From skeletal remains found among ancient owl pellets, a team of scientists has recovered the first ancient DNA of the extinct West Indian mammal Nesophontes, meaning "island murder." They traced its evolutionary history back to the dawn of mammals 70 million years ago.
The Solenodon taxa is the closest living relative to the extinct Nesophontes [Credit: Natural History Museum, London UK]
The authors, including Selina Brace, Jessica Thomas, Ian Barnes et al., published their findings in the advanced online edition of >Molecular Biology and Evolution.
The insect-eating creature existed in the Caribbean islands until the 16th century when, perhaps, they were outcompeted as the first Spanish ships arrived—-introducing rats as stowaways. "Nesophontes was just one of the dozens of mammals that went extinct in the Caribbean during recent times," said Professor Ian Barnes, Research Leader at London's Natural History Museum.
The relationship of Nesophontes to other mammals [Credit: Natural History Museum, London UK]
Scientists used a 750-year-old specimen to generate many thousands of base pairs of DNA sequence data. This allowed the research team to uncover its evolutionary origins and finally resolve the relationships between its closest relatives, the insectivores, a group including shrews, hedgehogs and moles. Phylogenetic and divergence time scenarios clearly demonstrate that Nesophontes is a deeply distinct sister group to another group of living native Caribbean insectivores, the solenodons. The time of the split between these two correlates with an era when the northern Caribbean was formed of volcanic islands, well before the origins of the islands we see today.
Obtaining DNA from tropical fossils is notoriously difficult, and the team made use of the latest developments in ancient DNA technology to conduct the study.
Nesophontes sample used in the investigation, recovered from skeletal remains in owl pellets. (a) Map of the Carribean and Hispaniola (b) where the sample was recovered, and a skull from the collection locality (c) [Credit: Natural History Museum, London UK]
"Once we'd dealt with the tiny size of the bone samples, the highly degraded state of the DNA, and the lack of any similar genomes to compare to, the analysis was a piece of cake," said Natural History Museum scientist Dr. Selina Brace.
The findings will be of considerable interest for evolutionary biologists studying mammalian biogeography, and the significant role that humans may have played in a recent extinction.
Source: Oxford University Press [September 13, 2016]
By comparing the genes of current-day North and South Americans with African and European populations, an Oxford University study has found the genetic fingerprints of the slave trade and colonization that shaped migrations to the Americas hundreds of years ago.
A 1770 painting showing Spanish, Peruvian and mixed-race people [Credit: WikiCommons]
The study published in Nature Communications found that:
While Spaniards provide the majority of European ancestry in continental American Hispanic/Latino populations, the most common European genetic source in African-Americans and Barbadians comes from Great Britain.
The Basques, a distinct ethnic group spread across current-day Spain and France, provided a small but distinct genetic contribution to current-day Continental South American populations, including the Maya in Mexico.
The Caribbean Islands of Puerto Rico and the Dominican Republic are genetically similar to each other and distinct from the other populations, probably reflecting a different migration pattern between the Caribbean and mainland America.
Compared to South Americans, people from Caribbean countries (such as the Barbados) had a larger genetic contribution from Africa.
The ancestors of current-day Yoruba people from West Africa (one of the largest African ethnic groups) provided the largest contribution of genes from Africa to all current-day American populations.
The proportion of African ancestry varied across the continent, from virtually zero (in the Maya people from Mexico) to 87% in current-day Barbados.
South Italy and Sicily also provided a significant European genetic contribution to Colombia and Puerto Rico, in line with the known history of Italian emigrants to the Americas in the late 19th and early 20th century.
One of the African-American groups from the USA had French ancestry, in agreement with historical French immigration into the colonial Southern United States.
The proportion of genes from European versus African sources varied greatly from individual to individual within recipient populations.
The team, which also included researchers from UCL (University College London) and the Universita' del Sacro Cuore of Rome, analysed more than 4,000 previously collected DNA samples from 64 different populations, covering multiple locations in Europe, Africa and the Americas. Since migration has generally flowed from Africa and Europe to the Americas over the last few hundred years, the team compared the 'donor' African and European populations with 'recipient' American populations to track where the ancestors of current-day North and South Americans came from.
'We found that the genetic profile of Americans is much more complex than previously thought,' said study leader Professor Cristian Capelli from the Department of Zoology.
The research team analysed DNA samples collected from people in Barbados, Columbia, the Dominican Republic, Ecuador, Mexico, Puerto Rico and African-Americans in the USA.
They used a technique called haplotype-based analysis to compare the pattern of genes in these 'recipient populations' to 'donor populations' in areas where migrants to America came from.
'We firstly grouped subsets of people in Africa and Europe who were genetically similar and used this fine scale resolution to find which combinations of these clusters resulted in the sort of mixtures that we now see in people across the Americas', said the study's first author, Dr Francesco Montinaro from the Department of Zoology.
'We can see the huge genetic impact that the slave trade had on American populations and our data match historical records', said study author Dr Garrett Hellenthal from the UCL Genetics Institute, 'The majority of African Americans have ancestry similar to the Yoruba people in West Africa, confirming that most African slaves came from this region. In areas of the Americas historically under Spanish rule, populations also have ancestry related to what is now Senegal and Gambia. Records show that around a third of the slaves sent to Spanish America in the 17th Century came from this region, and we can see the genetic evidence of this in modern Americans really clearly.'
These genetic findings also uncover previously unknown migration. ‘We found a clear genetic contribution from the Basques in modern-day Maya in Mexico’, said Professor Capelli. ‘This suggests that the Basque also took part in the colonisation of the Americas, coming over either with the Spanish conquistadores or in later waves of migration’.
'The differences in European ancestry between the Caribbean islands and mainland American population that we found were also previously unknown. It is likely that these differences reflect different patterns of migration between the Caribbean and mainland America.'
'These results show just how powerful a genetic approach can be when it comes to uncovering hidden patterns of ancestry. We hope to use the same approach to look at other populations with diverse genetic contributions, such as Brazilians,' said Professor Capelli.
The first annual State of the World's Plants report, which involved more than 80 scientists and took a year to produce, is a baseline assessment of current knowledge on the diversity of plants on earth, the global threats these plants currently face, as well as the policies in place and their effectiveness in dealing with threats.
A fifth of the world's plant species are at risk of extinction, according to a survey by Britain's Royal Botanic Gardens at Kew [Credit: AFP/Daniel Leal-Olivas]
"This is the first ever global assessment on the state of the world's plants. We already have a 'State of the World's ...birds, sea-turtles, forests, cities, mothers, fathers, children even antibiotics' but not plants. I find this remarkable given the importance of plants to all of our lives- from food, medicines, clothing, building materials and biofuels, to climate regulation. This report therefore provides the first step in filling this critical knowledge gap." said Professor Kathy Willis, Director of Science at the Royal Botanic Gardens, Kew at the report launch on Monday.
"But to have effect, the findings must serve to galvanise the international scientific, conservation, business and governmental communities to work together to fill the knowledge gaps we've highlighted and expand international collaboration, partnerships and frameworks for plant conservation and use," she added.
The status of plants outlined in the report is based on the most up to date knowledge from around the world as of 2016 and is divided into three sections; describing the world's plants, global threats to plants and policies and international trade.
Naming and Counting
The first section focuses on the diversity of plants on earth, noting that there are now an estimated 391,000 vascular plants known to science of which 369,000 are flowering plants -- with around 2,000 new vascular plant species described annually. Some of the most exciting were found during fieldwork while many others were detected only after they have already been preserved and filed as herbarium specimens and a few have been discovered in the glasshouses at Kew.
Logging at the Amazon and other rainforests represents 21.3 percent of the total risk to plant species, according to a study by Britain's Royal Botanic Gardens [Credit: AFP/Raphael Alves]
One of the largest carnivorous plants known (1.5m in height), a new insect-eating plant of the sundew genus called Drosera magnifica was even first discovered on Facebook. Eighteen new species of the genus Ipomoea in the morning glory family, were described from Bolivia last year, among them a close relative of the sweet potato, Ipomoea batatas, offering exciting options for the future of this crop.
"But there are still large parts of the world where very little is known about plants. Identification of these important plant areas is now critical." said Steve Bachman, strategic output leader for the State of the World´s Plants report, RBG Kew. "Similarly, we still only know a fraction of the genetic diversity of plants and whole-genome sequences are currently available for just 139 species of vascular plants. Activity in this area needs to speed up," he added.
Useful plants
In terms of the uses of plants, the report collates data from multiple data sources to reveal that at least 31,000 plant species have a documented use for medicines, food, materials and so on. The majority (17,810 plants) of those now documented have a medicinal use.
British scientists warn that farming -- such as mangroves being transformed into shrimp farms -- poses the biggest extinction threat to plant species [Credit: AFP/Sebastien Blanc]
Aside from the plants that are currently in use, the report looks at where collection efforts should focus to include plants that will be useful in the future. One set of plant species of critical importance to global food security are the wild relatives of crops, a pool of genetic variation that can help to drive the improvement of our crops into the future. A recent inventory has revealed that there are currently 3,546 prioritised global plant taxa identified as 'crop wild relatives' and Kew's Millennium Seed Bank (MSB) includes 688 crop wild relatives among its over 78,000 accessions, but there are still substantial gaps.
Research in this sector has found that the traits that have been bred into crops over years of domestication are not necessarily the same ones that will provide the greatest climate resilience. Given that many of the wild populations of these species are under considerable threat due to land-use and climate change there is an urgent need to conserve those species not adequately represented in current collections. More seed banking will help preserve a wider range of alternatives to the crops on which the world over relies today (report pages 20-23).
Climate change
The report also explores current knowledge around the impact of climate change on plants and finds that while there is a good understanding for some regions of the world, there are still large areas for which little or no research exists. In those areas where good data is available, clear impacts are visible, including changes in flowering times, turnover in plant communities and movement of species with changing climates.
Tim Utteridge of Kew Gardens shows a preserved Ferocactus fordii [Credit: AFP/Daniel Leal-Olivas]
Research referenced in the report shows that all but one of the world's biomes have experienced more than 10% change in land-cover type in the past decade due to the combined impacts of land-use and climate change.
This research, led by teams at the International Center for Tropical Agriculture in Colombia is also the first of its kind to allocate timeframes for the changes in policy and practice needed to maintain food production and security in Africa. It identifies that up to 30% of areas growing maize and bananas, and up to 60% of those growing beans, are likely to become unviable by the end of the century. But it also highlights some crops like cassava and yams that are showing much greater resilience and could worth focusing on in years to come (report pages 36-39).
"Having proof that root crops like cassava and yams are among the climate-smart crops of the future for sub Saharan Africa is vital for informing policy and planning today," added Professor Willis.
Further research into building a climate resilient coffee economy in Ethiopia published in this report highlights how coffee production is likely to be drastically affected by climate change, but claims that this could be offset if there were interventions now to develop new areas for coffee plantations, which may even lead to gains in coffee production.
Kew Gardens in southwest London has one of the world's largest plant collections [Credit: AFP/Daniel Leal-Olivas]
Important plant areas
1,771 important plant areas have been identified globally but very few currently have conservation protection. In the UK alone, 165 such sites have been recognised, including parts of the Atlantic woodlands and the Celtic rainforests which are considered to be globally important. These sites include the Lizard in Cornwall, the Brecklands in East Anglia and parts of the west coast of Scotland. Important plant areas have also been identified in several of the UK Overseas Territories including the Falkland Islands and plans are underway to extend this programme to the Caribbean UK Overseas Territories.
Invasive species
A large movement of invasive alien plant species is also occurring. Nearly 5000 plant species are now documented as invasive in global surveys. These plants are causing large declines in native plants, damaging natural ecosystems, transforming land-cover and often causing huge economic losses. In the UK, this includes the highly invasive Japanese knotweed (Reynoutria japonica), introduced as an ornamental plant to Britain in the mid-19th century and costing Great Britain more than £165 million annually to control (report pages 48-51).
The report calls for closer collaboration between institutions and organisations working with invasive species to enable the establishment of a single global list that documents taxonomy, threat, distribution, control and other relevant information. Stricter enforcement of legislation and increased implementation of quarantine procedures would minimise the risk of further.
A technician picks up a sample of frozen DNA from a Ficus hispida at Kew Gardens [Credit: AFP/Daniel Leal-Olivas]
Plant diseases
There are many emerging threats also occurring with plant diseases, and research effort into these diseases is skewed towards countries with a wealthier research infrastructure.
Threats and extinction
Best estimates lead us to believe that 21% of the world's plants are currently threatened with extinction and ongoing monitoring will allow us to determine whether the trend is of plants slipping closer towards extinction or becoming less threatened.
Plants and policies
Although trade in plants supports livelihoods worldwide, illegal or unsustainable trade is causing additional pressure on wild biodiversity and strict enforcement of international legislation is crucial. Adoption and implementation of policies such as CITES (Convention on International Trade in Endangered Species) have had demonstrable benefits and there is cause for optimism that the Nagoya Protocol will enhance the effectiveness with which countries conserve and utilise their biodiversity.
One of the main plant groups that are still widely traded are orchids, a fact confirmed by data from the UK borderforce. Of all plants plants seized at Heathrow airport in 2015 over 42% were wild orchids.
"This is the most significant horizon-scanning document to be released by Kew in recent decades and I hope as many people as possible will access the findings," said Richard Deverell, Director of the Royal Botanic Gardens, Kew.
"Plants represent one of the most important constituents of biodiversity, the foundation of most of the world's ecosystems and hold the potential to tackle many of the world's present and future challenges. We are uniquely placed to unlock their importance and are proud to have both the catalogue of over 250 years of collections and active scientific field work globally that allows us to interpret the data so it will have multiple uses for generations to come," he added.
