x-ray astronomy: peeking into the obscured universe

3
than 99% has been determined. The critical question is how much important sequence might still be missing. The problem can be assessed objectively, because partial or com- plete sequence data are already available for 2,783 fly genes. Only six of these known genes were found to be missing from the assembled sequence, so a reasonable finish- ing line has been reached. Now the fun begins for the annotators and the rest of the scientific community. Many broad features of the genome immedi- ately become apparent. One long-standing question, the number of genes in Drosophila, has a surprising answer: annotation and gene-prediction programs suggest that there are 13,600, barely twice the number found in yeast and decidedly lower than the estimates for Caenorhabditis elegans (more than 19,000, according to current annotation) 3 and the flowering plant Arabidopsis thaliana (around 27,000) 10 , although all three organ- isms have much the same DNA content (excluding heterochromatin). So the num- bers of genes in fly, worm and weed are ranked in exactly the opposite order to that expected from simple estimates of anatomi- cal complexity, cell-type diversity and so on. However, the differences might be illuso- ry: plants might make less use of alternative splicing of messenger RNA than do animals, instead employing larger gene families. Caenorhabditis elegans also carries more duplicated genome segments than Drosophi- la melanogaster, again resulting in more genes. Overall, the effective complexity of the protein complements of the three organ- isms might be similar. In addition, by some criteria fly proteins are more complex, in that many carry multiple different domains. In the most fascinating of the articles accompanying the Drosophila genome sequence, Rubin et al. 5 compare the contents of the three eukaryotic genomes now avail- able for comprehensive scrutiny. As expect- ed, about 3,000 genes are shared between yeast, fruitfly and nematode, encoding the basic machineries of eukaryotic cell biology. The two animal genomes, however, share many features that are not found in yeast. Rubin et al. provide a list of the 200 most fre- quently occurring protein-coding domains in the fly genome, of which about 25% are completely absent from yeast. In contrast, members of almost all 200 families occur in both fly and nematode, often in remarkably similar numbers. There are some disparities, but many are explicable: for example, flies have many genes encoding cuticle proteins and chitin- binding proteins, whereas nematodes lack these but have many collagen genes, required for their collagenous cuticles. Some other differences are more a matter of relative usage in major transcription-factor families: flies have more C2H2-class zinc-finger proteins, more homeobox proteins, fewer nuclear receptors and so on. The general conservation between fruitfly and nematode strongly reinforces the belief that there is a basic gene kit for all animal development and physiology, and one can therefore expect that the distribution of gene families in vertebrates will not be very different. This expectation is supported by a search for counterparts of human disease genes in the fly genome. Of 289 such genes, 177 (61%) have clear equivalents in the Drosophila sequence, several of them being identified for the first time. Examples of new discoveries include genes encoding the tumour suppressor p53 (the ‘guardian of the genome’), MEN (involved in multiple endocrine neoplasia), tau and Parkin (both involved in neurological disease). The avail- ability of these as complete sequences in a model organism with so many practical advantages creates a host of new experimen- tal opportunities. Some properties of the fly genome look both idiosyncratic and intriguing, such as the large number of trypsin-like proteases (199 in all). No other organism known con- tains anything resembling this enormously amplified family of proteins. Most striking, however, is the substantial percentage of pre- dicted genes with unknown function and no obvious homologue in any other organism: about 22%. This is a good reminder that even after 90 years of research on the geneticist’s favourite animal 7 , there is still a lot to be learned. Jonathan Hodgkin is in the Genetics Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK. e-mail: [email protected] 1. Adams, M. D. et al. Science 287, 2185–2195 (2000). 2. Goffeau, A. et al. Science 274, 546–567 (1996). 3. C. elegans Sequencing Consortium Science 282, 2012–2018 (1998). 4. Myers, E. W. et al. Science 287, 2196–2204 (2000). 5. Rubin, G. M. et al. Science 287, 2204–2215 (2000). 6. Rubin, G. M. et al. Science 287, 2222–2224 (2000). 7. Rubin, G. M. & Lewis, E. B. Science 287, 2216–2218 (2000). 8. Kornberg, T. B. & Krasnow, M. Science 287, 2218–2220 (2000). 9. Benos, P. V. et al. Science 287, 2220–2222 (2000). 10. Lin, X. et al. Nature 402, 761–768 (1999). news and views NATURE | VOL 404 | 30 MARCH 2000 | www.nature.com 443 W hy is it dark at night? If we lived in an infinite Universe uniformly filled with stars, then every line of sight should eventually end up on the surface of a star and the night sky should appear as bright as the surface of the Sun 1 . It was Edgar Allan Poe 2 who eventually found a solution to this puzzle, known as Olbers’ paradox: the stars have not had enough time to fill the Universe with light. Today the brightness of the Uni- verse has been measured over a wide range of electromagnetic frequencies, from radio to high-energy gamma rays (Fig. 1, overleaf), and cosmologists are turning Olbers’ ques- tion around. What can we learn from the brightness of the sky about the nature and cosmological evolution of objects in our Universe? On page 459 of this issue, Mushotzky et al. 3 report the first deep obser- vations of the cosmic X-ray background (CXB) with the Chandra satellite — the sharpest X-ray eye around. The question of whether the CXB is pro- duced by uniform emission from a diffuse intergalactic gas at a temperature of a few million degrees, or by radiation from many individual sources, was settled in the 1990s. First, the COBE satellite did not detect a tiny deviation from the perfect 2.7 K blackbody spectrum of the cosmic micro- wave background (CMB; Fig. 1), which would be expected if the radiation were seen through a screen of hot intergalactic gas. Second, the majority of the ‘soft’ X-ray background (1210 17 –5210 17 Hz) was re- solved into discrete sources by the X-ray satellite ROSAT. These sources are mostly distant active galaxies (active galactic nuclei, or AGN), containing massive black holes accreting matter from their environ- ment 4 . The X-ray background should represent the summed emission of all these discrete sources, but the CXB has a spectral shape completely different from the spectra of individual AGN measured at X-ray frequen- cies. The spectrum of the CXB has a charac- teristic peak at about 10 19 Hz (Fig. 1), corre- sponding roughly to the radiation that medical doctors use to ‘X-ray’ our bones, whereas the AGN have a flat or slightly concave distribution over the whole X-ray range. A solution to this long-standing puz- zle was proposed in 1989, namely that most sources of the X-ray background could be heavily obscured by gas and dust clouds 5 , much like our bones absorb the doctor’s X-rays. The higher-energy (‘hard’) X-rays can penetrate the obscuring clouds, whereas ‘soft’ photons are absorbed, so that the over- all spectrum is different from that of individ- ual AGN. Models using this idea can reproduce the shape of the observed CXB by assuming sources at various distances and obscured by different amounts of gas 6 . The most impor- tant conclusion from these models is that most (80–90%) of the light produced by X-ray astronomy Peeking into the obscured Universe Günther Hasinger © 2000 Macmillan Magazines Ltd

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Page 1: X-ray astronomy: Peeking into the obscured Universe

than 99% has been determined. The criticalquestion is how much important sequencemight still be missing. The problem can beassessed objectively, because partial or com-plete sequence data are already available for2,783 fly genes. Only six of these knowngenes were found to be missing from theassembled sequence, so a reasonable finish-ing line has been reached.

Now the fun begins for the annotatorsand the rest of the scientific community.Many broad features of the genome immedi-ately become apparent. One long-standingquestion, the number of genes in Drosophila,has a surprising answer: annotation andgene-prediction programs suggest that thereare 13,600, barely twice the number found inyeast and decidedly lower than the estimatesfor Caenorhabditis elegans (more than19,000, according to current annotation)3

and the flowering plant Arabidopsis thaliana(around 27,000)10, although all three organ-isms have much the same DNA content(excluding heterochromatin). So the num-bers of genes in fly, worm and weed areranked in exactly the opposite order to thatexpected from simple estimates of anatomi-cal complexity, cell-type diversity and so on.

However, the differences might be illuso-ry: plants might make less use of alternativesplicing of messenger RNA than do animals,instead employing larger gene families.Caenorhabditis elegans also carries moreduplicated genome segments than Drosophi-la melanogaster, again resulting in moregenes. Overall, the effective complexity ofthe protein complements of the three organ-isms might be similar. In addition, by somecriteria fly proteins are more complex, in thatmany carry multiple different domains.

In the most fascinating of the articlesaccompanying the Drosophila genomesequence, Rubin et al.5 compare the contentsof the three eukaryotic genomes now avail-able for comprehensive scrutiny. As expect-ed, about 3,000 genes are shared betweenyeast, fruitfly and nematode, encoding thebasic machineries of eukaryotic cell biology.The two animal genomes, however, sharemany features that are not found in yeast.Rubin et al. provide a list of the 200 most fre-quently occurring protein-coding domainsin the fly genome, of which about 25% arecompletely absent from yeast. In contrast,members of almost all 200 families occur inboth fly and nematode, often in remarkablysimilar numbers.

There are some disparities, but many areexplicable: for example, flies have manygenes encoding cuticle proteins and chitin-binding proteins, whereas nematodes lackthese but have many collagen genes, requiredfor their collagenous cuticles. Some otherdifferences are more a matter of relativeusage in major transcription-factor families:flies have more C2H2-class zinc-fingerproteins, more homeobox proteins, fewer

nuclear receptors and so on. The generalconservation between fruitfly and nematodestrongly reinforces the belief that there is abasic gene kit for all animal development andphysiology, and one can therefore expectthat the distribution of gene families invertebrates will not be very different.

This expectation is supported by a searchfor counterparts of human disease genesin the fly genome. Of 289 such genes, 177(61%) have clear equivalents in theDrosophila sequence, several of them beingidentified for the first time. Examples of newdiscoveries include genes encoding thetumour suppressor p53 (the ‘guardian of thegenome’), MEN (involved in multipleendocrine neoplasia), tau and Parkin (bothinvolved in neurological disease). The avail-ability of these as complete sequences in amodel organism with so many practicaladvantages creates a host of new experimen-tal opportunities.

Some properties of the fly genome lookboth idiosyncratic and intriguing, such as

the large number of trypsin-like proteases(199 in all). No other organism known con-tains anything resembling this enormouslyamplified family of proteins. Most striking,however, is the substantial percentage of pre-dicted genes with unknown function and noobvious homologue in any other organism:about 22%. This is a good reminder that evenafter 90 years of research on the geneticist’sfavourite animal7, there is still a lot to belearned. ■Jonathan Hodgkin is in the Genetics Unit,Department of Biochemistry, University of Oxford,South Parks Road, Oxford OX1 3QU, UK.e-mail: [email protected]

1. Adams, M. D. et al. Science 287, 2185–2195 (2000).

2. Goffeau, A. et al. Science 274, 546–567 (1996).

3. C. elegans Sequencing Consortium Science 282, 2012–2018

(1998).

4. Myers, E. W. et al. Science 287, 2196–2204 (2000).

5. Rubin, G. M. et al. Science 287, 2204–2215 (2000).

6. Rubin, G. M. et al. Science 287, 2222–2224 (2000).

7. Rubin, G. M. & Lewis, E. B. Science 287, 2216–2218 (2000).

8. Kornberg, T. B. & Krasnow, M. Science 287, 2218–2220 (2000).

9. Benos, P. V. et al. Science 287, 2220–2222 (2000).

10.Lin, X. et al. Nature 402, 761–768 (1999).

news and views

NATURE | VOL 404 | 30 MARCH 2000 | www.nature.com 443

Why is it dark at night? If we lived inan infinite Universe uniformly filledwith stars, then every line of sight

should eventually end up on the surface of astar and the night sky should appear as brightas the surface of the Sun1. It was Edgar AllanPoe2 who eventually found a solution to thispuzzle, known as Olbers’ paradox: the starshave not had enough time to fill the Universewith light. Today the brightness of the Uni-verse has been measured over a wide range ofelectromagnetic frequencies, from radio tohigh-energy gamma rays (Fig. 1, overleaf),and cosmologists are turning Olbers’ ques-tion around. What can we learn from thebrightness of the sky about the nature andcosmological evolution of objects in ourUniverse? On page 459 of this issue,Mushotzky et al.3 report the first deep obser-vations of the cosmic X-ray background(CXB) with the Chandra satellite — thesharpest X-ray eye around.

The question of whether the CXB is pro-duced by uniform emission from a diffuseintergalactic gas at a temperature of afew million degrees, or by radiation frommany individual sources, was settled in the1990s. First, the COBE satellite did notdetect a tiny deviation from the perfect 2.7 Kblackbody spectrum of the cosmic micro-wave background (CMB; Fig. 1), whichwould be expected if the radiation were seenthrough a screen of hot intergalactic gas.Second, the majority of the ‘soft’ X-ray

background (121017–521017 Hz) was re-solved into discrete sources by the X-raysatellite ROSAT. These sources are mostlydistant active galaxies (active galacticnuclei, or AGN), containing massive blackholes accreting matter from their environ-ment4.

The X-ray background should representthe summed emission of all these discretesources, but the CXB has a spectral shapecompletely different from the spectra ofindividual AGN measured at X-ray frequen-cies. The spectrum of the CXB has a charac-teristic peak at about 1019 Hz (Fig. 1), corre-sponding roughly to the radiation thatmedical doctors use to ‘X-ray’ our bones,whereas the AGN have a flat or slightlyconcave distribution over the whole X-rayrange. A solution to this long-standing puz-zle was proposed in 1989, namely that mostsources of the X-ray background could beheavily obscured by gas and dust clouds5,much like our bones absorb the doctor’sX-rays. The higher-energy (‘hard’) X-rayscan penetrate the obscuring clouds, whereas‘soft’ photons are absorbed, so that the over-all spectrum is different from that of individ-ual AGN.

Models using this idea can reproduce theshape of the observed CXB by assumingsources at various distances and obscured bydifferent amounts of gas6. The most impor-tant conclusion from these models is thatmost (80–90%) of the light produced by

X-ray astronomy

Peeking into the obscured UniverseGünther Hasinger

© 2000 Macmillan Magazines Ltd

Page 2: X-ray astronomy: Peeking into the obscured Universe

accretion onto black holes in the early Uni-verse should be obscured, and is probablyre-radiated, by warm dust in the cosmicinfrared background (CIB; Fig. 1). Butbecause of several uncertain ingredients, thepredictive power of these models remainslimited.

The new Chandra data expand the rangeof previous observations significantly. In thesoft X-ray band they beautifully confirm andextend the ROSAT results to roughly four-fold fainter limits. In the hard X-ray band(521017–2521017 Hz) they provide the firsthigh-quality images ever. The new Chandrasources must therefore be further away (athigher redshifts) or more obscured thanthose previously found. The Chandraimages resolve at least 75% of the hard X-raybackground into discrete sources, and it isreassuring to find that the average spectrumof Chandra sources is now consistent withthe background spectrum. The Chandraresults broadly agree with models thatassume a large population of obscured galac-tic nuclei, which at optical wavelengths areexpected to be very faint or to reside in nor-mal-looking galaxies. This seems to be exact-ly what Chandra has found.

The most tedious work lies ahead in theoptical identification and classification ofthe X-ray sources and the determination of

their redshift, which is a crucial ingredientfor the models. The location of this Chandrasurvey — the Hawaii deep field — was wellchosen for this purpose, because a largenumber of deep multiwavelength dataalready exists. But Mushotzky et al.3 showthat there are many optically faint objects,for which even the giant Keck telescope is notpowerful enough to obtain redshifts — theobscured Universe is a hard subject to study.Future observatories such as the Next Gener-ation Space Telescope or the Atacama LargeMillimeter Array will be required to studysome of the objects that Chandra detected.X-ray spectrophotometry with more power-ful X-ray telescopes such as the recentlylaunched Newton (XMM) observatory,or the planned XEUS mission in thedistant future, may also help because theymight be able to estimate redshifts fromX-ray data alone.

One concern in the present study3 is therelatively small size of the chosen survey. TheROSAT experience has shown that a largenumber of survey fields with different sensi-tivities and coverages are required for deter-mining the distribution of AGN and theircosmological evolution. In particular thequestion of whether massive black holesformed at the same time as, or even before,the first galaxies requires much larger sur-

news and views

NATURE | VOL 404 | 30 MARCH 2000 | www.nature.com 445

Figure 1 The energy density spectrum of the Universe over the whole electromagnetic spectrum fromradio to gamma rays7. The four distinct peaks correspond to different cosmologically importantemission processes.The 2.7 K cosmic microwave background (CMB) reflects the ‘echo of the hot BigBang’. The recently discovered cosmic infrared (CIB) and optical (COB) backgrounds are probablyemitted by warm dust and normal stars, respectively, with an unknown contribution from activegalactic nuclei (AGN). The cosmic X-ray background (CXB), discovered 38 years ago, shows acharacteristic peak at 1019 Hz , which is probably shaped by AGN obscured by dust. The energy bandcovered by the new Chandra observations3 is shown in white. The vertical axis corresponds to thepower emitted by the Universe per energy decade, making it clear that the CMB dominates the totalenergy output of the Universe.

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100 YEARS AGOThere are many people who write aboutexperiments upon animals, but only very fewwho have under their constant notice theactual facts relevant to the subject. In thisconnection, not merely is a knowledge offact required, but an intellectuality capableof appreciating the significance of fact. Theperson most competent from this standpointis one of the Inspectors under the Act. TheseInspectors are most carefully chosen by theHome Office on account of specialqualifications which they possess…. Itwould not, however, be comely for a personholding an official appointment to write abook upon the subject-matter of his office.Every vivisector, a terrible term by which todesignate any one who merely pricks aguinea-pig, knows full well that no one, withthe above exceptions, is more entitled towrite upon the subject of animalexperiments than Mr. Stephen Paget, who fortwelve years was the active and long-suffering secretary of the Society for theAdvancement of Medicine by Research.From Nature 29 March 1900.

50 YEARS AGOFor the past three or four years, there hasbeen great congestion of the portion ofNature appearing under the title of “Lettersto the Editors”. Since these ‘letters’ havecome to be regarded as the usual mode ofannouncement of the results of new work —interim reports in most cases — this wasperhaps inevitable in view of the greatoutburst of scientific activity throughout theworld. A further factor was the enforcedreduction in size, or even the disappearance,of many of the specialist organs of scientificpublication during the war period. Oneunfortunate result of the great pressure onour space has been the irritating butunavoidable delays in publication, whichhave been, and are still, a matter of graveconcern to the Editors, correspondents andreaders. At one period an attempt was madeto reduce such delays by using smaller type,so that a greater number of letters could befitted into the same amount of space.Experience showed, however, that the greatinconvenience and strain caused by the useof this small type were not worth the space‘gained’. As soon, therefore, as more papercould be used, we reverted to the usual typeand the number of pages devoted to ‘letters’was increased. From Nature 1 April 1950.

© 2000 Macmillan Magazines Ltd

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veys. Fortunately, several groups around theworld have started deep Chandra and New-ton observations in other, well-studiedfields. A great deal of interesting work liesahead. ■

Günther Hasinger is at the Astrophysical InstitutePotsdam, An der Sternwarte 16, 14482 Potsdam,Germany.e-mail: [email protected]

1. Olbers, H. W. M. in Astron. Jahrb. für das Jahr 1826 (ed.Bode, J.) 110–121 (Späthen, Berlin, 1923).

2. Poe, E. A. Eureka, a Prose Poem (1848).3. Mushotzky, R., Cowie, L., Barger, A. & Arnaud, K. Nature 404,

459–464 (2000).4. Schmidt, M. et al. Astron. Astrophys. 329, 495–503 (1998).5. Setti, G. & Woltjer, L. Astron. Astrophys. 224, L21–L24 (1989).6. Comastri, A., Setti, G., Zamorani, G. & Hasinger, G. Astron.

Astrophys. 296, 1–12 (1995).7. Hasinger, G. in ISO Surveys of a Dusty Universe (eds Lemke, D.,

Stickel, M. & Wilke, K.)(Springer Lecture Notes, Berlin, in thepress).

important insectivorous birds of the region.The authors also surveyed the hunting activ-ity of avian predators, including raptors suchas kestrel (Falco tinnunculus), sparrowhawk(Accipiter nisus), rough-legged buzzard(Buteo lagopus), northern goshawk (Accip-iter gentilis) and hawk owl (Surnia ulula).

Migratory insectivorous birds, such asthe sand martin, are able to exploit the abun-dant insect life of the high-latitude summersand are thought to find the long days advan-tageous when feeding their young. Speak-man et al.’s observations showed, however,that there was a period between 24:00 and3:00 when sand-martin activity ceased andthe adult birds were believed to be resting intheir nest burrows. Excessive physical stresscan suppress the immune system of birdsand leave them susceptible to disease3, so a‘nocturnal’ rest period seems to be needed.The density of aerial insects correspondedclosely with the aerial temperature curve,with lowest insect abundance occurringbetween 22:00 and 6:00. So, the sand martinschoose to rest at a time when insects are lessavailable.

The records of the raptors’ activity areless reliable because of their fewer numbers,but overall hunting appeared to be equallyintense at all times of the 24-hour day,although different species and individualswere probably involved at different times.The bat activity, on the other hand, was con-centrated in the period 22:00 to 2:00. Duringthis time, insect density was at its lowest, butraptor activity continued unabated. Faecalanalysis showed that the bats were feedinglargely upon small flies of the order Diptera,which are also the preferred food of thesand martins, so there was no indication ofinsectivores partitioning their resources byhunting different prey, such as moths,during the ‘night’.

The evidence indicates, therefore, thatbats avoid the feeding time of the birds andare competing for the same food resource.Their pattern of activity does not seem to berelated to the risk of predation by predatorybirds. But the case is not closed because a fewalternative explanations remain. Speakmanet al.1 are concerned that their measure-ments of raptor activity may not correspondwith actual risks of predation. As these birdsdepend on vision for their hunting, the low-ering of light intensities in the middle of the‘night’ could reduce their efficiency andimprove the bats’ survival chances. This isnot true of all raptors, however. Observa-tions of the kestrel in lower latitudes haveshown that this falcon eats bats and can huntin low-light, crepuscular conditions. It oftenhunts wood mice (Apodemus sylvaticus), anocturnal mammal, and has even beenobserved hunting by moonlight4.

There is also the problem of the relativelylow overall density of both bats and sandmartins, which raises the question of

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446 NATURE | VOL 404 | 30 MARCH 2000 | www.nature.com

Why do bats fly at night rather thanduring the day? There are exceptions,of course, but most bats confine their

activities to dusk and the depths of night.The insect-eating bats of the higher latitudes,in particular, are night-time hunters and areequipped with sophisticated techniques forthe non-visual location of prey. There areseveral possible advantages that could beassociated with nocturnal feeding, such asthe avoidance of predators or mobbing bybirds, the tapping of a food resource unex-ploited by other insectivores, or sensitivity tothe problems of overheating when active indaylight. In a study of bats, insectivorousbirds and predators in northern Norway,Speakman and colleagues1, reporting inOikos, conclude that the avoidance ofcompetition for food is the most likelyanswer.

The question has been debated for manyyears. Nearly ten years ago, Speakman2

measured the effects of day-time flying onthe activity of bats, and found that they werereluctant to fly in the light, but were notfurther deterred by high temperatures. Thebody temperatures of bats after they hadflown in the light and in the dark did not dif-fer significantly, so the overheating hypothe-sis can be rejected. It is also unlikely that batsfly at night to avoid being mobbed by birds,as there are relatively few observations of thisoccurring and no records of serious harmbeing done to any bullied bat.

Avoidance of predation or of competitionfor food therefore remain the most plausibleexplanations for night flying. Speakman etal.1 have now investigated the relative impor-tance of these two possibilities by choosing astudy site within the Arctic circle in summer,for which there is no distinctly dark periodand where one might expect to see some cor-responding response from birds and bats,together with the higher predators. Theirstudy was based in northern Norway, at lati-tude 69° N, in early July, when the daylightintensity declines during the period 23:00 to4:00, but darkness is never total. The temper-ature also declined during the ‘night’, from a

‘daytime’ high of around 22 °C to a low ofabout 9 °C between 2:00 and 4:00.

The authors surveyed the abundance offlying insects throughout the day and night,using a simple technique of sweep-nettingthe air over a defined sample route. Byobserving a bat roost (an abandoned humandwelling), Speakman et al. were able to esti-mate the activity and flight periods of thenorthern bat, Eptesicus nilssonii (Fig. 1).Similar 24-hour observations of a colony ofnesting sand martins (Riparia riparia; Fig. 1)provided data about the activity of one of the

Ecology

Bats about the ArcticPeter D. Moore

Figure 1 The northern bat (top) and nesting sandmartins (bottom). It seems that northern batshunt at night to avoid competing with sandmartins for prey1. This may provide a generalexplanation for nocturnal flight in bats.

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© 2000 Macmillan Magazines Ltd