quinta-feira, 29 de março de 2018

Divided by DNA: The uneasy relationship between archaeology and ancient genomics

Two fields in the midst of a technological revolution are struggling to reconcile their views of the past. 
 
 
 
 
  
The West Kennet long barrow served as a tomb and ceremonial site for more than a millennium. Credit: Robert Harvey/Natural World Photography.

Thirty kilometres north of Stonehenge, through the rolling countryside of southwest England, stands a less-famous window into Neolithic Britain. Established around 3600 bc by early farming communities, the West Kennet long barrow is an earthen mound with five chambers, adorned with giant stone slabs. At first, it served as a tomb for some three dozen men, women and children. But people continued to visit for more than 1,000 years, filling the chambers with relics such as pottery and beads that have been interpreted as tributes to ancestors or gods.

The artefacts offer a view of those visitors and their relationship with the wider world. Changes in pottery styles there sometimes echoed distant trends in continental Europe, such as the appearance of bell-shaped beakers — a connection that signals the arrival of new ideas and people in Britain. But many archaeologists think these material shifts meshed into a generally stable culture that continued to follow its traditions for centuries.

“The ways in which people are doing things are the same. They’re just using different material culture — different pots,” says Neil Carlin at University College Dublin, who studies Ireland and Britain’s transition from the Neolithic into the Copper and Bronze Ages.

But last year, reports started circulating that seemed to challenge this picture of stability. A study1 analysing genome-wide data from 170 ancient Europeans, including 100 associated with Bell Beaker-style artefacts, suggested that the people who had built the barrow and buried their dead there had all but vanished by 2000 bc. The genetic ancestry of Neolithic Britons, according to the study, was almost entirely displaced. Yet somehow the new arrivals carried on with many of the Britons’ traditions. “That didn’t fit for me,” says Carlin, who has been struggling to reconcile his research with the DNA findings.

The Bell Beaker ‘bombshell’ study appeared in Nature2 in February and included 230 more samples, to make it the largest ancient-genome study on record. But it is just the latest example of the disruptive influence that genetics has had on the study of the human past. Since 2010, when the first ancient-human genome was fully sequenced3, researchers have amassed data on more than 1,300 individuals (see ‘Ancient genomes’ graphic), and used them to chart the emergence of agriculture, the spread of languages and the disappearance of pottery styles — topics that archaeologists have laboured over for decades.

Some archaeologists are ecstatic over the possibilities offered by the new technology. Ancient-DNA work has breathed new life and excitement into their work, and they are beginning once-inconceivable investigations, such as sequencing the genome of every individual from a single graveyard. But others are cautious.

“Half the archaeologists think ancient DNA can solve everything. The other half think ancient DNA is the devil’s work,” quips Philipp Stockhammer, a researcher at Ludwig-Maximilians University in Munich, Germany, who works closely with geneticists and molecular biologists at an institute in Germany that was set up a few years ago to build bridges between the disciplines. The technology is no silver bullet, he says, but archaeologists ignore it at their peril.

Some archaeologists, however, worry that the molecular approach has robbed the field of nuance. They are concerned by sweeping DNA studies that they say make unwarranted, and even dangerous, assumptions about links between biology and culture. “They give the impression that they’ve sorted it out,” says Marc Vander Linden, an archaeologist at the University of Cambridge, UK. “That’s a little bit irritating.”

This isn’t the first time archaeologists have had to contend with transformative technology. “The study of prehistory today is in crisis,” wrote Cambridge archaeologist Colin Renfrew in his 1973 book Before Civilization, describing the impact of radiocarbon dating. Before the technique was developed by chemists and physicists in the 1940s and 50s, prehistorians determined the age of sites using ‘relative chronologies’, in some cases relying on ancient Egyptian calendars and false assumptions about the spread of ideas from the Near East. “Much of prehistory, as written in the existing textbooks is inadequate: some of it, quite simply wrong,” Renfrew surmised.
It wasn’t an easy changeover — early carbon-dating efforts were off by hundreds of years or more — but the technique eventually allowed archaeologists to stop spending most of their time worrying about the age of bones and artefacts and focus instead on what the remains meant, argues Kristian Kristiansen, who studies the Bronze Age at the University of Gothenburg in Sweden. “Suddenly there was a lot of free intellectual time to start thinking about prehistoric societies and how they are organized.” Ancient DNA now offers the same opportunity, says Kristiansen, who has become one of his field’s biggest cheerleaders for the technology.
Genetics and archaeology have been uneasy bedfellows for more than 30 years — the first ancient-human DNA paper4, in 1985, reported sequences from an Egyptian mummy (now thought to be contamination). But improvements in sequencing technology in the mid-to-late 2000s set the fields on a collision course.

In 2010, scientists led by Eske Willerslev at the Natural History Museum of Denmark used DNA from a lock of hair from a 4,000-year-old native Greenlander to generate the first complete sequence of an ancient-human genome3. Seeing the future of the field before his eyes, Kristiansen asked Willerslev to team up on a prestigious European Research Council grant that would allow them to examine human mobility as the late Neolithic gave way to the Bronze Age, some 4,000–5,000 years ago.

Association problems
Migration has been a major source of tension for archaeologists. They have debated at length whether human movements are responsible for cultural changes in the archaeological record, such as the Bell Beaker phenomenon, or whether it is simply the ideas that are moving through cultural exchanges. Populations identified by the artefacts they associated with came to be seen as a remnant of the science’s colonial past, and one that imposed artificial categories. “Pots are pots, not people,” goes a common refrain.

Most archaeologists have since cast aside the view that prehistory was like a game of Risk, in which homogenous cultural groups conquer their way across a map of the world. Instead, researchers tend to focus on understanding a small number of ancient sites and the lives of the people who lived there. “Archaeology had moved away from these grand narratives,” says Tom Booth, a bioarchaeologist at the Natural History Museum in London, who is part of a team using ancient DNA to trace the arrival of farming in Britain. “A lot of people thought you needed to understand change regionally to understand people’s lives.”
Ancient-DNA work — which has repeatedly shown that a region’s modern inhabitants are often distinct from populations that lived there in the past — promised, for better or worse, to bring back some of the broad focus on migration to human prehistory. “What genetics is particularly good at is detecting change in populations,” says David Reich, a population geneticist at Harvard Medical School in Boston, Massachusetts. Archaeologists, Kristiansen says, “were prepared to accept that individuals had travelled”. But for the Bronze Age period that he studies, “they were not prepared for major migrations. That was a new thing.”
Studies of strontium isotopes in teeth5, which vary with local geochemistry, had hinted that some Bronze Age individuals had moved hundreds of kilometres over their lifetimes, Kristiansen says. He and Willerslev wondered whether DNA analysis might detect movements of whole populations during this period.
Bell Beaker pots signal a period of unprecedented cultural intermingling for early Europeans.Credit: Ashmolean Museum/Univ. Oxford/Bridgeman
They would have competition. In 2012, David Anthony, an archaeologist at Hartwick College in Oneonta, New York, loaded his car with boxes of human remains that he and his colleagues had excavated from the steppes near the Russian city of Samara, including bones associated with a Bronze Age pastoralist culture called the Yamnaya. He was bringing them to the ancient-DNA lab just established by Reich in Boston. Like Kristiansen, Anthony was comfortable theorizing about the past on a grand scale. His 2007 book The Horse, the Wheel and Language proposed that the Eurasian steppe had been a melting pot for the modern developments of horse domestication and wheeled transport, which propelled the spread of a family of languages called Indo-European across Europe and parts of Asia.
In duelling 2015 Nature papers6,7, the teams arrived at broadly similar conclusions: an influx of herders from the grassland steppes of present-day Russia and Ukraine — linked to Yamnaya cultural artefacts and practices such as pit burial mounds — had replaced much of the gene pool of central and Western Europe around 4,500–5,000 years ago. This was coincident with the disappearance of Neolithic pottery, burial styles and other cultural expressions and the emergence of Corded Ware cultural artefacts, which are distributed throughout northern and central Europe. “These results were a shock to the archaeological community,” Kristiansen says.
Cord cutters
The conclusions immediately met with push-back. Some of it began even before the papers were published, says Reich. When he circulated a draft among his dozens of collaborators, several archaeologists quit the project. To many, the idea that people linked to Corded Ware had replaced Neolithic groups in Western Europe was eerily reminiscent of the ideas of Gustaf Kossinna, the early-twentieth-century German archaeologist who had connected Corded Ware culture to the people of modern Germany and promoted a ‘Risk board’ view of prehistory known as settlement archaeology. The idea later fed into Nazi ideology.
Reich won his co-authors back by explicitly rejecting Kossinna’s ideas in an essay included in the paper’s 141-page supplementary material7. He says the episode was eye-opening in showing how a wider audience would perceive genetic studies claiming large-scale ancient migrations.
Still, not everyone was satisfied. In an essay8 titled ‘Kossinna’s Smile’, archaeologist Volker Heyd at the University of Bristol, UK, disagreed, not with the conclusion that people moved west from the steppe, but with how their genetic signatures were conflated with complex cultural expressions. Corded Ware and Yamnaya burials are more different than they are similar, and there is evidence of cultural exchange, at least, between the Russian steppe and regions west that predate Yamnaya culture, he says. None of these facts negates the conclusions of the genetics papers, but they underscore the insufficiency of the articles in addressing the questions that archaeologists are interested in, he argued. “While I have no doubt they are basically right, it is the complexity of the past that is not reflected,” Heyd wrote, before issuing a call to arms. “Instead of letting geneticists determine the agenda and set the message, we should teach them about complexity in past human actions.”
Ann Horsburgh, a molecular anthropologist and prehistorian at Southern Methodist University in Dallas, Texas, attributes such tensions to communication problems. Archaeology and genetics say distinct things about the past, but often use similar terms, such as the name of a material culture. “It’s C. P. Snow all over again,” she says, referring to the influential ‘Two Cultures’ lectures by the British scientist lamenting the deep intellectual divide between the sciences and the humanities. Horsburgh complains that genetic results are too often given precedence over inferences about the past from archaeology and anthropology, and that such “molecular chauvinism” prevents meaningful engagement9. “It’s as though genetic data, because they’re generated by people in lab coats, have some sort of unalloyed truth about the Universe.”
Horsburgh, who is seeing her own field of African prehistory start to feel the tremors of ancient genomics, says that archaeologists frustrated at having their work misinterpreted should wield their power over archaeological remains to demand more equitable partnerships with geneticists. “Collaboration doesn’t mean I send you an e-mail saying ‘hey, you’ve got some really cool bones. I’ll get you a Nature paper.’ That’s not a collaboration,” she says.
Many archaeologists are also trying to understand and engage with the inconvenient findings from genetics. Carlin, for instance, says that the Bell Beaker genome study sent him on “a journey of reflection” in which he questioned his own views about the past. He has pored over the selection of DNA samples included in the study as well as the basis for its conclusion that the appearance of Bell Beaker artefacts coincided with a greater than 90% replacement in Britain’s gene pool. “I didn’t want to be questioning it from a position of ignorance,” Carlin says.
Like Heyd, he accepts that a shift in ancestry occurred (although he has questions about its timing and scale). Those results, in fact, now have him wondering about how cultural practices such as leaving pottery and other tributes at the West Kennet long barrow persisted in the face of such upheavals. “I would characterize a lot of these papers as ‘map and describe’. They’re looking at the movement of genetic signatures, but in terms of how or why that’s happening, those things aren’t being explored,” says Carlin, who is no longer disturbed by the disconnect. “I am increasingly reconciling myself to the view that archaeology and ancient DNA are telling different stories.” The changes in cultural and social practices that he studies might coincide with the population shifts that Reich and his team are uncovering, but they don’t necessarily have to. And such biological insights will never fully explain the human experiences captured in the archaeological record.
Reich agrees that his field is in a “map-making phase”, and that genetics is only sketching out the rough contours of the past. Sweeping conclusions, such as those put forth in the 2015 steppe migration papers, will give way to regionally focused studies with more subtlety.
This is already starting to happen. Although the Bell Beaker study found a profound shift in the genetic make-up of Britain, it rejected the notion that the cultural phenomenon was associated with a single population. In Iberia, individuals buried with Bell Beaker goods were closely related to earlier local populations and shared little ancestry with Beaker-associated individuals from northern Europe (who were related to steppe groups such as the Yamnaya). The pots did the moving, not the people.
Reich describes his role as that of a ‘midwife’ delivering ancient-DNA technology to archaeologists, who can apply it as they see fit. “Archaeologists will embrace this technology and will not be Luddites,” he predicts, “and they’ll make it their own.”
A stronger partnership
Nestled in a sleepy valley in the state of Thuringia in former East Germany, the city of Jena has become an unlikely hub for the convergence of archaeology and genetics. In 2014, the prestigious Max Planck Society established an Institute for the Science of Human History there and installed a rising star in ancient-DNA research, Johannes Krause, as a director. Krause was a protégé of the geneticist Svante Pääbo, at the Max Planck Institute for Evolutionary Anthropology in Leipzig. There, Krause worked on the Neanderthal genome10 and helped discover a new archaic human group, known as Denisovans11.
Whereas Pääbo was focused on applying genetics to biological questions about ancient humans and their relatives, Krause saw a wider scope for the technology. Before leading the Jena institute, his team identified DNA from plague-causing bacteria in the teeth of people who died from the Black Death in the fourteenth century, the first direct evidence of a potential cause for the pandemic12. At Jena, Krause hoped to bring genetics to bear, not just on ‘prehistorical’ periods such as the Neolithic and the Bronze Age, where archaeological methods are the main tool for reconstructing the past, but also on more-recent times. Outreach with historians is still a work in progress, but archaeology and genetics are thoroughly embedded at the institute. The department Krause directs is even called archaeogenetics. “We have to be interdisciplinary,” he says, because geneticists are addressing questions and time periods that archaeologists, linguists and historians have been poring over for decades.
Krause and his team have been heavily involved in the map-making phase of ancient genomics (he worked closely with Reich’s team on many such projects). But a study published late last year13 that focused on the transition between the Neolithic and Bronze Age in Germany won plaudits from archaeologists who have been dubious of the larger-scale ancient-DNA studies.
Led by Stockhammer, who also has a post at the Jena institute, the team analysed 84 Neolithic and Bronze Age skeletons from southern Bavaria’s Lech River Valley dating to between 2500 and 1700 bc. The diversity in the genomes of cellular structures known as mitochondria, which are inherited maternally, rose during this period, suggesting an influx of women. Meanwhile, strontium isotope levels in teeth — which are set during childhood — suggested that most females weren’t local. In one case, two related individuals who lived within a few generations of each other were found buried with different material cultures. In other words, some cultural shifts in the archaeological record could be due not to massive migrations, but to the systematic mobility of individual women.
It is the prospect of more such studies that has archaeologists salivating over ancient DNA. In the near future, says Stockhammer, archaeologists will be able to sequence the genomes of all the individuals at a burial site and build a local family tree, while also determining how individuals fit into larger ancestry patterns. This should allow researchers to ask how biological kinship relates to the inheritance of material culture or status. “These are the big questions of history. They can be solved now only with collaboration,” says Stockhammer.
Another glimpse of this approach appeared in February on the bioRxiv preprint server14. The paper explores Europe’s migration period, when ‘barbarian hordes’ filled the void left after the fall of the Roman Empire. In the paper, a team of geneticists, archaeologists and historians built family trees of 63 individuals from two medieval cemeteries in Hungary and northern Italy associated with a group known as the Longobards. They found evidence of high-status outsiders buried in the cemetery: most bore central and northern European genetic ancestry that differed from that of local people, who tended to be buried without goods — offering tentative support to the idea that some barbarian groups included outsiders.
Patrick Geary, a medieval historian at the Institute for Advanced Study in Princeton, New Jersey, who co-led the Longobard study, would not comment on the research because it is now being peer reviewed. But he says that genetic studies of historical times, such as the migration period, carry pitfalls, too. Historians are increasingly incorporating data such as palaeoclimate records into their work, and will do likewise with ancient DNA, Geary says. But they share archaeologists’ fears that biology and culture will be conflated, and that problematic designations such as Franks or Goths or Vikings will be reified by genetic profiles, overriding insights into how ancient peoples viewed themselves. “These days, what historians want to know about is identity,” he says. “Genetics cannot answer these questions.”
Reich concedes that his field hasn’t always handled the past with the nuance or accuracy that archaeologists and historians would like. But he hopes they will eventually be swayed by the insights his field can bring. “We’re barbarians coming late to the study of the human past,” Reich says. “But it’s dangerous to ignore barbarians.”
Nature 555, 573-576 (2018)
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References

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    Amorim, C. E. G. et al. Preprint at bioRxiv http://dx.doi.org/10.1101/268250 (2018).

Reconstructing the genetic history of late Neanderthals

Received:
Accepted:
Published:
  • Corrected online 28 March 2018

Abstract

Although it has previously been shown that Neanderthals contributed DNA to modern humans1,2, not much is known about the genetic diversity of Neanderthals or the relationship between late Neanderthal populations at the time at which their last interactions with early modern humans occurred and before they eventually disappeared.

Our ability to retrieve DNA from a larger number of Neanderthal individuals has been limited by poor preservation of endogenous DNA3 and contamination of Neanderthal skeletal remains by large amounts of microbial and present-day human DNA3,4,5.

Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five Neanderthals who lived around 39,000 to 47,000 years ago (that is, late Neanderthals), thereby doubling the number of Neanderthals for which genome sequences are available.

Genetic similarity among late Neanderthals is well predicted by their geographical location, and comparison to the genome of an older Neanderthal from the Caucasus2,7 indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neanderthal history. We find that the bulk of Neanderthal gene flow into early modern humans originated from one or more source populations that diverged from the Neanderthals that were studied here at least 70,000 years ago, but after they split from a previously sequenced Neanderthal from Siberia2 around 150,000 years ago.

Although four of the Neanderthals studied here post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.

On the use and abuse of ancient DNA

Researchers in several disciplines need to tread carefully over shared landscapes of the past. 
The reflection of a human skull on a museum case covering a mans face  
Ancient remains must be analysed carefully to avoid misle.
 
History might, as historian Arnold Toynbee allegedly said, be one damned thing after another, but historians and archaeologists spend a lot of their time trying to put those things into the right order. Assistance from science over the decades has been transformative, but not without difficulty: it took years for some archaeologists to be won over by radiocarbon dating.

Now, historians and archaeologists are grappling with a new scientific technique. As we discuss in a News Feature, the genetic study of ancient DNA is exploding, and the findings are posing several problems. One is a need for geneticists, archaeologists, historians and anthropologists to understand exactly how their skills and insights complement each other’s. It is clear, for example, that although genetics has useful things to say about the sweep of population history, the more conventional disciplines provide essential context.
Another problem is fear that simplistic takes on ancient DNA will mirror damaging uses of the idea of ‘culture history’. Culture history views the discovery of old artefacts as a proxy for the movement of the people who made them. According to this idea, a particular floral design on a pot that spread from south to north over a few centuries, for example, would indicate that the specific group of people that painted it was on the move — and carried the design with it.

These fears are not just about scholarship. Simplistic readings of culture history have encouraged people with political agendas to falsely draw clear boundaries between the behaviour and the claimed territory of some ancient (and not-so-ancient) populations — and to infer similarities with their claimed modern equivalents. For example, they often refer to the work of early-twentieth-century German archaeologist Gustaf Kossinna, who used culture history to trace the supposed origins of modern Germany to the spread of Corded Ware, a type of ceramic found throughout central Europe in the Bronze Age. Kossinna’s ideas, although influential, have proved to be scientifically simplistic. They became notorious following their use by the Nazi party to legitimize its territorial goals and beliefs about the racial superiority of German-speaking peoples.

Scholars are anxious because extremists are scrutinizing the results of ancient-DNA studies and trying to use them for similar misleading ends. Ancient DNA, for example, offers evidence of large migrations that coincide with cultural changes in the archaeological record, including the emergence of Corded Ware. Some archaeologists have expressed fears that the extremists will wrongly present such conclusions as backing for Kossinna’s theories.

Another problem for archaeologists and historians relates to the potential for abuse of the results of ancient-DNA studies looking at more recent times, such as the Migration Period around the fall of the Roman Empire or the era covered by the Viking sagas. They worry that DNA studies of groups described as Franks or Anglo-Saxons or Vikings will reify them by attaching misleading genetic profiles to categories that were devised by historians, and are not representative of how individuals viewed themselves at the time. Already, some people have picked up on such studies as a way to try to trace their roots to such supposed populations, to justify claims they have a right to some territory or other (L.-J. Richardson and T. Booth Papers Inst. Archaeol. 27, 25; 2017).

On the contrary, genetic and historical evidence suggests that there was widespread mixing during these periods, across populations and geography. Indeed, presented correctly alongside insights from other disciplines, ancient-DNA research can be a powerful weapon against bigotry. Studies documenting migrations can drive home the point that present-day peoples in one area often share few genetic links with ancient peoples who lived in the same place. And when they do focus on relatively recent times, DNA projects can highlight the diversity of past peoples who otherwise might be seen as homogenous. A 2016 study of Anglo-Saxon burials, for example, found a mix of ancestry, with some people related to earlier inhabitants of England and others tracing their ancestry across the Channel (S. Schiffels et al. Nature Commun. 7, 10408; 2016).

Two recommendations can be made for the public behaviour of scientists and other scholars. The first: give ample credit to the insights of complementary disciplines. The second: refute statements that misconstrue what your insights actually reveal and that can be used politically to justify disrespect, or worse, to groups of people.
Nature 555, 559 (2018)
 

terça-feira, 27 de março de 2018

Desmatamento favorece ação de fungo que dizima anfíbios

20 de março de 2018


Peter Moon  |  Agência FAPESP – Pesquisadores da Universidade Estadual Paulista (Unesp) estão investigando como o desflorestamento pode afetar a ação de patógenos que causam doenças como a quitridiomicose, que tem devastado populações de sapos e rãs no mundo nas últimas décadas.

Desmatamento favorece ação de fungo que dizima anfíbios Pesquisadores investigam relação entre o desflorestamento e a quitridiomicose, doença que tem devastado populações de sapos e rãs em vários países (foto: Guilherme Becker) 
 
Em artigo publicado na revista Proceedings of the Royal Society of London B – Biological Sciences os pesquisadores analisaram como a interação entre o desmatamento e o microbioma da pele pode afetar os anfíbios atingidos por fungos como o Batrachochytrium dendrobatidis, causador da quitridiomicose.

“Existe a suspeita de que esse fungo possa ter mais dificuldade de se estabelecer e proliferar em um animal cuja biota cutânea encontra-se íntegra”, disse Célio Haddad, professor do Instituto de Biociências da Unesp. A pesquisa integra o Projeto Temático “Diversity and conservation of Brazilian amphibians”, coordenado por Haddad e financiado pela FAPESP no âmbito do programa BIOTA.

O microbioma funciona como uma espécie de ecossistema que dificulta a ação de patógenos invasores. Para verificar qual seria a composição do microbioma na pele dos anfíbios da Mata Atlântica, habitando áreas de mata contínua ou mata degradada, os pesquisadores precisavam escolher uma espécie que não fosse exclusiva e que vivesse em ambas.

Precisaria também ser uma espécie com certo grau de tolerância ao fungo Batrachochytrium dendrobatidis, ou Bd. Ou seja, uma espécie cujo maior ou menor grau de tolerância individual pudesse ser associada à diversidade do microbioma cutâneo de cada indivíduo e avaliada de acordo com o local que habita.

A candidata eleita foi a pererequinha-do-brejo (Dendropsophus minutus), com moderada tolerância ao fungo e distribuição ampla na Mata Atlântica, tanto em ambientes de mata fechada como em áreas fragmentadas ou abertas.
Em 2010, os pesquisadores estudaram 10 populações de D. minutus em áreas da Mata Atlântica em São Luiz do Paraitinga (SP) e outras 10 populações da Mata de Araucárias, na Serra Gaúcha, em áreas degradadas e íntegras.
Foram amostrados cerca de 600 indivíduos. Entre esses, foram selecionados 187 indivíduos para estudo molecular. “Usamos luvas descartáveis para manusear cada animal, que foram limpos em campo com água destilada. Em seguida, usamos cotonetes para coletar material cutâneo de cada espécime, que foi armazenado em frascos estéreis”, disse outro autor do estudo, Guilherme Becker, pós-doutorando na Unesp na época e atualmente professor visitante do PPG de Ecologia da Unicamp.

Foi realizado o sequenciamento genético do material cutâneo coletado de cada indivíduo. “O processo gerou uma lista de bactérias presentes em cada indivíduo e em qual abundância. O resultado foi uma base de dados enorme, uma vez que cada indivíduo tinha centenas de bactérias”, disse Becker.
Os pesquisadores empregaram técnicas estatísticas para estabelecer relações e inferir padrões na base de dados. “Pela abordagem molecular, podemos verificar a carga de infecção do patógeno em relação à diversidade da biota cutânea de cada indivíduo. A partir daquele banco de dados, conseguimos gerar outros índices de diversidade, como o número de espécies de bactérias, sua abundância relativa e sua diversidade filogenética”, disse Becker.

Haddad conta que foi observado, em áreas abertas ou degradadas, que a composição do microbioma cutâneo é menos diversificada em termos de espécies de bactérias e menos homogênea entre os indivíduos.

“Em contraposição, nas áreas de floresta íntegra a composição do microbioma mostrou-se mais homogênea entre os indivíduos e mais diversificada em termos de microrganismos”, disse.
Os autores do estudo constataram que nas pererequinhas-do-brejo dos ambientes de floresta natural a diversidade do microbioma era maior. “O desmatamento diminuiu a diversidade da microbiota cutânea das pererequinhas, mas é difícil afirmar categoricamente que este empobrecimento da microbiota aumenta o risco de infecção pelo fungo”, disse Becker.

O pesquisador explica que, uma vez que um anfíbio é infectado pelo fungo Bd, a quantidade de bactérias aumenta muito em um primeiro momento, talvez pelo comprometimento do sistema imune causado pelo ataque de bactérias oportunistas.

“Os animais começam a ficar doentes, a pele fica mais grossa, o fungo cobre a pele. Uma vez que eles ficam muito doentes a carga de bactérias despenca. É um sinal ruim.

Significa que o microbioma está em disbiose [ou em crise]. Quando a quantidade de bactérias cai dramaticamente, o anfíbio geralmente morre”, disse Becker.
A ecologia da quitridiomicose é ainda mais complexa. O fungo Bd se espalha pelo meio ambiente por meio de esporos suspensos na água de lagoas e rios.

“É uma das piores epidemias atuais. Nenhuma outra doença de vertebrados atua como o fungo Bd. Trata-se de um patógeno generalista que prolifera melhor nos ambientes naturais, o que não favorece em nada os anfíbios. Por isso a quitridiomicose é tão devastadora”, disse Becker.

Endêmica na Mata Atlântica

A quitridiomicose está dizimando não apenas as espécies conhecidas de anfíbios, mas centenas ainda desconhecidas da ciência. Na doença, o fungo Bd se instala na pele, afetando a respiração e a fisiologia dos hospedeiros. O Bd é endêmico na Mata Atlântica brasileira, onde infecta inúmeras espécies, com maior ou menor suscetibilidade.

A suscetibilidade dos anfíbios ao fungo Bd varia bastante. Há espécies muito tolerantes, como é o caso da rã-touro norte-americana (Lithobates catesbeianus), espécies com tolerância intermediária e muitas outras onde a mortalidade pode chegar a 100%. A doença está espalhada pelas três Américas, mas também atinge a Austrália, Europa, Nova Zelândia e partes da África.

Os anfíbios apresentam mais de um sistema respiratório. Na fase do girino, respiram por meio de brânquias, como os peixes. Já na fase adulta, os anfíbios dependem principalmente da respiração cutânea, que podem associar ou não, dependendo do grupo, à respiração pulmonar e à respiração por meio da cavidade oral.

Quando o fungo Bd se instala na pele, ele ataca a queratina, principal proteína constituinte do tecido cutâneo, levando a uma maior impermeabilidade da pele do anfíbio, o que interfere na troca de gases com o meio ambiente.
A quitridiomicose atualmente é endêmica na Mata Atlântica brasileira, ainda que aqui ela ainda não seja tão devastadora como nas matas da Costa Rica, por exemplo, onde diversas espécies de anfíbios já desapareceram. Há relatos de pesquisadores dando conta de áreas antes livres da doença e que, em um ano, encontravam-se repletas de anfíbios, e no ano seguinte não se achou mais nenhum.

Não se sabe ao certo a razão pela qual a quitridiomicose é mais severa na Costa Rica e, aparentemente, mais branda entre as populações de anfíbios da Mata Atlântica. Talvez nem sempre tenha sido assim. Sabe-se que, no final dos anos 1970, houve um grande declínio entre as populações de anfíbios da Mata Atlântica.

“No fim da década de 1970 observamos o pico da prevalência do fungo Bd na pele de anfíbios depositados em museus, em relação aos animais depositados antes ou depois. Possivelmente, foi esse fungo que causou os declínios de populações de anfíbios na Mata Atlântica daquela época. Tudo isso coincide com declínios em massa ocorridos na mesma época em outros locais, como os Estados Unidos, os Andes e a Austrália”, disse Becker.

Segundo ele, o próximo passo da pesquisa é identificar se existem bactérias do microbioma dos anfíbios que conferem maior resistência à proliferação do fungo Bd na Mata Atlântica. Ao descobrir qual agente combate o fungo, pode ser possível formular probióticos para tentar proteger populações de anfíbios endêmicos ainda não afetadas, ajudando o microbioma a combater o fungo.
O artigo Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome (doi: 10.1098/rspb.2017.0582), de C. G. Becker, A. V. Longo, C. F. B. Haddad e K. R. Zamudio, está publicado em http://rspb.royalsocietypublishing.org/content/284/1861/20170582
 
 

segunda-feira, 26 de março de 2018

Amur Leopard: One of the World's Most Endangered Cats

With a Wild Population of 40, Amur Leopards are Close to Going Extinct 

 

Amur Leopard
 
 
 
 
 
 
 
Kathleen Reeder Wildlife Photography / Getty Images
The Far Eastern or Amur leopard (Panthera pardus orientalis) is one of the world's most endangered cats. It is a solitary, nocturnal leopard with a wild population estimated at under 40 individuals who mostly reside in the Amur River basin of eastern Russia with a few scattered in neighboring China. They are particularly vulnerable to extinction because Amur leopards have the lowest levels of genetic variation of any leopard subspecies.


The primary causes for their low population are habitat destruction from commercial logging and farming from 1970 to 1983 and illegal poaching for fur over the last 40 years. Fortunately, conservation efforts by organizations like the World Wildlife Fund and the Amur Leopard and Tiger Alliance (ALTA) are working to recover the species from extinction.

What Is an Amur Leopard?

Appearance: The Amur leopard is a subspecies of leopard with a thick coat of long, dense hair varying in color from creamy yellow to rusty orange, depending on their habitat.

Amur leopards in the snowier Amur River Basin of Russia develop lighter coats in the winter and tend to have more cream-colored coats than their Chinese kin. Their rosettes (spots) are more widely spaced with thicker black borders than other subspecies of leopards. They also have larger legs and wider paws than other subspecies, an adaptation that facilitates movement through deep snow.

Size: Both males and females range in height between 25 to 31 inches at the shoulder and are typically 42 to 54 inches long. Their tales measure approximately 32 inches in length. Males are typically heavier at 70 to 110 pounds while females typically weigh 55 to 75 pounds.
Diet: The Amur leopard is a strictly carnivorous predator that primarily hunts roe and sika deer but will also eat wild boar, Manchurian wapiti, musk deer, and moose.


It will opportunistically prey on hares, badgers, raccoon dogs, fowl, mice, and even young Eurasian black bears.

Reproduction: Amur leopards reach reproductive maturity between the ages of two and three years. Females' estrus period last from 12 to 18 days with gestation taking approximately 90 to 95 days. Cubs are typically born from the end of March through May and weigh a little over one pound at birth. Like domestic cats, their eyes remain closed for about a week and they begin to crawl 12 to 15 days after birth. Young Amur leopards have been reported to remain with their mother for up to two years.

Lifespan: Amur leopards have been known to live for up to 21 years in captivity, though their lifespan in the wild is typically 10 to 15 years.

Where Do Wild Amur Leopards Live?

Amur leopards can survive in temperate forest and mountain regions, keeping mostly to south-facing rocky slopes in winter (where less snow accumulates). Individuals' territories can range from 19 to 120 square miles, depending upon age, sex, and prey density — the latter of which has greatly diminished in recent years, increasing the decline in Amur leopard population.
Historically, Amur leopards have been found in eastern China, southeastern Russia, and throughout the Korean Peninsula.

The first known documentation was a skin found by German zoologist Hermann Schlegel in 1857 in Korea. Today, the few remaining leopards are scattered throughout approximately 1,200 square miles in the area where the borders of Russia, China, and North Korea meet the Sea of Japan.

According to the World Wildlife Fund, "The last remaining viable wild population, estimated 20-25 individuals, is found in a small area in the Russian Province of Primorsky Krai, between Vladivostok and the Chinese border. In adjacent China, 7 to 12 scattered individuals are estimated to remain. In South Korea, the last record of an Amur leopard dates back to 1969, when a leopard was captured on the slopes of Odo Mountain, in South Kyongsang Province."
As of December 2011, there were 176 captive Amur leopards in zoos worldwide.

How Many Amur Leopards Are Still Alive? 

The IUCN Species Survival Commission has considered Amur leopards Critically Endangered (IUCN 1996) since 1996. As of 2016, approximately 30 to 40 individuals remain in the wild and 170 to 180 live in captivity, but the population trend continues to decrease.

What Caused Amur Leopards to Become Endangered?

Although human interference plays a key role in Amur leopards' endangered status, their low level of genetic variation due to recent dwindling population size has led to many health complications including reduced fertility.

Habitat destructionBetween 1970 and 1983, 80 percent of the Amur leopard's habitat was lost due to logging, forest fires, and agricultural land conversion projects (this loss of habitat also affected the leopard's prey species, which have become increasingly scarce as well).

Human Conflict: With less wild prey to hunt, leopards have gravitated to deer farms where they have been killed by farmers.

Poaching: The Amur leopard is illegally hunted for its fur, which is sold on the black market. Habitat loss has made it easier to locate and kill leopards within the past 40 years.
Small Population Size: The Amur leopard's critically low population is at risk from disease or environmental catastrophes that could wipe out all remaining individuals.

Lack of Genetic Variation: Because there are so few individual leopards left in the wild, they are subject to inbreeding. Inbred offspring are prone to health problems, including reduced fertility which further reduces the population's chance of survival.

Are There Conservation Efforts Helping Amur Leopards Now?

The Amur Leopard and Tiger Alliance (ALTA) works in close cooperation with local, regional, and federal organizations to protect the region's biological wealth through conservation, sustainable development, and local community involvement. They maintain four anti-poaching teams with a total of 15 members in the Amur leopard range, monitor the Amur leopard population through snow track counts and camera trap counts, restore leopard habitats, support ungulate recovery, and run a media campaign to create awareness about the Amur leopard's plight.

The World Wildlife Fund (WWF) has established anti-poaching teams and environmental education programs to increase appreciation for the leopard among local communities within the leopard's range. WWF also implements programs to stop the traffic in Amur leopard parts and to increase the population of prey species in the leopard's habitat such as the 2003 Forest Conservation Programme in the Russian Far East Ecoregion Complex.

In 2007, WWF and other conservationists successfully lobbied the Russian government to reroute a planned oil pipeline that would have endangered the leopard's habitat.

How Can You Help Save Amur Leopards?

Adopt an Amur Leopard through the World Wildlife Fund to support their efforts to save the Amur leopard from extinction.


Buy an Amur leopard t-shirt or donate to support the  Amur Leopard and Tiger Alliance. All proceeds from sales of these shirts go directly to the conservation of Amur leopards and their habitat in the wild.

Why It Matters When Species Go Extinct

Animal extinction can effect entire ecosystems and in turn the world.

Javan rhino
Javan rhinos are the most threatened of the five rhino species, with only 60 individuals surviving in Ujung Kulon National Park in Java, Indonesia. Mary Plage/Getty Images
We are surrounded by endangered species every day. Majestic tigers grace posters on bedroom walls, stuffed toy pandas stare blankly from shopping mall shelves; with the click of a button, we can watch the elaborate courtship rituals of whooping cranes and the strategic hunting habits of the Amur leopard on the Discovery Channel. No matter where we look, images and information about the world's rarest animals are readily available, but do we ever stop to think about the effects endangered species have on their environments, what happens after they disappear?


Let's face it, few of us have crossed paths with a real, live endangered species today — one that is teetering on a tightrope of existence, ready to slip into the chasm of extinction, like the Santa Barbara Song Sparrow or the Jovan Rhino, much less consider the implications of their loss.

So, does it really matter if an animal goes extinct when we can still watch it on television, even after it's gone? A single species' disappearance can, in fact, make a huge difference on a global scale. Like pieces of yarn in a woven tapestry, the removal of one can start unraveling the whole system.

The Worldwide Web

Before the internet, the "worldwide web" could have referred to the intricate systems of connections between living organisms and their environments. We often call it the food web, although it encompasses many more factors than just diet. The living web, like a tapestry, is held together not by tacks or glue, but by interdependence — one strand stays in place because it is entwined with many others.

The same concept keeps our planet working. Plants and animals (including humans) depend on each other as well as microorganisms, land, water, and climate to keep our entire system alive and well.
Remove one piece, one species, and small changes lead to big problems that aren't easy to fix. In the words of the World Wildlife Fund, "When you remove one element from a fragile ecosystem, it has far-reaching and long-lasting effects on biodiversity."

Balance and Biodiversity

Many endangered species are top predators whose numbers are dwindling due to conflicts with humans. We kill predators all over the world because we fear for our own lives as well as pets and livestock, we compete with them for prey and we destroy their habitats to expand our communities and agricultural operations.

Take for example the effect human intervention had on the gray wolf and the subsequential effects their dwindling population numbers had on its environment and biodiversity.
Before a mass extermination effort in the U.S. that decimated wolf populations in the first half of the 20th century, wolves kept other animals' populations from growing exponentially. They hunted elk, deer, and moose and also killed smaller animals such as coyotes, raccoons, and beavers.
Without wolves to keep other animals' numbers in check, prey populations grew larger. Exploding elk populations in the western United States wiped out so many willows and other riparian plants that songbirds no longer had sufficient food or cover in these areas, threatening their survival and increasing numbers of insects like mosquitos that the songbirds were meant to control.
"Oregon State University scientists point to the intricacy of the Yellowstone ecosystem," reported EarthSky in 2011.

"The wolves prey on the elk, for example, which in turn graze on young aspen and willow trees in Yellowstone, which in their turn provide cover and food for songbirds and other species. As the elks' fear of wolves has increased over the past 15 years, elk 'browse' less — that is, eat fewer twigs, leaves, and shoots from the park's young trees — and that is why, the scientists say, trees and shrubs have begun recovering along some of Yellowstone's streams. These streams are now providing improved habitat for beaver and fish, with more food for birds and bears."
But it's not only large beasts of prey that can impact the ecosystem in their absence, small species can have just as big of an effect.

Extinctions of Small Species Matter, Too

While the losses of large, iconic species like the wolf, tiger, rhino, and polar bear may make for more stimulating news stories than the disappearance of moths or mussels, even small species can affect ecosystems in significant ways.

Consider the meager freshwater mussel: There are nearly 300 species of mussel in North American river and lakes, and most of them are threatened. How does this affect the water we all depend on?
"Mussels play an important role in the aquatic ecosystem," explains the U.S. Fish and Wildlife Service. "Many different kinds of wildlife eat mussels, including raccoon, otters, herons and egrets. Mussels filter water for food and thus are a purification system. They are usually present in groups called beds. Beds of mussels may range in size from smaller than a square foot to many acres; these mussel beds can be a hard 'cobble' on the lake, river, or stream bottom which supports other species of fish, aquatic insects and worms."
In their absence, these dependent species settle elsewhere, lower the available food source for their predators and in turn causing those predators to leave the area. Like the gray wolf, even the small mussel's disappearance acts like a domino, toppling the entire ecosystem one related species at a time.

Keeping the Web Intact

We may not see wolves on a regular basis, and nobody really wants a poster of a Higgins eye pearly mussel on the wall, but the presence of these creatures is interwoven with the environment we all share. Losing even a small strand in the web of life contributes to the unraveling of our planet's sustainability, the fine balance of biodiversity that affects each and every one of us.

Once Written Off for Dead, the Aral Sea Is Now Full of Life

Thanks to large-scale restoration efforts, the North Aral Sea has seen a resurgence of fish—a boon to the communities that rely on it.

Omirserik Ibragimov, 25, uses a net to ice fish on the frozen surface of the North Aral Sea near Tastubek, Kazakhstan.

Reporting on this story was supported by a grant from the Pulitzer Center on Crisis Reporting.
Omirserik Ibragimov fixed his gaze on the hole he had carved out from the frozen Aral Sea. The 25-year-old’s hands moved steadily, pulling out a fishing net that he and his father had left under the solid, snow-covered surface just three days earlier.
After a minute marked by tense silence, two breams emerged from the hole. Then three pike-perches, their silver scales shimmering as they struggled against the net’s green meshing.
“Here comes the gold,” Omirserik said with a smile as he continued tugging the net. The pike-perch, with its tender flesh and few bones, is considered to be the most valuable catch, selling for roughly 650 tenge (a little over $2) for a kilogram; local fishermen refer to them as “gold fish.”
His father, Kidirbai, worked with his bare hands to free the fish, his knuckles flush from the freezing water. After gathering all their nets, their total catch of the day was about 77 pounds (35 kilograms) of pike-perch and 44 pounds (20 kilograms) of bream—a sizable haul for a few hours of work.
The fishing has improved dramatically over the past few years on the North Aral Sea, indicating restoration efforts are working.

Just 15 years earlier, this would not have been possible. Once the world’s fourth-largest freshwater lake, with an area of some 26,000 square miles, the Aral Sea became the victim of the Soviet Union’s agricultural policies in the 1950s. Water from its two river sources—the Amu Darya and Syr Darya—was intentionally diverted for cotton cultivation. (See other rivers that have been run dry.)
As decreasing water flow into the sea caused a rise in salinity, the abundant freshwater fish species began to die out. By the 1980s, the fishing industry in the Aralsk district—once a robust source of employment for the region—was wiped out, forcing a mass migration of people. The remaining population was hit by extreme weather, brought on by the dried-out Aral seabed, and deteriorating health.
“The people destroyed the sea and then nature took revenge on the people,” said Madi Zhasekenov, the director of the Aralsk Regional Museum and Fishermen Museum.
Ice fishing can be cold, yet lucrative, work.

Massive Disaster

This rapid collapse over less than three decades—which environmental scientists say is one of the planet’s worst ecological disasters—is marked today by the sea’s reduced size. Its total area of water, straddling Kazakhstan and Uzbekistan, is now a tenth of its original size. What’s left has broken into two distinct bodies: the North and South Aral Seas. In Uzbekistan, the entire eastern basin of the South Aral Sea is completely desiccated, leaving merely a single strip of water in the west. (Learn about other vanishing lakes around the world.)
But Kazakhstan’s North Aral Sea has seen a happier outcome, thanks to a nearly $86 million project financed in large part by the World Bank. Along with repairs to existing dikes around the basin to prevent spillage, an eight-mile dam was constructed just south of the Syr Darya River. Completed in the summer of 2005, this dam, named Kokaral, surpassed all expectations. It led to an 11-foot increase in water levels after just seven months—a goal that scientists initially expected would take three years.
Local people have long relied on camels as livestock, especially as fishing declined.

This turnaround in the North Aral Sea’s fate has meant that the fish stocks have returned to its waters, injecting new life into the local communities. Just as government policies had doomed the Aral Sea, careful planning and research helped revive at least part of it.
Kristopher White, a researcher and professor of Almaty’s KIMEP University who has studied the economic impacts of the Aral Sea’s desiccation, explained that while the sea will never return to its former size, the 18 percent increase in mass of the North Aral Sea is a testament to how political will and scientific research can benefit the environment.
“Anthropogenic ecological damage can be reversed by human intervention,” said White.
Children play on a snowdrift in Tastubek, Kazakhstan, where economic opportunities are improving with the health of the sea.

Optimism and Hope

At its peak in 1957, the Aral Sea produced more than 48,000 tons of fish, representing roughly 13 percent of the Soviet Union’s fish stocks. By the 1980s, due to the rising salinity of the sea, the 20 native species of fish were decimated; commercial harvests plummeted to zero by 1987. The water from the sea receded, and today, the shore is about 12 miles (20 kilometers) from Aralsk.
“The major source of employment was gone, and with it optimism and hope for the future,” said White. “And that really prevailed throughout the region until the completion of this dam.”
Workers process fish at a plant in Aralsk, Kazakhstan.

During those decades, flounder was the only fish that could survive the high-salinity North Aral Sea. But after the Kokaral Dam was finished, the average salinity dropped from 30 grams to 8 grams per liter, prompting the return of almost two dozen freshwater species through the Syr Darya river.
According to the Aralsk Fish Inspection Unit, fish catch in the North Aral Sea has grown six-fold since 2006, when the bulk of the 1,360 tons caught was flounder. By 2016, 7,106 tons of fish was caught, with bream being the most common, followed by roach and the sought-after pike-perch. For 2018, the fishing limit is set at 8,200 tons, said head inspector Esenbai Ensepov.
A worker prepares fish for smoking.

This return has brought commerce back to the inland town of Aralsk. Askar Zhumashev, 42, a supervisor at Kambala Balyk Processing Plant, said that his team processed roughly 500 tons of fish two years ago, the biggest amount since he started working there.
“When I was born, the sea was already gone,” said Zhumashev. “I went to the Aral Sea for the first time only two years ago. My parents used to tell me that the boats would come in and out everyday from the old port.” (Learn why a giant green lake turned red.)
Kiderbai Ibragimov, 45, prepares a fish meal at home in Tastubek.

Growing Prosperity—and Problems

In the winter, the village of Tastubek, about four hours from Aralsk, appears desolate. But around 10 AM every morning, the town hums to life as the fishermen begin gathering to inspect their gear and discuss the day’s plans. With the Aral Sea just an hour’s drive away, they can be back in the village by the late afternoon with a successful haul.
Kidirbai, the patriarch of the Ibragimov family, has witnessed the changing fortunes of Tastubek. He was born here in 1973. Unlike those forced to move during the bleak years, his family relied on their livestock of camels and horses for income. When he was a young boy, there were 90 houses in Tastubek.
“By the mid-90s, there were only nine houses left,” he said. This year, he counted 34, an increase from last year’s 29. The newcomers are young fishermen attempting to strike gold. “I am happy the village is growing because then maybe the government will pay more attention to us, like they would build a road or support the village,” said Kidirbai.
People wait for a train under a Soviet-era mural in Aralsk.

But prosperity has also generated some negative effects, like the raft of illegal fishing during the breeding season of May to July. Aldanbek Kerinov, a former taxi driver from Aralsk who started fishing full-time with his brothers seven years ago, explained that this period, well legally off limits, is considered the most bountiful because fish swim closer to the shore to lay their eggs.
“Everyone usually goes late at night, because during the day, everyone is afraid the fish inspectors will come,” he said. “There are no other jobs and fishing is the main source of income, so they will always continue to fish.”
Aldanbek was unconcerned about the impact this would have on the fisheries, as the World Bank’s second phase to the dam is touted to bring more water and thus more fish, he said. (While a plan to raise the Kokaral Dam’s walls to increase water levels has been in the works for years, a World Bank representative said that the government needs to approve the project in order for it to move forward.)
Yet the illegal fishing does worry experts like White, who points out that illicit harvests are much harder to track for management purposes. And the history of fishing has been rife with loose or no management, followed by collapse of stocks. (Learn about vanishing aquifers.)
A Muslim graveyard is seen at sunrise near Tastubek.

An Unpredictable Force

For Kirdirbai, the sea has been an unpredictable force in his life. In 1987, the water froze unexpectedly early in November, and his family’s fishing boat was stuck a thousand feet (300 meters) out in the sea. His father, worried about thin ice, tied a rope to himself and shuffled out from shore to retrieve it. Fourteen-year-old Kidirbai watched as his father freed the craft from the ice with a metal spike and dragged it back, without incident.
Five years later, Kidirbai was not so lucky. He and his friend were fishing in the summer when a big storm hit. The boat overturned and his friend drowned. Kidirbai, traumatized by the incident, stopped fishing for three years.
Yes, it is bad to fish during the breeding season, Kidirbai said. But after decades of poverty and harsh living, they were all hungry for prosperity. “Now the locals are thinking only about how to earn as much as possible,” he said.
His faith in the Aral Sea remains unwavering. Since the freshwater fish species have returned, Kidirbai—who could never fathom living anywhere else—is determined that his son has a future there as well.
“The sea is the source of life for us,” he said. “Next year, I am going to build a new house for him. My son will get married and he will continue fishing.”
With reporting contributions by Serik Dyussenbayev