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Sunday, 19 October 2014

Out of Africa: Gorilla Happiness, while there's still time

 Western Lowland Gorilla brothers Kesho and Alf are reunited at Longleat Safari Park, Wiltshire, after three years apart. Native to central Africa, Western Lowland Gorillas are threatened by hunting and the Ebola virus. The surviving population is classified as "Critically Endangered" on the IUCN Red List of Threatened Species: photo by Ian Turner/BNPS, 16 August 2012

Kesho (on the left) and Alf embrace each other in a hug at Longleat Safari Park
Kesho, age 13, and Alf, age 9, were born at Dublin Zoo, but separated when Kesho was sent to London Zoo to take part in a breeding program. When he proved infertile, it was decided to reunite the animals: photo by Ian Turner/BNPS, 16 August 2012

Longleat keeper Mark Tye: "The keepers from Dublin weren't entirely sure the brothers would even know each other, but the moment they met you could just see the recognition in their eyes...": photo by Ian Turner/BNPS, 16 August 2012

"...We had been slightly concerned how they would react to each other and whether the big brother could put up with little Alf's playfulness...": photo by Ian Turner/BNPS, 16 August 2012

"However they have formed a really tight bond in just a few weeks...": photo by Ian Turner/BNPS, 16 August 2012

Kesho (on the left) and Alf play at Longleat Safari Park
"...Kesho is actually incredibly tolerant; allowing both Alf and six-year-old Evindi to jump all over him.": photo by Ian Turner/BNPS, 16 August 2012

"What you're seeing is exactly what you think you're seeing. Two intelligent social mammals, who were separate, are pleased to see each other again and play together. It is gorilla joy, being reunited with someone you used to have good times with and now you can again, so it's gorilla happiness.": photo by Ian Turner/BNPS, 16 August 2012

Insights into human evolution from the gorilla genome sequence

Humans share many elements of their anatomy and physiology with both gorillas and chimpanzees, and our similarity to these species was emphasized by Darwin and Huxley in the first evolutionary accounts of human origins. Molecular studies confirmed that we are closer to the African apes than to orang-utans, and on average closer to chimpanzees than gorillas. Subsequent analyses have explored functional differences between the great apes and their relevance to human evolution, assisted recently by reference genome sequences for chimpanzee and orang-utan.

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing.

Insights into human evolution from the gorilla genome sequence (from Introduction and Abstract): Aylwyn Scally et al., Nature 883, 8 March 2012

gorilla baby

The first full genome analysis has revealed that 30% of gorillas' genetic makeup is closer to human or chimpanzee than the latter are to each other: photo by Luanne Cadd via The Guardian, 7 March 2012

Gorilla genome analysis reveals new human links
First full sequence of gorilla genome shows 96% share with humans, with close parallels in sensory perception and hearing: Alok Jha, science correspondent, The Guardian, 7 March 2012

Humans and gorillas last shared a common ancestor 10 million years ago, according to an analysis of the first full sequence of the gorilla genome. The gorilla is the last of the living great apes –- humans, chimpanzees, gorillas and orangutans -– to have its complete genetic sequence catalogued.

Scientists, led by researchers from the Wellcome Trust Sanger Institute near Cambridge and Baylor College of Medicine in Houston, also found that 15% of the gorilla's genome is closer between humans and gorillas than it is between humans and chimpanzees, our closest animal relative. The genomes of all three species are, in any case, highly similar: humans and chimpanzees share more than 98% of their genes, while humans and gorillas share more than 96%.

The genetic sequence was taken from a female western lowland gorilla (Gorilla gorilla gorilla) named Kamilah and published in Nature.

An initial analysis also showed similarities in genes involved in sensory perception and hearing, and brain development showed accelerated evolution in all three species. Genes associated with proteins that harden up skin were also particularly active in gorillas -– which goes some way to explaining the large, tough knuckle pads on gorillas' hands.

"Gorillas are an interesting animal in their own right but the main reason they are of particular interest is because of their evolutionary closeness to us," said Aylwyn Scally, an author of the research from the Wellcome Trust Sanger Institute. "They're our second-closest evolutionary cousins after chimpanzees and knowing the content of the gorilla genome enables us to say quite a lot about an important period in human evolution when we were diverging from chimpanzees."

Comparing the sequences of humans, chimpanzees and gorillas has enabled scientists to put a more accurate clock on when the three species split from their last common ancestors. It was traditionally thought that the emergence of new species (known as "speciation") happens at a relatively localised point in time but emerging evidence suggests that this is not necessarily the case, that species split over an extended period. 

Studying the gorilla genome suggests that the divergence of gorillas from the common ancestor of humans and chimpanzees happened around 10 million years ago. Humans and chimpanzees last shared a common ancestor around 6 million years ago. Eastern and western gorillas split some time in the last million years.

First-time mother Mjukuu, a western lowland gorilla with her newly born male baby –- the first gorilla to be born there in 20 years -– resting on straw in an enclosure at the London zoo: photo by Iona Stewart/AP via the Guardian, 29 October 2010

One curious find was the evolution of genes associated with hearing, which seem very similar between humans and gorillas. "Scientists had suggested that the rapid evolution of human hearing genes was linked to the evolution of language," said Chris Tyler-Smith, senior author from the Wellcome Trust Sanger Institute. "Our results cast doubt on this, as hearing genes have evolved in gorillas at a similar rate to those in humans."

Scally adds that it could well be that there has been a parallel acceleration in these genes for two entirely different reasons –- that human hearing has developed because of speech and gorilla hearing has developed to serve an entirely different, but as-yet-unknown, purpose.

The researchers said that studying the gorilla genome would shed light on a time when apes were fighting for survival across the world.

"There's an interesting background story of great ape evolution," says Scally. "The common ancestor of all four great apes was sometime back in 15 to 20 million years ago. At that time, it seems to have been a nice time to have been an ape -– it was a golden age -– a lot of the world was just right for the kind of environment for apes to live in. Since that time, the story has been of fragmentation and extinction –- most of the great ape species that have existed have gone. Today, all the non-human apes are really endangered populations, they're living in forest refuges and population numbers are quite low. Humans look like an exception to that -– we're all over the world now and live in places where you could never have had a primate beforehand."

Today, gorillas are classified as critically endangered and populations have plummeted to below 100,000 individuals in recent decades due to poaching and disease. They are restricted to equatorial forests in countries including Cameroon, Central African Republic, Gabon, Nigeria, Republic of Congo and Angola.

"As well as teaching us about human evolution, the study of great apes connects us to a time when our existence was more tenuous," say the researchers in Nature. "And in doing so, highlights the importance of protecting and conserving these remarkable species."

Daring: Brave Alf, the western lowland gorilla, stunned keepers at Longleat Safari Park, when he scaled the great heights of a 40ft oak tree
Fourteen months after his arrival at the park, Alf stunned keepers when he scaled a 40-foot oak tree in search of acorns: photo by BNPS, 23 October 2013

Intrigued: After foraging around in the grass at the foot of the oak tree, Alf, the 10-year-old ape, gazes skywards at the bounty of acorns hanging above his head

After foraging around in the grass at the foot of the oak tree, Alf gazes skywards at the bounty of acorns hanging above his head
photo by BNPS, 23 October 2013
Tentative: The bright beast carefully tested each precarious branch checking they could take his 17-stone weight

He carefully tests each branch to check if it can bear his 17-stone weight:
photo by BNPS, 23 October 2013
Bemused: Watching on, Alf's older brothers Evindi, seven, and 14-year-old silverback Kesho kept their feet firmly rooted to the ground

  Looking on from far below as he climbed, Alf's bemused older brothers Evindi, seven, and 14-year-old silverback Kesho kept their feet firmly rooted to the ground. Keeper Mark Tye: "Alf has always been the more adventurous of the brothers and he also seems to be the most fearless. We’re not entirely sure why he felt the need to climb up quite so high to collect the acorns as there were plenty lying on the ground but perhaps he was looking for a bit of peace and quiet and knew the others weren’t going to join him. Although the branches look quite delicate, Alf is a very smart gorilla and he carefully tested them before venturing out along them.": photo by BNPS, 23 October 2013
Foraging: Scouring the branches Alf feasts on the tasty autumnal treats

 Alf's perseverance rewarded with a feast of autumnal acorns. A park spokesman: "Naturally gorillas forage for their food, for whatever is around, be it nuts or fruit. They are good climbers but don't normally climb that high. Alf clearly has a head for heights. He is a bit of a daredevil."
photo by BNPS, 23 October 2013

Satisfied: Edging closer to his goal, the western lowland gorilla perched precariously in the tree, tucking into his well-earned snack
Perched  high in the tree, Alf tucks into his well-earned snack: photo by BNPS, 23 October 2013

Ebola Outbreak Killed 5000 Gorillas: Magdalena Bernejo, José Domingo Rodriguez-Teijeiro, Alex Barroso, Carlos Vilà, Peter D. Walsh, Science 314, 8 December 2006 (Abstract)
Over the past decade, the Zaire strain of Ebola virus (ZEBOV) has repeatedly emerged in Gabon and Congo. Each human outbreak has been accompanied by reports of gorilla and chimpanzee carcasses in neighboring forests, but both the extent of ape mortality and the causal role of ZEBOV have been hotly debated. Here, we present data suggesting that in 2002 and 2003 ZEBOV killed about 5000 gorillas in our study area. The lag between neighboring gorilla groups in mortality onset was close to the ZEBOV disease cycle length, evidence that group-to-group transmission has amplified gorilla die-offs.

Over the past decade, the Zaire strain of Ebola virus (ZEBOV) has emerged repeatedly in Gabon and Congo. During each human outbreak, carcasses of western gorillas (Gorilla gorilla) and chimpanzees (Pan troglodytes) have been found in neighboring forests. Opinions have differed as to the conservation implications. Were these isolated mortality events of limited impact? Was ZEBOV even the cause? Or, were they part of a massive die-off that threatens the very survival of these species? Here, we report observations made at the Lossi Sanctuary in northwest Republic of Congo, where ZEBOV was the confirmed cause of ape die-offs in 2002 and 2003. Our results strongly support the massive die-off scenario, with gorilla mortality rates of 90 to 95% indicated both by observations on 238 gorillas in known social groups and by nest surveys covering almost 5000 km2. ZEBOV killed about 5000 gorillas in our study area alone.

Starting in 1995, we habituated gorillas to our presence, and by 2002 we had identified 10 social groups with 143 individuals. In late 2001 and early 2002, human outbreaks of ZEBOV had flared up along the Gabon-Congo border. In June 2002, a gorilla carcass was found 15 km west of the sanctuary. By October, gorilla and chimpanzee carcasses began appearing inside the sanctuary. In the next 4 months, we found 32 carcasses. Twelve of the carcasses were assayed for ZEBOV, and 9 tested positive. From October 2002 to January 2003, 91% (130/143) of the individually known gorillas in our study groups had disappeared.

In June 2003, one fresh carcass appeared south of the sanctuary. In September, we identified seven new social groups with home ranges straddling and to the east of the two rivers and monitored their sleeping nests on a biweekly basis. Then in October carcasses again appeared within the sanctuary. Ten carcasses were found in the following 3 months. From October 2003 to January 2004, Ebola spread sequentially from north to south, killing 91 of the 95 individuals (95.8%) in the newly monitored groups. One remarkable feature of this spread was that the onset of ZEBOV deaths in each group was predicted by the number of home ranges separating it from the first group to experience deaths. In particular, the estimated time lag between deaths in successive groups (11.2 days) was very similar to the typical length of the ZEBOV disease cycle of about 12 days. Assuming deaths were caused by spillover from a north-south reservoir epizootic did not fit the mortality pattern well. This implies that recent ape die-offs may not have been caused only by massive spillover from a reservoir host. Rather, group-to-group transmission may have also played a role in amplifying outbreaks, as transmission within gorilla groups apparently has.

Peter D. Walsh with friend: photo via Peter D. Walsh@ApesInc, 2014

Peter D. Walsh @ApesInc - Jul 30

In the last thirty years Ebola has killed at least 10 times as many gorillas as humans

Peter D. Walsh

Peter D. Walsh with friend: photo via Peter D. Walsh@ApesInc, 2014

Peter D. Walsh @ApesInc - Oct 17

Mountain Gorilla Veterinary Project advocates vaccinating wild gorillas against #Ebola. Wish I had thought of that first! Oh, yeah. I did...

Adult Silverback Western Lowland Gorilla (Gorilla gorilla gorilla): photo by Raul654, 2005

Gorilla gorilla ssp. gorilla: from The IUCN Red List of Threatened Species (P.D. Walsh et al., 19 October 2014)

There are two primary drivers of rapid western lowland gorilla decline: commercial hunting and the Ebola virus. Until the early 1980s, the interior of western lowland gorilla range included a series of vast, road-less blocks of forest where hunting access was extremely difficult and gorilla densities were high. Since then improvements in transportation infrastructure, devaluation of the regional currency, declining oil stocks, and timber depletion in other tropical regions have led to an explosion in mechanized logging. Regional timber production nearly doubled between 1991 and 2000 (Minnemeyer et al. 2002). Vast tracts of previously inaccessible forest have recently been penetrated by logging roads, which provide commercial hunters ready access to remote areas with high ape densities, and to markets. Logging vehicles are also used to transport bushmeat, and logging employees eat more bushmeat than do local villagers.

The gorillas’ very low reproductive rates (3% maximum observed rate of population increase, Steklis and Gerald-Steklis 2001) mean that even low levels of hunting are enough to cause population decline. Consequently, the logging boom has caused a rapid crash in gorilla numbers. For example, Gabon experienced an estimated 56% decline in ape abundance from 1983 to 2000, most of which was attributed to hunting (Walsh et al. 2005). Given that Gabon is the least heavily human populated country in the region, hunting impact is likely as high or higher in other range states. The threat posed by logging promises to continue and even intensify in the foreseeable future. Rates of timber production in the region are increasing (Minnemeyer et al. 2002), in the case of Gabon exponentially. Profits in the industry are derived largely through exploitation of previously unlogged areas rather than sustainable harvesting in older concessions. The current trajectory predicts that the last remaining tracts of inaccessible forest will be opened to logging in the next 10 to 20 years.

The second major driver of rapid gorilla decline is disease, specifically the Ebola virus. Since the early 1990s, Ebola has caused a series of massive gorilla and chimpanzee die-offs in remote forest blocks at the heart of their range. Outbreaks were first noted in 1994 in the Minkébé forest block of northern Gabon (Huijbregts et al. 2003). Before Ebola’s arrival, what is now Minkébé National Park held what was probably the second largest protected gorilla and chimpanzee population in the world. In 1996 Ebola emerged in the Lopé Reserve (now National Park) in central Gabon, in 2001 in the Mwagné forest block of eastern Gabon, in 2002 to 2003 in the adjoining Lossi forest block of north-west Congo, and in 2003 to 2005 in the Odzala National Park in north-west Congo. The Ivindo forest block of central Gabon was not monitored during the outbreak period, but it lies directly adjacent to the 1996 human outbreak zone around Booué and recent observations suggest an ape die-off there too.

Both phylogenetic analyses of the Ebola virus genome and analyses of the spatio-temporal pattern of outbreaks in humans and wild apes (Walsh et al. 2005, Lahm et al. 2006) suggest that these outbreaks were not isolated events but part of a spreading epizootic of Ebola in its reservoir host (probably bats, Leroy et al. 2005). Moving at about 40 to 45 km/year, this epizootic has for the last decade spread in an east/north-easterly direction across the region. Although continued spread is not guaranteed, the epizootic’s past spread rate has been highly consistent, making it possible to accurately predict the timing of the Odzala die-off well before it occurred (Walsh et al. 2003, 2005).

During Ebola outbreaks, gorilla mortality rates have been extremely high. During three different outbreaks at two different study sites, individually known social groups containing almost 600 gorillas were monitored. In all three outbreaks about 95% of known individuals died (Caillaud et al. 2006, Bermejo et al. 2007). Higher survival rates amongst solitary individuals suggest that most of the remaining 5% may be individuals who were never infected rather than resistant survivors (Caillaud et al. 2006). Nest surveys at four different sites exhibit an “all or none” pattern of Ebola impact. Areas of 10,000 km² or more showing 95% declines in abundance transition abruptly into areas with little or no mortality (Bermejo et al. 2007, WCS and Government of Congo MEF unpublished data). These low ape densities are not reasonably attributed to hunting pressure as most of the remote survey zones had high ape densities just a few years before the declines were detected and because densities of other preferred target species (e.g., elephants and duiker) were still high after the Ebola outbreaks (Walsh et al. 2003, Bermejo et al. 2007). The proportion of habitat in the 95% mortality class varied amongst outbreak sites, from little or none at Lopé to the entire Mwagné survey zone. In Odzala National Park, which held what were by far the largest protected populations of gorillas and chimpanzees in the world, the outbreak zone covered about 58% of the park.

In the Lossi and Odzala zones, extensive survey data allowed a fairly precise mapping of outbreak and non-outbreak zones. Therefore, the number presented for these two zones is based on the proportion of the survey zone in each outbreak class (Outbrk vs. NonOutbrk) and the assumption of 95% mortality in outbreak areas. This approach was not possible for the Mwagné and Minkébé sites where virtually the entire populations were wiped out, or for the Ivindo site where survey intensity was not high enough to precisely map outbreak and non-outbreak zones. For these sites, nest encounter rates for surveys conducted before Ebola emergence are compared with nest encounter rates after Ebola emergence (Pre-Ebola vs. Post-Ebola). No attempt was made to estimate % decline for Lopé because it was the only zone to be logged before Ebola arrival and the only area in which a substantial proportion of the survey zone has experienced high rates of hunting. This makes it difficult to discriminate Ebola impact from hunting impact. Therefore, for the purposes of this analysis, Ebola is assumed to have had zero impact at Lopé. Estimated declines in gorilla abundance for the five zones for which estimates have been made range from 56% at Odzala to more than 95% at Mwagné and Minkébé. When decline rates are averaged across all six zones (with the contribution of each zone weighted by its surface area) the mean decline is 74% . The assumption of zero impact at Lopé has a conservative effect on this mean value.

These six protected areas account for 45% of the total protected area habitat (67,250 km²) in which significant western lowland gorilla populations were found before Ebola emergence. If we assume that all major protected areas had the same pre-Ebola density, this implies that 33% of the total protected area population of western lowland gorilla (100*(0.45*0.26+0.55*1) = 33%) has been killed by Ebola just over the last 13 to 14 years. This estimate is highly conservative in that pre-Ebola density estimates for protected areas with Ebola impact were typically much higher than for protected areas without recorded Ebola impact.

If the Ebola epizootic continues at the same rate and trajectory, it could reach most of the remaining protected areas with large populations of western lowland gorillas within the next 5 to 10 years...

Walsh, P.D., Tutin, C.E.G., Baillie, J.E.M., Maisels, F., Stokes, E.J. & Gatti, S. 2008. Gorilla gorilla ssp. gorilla. The IUCN Red List of Threatened Species. Version 2014.2, 19 October 2014.

File:Gorilla gorilla11.jpg

Western Lowland Gorilla (Gorilla gorilla gorilla), Republic of the Congo: photo by Pierre Fidenci, September 2008

Western Lowland Gorillas (Gorilla gorilla gorilla), Odzala-Kokoua National Park, Republic of the Congo: photo © Céline Genton, 2009 via LiveScience, 18 June 2012

Western Lowland Gorilla What WWF Is Doing

Western Lowland Gorilla (Gorilla gorilla gorilla): photo © Richard Carroll / WWF-US  via WWF

Western Lowland Gorilla

Western Lowland Gorilla (Gorilla gorilla gorilla): photo © Martin Harvey / WWF-Canon via WWF


Hazen said...

Faced with these sobering facts about species decline among our primate cousins, and their possible extinction, and the hard reality that this implies for us all, there’s still a sense of delight, albeit cautious and momentary. It comes from the gorillas in those pictures, brothers finding one another at long last, disporting themselves, or even wanting to climb away from it all for a time, when the genome gets to feeling a little crowded and put upon. What a difference that four percent, or that two percent, has made in the history of the planet.

TC said...


Yes, I too was deeply affected by the sight of that brotherly reunion. Following the small group since then, as possible... it does seem Alf has developed something comparable to a sensitive teenager's tendency to go off by himself.

The necessary acknowledgment of the pathos of any zoo environment perhaps mitigated to some extent by the knowledge that any Western Lowland Gorilla to have escaped the pathogenic outbreaks of c. a decade ago might well be fortunate to be alive at all.

Impossible for that matter not to think all the many fateful what-might-have-beens in the primate evolution story...

"The common ancestor of all four great apes was sometime back in 15 to 20 million years ago. At that time, it seems to have been a nice time to have been an ape -– it was a golden age -– a lot of the world was just right for the kind of environment for apes to live in. Since that time, the story has been of fragmentation and extinction –- most of the great ape species that have existed have gone. Today, all the non-human apes are really endangered populations, they're living in forest refuges and population numbers are quite low. Humans look like an exception to that -– we're all over the world now and live in places where you could never have had a primate beforehand."

(Another way of saying that, maybe, would have been: " places where primates were never meant to go." With the possible further annotation: "...and doing things primates were never meant to be doing.")

By the by, three years ago there came out (and quickly disappeared) a very interesting Hollywood "summer vehicle" marketed as a "reboot" of the Planet of the Apes saga: The Rise of the Planet of the Apes.

In the film, biological testing of an Alzheimer's drug on apes leads to a sudden and surprising ape uprising -- along with an "accidental" release of the drug, now seen to be a deadly pathogen, into the human population, with an ominous final scene at San Francisco International Airport (an infected pilot, a few drops of blood), anticipating global spread of the outbreak among homo sapiens.

In that scenario, there would be not much future for the "dominant" chain of great apes; though the fact that a sequel to the "reboot" came out this year does suggest that the extermination of the Humans remains, at this date in the marketing cycle, as yet incomplete.