paleontologybut large-scale genome writing …jast239/courses/biogeo/readings/extinctions.pdflian...

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W here humans tread, extinction fol- lows. So researchers have thought for decades, persuaded by ample evidence that—in the last few thousand years, at least—the ar- rival of humans almost always brought overhunting, habitat destruction, or invasive species that killed off native crea- tures. Nowhere did the maxim seem truer than on islands, with their limited resources and naïve prey. But evidence presented by an international group of paleontologists and archaeologists at a meeting here at Austra- lian National University (ANU) last month suggests that in the more distant past, the story was different: When humans first landed on isolated islands during the Pleis- tocene, 10,000 years ago and more, their im- pact was surprisingly light. Few question the destruction wrought by later colonizations, such as the arrival of the Polynesians in New Zealand some 700 years ago, which precipitated the de- mise of creatures including the giant flight- less moa. But new evidence from Sri Lanka, the Indonesian island of Flores, and else- where persuaded many participants in the workshop, called “First Contact: Impact of Pleistocene Hominins on Island Ecosys- tems,” that humanity’s early record hasn’t always been so dismal. “I (and others) have in the past argued that when humans first reach islands, the extinction of endemic animals is quick and certain,” archaeologist Alan Simmons of the University of Nevada in Las Vegas commented later in an email to Science. “But it now appears that in many cases, there was, in fact, a long co-existence of humans with now extinct animals.” The new insights are hard-won—and preliminary. So far, only a few islands have yielded enough artifacts and bones for re- searchers to begin piecing together when early humans arrived, what extinctions occurred, and whether people had a hand in them. In a few cases early humans do appear to be guilty. On the island of Cyprus, a cache of dwarf hippo bones found 20 years ago by an 11-year-old boy at a site called Ak- rotiri Aetokremnos suggests the species went extinct on the island about 12,000 years ago, shortly after people arrived. The timing convinces Simmons that the arrival of humans, together with a sud- den cold, dry spell, killed off the hippos. Although critics point out that the bones lack the tell-tale cut marks of a human kill, “you don’t need big tools to kill hippos,” he said at the workshop. “These were naïve animals, they had no predators and they would have been easy prey for the ultimate predators—humans.” “That was one of the better lines of evidence of extinction,” says ANU paleo- ecologist Julien Louys, who co-organized the meeting with ANU archaeologist Sue O’Connor. But as researchers presented case studies from other islands, Louys says, “it became clear that it was more the ex- ception, not the rule.” By 100,000 years ago, for example, the island of Flores already had human inhab- itants: the hobbitlike Homo floresiensis. Hanneke Meijer, a vertebrate paleontologist from the University of Bergen in Norway, has excavated animal bones from Liang Bua cave, where the hobbit was found. At the conference, she reported finding fossils of 2-meter-tall storks, dwarf elephants, scav- enging birds, and other animals in the same geologic layer that yielded the hobbit. A few NEWS | IN DEPTH 674 19 MAY 2017 • VOL 356 ISSUE 6339 sciencemag.org SCIENCE Island extinctions weren’t inevitable During the ice age, human colonizers often coexisted with vulnerable island fauna By April Reese, in Canberra PALEONTOLOGY But large-scale genome writing faces technical barriers. Although the cost of DNA synthesis has decreased over the last decade, it still hovers around $0.10 per base pair. For now, companies supplying syn- thetic DNA routinely produce fragments of just 2000 to 5000 bases in length, notes NYU Langone geneticist Leslie Mitchell. Longer fragments, on the order of 10,000 bases, “come with a pretty penny price tag.” As DNA strands get longer, they become more prone to tearing when manipulated outside of cells. At about 30,000 bases, “you start to hit sort of the danger zone,” Mitchell says. Yeast is an ideal host for bigger strands because it can take up, assemble, and du- plicate DNA much more quickly and read- ily than human cells. Mitchell is part of an ongoing international collaboration, born from Boeke’s lab, to build synthetic versions of all 16 chromosomes in the yeast spe- cies Saccharomyces cerevisiae by overwrit- ing segments of the native chromosomes (Science, 28 March 2014, p. 1426). For mammalian genome writing, scien- tists will have to swap in large chunks of DNA from yeast or another carrier without disrupting the receiving cell’s vital func- tions. At the meeting, Mitchell hinted at a system her team is developing, which fuses the DNA-containing yeast cell with a mam- malian cell, targets the synthetic DNA to a place in that cell’s genome with specially engineered “landing pad” sequences, and swaps it for the native sequence with help from enzymes known as recombinases. The meeting’s technical talks largely left aside a central challenge for genome writers: understanding natural DNA se- quences well enough to improve on them. “We complain about how much DNA syn- thesis costs, but it actually costs a lot more to design a million base pairs’ worth of complicated circuitry,” Harvard synthetic biologist Jeffrey Way said. Geneticist Yasunori Aizawa at the Tokyo Institute of Technology wants to probe the importance of certain introns—DNA seg- ments within genes that don’t code for pro- teins but may still influence how other genes are expressed—by designing DNA frag- ments that lack them. William Efcavitch, chief scientific officer of San Diego, California–based Molecular Assemblies, one of several companies developing new synthesis methods, wondered to the techni- cal working group whether GP-write should first design a minimal human genome con- taining only the necessary bits of code. At that, Hessel’s imagination escaped the confines of the project. “I think that’s really interesting,” he chimed in. “I read a science fiction book where one of the char- acters was intron-free.” j ILLUSTRATION: LARS GRANT-WEST/NATIONAL GEOGRAPHIC CREATIVE Published by AAAS on May 18, 2017 http://science.sciencemag.org/ Downloaded from

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Where humans tread, extinction fol-

lows. So researchers have thought

for decades, persuaded by ample

evidence that—in the last few

thousand years, at least—the ar-

rival of humans almost always

brought overhunting, habitat destruction,

or invasive species that killed off native crea-

tures. Nowhere did the maxim seem truer

than on islands, with their limited resources

and naïve prey. But evidence presented by an

international group of paleontologists and

archaeologists at a meeting here at Austra-

lian National University (ANU) last month

suggests that in the more distant past, the

story was different: When humans first

landed on isolated islands during the Pleis-

tocene, 10,000 years ago and more, their im-

pact was surprisingly light.

Few question the destruction wrought

by later colonizations, such as the arrival

of the Polynesians in New Zealand some

700 years ago, which precipitated the de-

mise of creatures including the giant flight-

less moa. But new evidence from Sri Lanka,

the Indonesian island of Flores, and else-

where persuaded many participants in the

workshop, called “First Contact: Impact of

Pleistocene Hominins on Island Ecosys-

tems,” that humanity’s early record hasn’t

always been so dismal. “I (and others) have

in the past argued that when humans first

reach islands, the extinction of endemic

animals is quick and certain,” archaeologist

Alan Simmons of the University of Nevada

in Las Vegas commented later in an email

to Science. “But it now appears that in many

cases, there was, in fact, a long co-existence

of humans with now extinct animals.”

The new insights are hard-won—and

preliminary. So far, only a few islands have

yielded enough artifacts and bones for re-

searchers to begin piecing together when

early humans arrived, what extinctions

occurred, and whether people had a hand

in them.

In a few cases early humans do appear to

be guilty. On the island of Cyprus, a cache

of dwarf hippo bones found 20 years ago

by an 11-year-old boy at a site called Ak-

rotiri Aetokremnos suggests the species

went extinct on the island about 12,000

years ago, shortly after people arrived.

The timing convinces Simmons that the

arrival of humans, together with a sud-

den cold, dry spell, killed off the hippos.

Although critics point out that the bones

lack the tell-tale cut marks of a human kill,

“you don’t need big tools to kill hippos,” he

said at the workshop. “These were naïve

animals, they had no predators and they

would have been easy prey for the ultimate

predators—humans.”

“That was one of the better lines of

evidence of extinction,” says ANU paleo-

ecologist Julien Louys, who co-organized

the meeting with ANU archaeologist Sue

O’Connor. But as researchers presented

case studies from other islands, Louys says,

“it became clear that it was more the ex-

ception, not the rule.”

By 100,000 years ago, for example, the

island of Flores already had human inhab-

itants: the hobbitlike Homo floresiensis.

Hanneke Meijer, a vertebrate paleontologist

from the University of Bergen in Norway,

has excavated animal bones from Liang Bua

cave, where the hobbit was found. At the

conference, she reported finding fossils of

2-meter-tall storks, dwarf elephants, scav-

enging birds, and other animals in the same

geologic layer that yielded the hobbit. A few

NEWS | IN DEPTH

674 19 MAY 2017 • VOL 356 ISSUE 6339 sciencemag.org SCIENCE

Island

extinctions

weren’t

inevitableDuring the ice age, human colonizers often coexisted with vulnerable island fauna

By April Reese, in Canberra

PALEONTOLOGY But large-scale genome writing faces

technical barriers. Although the cost of

DNA synthesis has decreased over the last

decade, it still hovers around $0.10 per base

pair. For now, companies supplying syn-

thetic DNA routinely produce fragments

of just 2000 to 5000 bases in length, notes

NYU Langone geneticist Leslie Mitchell.

Longer fragments, on the order of 10,000

bases, “come with a pretty penny price tag.”

As DNA strands get longer, they become

more prone to tearing when manipulated

outside of cells. At about 30,000 bases, “you

start to hit sort of the danger zone,” Mitchell

says. Yeast is an ideal host for bigger strands

because it can take up, assemble, and du-

plicate DNA much more quickly and read-

ily than human cells. Mitchell is part of an

ongoing international collaboration, born

from Boeke’s lab, to build synthetic versions

of all 16 chromosomes in the yeast spe-

cies Saccharomyces cerevisiae by overwrit-

ing segments of the native chromosomes

(Science, 28 March 2014, p. 1426).

For mammalian genome writing, scien-

tists will have to swap in large chunks of

DNA from yeast or another carrier without

disrupting the receiving cell’s vital func-

tions. At the meeting, Mitchell hinted at a

system her team is developing, which fuses

the DNA-containing yeast cell with a mam-

malian cell, targets the synthetic DNA to a

place in that cell’s genome with specially

engineered “landing pad” sequences, and

swaps it for the native sequence with help

from enzymes known as recombinases.

The meeting’s technical talks largely

left aside a central challenge for genome

writers: understanding natural DNA se-

quences well enough to improve on them.

“We complain about how much DNA syn-

thesis costs, but it actually costs a lot more

to design a million base pairs’ worth of

complicated circuitry,” Harvard synthetic

biologist Jeffrey Way said.

Geneticist Yasunori Aizawa at the Tokyo

Institute of Technology wants to probe the

importance of certain introns—DNA seg-

ments within genes that don’t code for pro-

teins but may still influence how other genes

are expressed—by designing DNA frag-

ments that lack them. William Efcavitch,

chief scientific officer of San Diego,

California–based Molecular Assemblies,

one of several companies developing new

synthesis methods, wondered to the techni-

cal working group whether GP-write should

first design a minimal human genome con-

taining only the necessary bits of code.

At that, Hessel’s imagination escaped

the confines of the project. “I think that’s

really interesting,” he chimed in. “I read a

science fiction book where one of the char-

acters was intron-free.” j ILL

US

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DA_0519NewsInDepth.indd 674 5/17/17 10:58 AM

Published by AAAS

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of those creatures, including the elephants

and the avian scavengers, later vanished.

Climate change seems a more likely cause

than hunting, though—H. floresiensis may

have been a scavenger rather than a hunter

and could easily have become prey itself.

“It is not unlikely … that storks would have

gobbled up a baby hobbit if it happened to

run by,” Meijer said.

Even when modern humans landed on is-

lands, they sometimes hunted in a sustain-

able way. In Sri Lanka,

Patrick Roberts of the

Max Planck Institute for

the Science of Human

History in Jena, Ger-

many, analyzed animal

bones found at archaeo-

logical sites between

3000 and 36,000 years

old. He found that three

species of monkeys—the

toque macaque, gray

langur, and purple-faced

leaf monkey—accounted for about 70% to

80% of human kills.

Monkeys are big, easy to find, and slow to

reproduce, which makes them particularly

vulnerable to overhunting, Roberts noted.

Yet all three primates are still around to-

day, and they’re still hunted by indigenous

people “with limited effects,” Roberts wrote

in a later email. (The gray langur and the

purple-faced leaf monkey are endangered,

but because of development and deforesta-

tion, not hunting, he added.)

Studies from other islands, including

Tasmania, the Philippines, the Channel Is-

lands, and Taiwan, also suggest Pleistocene

humans had a light ecological footprint,

leaving workshop participants to speculate

why. Smaller populations and simpler tech-

nologies than those of later arrivals might

have lessened their impact. The evidence

also hints that unlike later colonizers, the

early arrivals did not introduce invasive

species such as rats and dogs.

This emerging picture raises a new puzzle,

however. On continents such as North Amer-

ica and Australia, ice age immigrants are

blamed for widespread

extinctions of ice age

megafauna—think mam-

moths, giant sloths, and

giant kangaroos. “If we

cannot locate a definite

Pleistocene megafaunal

extinction on an island,”

says Roberts, “then what

does this mean for argu-

ments on the continents?”

Generalizing from the

studies so far is risky,

researchers emphasized. Environmental

conditions, the timing of settlement and ex-

tinctions, the technologies the new arrivals

brought—all vary from island to island, and

none of those factors is fully understood at

any site. But Louys finds a hopeful message

in the stories these islands are beginning to

tell. “Extinctions aren’t necessarily a char-

acteristic of our species—it’s something we

learned to do,” he said. “And if it’s some-

thing we learned to do, it’s something we

can learn to undo.” j

April Reese is a journalist in

Townsville, Australia.

SCIENCE sciencemag.org

“Extinctions aren’t necessarily a characteristic of our species—it’s something we learned to do.” Julien Louys, Australian

National University

Homo floresiensis shared the island

of Flores with giant lizards, dwarf

elephants, and other exotic species.

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(6339), 674-675. [doi: 10.1126/science.356.6339.674]356Science April Reese (May 18, 2017) Island extinctions weren't inevitable

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