes), whereas owl monkeys (Aotus) are members of a clade in which the other members are squirrel monkeys (Saimiri), capuchin monkeys (Cebus) and callitrichines – tamarins (Saguinus), lion tamarins (Leontopithecus), marmosets (Callithrix) and Goeldi’s monkeys (Callimico) [16–18]. Among the strepsirrhines, are the aye-ayes (family Daubentoniidae) sister to all other members of Lemuriformes or all other strepsirrhines? The DNA evidence clearly places Daubentoniidae as sister to all other lemuriforms [21,22].
To understand fully the genetic basis of humankind it is important to obtain comparative genomic data from many primate clades. Admirably, projects such as the Encyclopedia of DNA Elements (ENCODE) are obtaining a large set of comparative data from strepsirrhines, New World monkeys, Old World monkeys and apes. Additional large-scale cDNA and BAC-end sequencing projects will greatly improve our understanding of primate genomics in the coming years. It is our hope that one day there will be a complete genome sequence for every genus of living primate and also comprehensive data on the expression patterns of its genes. At minimum, we would like to see all primate families, and in some cases subfamilies or tribes, so represented in order that the genomic correlates of the adaptive diversity of primates can be better assessed. Thus we suggest that sequencing projects should be initiated on the following species to supplement current sequencing efforts: (i) Apes: gorilla and gibbon. (ii) Old World monkeys: langur or colobus, green monkey or guenon. (iii) New World monkeys: seven genomes; one from each of the major clades – pitheciids (titi and saki monkeys), cebids (capuchin, squirrel and owl monkey) and atelids [i.e. Ateles (spider monkey) and Alouatta (howler monkey)]. (iv) Tarsiers: one species is necessary but two would be better. (v) Strepsirrhines: one species from each family. (vi) Outgroups: the sister group of primates has not yet been determined. Candidates include one, some or all of the following orders: Dermoptera, Scandentia, Lagomorpha and Rodentia. We need at least genomes from the three non-rodent candidate sister taxa.
that possibly is associated with the process of encephalization. These cases involve phylogenetic comparisons carried out for each of the following genes: ASPM (abnormal spindle-like microcephaly associated), MCPH1 (microcephalin) and COX8 (cytochrome c oxidase subunit 8). These genes are not brain-specific, although ASPM and MCPH1 are thought to have their largest phenotypic impact on brain anatomy. Because certain mutations in MCPH1 apparently cause severe reductions in brain size (microcephaly), Evans et al. [34] and Wang and Su [35] suggested that the molecular evolution of microcephalin could have contributed to the brain expansion. COX8 encodes one of the many protein components in the machinery for aerobic energy production. Cytochrome c oxidase itself contains 13 different protein subunits, nine of which show bursts of change within the Anthropoidea but are slow evolving in nonanthropoid lineages [29,36]. It has been suggested that darwinian evolution optimized the biochemical machinery required to satisfy the rapacious need anthropoid brains have for aerobically produced energy [28,36]. In addition to the evidence for positive selection, several recent studies have focused on differences and similarities in gene expression in the brains of primates (e.g. Refs [37,38]). The published phylogenetic comparisons of ASPM orthologs [11,31,33] as yet do not represent enough branches of the order Primates to determine whether or not accelerated nonsynonymous changes occurred in the anthropoid stem. However, the phylogenetic comparisons that have been published show marked acceleration in the human lineage and, in the study of Kouprina et al. [11], almost as much in the gorilla lineage, somewhat weaker acceleration in the chimpanzee lineage and in the stem of the African great ape (human, chimpanzee, gorilla) clade or, in the study of Evans et al. [33], the great ape (human, chimpanzee, gorilla, orangutan) clade. Kouprina et al. [11] suggested that the ASPM coding sequence changes were positively selected and that their phenotypic impact was originally on some as yet undiscovered feature of www.sciencedirect.com
embryonic neurogenesis shared by gorillas, humans and chimpanzees but not orangutans or other primates. MCPH1 presents a somewhat different pattern of darwinian evolution. Again, not enough primate branches were compared to determine whether the anthropoid stem lineage showed an accelerated rate of MCPH1 evolution [34,35]. However, accelerated rates are evident on the catarrhine, ape, gre at ape and chimpanzee–human stems, with the most elevated rate being on the ape stem. Other than these stems none of the remaining lineages, including the terminal human and terminal chimpanzee lineages, showed elevated rates. The signature of positive selection is clearly evident on the ape stem, where the rate of nonsynonymous substitutions was two-and-a-half times greater than the rate of synonymous (amino acidunchanging) substitutions [34] in earlier ape ancestors in the lineage leading eventually to humans and chimpanzees. Phylogenetic comparisons of COX8 coding sequences were carried out with orthologs from 17 primates and four non-primate eutherians [28]. Accelerated rates showing the signature of positive selection occurred on the anthropoid stem, the platyrrhine stem, the Old World monkey stem and in papionans, the ape stem, and the terminal human lineage. The COX8 Old World monkey lineage to Trachypithecus (a leaf-eating Old World monkey) did not show an elevated nonsynonymous rate in contrast to the marked elevation in the cheek-pouched Old World monkeys, whose diet is much more diverse than that of the leaf-eaters. Of possible significance, the Old World monkeys with the longest life spans and largest brains are cheek-pouched monkeys such as mandrills and baboons, and those with the shortest life spans and
516
Review
TRENDS in Genetics Vol.21 No.9 September 2005
smaller brains are the colobins (leaf-eating Old World monkeys). Similar results were found for COX6C and for a complex III protein of the electron transport chain (iron sulfur protein, ISP) [29,39]. It would be well worth finding out if the pattern of accelerated rates afforded by these three electron transport proteins exists more widely among genes that encode brain-important proteins. Comparative studies of brain evolution have already established that enlarged brains evolved independently in several clades but not in their sister clades. Thus it is feasible to explore in each such pair of closely related clades if the proteins important for brain function evolved faster in the clade showing the most encephalization. Outlook and conclusion The nearly complete human genome sequence (build 35) suggests that there are between 20 000 and 25 000 genes in our species [40]. Complete primate genome sequences will enable us to trace the evolution of all of these genes and their regulatory sequences. The upsurges in nonsynonymous substitutions, indicative of positive selection for protein sequence changes, should be readily detectable. In addition, via a variety of techniques including phylogenetic footprinting [41,42], phylogenetic shadowing [43,44] and differential phylogenetic footprinting [45], it should eventually be possible to tabulate virtually all the functionally important cis-acting noncoding elements. The data gathered should detect any probable positively selected bursts of nucleotide change within normally conserved elements and should also map any changes in the genomic locations of those annotated DNA sequences judged to be functionally important. These data along with those gathered on gene expression patterns during different developmental stages – both those patterns shared by different species and those that are speciesspecific – would permit a more probing analysis of the genetic changes responsible for shaping the uniqueness of each primate lineage. No doubt, thousands and thousands of positively selected genetic changes will be implicated in the evolutionary history of that primate lineage that ultimately led to humankind and shaped such features as bipedalism, enlarged brains, tool use, speech and complex social relationships. Evolutionary genetic changes that have occurred on other lineages will also provide valuable clues about the development and function of key organismal features. Different primate species possess disease resistance capabilities not shared with humans (e.g. chimpanzees are resistant to AIDS). Finding the genetic loci that enable disease resistance in non-human primates will provide candidate loci for human therapeutic interventions. Availability of a draft sequence of the common chimpanzee genome, together with the detailed sequence of the human genome, only marks the beginning of largescale primate comparative genomics. In this review, we have argued that a fully resolved primate phylogenetic tree, validated by many sequenced genomes, is a prerequisite for uncovering the genetic basis of being human, and for testing the supposed human uniqueness of these traits. Of course, the goal of understanding the www.sciencedirect.com
genetic basis of human uniqueness is central to comparative primate genomics, but that goal would be only partially achieved if we had a detailed list of all the structural and functional genomic differences between humans and chimpanzees. To understand fully why humans are humans, it is necessary to discover, for instance, why primates as a group are not rodents or ungulates, why monkeys are not lemurs and why the gorilla–chimpanzee–human phyletic group is separate from the orangutan. Perhaps the most remarkable aspect of the current status of comparative primate genomics is that answering such questions is becoming feasible. We confidently anticipate rapid progress and look forward to often being astonished by exciting discoveries. Update Nielsen et al. [52] have recently compared 13 731 annotated human genes with their chimpanzee orthologs and found that the strongest evidence of positive selection is afforded by genes involved in sensory perception or immune defenses, including tumor suppression and apoptosis as well as spermatogenesis. The design of these comparisons precluded investigating the evolutionary history of these genes showing evidence of more recently occurring positive selection in either humans or chimpanzees or both. Acknowledgements We thank Edwin McConkey, Jianzhi Zhang, Robert Shields and two anonymous reviewers for providing stimulating and thoughtful comments on this manuscript. We also acknowledge the generous support of the National Institutes of Health (DK-56927, GM-65580) and the National Science Foundation (BCS-0318375).
References 1 Miyamoto, M.M. et al. (1987) Phylogenetic relations of humans and African apes from DNA sequences in the psi eta-globin region. Science 238, 369–373 2 Sibley, C.G. and Ahlquist, J.E. (1987) DNA hybridization evidence of hominoid phylogeny: results from an expanded data set. J. Mol. Evol. 26, 99–121 3 Bailey, W.J. et al. (1992) Reexamination of the African hominoid trichotomy with additional sequences from the primate beta-globin gene cluster. Mol. Phylogenet. Evol. 1, 97–135 4 Horai, S. et al. (1995) Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. U. S. A. 92, 532–536 5 Arnason, U. et al. (1996) Pattern and timing of evolutionary divergences among hominoids based on analyses of complete mtDNAs. J. Mol. Evol. 43, 650–661 6 Chen, F.C. and Li, W.H. (2001) Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am. J. Hum. Genet. 68, 444–456 7 Salem, A.H. et al. (2003) Alu elements and hominid phylogenetics. Proc. Natl. Acad. Sci. U. S. A. 100, 12787–12791 8 Shi, J. et al. (2003) Divergence of the genes on human chromosome 21 between human and other hominoids and variation of substitution rates among transcription units. Proc. Natl. Acad. Sci. U. S. A. 100, 8331–8336 9 Wildman, D.E. et al. (2003) Implications of natural selection in shaping 99.4% nonsynonymous DNA identity between humans and chimpanzees: Enlarging genus Homo. Proc. Natl. Acad. Sci. U. S. A. 100, 7181–7188 10 Kitano, T. et al. (2004) Human-specific amino acid changes found in 103 protein-coding genes. Mol. Biol. Evol. 21, 936–944
Review
TRENDS in Genetics Vol.21 No.9 September 2005
11 Kouprina, N. et al. (2004) Accelerated evolution of the ASPN gene controlling brain size begins prior to human brain expansion. PLoS Biol. 2, e126. doi: 10.1371/journal.pbio.0020126 (http://www.plos.org) 12 Pavlicek, A. et al. (2004) Evolution of the tumor suppressor BRCA1 locus in primates: implications for cancer predisposition. Hum. Mol. Genet. 13, 2737–2751 13 McConkey, E.H. and Goodman, M. (1997) A human genome evolution project is needed. Trends Genet. 13, 350–351 14 McConkey, E.H. et al. (2000) Proposal for a human genome evolution project. Mol. Phylogenet. Evol. 15, 1–4 15 Margulies, E.H. et al. (2005) An initial strategy for the systematic identification of functional elements in the human genome by lowredundancy comparative sequencing. Proc. Natl. Acad. Sci. U. S. A. 102, 4795–4800 16 Porter, C.A. et al. (1995) Evidence on primate phylogeny from epsilonglobin gene sequences and flanking regions. J. Mol. Evol. 40, 30–55 17 Porter, C.A. et al. (1997) Sequences of the primate epsilon-globin gene: implications for systematics of the marmosets and other New World primates. Gene 205, 59–71 18 Goodman, M. et al. (1998) Toward a phylogenetic classification of primates based on DNA evidence complemented by fossil evidence. Mol. Phylogenet. Evol. 9, 585–598 19 Page, S.L. and Goodman, M. (2001) Catarrhine phylogeny: noncoding DNA evidence for a diphyletic origin of the mangabeys and for a human-chimpanzee clade. Mol. Phylogenet. Evol. 18, 14–25 20 Poux, C. and Douzery, E.J. (2004) Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP. Am. J. Phys. Anthropol. 124, 1–16 21 Roos, C. et al. (2004) Primate jumping genes elucidate strepsirrhine phylogeny. Proc. Natl. Acad. Sci. U. S. A. 101, 10650–10654 22 Yoder, A.D. and Yang, Z. (2004) Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context. Mol. Ecol. 13, 757–773 23 Ray, D.A. et al. (2005) Alu insertion loci and platyrrhine primate phylogeny. Mol. Phylogenet. Evol. 35, 117–126 24 Tosi, A.J. et al. (2004) Sex chromosome phylogenetics indicate a single transition to terrestriality in the guenons (tribe Cercopithecini). J. Hum. Evol. 46, 223–237 25 Gibbons, R. et al. (2004) Distinguishing humans from great apes with AluYb8 repeats. J. Mol. Biol. 339, 721–729 26 Messier, W. and Stewart, C.B. (1997) Episodic adaptive evolution of primate lysozymes. Nature 385, 151–154 27 Zhang, J. et al. (2002) Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat. Genet. 30, 411–415 28 Goldberg, A. et al. (2003) Adaptive evolution of cytochrome c oxidase subunit VIII in anthropoid primates. Proc. Natl. Acad. Sci. U. S. A. 100, 5873–5878 29 Doan, J.W. et al. (2004) Coadaptive evolution in cytochrome c oxidase: 9 of 13 subunits show accelerated rates of nonsynonymous substitution in anthropoid primates. Mol. Phylogenet. Evol. 33, 944–950 30 Dorus, S. et al. (2004) Rate of molecular evolution of the seminal protein gene SEMG2 correlates with levels of female promiscuity. Nat. Genet. 36, 1326–1329 31 Zhang, J. (2003) Evolution of the human ASPM gene, a major determinant of brain size. Genetics 165, 2063–2070
517
32 Dorus, S. et al. (2004) Accelerated evolution of nervous system genes in the origin of Homo sapiens. Cell 119, 1027–1040 33 Evans, P.D. et al. (2004) Adaptive evolution of ASPM, a major determinant of cerebral cortical size in humans. Hum. Mol. Genet. 13, 489–494 34 Evans, P.D. et al. (2004) Reconstructing the evolutionary history of microcephalin, a gene controlling human brain size. Hum. Mol. Genet. 13, 1139–1145 35 Wang, Y.Q. and Su, B. (2004) Molecular evolution of microcephalin, a gene determining human brain size. Hum. Mol. Genet. 13, 1131–1137 36 Grossman, L.I. et al. (2004) Accelerated evolution of the electron transport chain in anthropoid primates. Trends Genet. 20, 578–585 37 Uddin, M. et al. (2004) Sister grouping of chimpanzees and humans as revealed by genome-wide phylogenetic analysis of brain gene expression profiles. Proc. Natl. Acad. Sci. U. S. A. 101, 2957–2962 38 Caceres, M. et al. (2003) Elevated gene expression levels distinguish human from non-human primate brains. Proc. Natl. Acad. Sci. U. S. A. 100, 13030–13035 39 Doan, J.W. et al. (2005) Rapid nonsynonymous evolution of the iron sulfur protein in anthropoid primates. J. Bioenerg. Biomembr. 37, 35–41 40 Human Genome Sequencing Consortium. (2004) Finishing the euchromatic sequence of the human genome. Nature 431, 931–945 41 Tagle, D.A. et al. (1988) Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203, 439–455 42 Gumucio, D.L. et al. (1992) Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes. Mol. Cell. Biol. 12, 4919–4929 43 Boffelli, D. et al. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391–1394 44 Berezikov, E. et al. (2005) Phylogenetic shadowing and computational identification of human microRNA genes. Cell 120, 21–24 45 Gumucio, D.L. et al. (1994) Differential phylogenetic footprinting as a means to identify base changes responsible for recruitment of the anthropoid gamma gene to a fetal expression pattern. J. Biol. Chem. 269, 15371–15380 46 Roos, C. and Geissmann, T. (2001) Molecular phylogeny of the major hylobatid divisions. Mol. Phylogenet. Evol. 19, 486–494 47 Disotell, T.R. (1994) Generic level relationships of the Papionini (Cercopithecoidea). Am. J. Phys. Anthropol. 94, 47–57 48 Schmitz, J. et al. (2001) SINE insertions in cladistic analyses and the phylogenetic affiliations of Tarsius bancanus to other primates. Genetics 157, 777–784 49 Hasegawa, M. et al. (1990) Mitochondrial DNA evolution in primates: transition rate has been extremely low in the lemur. J. Mol. Evol. 31, 113–121 50 Murphy, W.J. et al. (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409, 614–618 51 Disotell, T.R. et al. (1992) Mitochondrial DNA phylogeny of the Old World monkey tribe Papionini. Mol. Biol. Evol. 9, 1–13 52 Nielsen, R. et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PloS Biol 3, e170. doi: 10.1371/ journal.pbio.0030170 (http://www.plos.org)
Elsevier.com – Dynamic New Site Links Scientists to New Research & Thinking Elsevier.com has had a makeover, inside and out. As a world-leading publisher of scientific, technical and health information, Elsevier is dedicated to linking researchers and professionals to the best thinking in their fields. We offer the widest and deepest coverage in a range of media types to enhance crosspollination of information, breakthroughs in research and discovery, and the sharing and preservation of knowledge. Visit us at Elsevier.com.
Elsevier. Building Insights. Breaking Boundaries www.sciencedirect.com