Unravelling arthropod genomic diversity over 500 million years of evolution

An international team of scientists report in the journal Genome Biology results from a pilot project, co-led by Robert Waterhouse, Group Leader at the SIB Swiss Institute of Bioinformatics and University of Lausanne, to kick-start the global sequencing initiative of thousands of arthropods. Comparative analyses across 76 species spanning 500 million years of evolution reveal dynamic genomic changes that point to key factors behind their success and open up many new areas of research.

The i5k pilot project sequenced, assembled, and annotated the genomes of 28 diverse arthropod species,
substantially increasing the current species sampling to explore arthropod genomic diversity over
500 million years of evolution [Credit: Created by Robert M. WaterhouseReuse licensed under
CC BY 4.0Milkweed Bug by Chiaki UedaLong-Horned Beetle by Robert Mitchell]

Friends and foes, arthropods rule the world

Arthropods make up the most species-rich and diverse group of animals on Earth, with numerous adaptations over 500 million years of evolution that have allowed them to exploit all major ecosystems. They play vital roles in the healthy ecology of our planet as well as being both beneficial and detrimental to the success of humankind through pollination and biowaste recycling, or destroying crops and spreading disease.

"By sequencing and comparing their genomes we can begin to identify some of the key genetic factors behind their evolutionary success," explains Waterhouse, "but will the impact of human activities in modern times bring an end to their rule, or will their ability to adapt and innovate ensure their survival?"

The i5k pilot project: kick-starting arthropod genome sequencing

The i5k initiative to sequence and annotate the genomes of 5000 species of insects and other arthropods, was launched in a letter to Science in 2011. From the outset, the initiative aimed to support the development of new genomic resources for understanding the molecular biology and evolution of arthropods.

Since then, the i5k has grown into a broad community of scientists using genomics to study insects and other arthropods in many different contexts from fundamental animal biology, to effects on ecology and the environment, and impacts on human health and agriculture.

To kick-start the i5k, a pilot project was launched at the Baylor College of Medicine led by Stephen Richards to sequence, assemble, and annotate the genomes of 28 diverse arthropod species carefully selected from 787 community nominations.

Large-scale multi-species genome comparisons

"The identification and annotation of thousands of genes from the i5k pilot project substantially increases our current genomic sampling of arthropods," says Waterhouse.

The evolutionary innovations of insects and other arthropods are as numerous as they are wondrous, from terrifying fangs 

and stingers to exquisitely coloured wings and ingenious feats of engineering. DNA sequencing allows us to chart the 

genomic blueprints underlying this incredible diversity that characterises the arthropods and makes them the most 

successful group of animals on Earth. An international team of scientists report in the journal Genome Biology results 

from a pilot project, co-led by SIB Group Leader Robert Waterhouse at the University of Lausanne, to kick-start the

 global sequencing initiative of thousands of arthropods. Comparative analyses across 76 species spanning 

500 million years of evolution reveal dynamic genomic changes that point to key factors behind 

their success and open up many new areas of research [Credit: Robert Waterhouse]

Combining these with previously sequenced genomes enabled the researchers to perform a large-scale comparative analysis across 76 diverse species including flies, butterflies, moths, beetles, bees, ants, wasps, true bugs, thrips, lice, cockroaches, termites, mayflies, dragonflies, damselflies, bristletails, crustaceans, centipedes, spiders, ticks, mites, and scorpions.

PhD students Gregg Thomas from Indiana University, USA, and Elias Dohmen from the University of Munster, Germany, used the annotated genomes to perform the computational evolutionary analyses of more than one million arthropod genes.

Dynamic gene family evolution - a key to success?

The team's analyses focused on tracing gene evolutionary histories to estimate changes in gene content and gene structure over 500 million years. This enabled identification of families of genes that have substantially increased or decreased in size, or newly emerged or disappeared, or rearranged their protein domains, between and within each of the major arthropod subgroups.

The gene families found to be most dynamically changing encode proteins involved in functions linked to digestion, chemical defence, and the building and remodelling of chitin - a major part of arthropod exoskeletons.

Adaptability of digestive processes and mechanisms to neutralise harmful chemicals undoubtedly served arthropods well as they conquered a wide variety of ecological niches. Perhaps even more importantly, the flexibility that comes with a segmented body plan and a dynamically remodellable exoskeleton allowed them to thrive by physically adapting to new ecosystems.

Innovation through invention and repurposing

Newly evolved gene families also reflect functions known to be important in different arthropod groups, such as visual learning and behaviour, pheromone and odorant detection, neuronal activity, and wing development. These may enhance food location abilities or fine-tune species self-recognition and communication.

In contrast, few changes were identified in the ancestor of insects that undergo complete metamorphosis: the dramatic change from the juvenile form to the fully developed adult (like a caterpillar transforming into a butterfly). This has traditionally been thought of as a major step in the evolution of insects from the original state of developing through gradual nymph stages until finally reaching the adult stage.

"These findings support the idea that this key transition is more likely to have occurred through the rewiring of existing gene networks or building new networks using existing genes, a scenario of new-tricks-for-old-genes" explains Waterhouse.

Genomic insights into arthropod biology and evolution

Several detailed genomic studies of individual i5k species have focused on their fascinating biological traits such as the feeding ecology and developmental biology of the milkweed bug, insecticide resistance, blood feeding, and traumatic sex of the bed bug, horizontal gene transfer from bacteria and fungi and digestion of plant materials by the Asian long-horned beetle, and parasite-host interactions and potential vaccines for the sheep blowfly. The combined analyses reveal dynamically changing and newly emerged gene families that will stimulate new areas of research.

"We can take these hypotheses into the lab and use them to directly study how the genome is translated into visible morphology at a resolution that cannot be achieved with any other animal group," says co-lead author, Ariel Chipman, from the Hebrew University of Jerusalem, Israel.

The new resources substantially advance progress towards building a comprehensive genomic catalogue of life on our planet, and with more than a million described arthropod species and estimates of seven times as many, there clearly remains a great deal to discover!

Next steps in arthropod genomics and beyond

More effective and cost-efficient DNA sequencing technologies mean that new ambitious initiatives are already underway to sequence the genomes of additional arthropods. These include the Global Ant Genome Alliance and the Global Invertebrate Genomics Alliance, as well as the Darwin Tree of Life Project that is targeting all known species of animals in the British Isles, and the global network of communities coordinated by the Earth BioGenome Project (EBP) that aims to sequence all of Earth's eukaryotic biodiversity7.

The EBP's goals also include benefitting human welfare, where the roles of arthropods are clear and the hidden benefits are likely to be substantial, as well as protecting biodiversity and understanding ecosystems, where alarming reports of declining numbers make arthropods a priority.

"The completion of the i5k pilot project therefore represents an important milestone in the progress towards intensifying efforts to develop a comprehensive genomic catalogue of life on our planet", concludes Richards.

Source: Swiss Institute of Bioinformatics [January 23, 2020]

Platypus on brink of extinction

Australia's devastating drought is having a critical impact on the iconic platypus, a globally unique mammal, with increasing reports of rivers drying up and platypuses becoming stranded.

The platypus is one of the world's strangest animals
[Credit: Torsten Blackwood/AFP]

Platypuses were once considered widespread across the eastern Australian mainland and Tasmania, although not a lot is known about their distribution or abundance because of the species' secretive and nocturnal nature.

A new study led by UNSW Sydney's Centre for Ecosystem Science, funded through a UNSW-led Australian Research Council project and supported by the Taronga Conservation Society, has for the first time examined the risks of extinction for this intriguing animal.

Published in the international scientific journal Biological Conservation this month, the study examined the potentially devastating combination of threats to platypus populations, including water resource development, land clearing, climate change and increasingly severe periods of drought.

Lead author Dr Gilad Bino, a researcher at the UNSW Centre for Ecosystem Science, said action must be taken now to prevent the platypus from disappearing from our waterways.

"There is an urgent need for a national risk assessment for the platypus to assess its conservation status, evaluate risks and impacts, and prioritise management in order to minimise any risk of extinction," Dr Bino said.

Alarmingly, the study estimated that under current climate conditions and due to land clearing and fragmentation by dams, platypus numbers almost halved, leading to the extinction of local populations across about 40 per cent of the species' range, reflecting ongoing declines since European colonisation.

UNSW Sydney's Centre for Ecosystem Science leads new research into
the extinction risk of the platypus [Credit: Tahnael Hawke]

Under predicted climate change, the losses forecast were far greater because of increases in extreme drought frequencies and duration, such as the current dry spell.

Dr Bino added: "These dangers further expose the platypus to even worse local extinctions with no capacity to repopulate areas."

Documented declines and local extinctions of the platypus show a species facing considerable risks, while the International Union for Conservation of Nature (IUCN) recently downgraded the platypus' conservation status to "Near Threatened".

But the platypus remains unlisted in most jurisdictions in Australia - except South Australia, where it is endangered.

Director of the UNSW Centre for Ecosystem Science and study co-author Professor Richard Kingsford said it was unfortunate that platypuses lived in areas undergoing extensive human development that threatened their lives and long-term viability.

"These include dams that stop their movements, agriculture which can destroy their burrows, fishing gear and yabby traps which can drown them and invasive foxes which can kill them," Prof Kingsford said.

The UNSW-led project raises concerns about the decline
of platypus populations [Credit: UNSW Science]

Study co-author Professor Brendan Wintle at The University of Melbourne said it was important that preventative measures were taken now.

"Even for a presumed 'safe' species such as the platypus, mitigating or even stopping threats, such as new dams, is likely to be more effective than waiting for the risk of extinction to increase and possible failure," Prof Wintle said.

"We should learn from the peril facing the koala to understand what happens when we ignore the warning signs."

Dr Bino said the researchers' paper added to the increasing body of evidence which showed that the platypus, like many other native Australian species, was on the path to extinction.

"There is an urgent need to implement national conservation efforts for this unique mammal and other species by increasing monitoring, tracking trends, mitigating threats, and protecting and improving management of freshwater habitats," Dr Bino said.

The platypus research team is continuing to research the ecology and conservation of this enigmatic animal, collaborating with the Taronga Conservation Society, to ensure its future by providing information for effective policy and management.

Source: University of New South Wales [January 21, 2020]

Global study finds predators are most likely to be lost when habitats are converted for human use

A first of its kind, global study on the impacts of human land-use on different groups of animals has found that predators, especially small invertebrates like spiders and ladybirds, are the most likely to be lost when natural habitats are converted to agricultural land or towns and cities. The findings are published in the British Ecological Society journal Functional Ecology.

A Malaysian spider, one of the small predators found in our study to be
most affected by habitat loss [Credit: Tim Newbold]

Small ectotherms (cold blooded animals such as invertebrates, reptiles and amphibians), large endotherms (mammals and birds) and fungivores (animals that eat fungi) were also disproportionally affected, with reductions in abundance of 25-50% compared to natural habitats.

The researchers analysed over one million records of animal abundance at sites ranging from primary forest to intensively managed farmland and cities. The data represented over 25,000 species across 80 countries. Species were grouped by size, whether they were warm or cold blooded and by what they eat. Species ranged from the oribatid mite weighing only 2x10-6g, to an African elephant weighing 3,825kg.

Dr. Tim Newbold at UCL (University College London) and lead author of the research said: "Normally when we think of predators, we think of big animals like lions or tigers. These large predators did not decline as much as we expected with habitat loss, which we think may be because they have already declined because of human actions in the past (such as hunting). We find small predators - such as spiders and ladybirds - to show the biggest declines."

The results indicate that the world's ecosystems are being restructured with disproportionate losses at the highest trophic levels (top of the food chain). Knowing how different animal groups are impacted by changing land-use could help us better understand how these ecosystems function and the consequences of biodiversity change.

"We know that different types of animals play important roles within the environment - for example, predators control populations of other animals. If some types of animals decline a lot when we lose natural habitats, then they will no longer fulfil these important roles." said Dr. Tim Newbold.

The conversion of land to human use is associated with the removal of large amounts of natural plant biomass, usually to give space for livestock and crops. The limiting of the quantity and diversity of resources available at this level potentially explains the disproportionate reductions in predators seen in this study. As you go up the trophic levels (food chain), resource limitations are compounded through a process known as bottom-up resource limitation.

The study is part of the PREDICTS project which explores how biodiversity responds to human pressures. The researchers analysed 1,184,543 records of animal abundance in the PREDICTS database, gathered from 460 published scientific studies. This database included all major terrestrial vertebrate taxa and many invertebrate taxa (25,166 species, 1.8% of described animals).

Species were sorted into functional groups defined by their size, trophic level (what they consumed) and thermal regulation strategy (warm or cold blooded). The type of land-use at each of the 13,676 sample sites was classified from the description of the habitat in the source publication. The six broad categories were primary vegetation, secondary vegetation, plantation forest, cropland, pasture and urban. Three levels of human use intensity were also recorded: minimal, light and intense.

Dr. Tim Newbold explained that studies like this are limited by the available data: "As with all global studies, we are limited in the information that is available to us about where animals are found and what they eat. We were able to get information for more animals than ever before, but this was still only around 1 out of every 100 animals known to science."

The researchers also observed biases in the spread of data across types of land-use, animal groups and parts of the world. "Natural habitats and agricultural areas have been studied more than towns and cities. We think this is because ecologists tend to find these environments more interesting than urban areas as there tend to be more animals in them." said Dr. Tim Newbold. The researchers also found that large parts of Asia were under sampled for several functional groups. Birds were also better represented among vertebrates and insects better represented among invertebrates.

The researchers are now interested in exploring how groups of animals that play particularly important roles for agriculture, such as pollinating or controlling crop pests, are affected by habitat loss.

Author: Davy Falkner | Source: British Ecological Society [January 21, 2020]