genomic catastrophism and the origin of vertebrate immunity · i n which “catastrophism” refers...

A�

rchivum Immunologiae et Therapiae Experimentalis, 1999, 4�

7,� 347–353P�

L ISSN 0004-069X

Review

Genomic Catastrophism and the Origin of Vertebrate ImmunityA. L. Hughes: Catastrophism and Immunity

A�

USTIN L. HU�

GHES

Department of Biology, 208 Mueller Laboratory, Pennsylvania State University, University Park, PA 16802, USA

Abstract. G�

enomic catastrophism is the belief that unique genetic events, unlike those observed in recent evol-u� tionary history, played a key role in the origin of vertebrate adaptations. Catastrophist hypotheses have beenp� articularly popular is accounting for the origin of vertebrate specific immunity. Two majo r such hypothesesinvolve genome duplication by polyploidization and horizontal gene transfer. Recent analy ses lead to decisiver� ejection of the widely cited hypothesis that the vertebrate genome underwent two rounds of g� enome duplication,a nd theoretical considerations suggest that genome duplication is unlikely to lead to new adaptive advances.Likewise, the evidence that key elements of the vertebrate immune system arose by horizontal transfer froma bacterium or by incorporation of a transposable element into the vertebrate genome rema ins relatively weak.T

�hus, at present, a uniformitarian view of the origin of the vertebrate immune system seems more reasonable,

e� specially given the longer time-frame for vertebrate evolution indicated by molecular data.

Key words: g� enome duplication; horizontal gene transfer; immune system evolution; vertebrate evolution.

T�

he vertebrates are, as far as we know, uniquea mong all organisms in possessing an immune systemt

�hat is capable of recognizing a wide variety of foreigna ntigens and of mounting a response to each antigent

�hat is somatically plastic and thus highly specific. The

molecules involved in the specific immune system ofv� ertebrates (sometimes misleadingly called “adaptiveimmunity” , as if the immune responses of vertebrateinnate immunity or of the immune systems of othera nimals were not adaptive in the Darwinian sense) in-c� lude the immunoglobulins (Ig), T cell receptors(TCR), and class I and class II molecules of the majorh

�istocompatibility complex (MHC). All of these are

members of the Ig superfamily, whose members arec� haracterized by a distinct folding pattern consisting oft

�wo β sheets3

�. Although Ig superfamily members have

b�een found outside vertebrates, no animals except

j�awed vertebrates have been shown to possess Ig, TCR,

o r MHC. The origin of the complex suite of adaptations

a ssociated with vertebrate specific immunity has poseda problem for evolutionary biology. The basal group ofj

�awed vertebrates, the cartilaginous fishes (Chondrich-

t�yes) possess Ig, TCR, and MHC that resemble, in most

respects, those of other vertebrates3�

0.Thus, the vertebrate specific immune system seems

t�o have appeared rather suddenly in evolution. As

a consequence, biologists have struggled to devise sce-narios explaining this sudden appearance (called a “bigb

�ang” by MA

�RCHALONIS and colleagues24)

�. The problem

w� as aggravated by a widespread acceptance of in thee� volutionary scenario known as the “Cambrian explo-sion” . According to this hypothesis, the major animalp� hyla diverged from each other in the Cambrian period(roughly 590–505 million years ago). Since fossil re-m� ains of jawless vertebrates are known from the UpperC

�ambrian and those of sharks from the Upper Silurian

(over 408 million years ago)6�, it was believed that the

d�euterostome lineage itself, the chordate body plan, and

t�he genes of the vertebrate specific immune system

must all have appeared in a period of at most 100 mil-lion years.

T�

he response of many researches to this problemhas been to seek for solution in what I call “genomicc� atastrophism”. I use this term in analogy to geology,i

�n which “catastrophism” refers to theories holding that

features of the earth’s surface arose as a result of cata-strophic events early in the earth’s history which haven� o counterpart today. Genomic catastrophists hold thatt

�he immune system arose through one or more catastro-

p� hic events in the evolution of the vertebrate genome;t

�he most commonly invoked of such events are genome

d�uplication by polyploidization18, 19, 21 and horizontal

g� ene transfer21. The alternative view would be one ofg� enomic uniformitarianism. As in geology, genomicu� niformitarianism would hold that the events the oc-c� urred in the distant past are likely to have been of thesame sort as those we can observe today or in the recentp� ast.

H

ere I review recent evidence from molecular evol-u� tionary genetics relevant to deciding between the ca-t

�astrophist or uniformitarian views of the origin of the

v� ertebrate immune system. First, I discuss recent mole-c� ular evidence suggesting that vertebrate evolution tookp� lace over a much longer time period than was pre-v� iously supposed. Next I consider the widely held viewt

�hat vertebrates underwent polyploidization early in

t�heir history. Finally, I briefly discuss the hypothesist

�hat horizontal gene transfer may have played a role int

�he origin of vertebrate specific immunity. My assump-

t�ion is that genomic uniformitarianism should be the

n� ull hypothesis, which we should reject only if the evi-d

�ence for a unique, “catastrophic” event is strong.

V!

ertebrate Origins

Estimates of the timing of major events of cladogen-e� sis in the vertebrate lineage based on large numbers ofg� enes tested statistically for clock-live evolution haverevolutionized our understanding of vertebrate his-t

�ory22, 34. The results of these studies (summarized in

F"

ig. 1) call into question the idea of a Cambrian explo-sion. Rather, the deuterostome lineage, to which thev� ertebrates belong, had been evolving independentlyfor nearly a billion years.

If this interpretation is true, it helps explain somerecent findings regarding the evolution of vertebratei

�nnate immunity. In addition to the specific immune

system, vertebrates possess other less specific immuned

�efenses collectively called the innate immune system.

Because vertebrate innate immunity shows some

g� eneral resemblance to the immune mechanisms knownfrom invertebrates, it has frequently been suggested thatt

�hese mechanisms have been conserved since the com-

mon ancestors of vertebrates and protostome phylasuch as arthropods7

#, 16. However, phylogenies of gene

families having immune system representatives in bothv� ertebrates and invertebrates do not support this hypo-t

�hesis13. Rather, in mot cases, vertebrate and inverte-

b�rate immune functions seem to have evolved inde-

p� endently13. For example, insect hemolin, which isa member of the Ig superfamily and functions in theimmune response, is more closely related to Ig familym� embers expressed in insect and vertebrate nervoussystems than it is to the Ig family members involved inimmunity in vertebrates (Fig. 2). Thus, members of thissuperfamily independently evolved immune systemf

$unctions in deuterostomes (including vertebrates) and

p� rotostomes (including insects).G

�iven a longer time frame in which to evolve their

u� nique adaptations for dealing with parasites, it is notreally surprising that vertebrates developed a uniqueimmune system, any more than it is surprising that theye� volved a unique suite of nervous and sensory adapta-t

�ions. However, the time between most recent point

e� stimates of the divergence time of jawless vertebrates(about 564 million years ago) and that of cartilaginousfishes (528 million years ago) remains extremely short

Fig. 1. Diagram of major events of cladogenesis in the history ofthe vertebrates. Divergence time estimates in millions of years(Mya) ±

% standard error are based on references2

&2, 34

348 A. L. Hughes: Catastrophism and Immunity

(less than 30 million years). It is important to recognizet

�hat the standard errors of these estimates are quite

l'arge, bounding a range of 167 million years. Even so,t

�his may seem a short time for all of the mechanismso f specific immunity to appear and diversify.

O(

ne possibility is that the ancestors of modern jaw-less vertebrates had at least the rudiments of a specificimmune system. If so, such a system may remain inm� odern jawless vertebrates (lampreys and hagfish), butmay have been undetected as yet. Alternatively, al-t

�hough present in ancestral jawless vertebrates, the spe-

c� ific immune system may have subsequently been lostin their modern descendants. Lampreys and hagfish arehighly specialized organisms, and they may not bearm� uch resemblance physiologically to ancient jawlessv� ertebrates such as ostracoderms.

G)

enome Duplication

O(

ne of the most widely cited hypotheses in evol-u� tionary biology is Ohno’s hypothesis that two roundso f duplication of the entire genome by polyploidization

(the 2R hypothesis) occurred early in vertebrate his-t

�ory23, 25, 32, 33. A number of authors have asserted that

t�hese alleged events of genome duplication played

a major role in the evolution of vertebrate specific im-munity18, 19, 21, however, this literature is very incoher-e� nt, and none of the authors explains clearly howg� enome duplication is supposed to have done this. Ofc� ourse, genome duplication would provide a mechanismf

$or duplicating individual genes or gene clusters, but

t�he problem in this case is one of explaining the origin

o f the genes involved in vertebrate specific immunity,n� ot merely their duplication. For example, genome du-p� lication might seem a plausible way of explaining whyt

�here are 4 distinct types of TCR (α, β, δ a nd γ* )

�, but it

c� annot explain the origin of TCR themselves nor howt

�he interaction of TCR and MHC molecules evolved.

It is well known that polyploidization has occurredm� ore recently in certain lineages of bony fishes anda mphibians. For example, it is well known that repeatedp� olyploidization events have occurred in the frog genusX

+enopus5

,. Observing that there are 7 h

-ox c� lusters in

zebrafish but only 4 in tetrapods, AMORES et al.2. recent-

Fig. 2. Phylogenetic tree of insect hemolin and related proteins of insects and vertebrates, il lustrating the close relationship between hemolina/ nd insect neuroglians. The tree was constructed by the neighbor-joining method3

01 on the basis of the proportion of amino acid difference (p)

A. L. Hughes: Catastrophism and Immunity 349

l'y proposed that the ancestors of bony fish underwenta round of genome duplication. However, the conclu-sion that this duplication occurred in the ancestors ofa ll bony fish is unwarranted. Pufferfish have only 4 h

-ox

c� lusters, suggesting that the duplication may have oc-c� urred independently in the zebrafish lineage. In anye� vent, there is no compelling evidence of polyploidiza-t

�ion in the ancestors of all vertebrates12, 33.

Supporters of the 2R hypothesis point to the fact thatt

�here are certain gene families having one member in

Drosophila a nd 4 in vertebrates3�

2. If this situation infact results from 2 rounds of polyploidization, then thep� hylogeny of the vertebrate genes is expected to showa specific topology, showing 2 clusters of 2 genes each(Fig. 3A). I call this a topology of the form (AB) (CD).O

(n the other hand, a topology of the form (A) (BCD),

in which one vertebrate gene duplicated before theo thers (Fig. 3B), does not support the 2R hypothesis.L

1ikewise, if the vertebrate genes duplicated before the

o rigin of vertebrates, as indicated by a phylogeny liket

�hat of Fig. 3C, the 2R hypothesis is not supported.

H

U2

GHES12 tested the 2R hypothesis by examiningp� hylogenies of 13 developmentally important genefamilies having one member in Drosophila a nd 4 inv� ertebrates; these include the very families listed bySIDOW3

�2 as supporting the 2R hypothesis. In fact, only

o ne of these families showed a topology of the form

(AB) (CD), and that received weak statistical support.In 6 families, there was statistically significant supportfor a topology of the form (A) (BCD)12. In 2 families,t

�here was significant support for duplication of the ver-

t�ebrate genes before the divergence of deuterostomes

a nd protostomes, and in one family before the diver-g� ence of vertebrates and urochordates12. Thus, therew� as essentially no support for the 2R hypothesis.

Theoretical considerations also lead us to questionh

�ow duplication of the entire genome could realistically

lead genes encoding proteins with new functions. Therea re 2 models of how new protein function evolves:1) OHNO2

.6 proposed that, after gene duplication, one

g� ene copy is redundant and thus free to accumulatem� utations at random. Most such redundant copies wille� ventually become pseudogenes, but a few will byc� hance hit upon some new beneficial function; 2) vari-o us authors11, 14, 17, 27 have proposed that, when dupli-c� ate genes adapt to new functions, gene duplication iso rdinarily preceded by a period of “gene sharing”28,w� hen a single gene encodes a bifunctional protein pro-d

�uct. Under this latter model, positive Darwinian selec-

t�ion after gene duplication is expected to play a role ina daptation of daughter genes to their specific functions.M

3olecular evidence strongly argues against Ohno’s

model as a general explanation for the origin of newp� rotein function and generally supports the lattermodel11, 14.

In the case of duplication of the entire genome, ifO

(hno’s model were true, we would predict that the vast

m� ajority of duplicated genes would become pseu-d

�ogenes. Thus, contrary to the view of the genomic

c� atastrophists, ancient genome duplication would belargely irrelevant to modern functional genomics. Ont

�he alternative model, because of the role of positive

selection, simultaneous adaptation of large numbers ofd

�uplicate genes to new functions would impose a sub-

stitutional load8, 15 that no population could bear. Eitherm� odel, then, yields the prediction that polyploidizationin itself will not lead to major adaptive innovations.

This prediction is consistent with what is observedin recent polyploids. For example, the numerous poly-p� loidization events in the frogs of the genus X

+enopus5

,

have had no detectable phenotypic effects. They havec� ertainly led to no changes in body plan or other majora daptive advances. Contrary to Ohno’s hypothesis, du-p� licate genes in Xenopus laevis a re subject to purifyingselection as long as they are expressed20 and thus aren� ot free to accumulate mutations at random, but noneis known to have achieved an important new function.O

(n the uniformitarian view, this is to be expected, and

if recent polyploidization has had no major phenotypic

Fig. 3. Possible phylogenies of gene families having 4 members inv4 ertebrates (A-D). A – phylogeny of the form (AB) (CD), consist-e5 nt with the hypothesis of two rounds of genome duplication; B –p6 hylogeny of the form (A) (BCD); C – phylogeny indicating thato7 ne duplication of vertebrate genes preceded the divergence ofd8euterostomes (including vertebrates) and protostomes (including

a/ rthropods)


e� ffects, there is no reason to believe that more ancientp� olyploidizations did either.

Horizontal Gene Transfer

The process of segmental joining by which verte-b

�rate Ig and TCR are assembled involves a number of

u� nique proteins, including the recombination activatorsg� enes 1 (RAG1) and RAG2. BERNSTEIN et al.4

9 observed

some amino acid sequence similarity between RAG1a nd RAG2 and certain bacterial integrases, involved int

�he bacterial site-specific recombination system, and

p� roposed that the ancestors of RAG1 and RAG2 wereh

�orizontally transferred from bacteria to vertebrates

e� arly in vertebrate history. However, RAG1 and RAG2

a lso show similarity to eukaryotic DNA-binding pro-t

�eins. For example, RAG1 shows similarity throughout

its length to yeast RAD18 and related fungal DNA--binding proteins; the regions of greatest similarity arei

�llustrated in Fig. 4. These are the zinc-finger domain

a nd two other regions of unknown function, one ofw� hich overlaps the region of similarity with bacterialF

"im B pointed out by BE

:RNSTEIN et al.4 RAG2 shows

similarity to another yeast DNA-binding protein, SAS.These resemblances suggest that the ancestors of RAG1a nd RAG2 may have been present in the eukaryotica ncestors. Thus, sequence comparisons alone providen� o compelling reason for accepting the extraordinarym� echanism of horizontal gene transfer.

Recently, experimental evidence that RAG1 and

Fig. 4. Portions of an alignment (constructed with the CLUSTAL V program9;) of vertebrate RAG1 with RAD18 of yeast (S

<accharomyces

c= erevisiae) and related fungal DNA-binding proteins (from Emericella nidulans a/ nd N>

eurospora crassa). The numbers of residues inh?uman RAG1 are indicated. “ * ” indicates a residue conserved in all sequences; “ .” indicates a position having chemically similar residues

in all sequences

3�

– Archivum Immunologiae... 6/99


R@

AG2 together can act as a transposase in vitro h�as

b�een taken as supporting the hypothesis that these genes

o riginated in an ancient transposable element that wassomehow “ tamed” and adapted to its immune systemfunction by ancient vertebrates1, 10, 32. While consistentw� ith this hypothesis, the transposase-like features ofR

@AG1 and RAG2 do not in themselves prove it. We

know at present essentially nothing about the origin oft

�ransposable elements. For example, it is possible that

t�ransposable elements have themselves originated from

recombination-promoting genes that have “escaped”from genomes of cellular organisms, rather than suchg� enes being “ tamed” transposable elements. Further-more, it is possible that the transposase-like featrues ofR

@AG1 and RAG2 have simply arisen as a fortuitous

b�y-product of these molecules’ function in segmental

rearrangement. Certainly, these results raise an interes-t

�ing possibility regarding the origin of RAG1 and

R@

AG2, but at present it is no more than a possibility.

Conclusions

Two major types of “catastrophic” events have beena lleged to play a role in the origin of vertebrate specifici

�mmunity: 1) genome duplication; and 2) horizontalg� ene transfer. There is no good evidence for the former,a nd indeed there are theoretical reasons for doubtingt

�hat genome duplication could give rise to important

a daptive changes. As regards the exogenous origin ofRAG1 and RAG2, it remains only one of several viableh

�ypotheses. From the point of view of scientific

method, it seems important to be skeptical of claims ofu� nique genetic events early in vertebrate history untilmore substantial evidence becomes available. Molecu-lar data are now giving us indications that the inde-p� endent evolution of the vertebrate lineage has occu-p� ied a much longer time than was previously supposed.This longer time frame makes it quite conceivable thatt

�he unique adaptations of vertebrates, including those

o f the specific immune system, arose by the ordinaryp� rocesses of gene duplication, recombination, drift, andnatural selection that we can observe in more recentp� opulations.

References

1. AGA

RAWAL A., EASTMANN Q. E. and SCB

HATZ D. G. (1998):Transposition mediated by RAG1 and RAG2 and its implica-tions for the evolution of the immune system. Nature, 394,�744–751.

2. AMC

ORES A., FOD

RCE A., YAE

N Y. -L., JOD

LY L., AMC

EMIYA C.,FR

FITZ A., HO

D R. K., LAE

NGELAND J., PRF

INCE V., WAE

NG Y. -L.,WESTERFIELD M., EKKER M. and PO

DSTLETHWAIT J. H. (1998):

ZG

ebrafish hox clusters and vertebrate genome evolution.SH

cience, 282,� 1711–1714. 3. BA

ERCLAY A. N., BE

IYERS A. D., BI

JRKELAND M. L., BR

FOWN

M. H., DAVIS S. J., SOD

MOZA C. and WILLIAMS A. F. (1993):The leucocyte antigens factsbook. Academic Press, London.

4. BEI

RNSTEIN R. M., SCB

HLUTER S. F., BEI

RNSTEIN H. and MAE

R-

CB

HALONIS J. J. (1996): Primordial emergence of the recombina-tKion activating gene 1 (RAG1): sequence of the complete shark

gL ene indicates homology to microbial integrases. Proc. Natl.A�

cad. Sci. USA, 93,� 9454–9459. 5. BISBEE C. A., BAKER M. A., WILSON A. C., IRANDOKHT H. -A.

a/ nd FIJSCHBERG M. (1977): Albumin phylogeny for clawed

frogs (Xenopus). Science, 195, 785–787. 6. CA

ERROLL R. L. (1988): Vertebrate paleontology and evolution.

WM

. H. Freeman, New York. 7. HA

EBICHT G. S. (1994): Primordial immunity: foundations for

tKhe vertebrate immune system. Ann. NY Acad. Sci., 712, ix–xi.

8. HALDANE J. B. S. (1957): The cost of natural selection.JN. Genet., 55, 511–524.

9. HIGGINS D. G., BLEASBY A. J. and FUO

CHS R. (1992): ClustalVP

: improved software for multiple sequence alignment. Com-p6 ut. Appl. Biosci., 8

Q, 189–191.

10. HIJOM K., ME

ILEK M. and GE

ILLERT M. (1998): DNA transposi-

tKion by the RAG1 and RAG2 proteins: a possible source of

o7 ncogenic translocations. Cell, 94, 463–470.11. HU

OGHES A. L. (1994): The evolution of functionally novel pro-

tKeins after gene duplication. Proc. R. Soc. Lond. Biol. Sci., 256,

119–124.12. HU

OGHES A. L. (1999): Phylogenies of developmentally import-

a/ nt proteins do not support the hypothesis of two rounds ofgL enome duplication early in vertebrate history. J. Mol. Evol. 48,5R65–576.

13. HUO

GHES A. L. (1998): Protein phylogenies provide evidence ofa/ radical discontinuity between arthropod and vertebrate im-mune systems. Immunogenetics, 47, 283–296.

14. HUO

GHES A. L. (1999): Adaptive evolution of genes andgL enomes. Oxford University Press, New York.

15. HUO

GHES M. K. and HUO

GHES A. L. (1993): Evolution of dupli-cS ate genes in a tetraploid animal, Xenopus laevis.T Mol. Biol.EU

vol., 1V

0,� 1360–1369.16. HU

OLTMARK D. (1993): Immune reactions in Drosophila and

o7 ther insects: a model for innate immunity. Trends Genet.,9W, 178–183.

17. JENSEN R. A. (1976): Enzyme recruitment in the evolution ofnX ew function. Ann. Rev. Microbiol., 30, 409–425.

18. KAE

SAHARA M. (1998): What to the paralogous regions in thegL enome tell us about the origin of the adaptive immune system?Immunol. Rev., 166,� 159–175.

19. KAE

SAHARA M., NAE

KAYA J., SAE

TTA Y. and TAE

KAHATA

NY

. (1997): Chromosomal duplication and the emergence of thea/ daptive immune system. Trends Genet., 1

V3,� 90–92.

20. KIMURA M. (1968): Evolutionary rate at the molecular level.NY

ature, 217,� 624–626.21. KLEIN J., SATO A. and O’HU

OIGIN C. (1998): Evolution by gene

d8uplication in the major histocompatibility complex. Cytogenet.

CZ

ell Genet., 80, 123–127.22. KU

OMAR S. and HEDGES S. B. (1998): A molecular timescale for

v4 ertebrate evolution. Nature, 3[

92, 917–920.23. LU

ONDIN L. G. (1993): Evolution of the vertebrate genome as

reflected in paralogous chromosomal regions in man and housemouse. Genomics, 16, 1–19.


2\4. MA

ERCHALONIS J. J., SC

BHLUSTER S. F., BE

IRNSTEIN R. M. and

HOD

HMAN V. S. (1998): Antibodies of sharks: revolution andevolution. Immunol. Rev., 1

V66, 103–122.

25. OHNO S. (1970): Evolution by gene duplication. Springer, NewYork.

2\6. OH

]NO S. (1973): Ancient linkage groups and frozen accidents.

Nature, 244, 259–262.27. ORGEL L. E. (1977): Gene-duplication and the origin of pro-

teins with novel functions. J. Theor. Biol., 67,� 773.2\8. PI

JATIGORSKY J. and WI

JSTOW G. (1991): The recruitment of

crystallins: new functions precede gene duplication. Science,252,� 1078–1079.

29. PLASTERK R. (1998): Ragtime jumping. Nature, 3[

94, 718–719.3^0. RA

EST J. P. and LI

JTMAN G. W. (1998): Towards understanding

the evolutionary origins and early diversification of rearrangingantigen receptors. Immunol. Rev., 166, 79–86.

31. SAE

ITOU N. and NEI

I M. (1987): The neighbor-joining method:a/ new method for reconstructing phylogenetic trees. Mol. Biol.EU

vol., 4�, 406–425.

32. SIDOW A. (1996): Gen(om)e duplications in the evolution ofe5 arly vertebrates. Curr. Opin. Genet. Dev., 6

_, 715–722.

33. SK`

RABANEK L. and WOD

LFE K. H. (1998): Eukaryote genomed8uplication: where is the evidence? Curr. Opin. Genet. Dev.,

8Q, 694–700.

34. WANG D. Y., KUO

MAR S. and HEDGES S. B. (1999): DivergencetKime estimates for the early history of animal phyla and the

o7 rigin of plants, animals, and fungi. Proc. R. Soc. Lond. Biol.SH

ci., 266,� 163–171.

Received in April 1999Accepted in June 1999


genomic catastrophism and the origin of vertebrate immunity · i n which “catastrophism” refers...

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