- Email: [email protected]
To boldly sequence
Update
TRENDS in Ecology and Evolution
amount of ‘paleo-pornography.’ Anyone who has seen the caves of southern France and northern Spain is familiar with the ever-present vulva-like triangles and the occasional phallic imagery. But Guthrie digs much deeper, featuring and interpreting couples in coitus in a diverse array of positions. One gathers from this section that, although Pleistocene life might have been relatively short and brutal, these were also fun-loving folks. Besides sex, there is plenty of violence (‘testosterone events’ in Guthrie’s parlance). Balancing the familiar scenes of speared and bleeding megafauna, there are less familiar scenes clearly depicting humans under attack by bears and other fearsome creatures. Yet there is a lack of evidence for warfare in the Pleistocene, a powerful contrast with Neolithic art. One of the most interesting parts of the book should challenge potentially skeptical anthropologists and art historians. Guthrie makes a compelling stab at the question that has goaded the experts from the beginning of Paleolithic art studies: Why is this art, spanning nearly 30 millennia, so stylistically consistent and realistic, almost photographically so? And why did it stop? What happened
Vol.21 No.11
603
to make subsequent art of Neolithic agrarian peoples more symbolic and, in general, less visually accurate? You will have to read the book to get the whole story, although the gist of the answer is that big-game hunters are obligate empiricists. Tracking, stalking and killing with rudimentary weapons animals that can easily kill you requires a certain devotion to the bare facts that settled life in the village does not. The no-nonsense biggame bowhunter in the author comes to the fore here, and appropriately so. This tome is well worth buying for many reasons. It is a scholarly work by an expert uniquely qualified to reinterpret a subject too long dominated by religious themes when a more literal interpretation might serve as well or better. It is also a superb ‘coffee-table’ book. His rendering of the art is clear and compelling. One can open the huge volume to any page and be drawn in, instantly transported to a Pleistocene campfire surrounded by surprisingly familiar folk. 0169-5347/$ – see front matter ß 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2006.06.014
To boldly sequence DNA Barcoding of Life edited by V. Savolainen, R.S. Cowan, A.P. Vogler and G.K. Roderick. Themed issue of the Philosophical Transactions of the Royal Society B 360, 1803–1980 (2005)
H. Charles J. Godfray NERC Centre for Population Biology, Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK, SL5 7PY
Pity the poor taxonomist! Although there is a growing consensus that serious biodiversity studies need robust and accessible taxonomy, this realisation is accompanied by rather little in the way of extra resources but by lots of helpful advice and injunctions. On the one hand, they are told to become cyberneticists, disseminating information solely through the web, while on the other, they are urged to abandon Linnean taxonomy and even species to enter a phylogenetic state of grace. Now, they must obtain diagnostic DNA sequences of all life on Earth, barcoding the biota. DNA Barcoding of Life is a collection of papers on the barcoding of life initiative, bringing together the leading enthusiasts in the field. The idea is to sequence small sections of the same gene from as many species as possible so that further specimens (including non-traditional specimens, such as juvenile stages, tissue or excreta) can be diagnosed purely by sequence comparison. Where a Corresponding author: Godfray, H.C.J. ([email protected]) Available online 30 June 2006. www.sciencedirect.com
sequence does not match, this flags up a possible undescribed species or at least the need for further research. The gene of choice for most (but not all groups) is the mitochondrial cox1, present at high copy numbers and for which fairly broad primers can be designed. The volume includes studies of a series of taxa where cox1 barcoding has worked well (e.g. tropical ants, beetles and moths, Australian fish and red algae) typically distinguishing between 95% and 100% of known species, and often revealing unappreciated diversity, both morphological and cryptic. Sometimes, problems are encountered with issues such as nonamplification and nuclear pseudogenes (e.g. in frogs and primates) and the authors suggest that further genes in addition to cox1 will need to be sequenced. In plants, cox1 is far too uniform but other plastid genes might fill the gap. Of course, barcoding by another name is routine in prokaryote taxonomy, and environmental sequence mining has revealed much new biological diversity. Eukaryote barcoding might be similarly valuable for otherwise intractable groups, as several papers on benthic meiofauna demonstrate. DNA Barcoding of Life also includes discussion on methods of scaling up the collection of barcode sequences, and the development of statistical techniques and software to handle this type of information.
Update
604
TRENDS in Ecology and Evolution Vol.21 No.11
This collection of papers suffers somewhat from the near absence of dissenting voices, given that barcoding has enraged a significant section of the taxonomic community; however, as the initiative matures and some of the early hype is tempered by experience, the role and value but also the limitations of the approach are becoming more clearly defined. In particular, barcode enthusiasts are now far more careful about claiming that this type of sequence can provide useful phylogenetic information. In general, I thought that the volume was an impressive shop window for what barcoding could deliver, and a tribute to the energy and vision of Paul Hebert, the pioneer of the movement. One aspect of barcoding that troubles many people is that it might suck resources away from more traditional taxonomy. To have barcodes for every species on Earth without further and richer information is akin to having a bare list of encyclopaedia entries. The paper by Janzen et al. in this volume eloquently emphasises the importance of marrying barcoding with traditional taxonomy, and I was also impressed by de Lay et al.’s description of an automated system for nematodes that both obtained a barcode and a multifocal digital image voucher. I do not think it naı¨ve to believe that barcoding will lead to more people using taxonomy and that this will build a constituency that will call for more support for the subject. I think that this will be infinitely easier if taxonomic
information, both new and traditional, is easily and freely available via the web. Another concern is the frequency with which barcoding enthusiasts herald the imminent development of a Star Trek style Tricorder that will enable any species to be identified instantaneously in the field (although perhaps it’s just me finding ‘trekkies’ rather scary). It is true that the pace of advance of DNA-sequencing technology is astounding [1] but we have no real idea what the technology will actually consist of ten-years hence, nor whether the painstakingly collected cox1 sequences will actually form its base. I tend to agree with the conclusion in Chase et al.’s contribution that we shall end up wanting to sequence multiple plastid and nuclear genes, although it is conceivable that totally different approaches will have been invented. But this is not an argument for delaying the barcoding initiative (although a strong one for museums and herbariums building DNA repositories), which will deliver useful tools in the near future. It’s taxonomy, Jim, but not as we know it! Reference 1 Service, R.F. (2006) Gene sequencing, the race for the $1000 genome. Science 311, 1544 0169-5347/$ – see front matter ß 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2006.06.010
Conservation, economics and celibacy: a tortoise-eye view Lonesome George: The Life and Loves of a Conservation Icon by Henry Nicholls, Macmillan, 2006. £16.99 hbk (231 pages) SBN-13 9781403945761; ISBN-10 1403945764
Justin Gerlach University Museum of Zoology, Department of Zoology, Downing Street, Cambridge, UK, CB2 3EJ
Of all known surviving animal species or subspecies, Lonesome George is the rarest, being the sole surviving Pinta island giant tortoise (‘Geochelone’ nigra abingdoni). As such, he symbolises the environmental destruction wrought by human activities, the process of extinction and the tenuous hope of recovery, and can justly be regarded as a conservation icon. Nicholls tells the story in detail, but with a light style. He has been conscientious in checking his facts and following the trail of the story. After talking to the main protagonists, he has been able to combine first-hand accounts with the few documents relating to Lonesome George. Given that the tortoise spent most of his days hidden on a remote island in the Galapagos, much remains unknown about his life, although the story since his discovery in 1971 Corresponding author: Gerlach, J. ([email protected]). Available online 27 June 2006. www.sciencedirect.com
is remarkable. Being a tortoise, most of this life has involved long years of sleeping and eating; however, in the Galapagos, nothing is constant and Lonesome George has experienced more than his fair share of upsets. He has been the reluctant participant in artificial insemination attempts and the recipient of death threats. A synopsis of his life reads like any far-fetched thriller, covering everything from bizarre sexual practices to riots and body doubles, but at a tortoise’s pace. The accidental discovery of Lonesome George in 1971 is wonderfully described by Nicholls and the story of the next 30 years makes thought-provoking reading. Despite his iconic status, no-one seems to know what to do with him. For two decades, he was kept in isolation; since 1992, attempts have been made to breed from him, but these efforts have been desultory and unsuccessful. Lonesome George symbolises the great dilemma in conservation biology: should we preserve unique taxa or recreate functioning ecosystems? Ideally the two go together, but there are situations where a genetic purity ideal might prove
TRENDS in Ecology and Evolution
amount of ‘paleo-pornography.’ Anyone who has seen the caves of southern France and northern Spain is familiar with the ever-present vulva-like triangles and the occasional phallic imagery. But Guthrie digs much deeper, featuring and interpreting couples in coitus in a diverse array of positions. One gathers from this section that, although Pleistocene life might have been relatively short and brutal, these were also fun-loving folks. Besides sex, there is plenty of violence (‘testosterone events’ in Guthrie’s parlance). Balancing the familiar scenes of speared and bleeding megafauna, there are less familiar scenes clearly depicting humans under attack by bears and other fearsome creatures. Yet there is a lack of evidence for warfare in the Pleistocene, a powerful contrast with Neolithic art. One of the most interesting parts of the book should challenge potentially skeptical anthropologists and art historians. Guthrie makes a compelling stab at the question that has goaded the experts from the beginning of Paleolithic art studies: Why is this art, spanning nearly 30 millennia, so stylistically consistent and realistic, almost photographically so? And why did it stop? What happened
Vol.21 No.11
603
to make subsequent art of Neolithic agrarian peoples more symbolic and, in general, less visually accurate? You will have to read the book to get the whole story, although the gist of the answer is that big-game hunters are obligate empiricists. Tracking, stalking and killing with rudimentary weapons animals that can easily kill you requires a certain devotion to the bare facts that settled life in the village does not. The no-nonsense biggame bowhunter in the author comes to the fore here, and appropriately so. This tome is well worth buying for many reasons. It is a scholarly work by an expert uniquely qualified to reinterpret a subject too long dominated by religious themes when a more literal interpretation might serve as well or better. It is also a superb ‘coffee-table’ book. His rendering of the art is clear and compelling. One can open the huge volume to any page and be drawn in, instantly transported to a Pleistocene campfire surrounded by surprisingly familiar folk. 0169-5347/$ – see front matter ß 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2006.06.014
To boldly sequence DNA Barcoding of Life edited by V. Savolainen, R.S. Cowan, A.P. Vogler and G.K. Roderick. Themed issue of the Philosophical Transactions of the Royal Society B 360, 1803–1980 (2005)
H. Charles J. Godfray NERC Centre for Population Biology, Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire, UK, SL5 7PY
Pity the poor taxonomist! Although there is a growing consensus that serious biodiversity studies need robust and accessible taxonomy, this realisation is accompanied by rather little in the way of extra resources but by lots of helpful advice and injunctions. On the one hand, they are told to become cyberneticists, disseminating information solely through the web, while on the other, they are urged to abandon Linnean taxonomy and even species to enter a phylogenetic state of grace. Now, they must obtain diagnostic DNA sequences of all life on Earth, barcoding the biota. DNA Barcoding of Life is a collection of papers on the barcoding of life initiative, bringing together the leading enthusiasts in the field. The idea is to sequence small sections of the same gene from as many species as possible so that further specimens (including non-traditional specimens, such as juvenile stages, tissue or excreta) can be diagnosed purely by sequence comparison. Where a Corresponding author: Godfray, H.C.J. ([email protected]) Available online 30 June 2006. www.sciencedirect.com
sequence does not match, this flags up a possible undescribed species or at least the need for further research. The gene of choice for most (but not all groups) is the mitochondrial cox1, present at high copy numbers and for which fairly broad primers can be designed. The volume includes studies of a series of taxa where cox1 barcoding has worked well (e.g. tropical ants, beetles and moths, Australian fish and red algae) typically distinguishing between 95% and 100% of known species, and often revealing unappreciated diversity, both morphological and cryptic. Sometimes, problems are encountered with issues such as nonamplification and nuclear pseudogenes (e.g. in frogs and primates) and the authors suggest that further genes in addition to cox1 will need to be sequenced. In plants, cox1 is far too uniform but other plastid genes might fill the gap. Of course, barcoding by another name is routine in prokaryote taxonomy, and environmental sequence mining has revealed much new biological diversity. Eukaryote barcoding might be similarly valuable for otherwise intractable groups, as several papers on benthic meiofauna demonstrate. DNA Barcoding of Life also includes discussion on methods of scaling up the collection of barcode sequences, and the development of statistical techniques and software to handle this type of information.
Update
604
TRENDS in Ecology and Evolution Vol.21 No.11
This collection of papers suffers somewhat from the near absence of dissenting voices, given that barcoding has enraged a significant section of the taxonomic community; however, as the initiative matures and some of the early hype is tempered by experience, the role and value but also the limitations of the approach are becoming more clearly defined. In particular, barcode enthusiasts are now far more careful about claiming that this type of sequence can provide useful phylogenetic information. In general, I thought that the volume was an impressive shop window for what barcoding could deliver, and a tribute to the energy and vision of Paul Hebert, the pioneer of the movement. One aspect of barcoding that troubles many people is that it might suck resources away from more traditional taxonomy. To have barcodes for every species on Earth without further and richer information is akin to having a bare list of encyclopaedia entries. The paper by Janzen et al. in this volume eloquently emphasises the importance of marrying barcoding with traditional taxonomy, and I was also impressed by de Lay et al.’s description of an automated system for nematodes that both obtained a barcode and a multifocal digital image voucher. I do not think it naı¨ve to believe that barcoding will lead to more people using taxonomy and that this will build a constituency that will call for more support for the subject. I think that this will be infinitely easier if taxonomic
information, both new and traditional, is easily and freely available via the web. Another concern is the frequency with which barcoding enthusiasts herald the imminent development of a Star Trek style Tricorder that will enable any species to be identified instantaneously in the field (although perhaps it’s just me finding ‘trekkies’ rather scary). It is true that the pace of advance of DNA-sequencing technology is astounding [1] but we have no real idea what the technology will actually consist of ten-years hence, nor whether the painstakingly collected cox1 sequences will actually form its base. I tend to agree with the conclusion in Chase et al.’s contribution that we shall end up wanting to sequence multiple plastid and nuclear genes, although it is conceivable that totally different approaches will have been invented. But this is not an argument for delaying the barcoding initiative (although a strong one for museums and herbariums building DNA repositories), which will deliver useful tools in the near future. It’s taxonomy, Jim, but not as we know it! Reference 1 Service, R.F. (2006) Gene sequencing, the race for the $1000 genome. Science 311, 1544 0169-5347/$ – see front matter ß 2006 Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2006.06.010
Conservation, economics and celibacy: a tortoise-eye view Lonesome George: The Life and Loves of a Conservation Icon by Henry Nicholls, Macmillan, 2006. £16.99 hbk (231 pages) SBN-13 9781403945761; ISBN-10 1403945764
Justin Gerlach University Museum of Zoology, Department of Zoology, Downing Street, Cambridge, UK, CB2 3EJ
Of all known surviving animal species or subspecies, Lonesome George is the rarest, being the sole surviving Pinta island giant tortoise (‘Geochelone’ nigra abingdoni). As such, he symbolises the environmental destruction wrought by human activities, the process of extinction and the tenuous hope of recovery, and can justly be regarded as a conservation icon. Nicholls tells the story in detail, but with a light style. He has been conscientious in checking his facts and following the trail of the story. After talking to the main protagonists, he has been able to combine first-hand accounts with the few documents relating to Lonesome George. Given that the tortoise spent most of his days hidden on a remote island in the Galapagos, much remains unknown about his life, although the story since his discovery in 1971 Corresponding author: Gerlach, J. ([email protected]). Available online 27 June 2006. www.sciencedirect.com
is remarkable. Being a tortoise, most of this life has involved long years of sleeping and eating; however, in the Galapagos, nothing is constant and Lonesome George has experienced more than his fair share of upsets. He has been the reluctant participant in artificial insemination attempts and the recipient of death threats. A synopsis of his life reads like any far-fetched thriller, covering everything from bizarre sexual practices to riots and body doubles, but at a tortoise’s pace. The accidental discovery of Lonesome George in 1971 is wonderfully described by Nicholls and the story of the next 30 years makes thought-provoking reading. Despite his iconic status, no-one seems to know what to do with him. For two decades, he was kept in isolation; since 1992, attempts have been made to breed from him, but these efforts have been desultory and unsuccessful. Lonesome George symbolises the great dilemma in conservation biology: should we preserve unique taxa or recreate functioning ecosystems? Ideally the two go together, but there are situations where a genetic purity ideal might prove