Social change may explain decline in genetic diversity of the Y chromosome at the end of the Neolithic period

The emergence in the Neolithic of patrilineal social systems, in which children are affiliated with their father's lineage, may explain a spectacular decline in the genetic diversity of the Y chromosome observed worldwide between 3,000 and 5,000 years ago. In a study to be published on 24 April in Nature Communications, a team of scientists from the CNRS, MNHN and Université Paris Cité suggest that these patrilineal organisations had a greater impact on the Y chromosome than mortality during conflict.

This conclusion was reached after analysing twenty years of anthropological field data -- from contemporary non-warlike patrilineal groups, particularly from the scientists' own fieldwork carried out in Asia -- and modelling various socio-demographic scenarios. The team compared warrior and non-warrior scenarios and showed that two processes play a major role in genetic diversity: the splitting of clans into several sub-clans and differences in social status that lead to the expansion of certain lineages to the detriment of others.

This study calls into question the previously proposed theory that violent clashes, supposedly due to competition between different clans, in which many men died, were at the origin of the loss of genetic diversity of the Y chromosome. The results of this study also provide new hypotheses on human social organisation in the Neolithic and Bronze Age.

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Probing the deep genetic structure of Africa

Using ancestry decomposition techniques an international research team has revealed a deeply divergent ancestry among admixed populations from the Angolan Namib desert. This unique genetic heritage brings the researchers closer to understanding the distribution of genetic variation in the broader region of southern Africa before the spread of food production.

Africa is the birthplace of modern humans and the continent with the highest level of genetic diversity. While ancient DNA studies are revealing some aspects of the genetic structure of Africa before the spread of food production, issues concerning DNA preservation have limited the insights from ancient DNA.

Hoping to find clues in modern populations, researchers from a Portuguese-Angolan TwinLab ventured into the Angolan Namib desert -- a remote, multi-ethnic region where different traditions met. "We were able to locate groups which were thought to have disappeared more than 50 years ago," states Jorge Rocha, a population geneticist from Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO, University of Porto) who led the fieldwork, together with Angolan anthropologists Samuel and Teresa Aço from the Centro de Estudos do Deserto (CEDO).

Among the communities the team encountered are the Kwepe, a pastoral group who used to speak a language known as Kwadi. "Kwadi was a click-language that shared a common ancestor with the Khoe languages spoken by foragers and herders across southern Africa," explains Anne-Maria Fehn, a linguist from CIBIO who participated in the fieldwork and was able to interview what may well be the last two speakers of Kwadi. "Khoe-Kwadi languages have been linked to a prehistoric migration of eastern African pastoralists," adds Rocha, whose research focuses on southern African population history. In addition, the team contacted Bantu-speaking groups that are part of the dominant pastoral tradition of southwest Africa, as well as marginalized groups whose origins have been associated with a foraging tradition, distinct from that of the neighboring Kalahari peoples, and whose original language was supposedly lost.

Modern DNA research can complement ancient DNA studies

The team's new study shows that the inhabitants of the Angolan Namib are quite divergent from other modern populations but also highly structured among themselves. "In agreement with our previous studies on the maternally-inherited DNA, most genome-wide diversity segregates according to socio-economic status. A lot of our efforts were placed in understanding how much of this local variation and global excentricity was caused by genetic drift -- a random process that disproportionally affects small populations -- and by admixture from vanished populations," says Sandra Oliveira, a researcher at the University of Bern in Switzerland who worked with these populations during her PhD and post-doc studies with Rocha and Mark Stoneking at CIBIO and the Max Planck Institute for Evolutionary Anthropology (MPI-EVA) in Leipzig, Germany. The team demonstrated that besides the high impact of genetic drift, which contributed to differences among neighboring groups of different socio-economic status, the descendants of Kwadi speakers and the marginalized communities of the Namib Desert retain a unique Pre-Bantu ancestry that is only found in populations from the Namib desert.

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Global macrogenetic map of marine habitat-forming species

Species known as marine habitat-forming species -- gorgonians, corals, algae, seaweeds, marine phanerogams, etc. -- are organisms that help generate and structure the underwater landscapes. These are natural refuges for other species, and provide biomass and complexity to the seabeds. But these key species in marine ecosystems are currently threatened by climate change and other perturbations derived from human activity. Now, a study published in the journal Global Ecology and Biogeography warns that even in the marine protected areas (MPAs) the genetic diversity of structural species is not protected, although it is essential for the response and adaptation of populations to changes that alter the natural environment.

The study was carried out by Laura Figuerola-Ferrando, Cristina Linares, Ignasi Montero-Serra and Marta Pagès-Escolà, from the Faculty of Biology of the University of Barcelona and the Biodiversity Research Institute of the UB (IRBio); Jean-Baptiste Ledoux and Aldo Barreiro, from the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) in Portugal, and Joaquim Garrabou, from the Institute of Marine Sciences (ICM-CSIC).

Genetic diversity is also a component of biodiversity

Traditionally, marine biodiversity management and conservation plans have considered factors such as species richness. Genetic diversity -- another major component of biodiversity -- reflects the genetic variation that exists among organisms of the same species and is a determining factor in the adaptive capacity of populations and their survival. Despite its importance, genetic diversity has so far been overlooked in management and conservation plans.

"Genetic diversity plays a key role in enhancing the ability of species, populations and communities to adapt to rapid environmental changes resulting from climate change and thus increase their resilience," says researcher Laura Figuerola-Ferrando, first author of the study.

"However, -- she continues -- so far, the vast majority of marine protected areas are implemented based on the presence of several species and habitats, without considering their genetic diversity. Another example would be the red list of the International Union for Conservation of Nature (IUCN), which does not consider genetic diversity either."

"In recent years, the need to focus conservation efforts on the protection of genetic diversity has been reinforced. Technological progress in the massive development of different techniques to determine genetic diversity (for example, through the use of microsatellites or small DNA fragments), as well as their affordable cost, can help to include genetic diversity in management and conservation plans," says the researcher from the Department of Evolutionary Biology, Ecology and Environmental Sciences of the UB.

From the northwest Atlantic to the Gulf of Guinea

The study applies macrogenetic techniques to identify general genetic patterns of diverse marine species at large spatial scales. The authors have analyzed data from a global database containing genetic diversity information (based on microsatellites) for more than 9,300 populations of 140 species in different marine regions around the globe.

The results outline a reference scenario of genetic patterns in marine habitat-forming species (corals, macroalgae, marine phanerogams, etc.) of potential interest for improving marine life management and conservation plans.

The northwest Atlantic provinces and the Bay of Bengal are the regions where the highest genetic diversity in marine landscape species has been identified. Quite high values (above the global average) have also been identified in the Mediterranean. In contrast, the marine provinces with the lowest values of genetic diversity are the Gulf of Guinea and the southwest Atlantic.

The findings also indicate a positive correlation between genetic diversity and species richness of both animal and plant marine habitat-forming species. However, the paper warns of a worrying result: the Network of Marine Protected Areas (RAMP) in the large oceanic ecoregions does not preserve areas where the genetic diversity of marine habitat-forming species is highest.

"What we have seen is that what is not being protected in MPAs is genetic diversity. In the study, the initial hypothesis was that within these areas there would be greater genetic diversity, but this has not been the case. In fact, we have seen, at a global level, that there are no differences in genetic diversity between inside and outside the MPAs," notes Laura Figuerola-Ferrando, who is doing her doctoral thesis under the supervision of Cristina Linares (UB) and Joaquim Garrabou (ICM-CSIC).

A new pattern of equatorial biodiversity at the poles

The authors have also identified a specific pattern in the distribution of genetic diversity of the marine habitat-forming species that differs from the traditional models known to date. "This is a bimodal latitudinal pattern: it is a complex biogeographic model and it implies that if we model how the genetic diversity of these species varies with latitude, we find two peaks in temperate zones and a small dip in genetic diversity at the equator," notes the ICREA Academia professor Cristina Linares (UB-IRBio), one of the coordinators of the study together with Jean-Baptiste Ledoux (CIIMAR).

This scientific discovery is relevant because until a few decades ago it was considered that the distribution of biodiversity on the planet followed a unimodal pattern, that is, it had maximum values at the equator and decreased towards the poles. "This is not always the case, especially in terms of species diversity in marine ecosystems. For example, in the case of benthic species, this pattern is biomodal rather than unimodal in terms of both species richness and genetic diversity," explains Cristina Linares.

"In our study, the bimodal latitudinal pattern is influenced by taxonomy: in the used model, we found statistically significant differences between animal species (more genetic diversity) and plant species (less genetic diversity). Furthermore, if we explore the latitudinal pattern separating animal and plant species, we can see that a bimodal pattern continues to be observed in animals, but the same cannot be said for plants," adds researcher Jean-Baptiste Ledoux (CIIMAR).

Genetic diversity: improving conservation management plans

The conclusions of the work recall the need to include the genetic diversity of populations in biodiversity management and conservation plans on the planet. "The importance of having genetic diversity in biodiversity management and conservation plans has just been reinforced with the 'Kunming-Montreal Global Biodiversity Framework' within the Convention on Biological Diversity (CBD/COP/15/L25, 2022). In this context, we believe that the baseline on genetic diversity patterns in marine habitat-forming species defined as our work can be very relevant," notes Jean-Baptiste Ledoux.

This study also reveals that the Mediterranean and Atlantic regions are among the most present in the scientific literature used in this work on macrogenetic patterns of deep-sea structural species.

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How fishermen benefit from reversing evolution of cod

Leipzig. Intense fishing and overexploitation have led to evolutionary changes in fish stocks like cod, reducing both their productivity and value on the market. These changes can be reversed by more sustainable and far-sighted fisheries management. The new study by researchers from the German Centre for Integrative Biodiversity Research (iDiv), Leipzig University and the Institute of Marine Research in Tromsø, which was published in Nature Sustainability, shows that reversal of evolutionary change would only slightly reduce the profit of fishing, but would help regain and conserve natural genetic diversity.

The impact of global fisheries on marine ecosystems is severe: fish stocks have declined and the degradation of marine habitats as well as the loss of biodiversity have been accelerated. Less visible, intense fishing has also affected the age and size structure of fish stocks and caused evolutionary change, often towards lower growth rates, smaller maturation sizes and earlier reproduction age. For example, cod in the North Sea, which has been heavily exploited in the past, matures at sizes just above 50 cm, compared to more than 70 cm expected in an unfished population.

Earlier reproduction can increase stock resilience in the short-term, but over time results in populations with smaller fish that have less offspring. "At the end of the day, this can reduce both the productivity of a stock and the value on the market," says first author Hanna Schenk from iDiv and Leipzig University. "Apart from this, we don't know much about potential consequences such as trophic cascades and other ecosystem changes that feed back onto the harvested species and may interfere with critical ecological functions."

Only long-term planning can reverse evolutionary decline

But evolution is not a one-way street. This is why the researchers from iDiv, Leipzig University and the Institute of Marine Research in Tromsø (Norway) wanted to find out what it takes to reverse evolutionary decline after decades of intensive exploitation, in particular with regard to planning horizons in fisheries management. For this, they developed a model that took various processes into account: Biological growth and reproduction as well as economic harvesting costs and consumer preferences. The researchers also analysed potential trade-offs between economic profit and conservation targets.

They found that evolutionary decline is profitable to reverse under century-long planning horizons. With more typical short-term planning, stock recovery in terms of biomass is achieved, but evolutionary decline continues, albeit at much lower rates. "Fisheries typically consider short planning horizons of a few years. This stands in contrast to long-term sustainability and biodiversity targets," says Hanna Schenk. The researchers found that more far-sighted planning horizons would help to rebuild the stock but evolutionary decline continues. According to Schenk, reversing this process takes much longer than the recovery of the stock biomass and is only achieved with century-long planning horizons.

Appropriate conservation targets only slightly reduce profit

The researchers also show that setting conservation targets for restoring not only fish stocks, but also their genetic composition would only slightly reduce profits. The cost and time of evolutionary reversal could be reduced further if fisheries can select fish depending on their genes, which may be possible to some extent by choosing the time and place of harvest. However, current conservation agendas do not include the restoration of genetic diversity, for example target 14 of the Sustainable Development Goals (SGDs), which calls for an end to overfishing.

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Corals pass mutations acquired during their lifetimes to offspring

In a discovery that challenges over a century of evolutionary conventional wisdom, corals have been shown to pass somatic mutations -- changes to the DNA sequence that occur in non-reproductive cells -- to their offspring. The finding, by an international team of scientists led by Penn State biologists, demonstrates a potential new route for the generation of genetic diversity, which is the raw material for evolutionary adaptation, and could be vital for allowing endangered corals to adapt to rapidly changing environmental conditions.

"For a trait, such as growth rate, to evolve, the genetic basis of that trait must be passed from generation to generation," said Iliana Baums, professor of biology at Penn State and leader of the research team. "For most animals, a new genetic mutation can only contribute to evolutionary change if it occurs in a germline or reproductive cell, for example in an egg or sperm cell. Mutations that occur in the rest of the body, in the somatic cells, were thought to be evolutionarily irrelevant because they do not get passed on to offspring. However, corals appear to have a way around this barrier that seems to allow them to break this evolutionary rule."

Since the time of Darwin, our understanding of evolution has become ever more detailed. We now know that an organism's traits are heavily determined by the sequence of their DNA. Individuals in a population vary in their DNA sequence, and this genetic variation can lead to the variation in traits, such as body size, that could give an individual a reproductive advantage. Only rarely does a new genetic mutation occur that gives an individual such a reproductive advantage and evolution can only proceed further if -- and this is the key -- the individual can pass the change to its offspring.

"In most animals, reproductive cells are segregated from body cells early in development," said Kate Vasquez Kuntz, a graduate student at Penn State and the co-lead author of the study. "So only genetic mutations that occur in the reproductive cells have the potential to contribute to the evolution of the species. This slow process of waiting for rare mutations in a particular set of cells can be particularly problematic given the rapid nature of climate change. However, for some organisms, like corals, the segregation of reproductive cells from all other cells may occur later in development or may never occur at all, allowing a path for genetic mutations to travel from a parent's body to its offspring. This would increase genetic variation and potentially even serve as a 'pre-screening' system for advantageous mutations."

Corals can reproduce both asexually (through budding and colony fragmentation) and sexually, by producing egg and sperm cells. For the Elkhorn corals studied here, which broadcast their egg and sperm cells into the water in spawning events, eggs from one coral colony are usually fertilized by sperm from a neighboring colony. However, the research team found that some Elkhorn coral eggs developed into viable offspring without a second coral being involved, a kind of single-parent sexual reproduction.

"This single-parent reproduction allowed us to more easily search for potential somatic mutations from the parent coral and track them into the offspring by simplifying the total number of genetic possibilities that could occur in the offspring," said Sheila Kitchen, co-lead author of the study, a postdoctoral researcher at Penn State and the California Institute of Technology co-lead author of the study.

The research team genotyped samples -- using a high-resolution molecular tool called a microarray to investigate DNA differences between the samples -- from ten different locations on a large Elkhorn coral colony that had produced single-parent offspring, and samples from five neighboring colonies at nearly 20,000 genetic locations. The results showed that all six of the separate coral colonies belonged to the same original coral genotype (known as a "genet"), meaning essentially that they were clones derived from a single original colony through asexual reproduction and colony fragmentation. Thus, any genetic variation found in these corals would have been the result of somatic mutation. The team found a total of 268 somatic mutations in the samples, with each coral sample harboring between 2 and 149 somatic mutations.

The team then looked at the single-parent offspring from the parent Elkhorn coral colony and found that 50% of the somatic mutations had been inherited. The exact mechanism of how the somatic mutations make their way into germline cells in the corals is still unknown, but the researchers suspect that the segregation between body and germline cells in corals may be incomplete and some body cells may retain the capacity to form germ cells, allowing somatic mutations to make their way into offspring. They also found evidence for the inheritance of somatic mutations in some offspring from the mating of two separate coral parents but will need additional studies to confirm this.

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Human land-use and climate change will have significant impact on animal genetic diversity

Over the last 200 years, researchers have worked towards understanding the global distribution of species and ecosystems. But so far even the basic knowledge on the global geography of genetic diversity was limited.

That now changes with a recent paper from Globe Institute. Professor David Nogues Bravo and his team has spent the last eight years combining data from scientific gene banks with scenarios of future climate and land-use change. The result is the first ever global assessment of how it will impact the genetic diversity of mammals, e.g. when tropical forests are converted to agricultural land.

'Our study identifies both genetically poor and highly diverse areas severely exposed to global change, paving the way to better estimate the vulnerability to global change such as rise in temperature as well as land-use changes. It could help countries to find out how much of the genetic diversity in their own country may be exposed to different global change impacts, while also establishing priorities and conservation policies', says David Nogues Bravo.

For example, Northern Scandinavia will be heavily impacted by climate change and not so much from land use change, whereas the tropical areas of the world will suffer from both climate change and land-use change. However, David Nogues Bravo underlines that it is difficult to compare areas.

'The genetic diversity in Scandinavia is always going to be lower than in the tropics, but that doesn't mean that the overall diversity there is not important. If we lose populations and species such as the polar bear, it's just one species but it will it will impact the total stability of ecosystems. However, the largest threat to genetic diversity will be in the tropical areas, which currently harbor the largest diversity of the bricks of life, genes. These regions include ecosystems like mangroves, jungles and grasslands', says David Nogues Bravo.

Putting it all together

The researchers have looked into gene banks with mitochondrial data from mammals. The mitochondria also regulate the metabolism, and by looking how it has changed over time, it can also unveil changes in diversity.

'The mitochondrial diversity is a broad estimate of adaptive capacity. We also used to think that mitochondria was a neutral marker, when it is in fact under selection. That means that some selection may relate to the physiological limits of a species in relation to climate, which makes it a very useful tool for researchers to track how global change impacts the genetic diversity in a specific area', explains David Nogues Bravo.

For many samples, there were not any geographical information available. The researchers used artificial intelligence to add geographical locations and then they built models predicting how much genetic exits in places without data.

Then the researchers analyzed maps of genetic diversity, future climate change and future land-use change, to reveal how and where global change will impact mammals.

Interest from the United Nations-agency

The research has attracted the attention of Secretariat of the United Nations Convention on Biological Diversity. David Nogues Bravo hope that the assessment map could become an important tool for the high-level summits among countries to help define policies for biodiversity protection.

'We are only now starting to have the tools, data and knowledge to understand how genetic diversity changes across the globe. In a decade from now, we will be able to know also how much of that genetic diversity has been lost since the Industrial Revolution for thousands of species and in a stronger position to bring effective measures to protect it', he says.

In the coming years, he hopes that scientists will map the global genetic diversity of many other forms of life, including plants, fungi and animals across the lands, rivers and oceans.

'Have been attempts to map the genetic diversity for amphibians, birds and reptiles, but we don't have maps for plants, insects or fungi. And whereas there are around 5000 mammal species, there are many more insect or fungi species, maybe millions. We don't even know how many, yet. So it will take longer, but it will come in the next decade', he says.

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New world map of fish genetic diversity

In a population of animals or plants, genetic diversity can decline much more quickly than species diversity in response to various stress factors: disease, changes to habitat or climate, and so on. Yet not much is known about fish genetic diversity around the world.

Help on that front is now on the way from an international team of scientists from French universities and ETH Zurich. They have produced the first global distribution map for genetic diversity among freshwater and marine fish. Furthermore, they identified the environmental factors that are instrumental in determining the distribution of genetic diversity. Their study was recently published in the journal Nature Communications.

Genetic diversity is unevenly distributed

To begin their study, the researchers analysed a database that contained the data of over 50,000 DNA sequences representing 3,815 species of marine fish and 1,611 species of freshwater fish. From this sequence data, the scientists estimated the average genetic diversity in sections of bodies of water, each section measuring 200 square kilometres.

Their analysis revealed that genetic diversity is unevenly distributed throughout marine and freshwater fish. The greatest genetic diversity was found among marine fish in the western Pacific Ocean, the northern Indian Ocean and the Caribbean. Among freshwater fish, genetic diversity was greatest in South America, but comparatively low in Europe.

In addition, the researchers determined that temperature is a key factor influencing genetic diversity among marine fish: as the temperature rises, so does diversity. By contrast, the key determinants of genetic diversity in freshwater fish were the complexity of their habitat structure and how their habitats have changed over time.

Impact on nature conservation strategies

The researchers see their study as a tool in efforts to improve conservation of genetic diversity and in turn biodiversity. Their map makes it easier to detect hotspots of species and genetic diversity and to plan appropriate protective action. Maintaining the genetic diversity is crucial, say the researchers. "The more diverse a population's gene pool is, the higher the potential for adaptation to environmental changes," explains Loïc Pellissier, co-?lead author of the study and Professor at ETH's Institute of Terrestrial Ecosystems.

Based on the findings, Pellissier predicts that fish populations will have potentially differing levels of adaptability in various areas of their range. "When setting up conservation areas, this characteristic has to be taken into account with respect to location, size and ecological connectivity," he says.

Protective measures thus far have concentrated primarily on maintaining species diversity. For example, several years ago Switzerland launched a programme for monitoring species diversity within its borders, but Pellissier believes this is not enough. "If we want to protect our biodiversity, we also have to monitor the genetic diversity of populations. This is the only way to ensure that the pool of varied genetic material is large enough to enable the survival of species under changing environmental conditions," he explains.

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