Peré Davids deer, Elaphurus davidianus. Now extinct in the wild.
About 90,000 years before creationist superstition says the Universe was created, humans, who had been evolving in Africa, began to expand their range into Eurasia and eventually into Austronesia and the Americas.
About 500,000 years later most large species show a sudden decline in their numbers, and now researchers led by Professor Jens-Christian Svenning, head of the Danish National Research Foundation's Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) at Aarhus University, believe they have shown that this was due to human predation and habitat destruction.
They reached this conclusion from an analysis of the genomes of 139 species. This involved crunching the data from 3 billion or so data points to build evolutionary trees of the mutations in the genomes. The bigger the population, the more mutations there will be in the species genome, so this data shows the population changes over time.
Their work is published, open access, in Nature and is explained in a news release from Aarhus University:
For years, scientists have debated whether humans or the climate have caused the population of large mammals to decline dramatically over the past several thousand years. A new study from Aarhus University confirms that climate cannot be the explanation.The team’s findings are explained in detail in their open access paper in Nature:
About 100,000 years ago, the first modern humans migrated out of Africa in large numbers. They were eminent at adapting to new habitats, and they settled in virtually every kind of landscape - from deserts to jungles to the icy taiga in the far north.
Part of the success was human's ability to hunt large animals. With clever hunting techniques and specially built weapons, they perfected the art of killing even the most dangerous mammals.
But unfortunately, the great success of our ancestors came at the expense of the other large mammals.
It is well-known that numerous large species went extinct during the time of the world-wide colonization by modern humans. Now, new research from Aarhus University reveals that those large mammals that survived, also experienced a dramatic decline.
By studying the DNA of 139 living species of large mammals, the scientists have been able to show that abundances of almost all species fell dramatically about 50,000 years ago.
The eastern gorilla is one of the mammals that have declined the most. Today it's only living in small areas in DR Congo.Foto: Michalsloviak / Creative Commons
This is according to Jens-Christian Svenning, a professor and head of the Danish National Research Foundation's Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) at Aarhus University, and the initiator of the study.
We’ve studied the evolution of large mammalian populations over the past 750,000 years. For the first 700,000 years, the populations were fairly stable, but 50,000 years ago the curve broke and populations fell dramatically and never recovered. For the past 800,000 years, the globe has fluctuated between ice ages and interglacial periods about every 100,000 years. If climate was the cause, we should see greater fluctuations when the climate changed prior to 50.000 years ago. But we don't. Humans are therefore the most likely explanation.
Professor Jens-Christian Svenning, Lead author
Center for Ecological Dynamics in a Novel Biosphere (ECONOVO)
Department of Biology
Aarhus University, Aarhus, Denmark.Who killed the large mammals?DNA contains the long-term history of the species
For decades, scientists have debated what is behind the extinction or rapid decline of large mammals over the past 50,000 years.
On one side are scientists who believe that rapid and severe fluctuations in the climate are the main explanation. For example, they believe that the woolly mammoth went extinct because the cold mammoth steppe largely disappeared.
On the opposite side are a group who believe that the prevalence of modern humans (Homo sapiens) is the explanation. They believe that our ancestors hunted the animals to such an extent that they either became completely extinct or were severely decimated.
So far, some of the most important evidence in the debate has been fossils from the past 50,000 years. They show that the strong, selective extinction of large animals in time and space roughly matches the spread of modern humans around the globe. Therefore, the extinction of animals can hardly be linked to climate. Nevertheless, the debate continues.
The new study presents brand new data that sheds new light on the debate. By looking at the DNA of 139 large living mammals – species that have survived for the past 50,000 years without becoming extinct – the researchers can show that the populations of these animals have also declined over the period. This development seems to be linked to the spread of humans and not climate change.
In the past 20 years, there has been a revolution within DNA sequencing. Mapping entire genomes has become both easy and inexpensive, and as a result the DNA of many species has now been mapped.
The mapped genomes of species all over the globe are freely accessible on the internet – and this is the data that the research group from Aarhus University has utilized, explains assistant professor Juraj Bergman, the lead researcher behind the new study.
We’ve collected data from 139 large living mammals and analysed the enormous amount of data. There are approximately 3 billion data points from each species, so it took a long time and a lot of computing power. DNA contains a lot of information about the past. Most people know the tree of life, which shows where the different species developed and what common ancestors they have. We’ve done the same with mutations in the DNA. By grouping the mutations and building a family tree, we can estimate the size of the population of a specific species over time.
The larger the population of an animal, the more mutations will occur. It’s really a question of simple mathematics. Take elephants, for example. Every time an elephant is conceived, there’s a chance that a number of mutations will occur, and it will pass these on to subsequent generations. More births means more mutations.
Assistant professor Juraj Bergman, First author
Center for Ecological Dynamics in a Novel Biosphere (ECONOVO)
Department of Biology
Aarhus University, Aarhus, Denmark.The large mammalsLooking at the neutral parts of the DNA
The 139 large mammals examined in the study are all species that exist today. They include elephants, bears, kangaroos and antelopes, among others.
It is estimated that there are 6,399 species of mammals on the Earth, but the 139 extant megafauna were selected in this study to test how their populations changed over the past 40,000 to 50,000 years, when similar large animals went extinct.
The large mammals are also called megafauna – and are defined as animals weighing more than 44 kg when fully grown. Humans are therefore also considered megafauna. In the study, however, the researchers examined species weighing as little as 22 kg, so that all continents have been represented - except Antarctica.
Source: Journal of Mammalogy
However, the size of the elephant population is not the only thing that affects the number of mutations.
If the area in which elephants live suddenly dries up, the animals come under pressure – and this affects the composition of mutations. The same applies if two isolated groups of elephants suddenly meet and mix genes.
If not only the size of the population affects how many mutations occur, you would think that the results are rather uncertain. But this is not the case, explains Juraj Bergman.
Only 10 per cent of mammalian genomes consist of active genes. Great selection pressure from the environment or migration will primarily lead to mutations in the genes. The remaining 90 percent, on the other hand, are more neutral. We have therefore examined mutations in those parts of the genome that are least susceptible to the environment. These parts primarily indicate something about the size of the population over time.
Assistant professor Juraj BergmanThe woolly mammoth is an atypical case
Peré Davids deer, shown in this picture, does not live in the wild anymore. The only animals left today is living in Zoos and animal parks.Foto: Tim Felce / Creative Commons.
Much of the debate about what caused the large animals to either become extinct or decline has centered around the woolly mammoth. But this is a bad example because the majority of the megafauna species that went were associated with temperate or tropical climates, as Jens-Christian Svenning explains.
The final full stop in the debate has probably yet to be set, but Jens-Christian Svenning finds it difficult to see how the arguments for the climate as an explanation can continue.The classic arguments for the climate as an explanatory model are based on the fact that the woolly mammoth and a number of other species associated with the so-called "mammoth steppe" disappeared when the ice melted and the habitat type disappeared. This is basically an unsatisfactory explanatory model, as the vast majority of the extinct megafauna species of the period did not live at all on the mammoth steppe. They lived in warm regions, such as temperate and tropical forests or savannahs. In our study, we also show a sharp decline during this period in populations of the many megafauna species that survived and come from all sorts of different regions and habitats.
It seems inconceivable that it is possible to come up with a climate model that explains how, across all continents and groups of large animals, there have been extinctions and continuous decline since about 50,000 years ago. And how this selective loss of megafauna is unique for the past 66 million years, despite huge climate change. Given the rich data we now have, it’s also hard to deny that instead it is because humans spread across the globe from Africa and subsequently grew in population.
Professor Jens-Christian Svenning
AbstractDuring that long period that creationists believe was before 'Creation Week', when they think Earth was magicked up out of nothing by a magic man made of nothing, mammalian megafauna such as elephants and mammoths, giraffes, kangaroos and antelopes had evolved, and the humans (who hadn't been created yet, but had been evolving in Africa for several millions of years) had spread out of Africa and across most of the Earth and were busy hunting and killing these large animals, leaving their descendants to tell the tale in the number of mutations in the neutral parts of the genome.
The worldwide extinction of megafauna during the Late Pleistocene and Early Holocene is evident from the fossil record, with dominant theories suggesting a climate, human or combined impact cause. Consequently, two disparate scenarios are possible for the surviving megafauna during this time period - they could have declined due to similar pressures, or increased in population size due to reductions in competition or other biotic pressures. We therefore infer population histories of 139 extant megafauna species using genomic data which reveal population declines in 91% of species throughout the Quaternary period, with larger species experiencing the strongest decreases. Declines become ubiquitous 32–76 kya across all landmasses, a pattern better explained by worldwide Homo sapiens expansion than by changes in climate. We estimate that, in consequence, total megafauna abundance, biomass, and energy turnover decreased by 92–95% over the past 50,000 years, implying major human-driven ecosystem restructuring at a global scale.
Introduction
The late-Quaternary extinction event1,2 is characterised by the selective extinction of large-bodied animals (megafauna) at a global scale. At the present date, only a small fraction of this prehistorically speciose group2,3,4,5 persists in rapidly diminishing communities, many of which face an immediate threat of extinction6,7. The causes of megafauna decline have been subject to long-standing debate, with fluctuations in paleoclimate and the spread of Homo sapiens emerging as the predominant explanatory factors3,5,8,9,10,11,12,13,14,15,16,17,18.
According to the climate-driven hypothesis of megafauna dynamics, a temporal dependency of population sizes on the glacial–interglacial cycle is expected. On the other hand, modern humans are expected to start influencing megafauna densities in recent times, mainly following the Last Interglacial period, corresponding to their worldwide expansion out of Africa19. To distinguish between these two scenarios, previous studies have focused on inferring past species distributions and extinction chronologies based on fossil data3,5,8,9,10,11,12,13,14,15,16,17,18. However, while the fossil record provides valuable insight into species’ histories, its fragmentary nature allows for only a limited temporal resolution of past population dynamics.
An alternative approach to fossil-based analyses is using genomic sequence data to reconstruct time-resolved trajectories of species population sizes20,21. Genomics-based methods commonly provide population size estimates for most of the Quaternary period (consisting of the Pleistocene period between 2.58 million and 11,700 years ago and the Holocene period between 11,700 years ago and present), thereby covering multiple glaciation cycles, as well as recent periods of human expansion22,23,24,25,26,27,28,29,30,31,32. Thus, genomics-based trajectories of population sizes should provide a more comprehensive framework for modelling the impact of climatic shifts and humans on megafauna dynamics compared to fossil-based approaches. However, a global analysis of genomics-based megafauna histories and their driving factors is currently lacking.
We focus our study on the Late Pleistocene and Early Holocene population trajectories of extant megafauna to address the following hypotheses. On the one hand, the surviving species may have experienced similar dynamics as the species undergoing extinction, showing widespread population declines linked to Homo sapiens or climate. Alternatively, surviving megafauna communities may have exhibited compensatory dynamics33, resulting in an increase in population size due to mechanisms such as competitive release. These scenarios have widely different ecological implications, whereby co-occurrence of population declines and extinctions would result in the exacerbation of ecosystem degradation, while compensatory dynamics would stabilise ecosystem functioning34. Thus, studying population dynamics of the surviving megafauna species during the Late Pleistocene and Early Holocene extinction period has major implications for our understanding of past and contemporary biosphere functioning4,35.
We curated a genomic dataset comprising 139 high-quality reference genome assemblies and short-read sequence data of extant terrestrial megafauna and implemented a bioinformatic pipeline to infer their Quaternary population histories. We studied the population dynamics of megafauna as a function of species’ ecology, geographical distribution, climate, and anthropogenic influence. We detect a global, severe decline in megafauna population sizes over the past 50,000 years and show that this observation is best explained by the influence of the worldwide expansion of H. sapiens rather than past climate dynamics. This lack of compensatory dynamics has had major impacts on ecosystem structure and functioning as reflected in a dramatic reduction of wild megafauna abundance, biomass and energy turnover.
Fig. 1: Effective population size (Ne) dynamics of 139 extant megafauna species. 
a Each step line represents changes in Ne with respect to time for a single megafauna species, coloured by a gradient based on average adult mass. The dashed line represents the fit of the piecewise linear model, as determined by breakpoint analysis. The grey-shaded area represents the 95% confidence interval of the linear model prediction. The blue rectangle represents the timespan of realm-specific breakpoints (Supplementary Fig. 2). Both axes are log10-transformed. Credit information for photographs of Antilocapra americana, Elephas maximus, Ursus arctos, Macropus giganteus and Giraffa tippelskirschi are available in Supplementary Table 2. All photographs are under CC-BY copyright (https://creativecommons.org/licenses/by/4.0/) and adapted for the purpose of the figure. b Relationship between species’ adult mass and the rate of population size change (slope). The x-axis is log10-transformed. Points are median slope values with 95% HPDI ranges indicated by bars (each distribution is derived using n = 1000 posterior samples). c Distribution of species’ decline severity. Source Data for this figure are in Source Data 1–4.
Creationists will need to ignore this evidence and the fact that the Theory of Evolution is the underpinning theory of biology that explains these observations.
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