New study switches from genetic to metabolic analysis to reconstitute evolutionary process

A new method for analyzing a living being chemical compositions is tested in Andean plants and attest the genesis of species by means of geographic isolation. Scientists analyzed chemical compounds which express specific biogeographic trends in the evolutionary process, validating a Smithsonian hypothesis on the evolution of the genus Espeletia in the process.

A new method for analyzing a living being chemical compositions is tested in Andean plants and attest the genesis 
of species by means of geographic isolation [Credit: Frederico Padilla]

With 72 species currently identified, Espeletia is a plant genus endemic to the paramo, a moist alpine biome unique to the northern Andes. This genus, which inhabits the world's most diverse high-altitude ecosystem, is considered an outstanding example of adaptive success.

Brazilian scientists investigated over Espeletia's diversity and geographic distribution in the paramo; the result, published in Scientific Reports, suggests that researchers might reconstitute more accurately the whole speciation process making use of a relatively unexplored bias in the study of evolutionary science: metabolomics.

Metabolomics refers to an area of study focusing on the chemical substances synthesized by a living organism -- a byproduct of its metabolism -- which is used to map chemical compounds inherent to a given species. In order to do so, a combination of techniques involving plant extracts, geographic data, and multivariate statistics is required. Studies of this kind are usually based on genomics, DNA marker analysis or morphological comparisons.

Researchers at the University of Sao Paulo's School of Pharmaceutical Sciences -- Ribeirao Preto campus (FCFRP-USP), in Brazil, use metabolic fingerprinting for the first time to explain the evolutionary histories and biogeographic characteristics of Espeletia.

"Basically, we took the chemical compositions of the species of Espeletia and their metabolome and found a correlation with their geographic origins. Species present in the same locations display similar chemical profiles. The same link had already been found using molecular markers but on a larger geographic scale. This shows that the geography of the Andes not only determined the evolution of this plant group, and possibly of other plant groups in the region but also shaped the chemical compositions of these species," said Federico Padilla, one of the authors of the article.

Based on a study supported by Sao Paulo Research Foundation (FAPESP) through regular research grant, the article confirms a hypothesis on the origin and migration routes of Espeletia along the northern Andes proposed by researchers at the US National Museum of Natural History, part of the Smithsonian Institution, in the 1990s, which was hitherto partially supported by molecular markers.

According to this hypothesis, the original stock of Espeletia diversified when the first population of the genus started expanding in two directions from the western part of the Cordillera de Merida, the largest massif in Venezuela. One branch moved along the Venezuelan Andes, while the other moved west and southwest along the Colombian Andes and into northern Ecuador.

"Historically, this kind of analysis has been based on molecular markers. However, genetic analysis is unable to determine specific biogeographic trends with satisfactory precisions in groups that have evolved recently, such as the genus Espeletia, for which it merely identifies two groups, the Venezuelan and Colombian species, " Padilla said.

Metabolites data point evolutionary adaptation

The Smithsonian hypothesis was confirmed by an analysis of the secondary metabolites (i.e., the chemical compounds involved in plants' adaptations to the ecosystem), which pointed to patterns of geographic distributions and chemical diversifications in the Andean paramos.

"Each kind of marker has advantages and disadvantages," said Professor Fernando Batista da Costa , Padilla's supervisor and a co-author of the article published in Scientific Reports. "Unlike animals, plants can't move in order to adapt to this or that environment. Instead, they produce a vast array of chemical compounds that help them adapt to the place where they grow."

The rugged topography of the Andes makes the paramo a highly fragmented biome, biologically and geographically comparable to an archipelago in which "islands" of open grassland vegetation are separated by dense forests or deep valleys that prevent plant species from communicating with other paramos.

According to the article, this geographic isolation is a particularly influential factor for species with limited seed dispersal and a lack of long-distance pollinators, as is the case for Espeletia.

"We prove that their isolation favored allopatric speciation, meaning speciation occurring in separate regions because of geographic barriers. Darwin proposed this kind of speciation in his evolutionary theory as a result of his observations in the Galapagos Archipelago. He saw there that different islands had different species and that these species were related to each other," Batista da Costa said.

The researchers' analyses of the chemical compositions showed that species of Espeletia in different paramos differ not only genetically and morphologically but also chemically.

"In each paramo, most species accumulate different chemical compounds that may possibly be linked to their adaptation to that particular geographic area," Padilla said. "We demonstrate, using chemical evidence, that allopatric speciation occurred in these paramos and groups of species, as had been proposed in the 1990s."

Application of metabolomics in other areas

According to the researchers, this approach can be used to study practically all of a plant's metabolites at the same time.

"In classical phytochemistry, we studied one plant at a time and usually identified a few chemical substances," Padilla said. "With the new techniques and equipment, such as the liquid chromatography coupled with mass spectrometry that we used, we can now assemble 100 or more plant extracts, analyze them all at the same time, and obtain a data matrix potentially representing more than 1,000 chemical compounds."

The researchers stress that analogous models to that described in the article can be used to obtain metabolic fingerprints for other plants with the aim of analyzing their biogeographic and evolutionary histories.

"This new model can be used in agriculture, or for medicinal plants, or even by the police, for example, to identify the origin of marijuana consumed in a particular region," said Batista.

Source: Fundação de Amparo à Pesquisa do Estado de São Paulo [September 19, 2017]

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When it comes to the threat of extinction, size matters

Animals in the Goldilocks zone -- neither too big, nor too small, but just the right size -- face a lower risk of extinction than do those on both ends of the scale, according to an extensive global analysis.

Extinction risks are greater for animals at the small and large ends of the scale 
[Credit: Oliver Day, Oregon State University]

Reporting today in the Proceedings of the National Academy of Sciences, researchers who determined body masses for thousands of vertebrate animal species showed that the largest and smallest species face a greater risk of extinction than do mid-sized animals.

Disproportionate losses at the large and small ends of the scale raise the likelihood of significant changes to the way natural ecosystems function in forests, grasslands, oceans and even rivers and streams -- "the living architecture of the planet," the researchers wrote.

"Knowing how animal body size correlates with the likelihood of a species being threatened provides us with a tool to assess extinction risk for the many species we know very little about," said William Ripple, a distinguished professor of ecology at Oregon State University and lead author of the study.

Ripple and colleagues from the United States, Australia and Switzerland looked at the more than 27,000 vertebrate animal species assessed by the International Union for the Conservation of Nature in the so-called Red List. About 4,400 are threatened with extinction.

Among the groups of animals evaluated were birds, reptiles, amphibians, bony fishes, cartilaginous fishes (mostly sharks and rays) and mammals.

The largest animals are threatened principally with harvesting by humans. "Many of the larger species are being killed and consumed by humans, and about 90 percent of all threatened species larger than 2.2 pounds (1 kilogram) in size are being threatened by harvesting," said Ripple.

"Harvesting of these larger animals takes a variety of forms including regulated and unregulated fishing, hunting and trapping for meat consumption, the use of body parts as medicine and killing due to unintentional bycatch," the authors wrote.

Meanwhile, threats to the smallest animals may be grossly underestimated. The smallest species with high extinction risk consist of tiny vertebrate animals generally less than about 3 ounces (77 grams) in body weight. These diminutive species are mostly threatened by loss or modification of habitat. Examples include the Clarke's banana frog, sapphire-bellied hummingbird, gray gecko, hog-nosed bat and the waterfall climbing cave fish. Small species that require freshwater habitats are especially imperiled.

Different conservation strategies will be needed to address threats to the largest and smallest animals, the scientists said. Well known mammals at the large end of the scale -- whales, elephants, rhinos, lions -- have been the target of protection programs, but conservation attention is also needed for large-bodied species that are not mammals. They include large fish, birds, amphibians and reptiles such as the whale shark, Atlantic sturgeon, Somali ostrich, Chinese giant salamander and the Komodo dragon.

Human activity seems poised to chop off both the head and tail of the size distribution of life, the authors added, which will fundamentally restructure many ecological communities.

Source: Oregon State University [September 18, 2017]

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New study contradicts assumption that true frogs diversified as they expanded their range around globe

Evolutionary biologists long have supposed that when species colonize new geographic regions they often develop new traits and adaptations to deal with their fresh surroundings. They branch from their ancestors and multiply in numbers of species.

Ranidae family are most diverse frog group in the world, found on all the world's continents except Antarctica 
[Credit: Chan Kin Onn]

Apparently, this isn't the story of "true frogs." The frog family scientists call Ranidae are found nearly everywhere in the world, and their family includes familiar amphibians like the American Bullfrog and the European common frog.

New research from the University of Kansas appearing in Royal Society Biology Letters shows, in contrast to expectations, "the rapid global range expansion of true frogs was not associated with increased net-diversification."

"First, we had to identify where these true frogs came from and when they started their dispersal all over the world," said lead author Chan Kin Onn, a doctoral student at KU's Biodiversity Institute. "We found a distinct pattern. The origin of these frogs was Indochina -- on the map today, it's most of mainland Asia, including Thailand, Vietnam, Cambodia and Burma. True frogs dispersed throughout every continent except Antarctica from there. That's not a new idea. But we found that a lot of this dispersal happened during a short period of time -- it was during the late Eocene, about 40 million years ago. That hadn't really been identified, until now."

Next, Chan and co-author Rafe Brown, curator-in-charge of the KU Biodiversity Institute's Herpetology Division, looked to see if this rapid dispersal of true frogs worldwide triggered a matching eruption of speciation.

To establish the actual timing of true frogs' diversification, Chan and Brown performed phylogenetic analysis of 402 genetic 
samples obtained from an online database called GenBank. These samples represented 292 of the known 380 true 
frog species in the world [Credit: Rafe Brown]

"That was our expectation," Chan said. "We thought they'd take off into all this new habitat and resources, with no competition -- and boom, you'd have a lot of new species. But we found the exact opposite was true. In most of the groups, nothing happened. There was no increase in speciation. In one of the groups, diversification significantly slowed down. That was the reverse of what was expected."

To establish the actual timing of true frogs' diversification, Chan and Brown performed phylogenetic analysis of 402 genetic samples obtained from an online database called GenBank. These samples represented 292 of the known 380 true frog species in the world.

"We mined all of these sequences and combined them into a giant analysis of the whole family," Chain said. "It is to my knowledge the most comprehensive Ranidae phylogenetic analysis ever performed that included most of the representative species from the family."

Chan and Brown focused on four genes that would help to establish the family tree of true frogs.

"It's a genealogical pedigree of specimens, a family tree of species," Chan said. "Normally, you think of family tree as everyone in one family and how the various people are related. But this is more expanded where we look at how species are related to each other, so you can trace ancestry back in time."

The researchers concluded true frogs didn't become one of the most biodiverse frog family due to dispersing 
into new ranges, or due to filling a gap created by a catastrophic die-off. Rather, the rich diversity of species 
in the Ranidae family comes from millions of years' worth of continual evolution influenced by 
a host of different environs [Credit: University of Kansas]

After completing the phylogenetic analysis, the KU researchers used several frog fossils to "time calibrate" the history of the frogs' global dispersal.

"We use fossil frogs because we can accurately date the fossils," Chan said. "We know we found the fossil in a certain rock deposit, and we know with confidence how old the deposit is, so then we can estimate the age of the fossil."

After Chan and Brown deduced similarities between fossilized true frogs as reported by paleontologists and contemporary true frogs, they placed fossils into groups of closely related species, which scientists call genera.

"Using data from paleontological studies, we can loosely place a fossil where in the phylogeny it belongs and can put a time stamp on that point," Chan said. "That's where calibration happens, each fossil is sort of like an anchor point. You can imagine with a really big phylogeny, the more anchor points or calibration points the better your time estimate."

Through this process, the KU researchers concluded true frogs didn't become one of the most biodiverse frog families due to dispersing into new ranges, or due to filling a gap created by a catastrophic die-off (such as the Eocene-Oligocene Extinction Event that triggered widespread extinctions from marine invertebrates to mammals in Asia and Europe).

Rather, the rich diversity of species in the Ranidae family comes from millions of years' worth of continual evolution influenced by a host of different environs.

"Our conclusion is kind of anticlimactic, but it's cool because it goes against expectations," Chan said. "We show the reason for species richness was just a really steady accumulation of species through time -- there wasn't a big event that caused this family to diversify like crazy."

Source: University of Kansas [September 13, 2017]

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Explosion in number of known life forms

A remarkable effort from University of Queensland researchers has helped increase the number of known genomes by almost 10 per cent.

A total of 7280 bacterial and 623 archaeal genomes were obtained [Credit: iStock]

UQ School of Chemistry and Molecular Biosciences ARC Future Fellow Professor Gene Tyson said researchers obtained 7280 bacterial and 623 archaeal genomes (genetic materials from microorganisms) from environmental samples.

That represents an almost 10 per cent increase on the 80,000 genomes currently in genome repositories.

"The real value of these genomes is that many are evolutionarily distinct from previously recovered genomes," said Professor Tyson, Deputy Director of the Australian Centre for Ecogenomics (ACE).

"They increase the evolutionary diversity spanned by both bacterial and archaeal genome trees by over 30 per cent, and are the first representatives within 17 bacterial and three archaeal phyla."

Professor Tyson said much microbial diversity remained to be discovered, with the majority of microbes seen under the microscope not being amendable to being grown under laboratory conditions.

"Less than one per cent can be cultured, due to challenging factors including slow growth rates, fastidious growth requirements, and the need to cross-feed off other species," he said.

However, recent advances in sequencing technology and computational techniques allowed microbial genomes to be recovered directly from environmental samples, bypassing the need for laboratory cultivation.

"The approximately 8000 genomes recovered move us closer to a comprehensive genomic representation of the microbial world, but also show that much remains to be discovered," he said.

ACE co-researcher Dr Donovan Parks said for the first time, science had the required tools to make substantial inroads into the vast diversity of phylogenetic and metabolic life.

"We anticipate that processing of environmental samples deposited in other public repositories will add tens of thousands of additional microbial genomes to the tree of life," he said.

"Numerous studies have been reported during the completion of this research which have dozens or hundreds of evolutionarily diverse genomes from varying environments.

"The tools for obtaining genomes from environmental samples are continually improving and we expect that reprocessing the samples considered in this study will result in the recovery of additional genomes."

"Constructing a comprehensive genomic repository of microbial diversity lays the foundation for furthering our understanding of the role of microorganisms in critical biogeochemical and industrial processes."

The study was published in Nature Microbiology.

Source: University of Queensland [September 12, 2017]

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Cold region 'tipping point' now inevitable

The decline of cold regions called periglacial zones is now inevitable due to climate change, researchers say.

Intense soil frost churning at Kilpisjarvi, northwestern Finland, at 800 metres above sea level 
[Credit: uha Aalto]

Periglacial zones, where there is often a layer of frozen ground known as permafrost, make up about a quarter of Earth's land surface and are mostly found in the far north and south, and at high altitudes.

Scientists from the universities of Exeter and Helsinki and the Finnish Meteorological Institute examined natural processes caused by frost and snow which take place in these zones.

Their findings suggest that -- even with optimistic estimates of future carbon emissions -- areas covered by periglacial zones will reduce dramatically by 2050, and they will "almost disappear" by 2100.

This would have a major impact on landscapes and biodiversity, and could trigger climate "feedbacks" -- processes that can amplify or diminish the effects of climate change.

"The results suggest that profound changes can be expected in current periglacial zones regardless of climate change mitigation policies," said Dr Juha Aalto, of the University of Helsinki and the Finnish Meteorological Institute.

"Unfortunately, it seems that many of the frost-driven processes we studied are already at the margin of the climate in which they can exist."

The scientists studied four processes which take place in periglacial zones, including snow accumulation sites and "frost churning" -- which refers to mixing of materials caused by freezing and thawing.

"Our results forecast a future tipping point in the operation of these processes, and predict fundamental changes in ground conditions and related atmospheric feedbacks," Dr Aalto added.

Dr Stephan Harrison, of the University of Exeter's Penryn Campus in Cornwall, said: "The project used very high-resolution climate and land surface models to demonstrate that geological processes and ecosystems in high latitudes (the far north and south) will be fundamentally altered by climate change during this century."

Even based on the optimistic RCP2.6 estimate for future carbon emissions, the researchers predict a 72% reduction in the current periglacial zone in the area of northern Europe they studied.

By 2100, periglacial zones in will only exist in high mountain regions, they say.

Professor Miska Luoto, of the University of Helsinki, said: "The anticipated changes in land surface processes can feedback to the regional climate system via alterations in carbon cycle and ground surface reflectance (light reflected by snow and ice) caused by the increase of shrub vegetation to alpine tundra.

"Our results indicate significant changes in Northern European plant life. Many rare species can only be sustained in areas of intense frost activity or late-lying snow packs, so the disappearance of such unique environments will reduce biodiversity."

The paper is published in the journal Nature Communications.

Source: University of Exeter [September 11, 2017]

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Hidden Inca treasure: Remarkable new tree genus discovered in the Andes

Hidden in plain sight -- that's how researchers describe their discovery of a new genus of large forest tree commonly found, yet previously scientifically unknown, in the tropical Andes. Researchers from the Smithsonian and Wake Forest University detailed their findings in a study just released in the journal PhytoKeys.

New canopy tree genus Incadendron esseri shown in this altitudinal transect of Manu National Park in Peru 
[Credit: Wake Forest University]

Named Incadendron esseri (literally "Esser's tree of the Inca"), the tree is a new genus and species commonly found along an ancient Inca path in Peru, the Trocha Union. Its association with the land of the Inca empire inspired its scientific name.

So how could a canopy tree stretching up to 100 feet tall and spanning nearly two feet in diameter go undetected until now?

"Incadendron tells us a lot about how little we understand life on our planet. Here is a tree that ranges from southern Peru to Ecuador, that is abundant on the landscape, and yet it was unknown. Finding this tree isn't like finding another species of oak or another species of hickory -- it's like finding oak or hickory in the first place," said Miles Silman, the Andrew Sabin Family Foundation Presidential Chair in Conservation Biology at Wake Forest.

"This tree perplexed researchers for several years before being named as new. It just goes to show that so much biodiversity is unknown and that obvious new species are awaiting discovery everywhere -- in remote ecological plots, as well as in our own backyards," said Kenneth Wurdack, a botanist with the Smithsonian's National Museum of Natural History.

Fruits and leaves of Incadendron esseri, new tree genus found in Peru and Ecuador 
[Credit: Jason Houston]

The tree belongs to the spurge family, Euphorbiaceae -- best known for rubber trees, cassava, and poinsettias -- and like many of its relatives, when damaged also bleeds white sap, known as latex, that serves to protect it from insects and diseases.

Its ecological success in a difficult environment suggests more study is needed to find the hidden secrets that are often inherent in newly discovered and poorly known biodiversity.

Currently the Incadendron is common in several research plots under intensive study as part of the Andes Biodiversity and Ecosystem Research Group, an international Andes-to-Amazon ecology program co-founded by Silman.

For nearly 25 years, Silman has worked to gain greater understanding of Andean species distributions, biodiversity, and the response of forest ecosystems to climate and land use changes over time.

Incadendron esseri branch [Credit: Wake Forest University]

"While Incadendron has a broad range along the Andes, it is susceptible to climate change because it lives in a narrow band of temperatures. As temperatures rise, the tree populations have to move up to cooler temperatures," said Silman.

One of the study's co-authors, William Farfan-Rios, is a Wake Forest graduate student researching tropical forest dynamics and responses to changing environments along the Andes-to-Amazon elevational gradient. Discovering the Incadendron hits particularly close to home for the Cusco, Peru-native. Not only is the new genus vulnerable to climate change, but it is also threatened by deforestation in nearby areas.

"It highlights the imperative role of parks and protected areas where it grows, such as Manu National Park and the Yanachaga-Chemillen National Park," he said. "Hopefully our ongoing study of the Incadendron and the intensive long-term forest monitoring will contribute to best practices in reforestation and forest management."

Source: Wake Forest University [September 07, 2017]

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