American mastodon mitochondrial genomes suggest multiple dispersal events in response to Pleistocene climate oscillations

A Million Years of Mammoth Mitogenome Evolution

The genomic study of specimens dating to the Early and Middle Pleistocene (EP and MP), a period spanning from 2.6 million years ago (Ma) to 126 thousand years ago (ka), has the potential to elucidate the evolutionary processes that shaped present-day biodiversity. Obtaining genomic data from this period is challenging, but mitochondrial DNA, given its higher abundance compared to nuclear DNA, could play an important role to understand evolutionary processes at this time scale. In this study, we report 34 new mitogenomes, including two EP and nine MP mammoth (Mammuthus spp.) specimens from Siberia and North America and analyze them jointly with >200 publicly available mitogenomes to reconstruct a transect of mammoth mitogenome diversity throughout the last million years. We find that our EP mitogenomes fall outside the diversity of all Late Pleistocene (LP) mammoths, while those derived from MP mammoths are basal to LP mammoth Clades 2 and 3, supporting an ancient Siberian origin of these lineages. In contrast, the geographical origin of Clade 1 remains unresolved. With these new deep-time mitogenomes, we observe diversification events across all clades that appear consistent with previously hypothesized MP and LP demographic changes. Furthermore, we improve upon an existing methodology for molecular clock dating of specimens >50 ka, demonstrating that specimens need to be individually dated to avoid biases in their age estimates. Both the molecular and analytical improvements presented here highlight the importance of deep-time genomic data to discover long-lost genetic diversity, enabling better assessments of evolutionary histories.

Re-evaluation of mastodon material from Oregon and Washington, USA, Alberta, Canada, and Hidalgo and Jalisco, Mexico

The presence of at least two contemporaneous Pleistocene mastodon taxa in North America (Mammut americanum and M. pacificus) invites re-examination of specimens at the geographic margins of each species in order to determine range boundaries, overlaps, and fluctuations. Third molars from Oregon in the United States, as well as from Hidalgo and Jalisco in Mexico, were found to be morphologically consistent with M. pacificus. Washington in the United States includes a number of specimens that could not be confidently assigned to either taxon. Alberta in Canada was found to have some specimens that were consistent with M. pacificus, but others that were identified as M. americanum. The Alberta specimen referred to M. pacificus is the same tooth found to have a Pliocene divergence time from M. americanum based on mitochondrial genome data from a previous study, suggesting a deep divergence time between the two taxa. The apparent presence of both mastodon taxa in close geographic proximity has interesting paleobiogeographic implications. It is not yet clear if both taxa were present simultaneously in a given location; if not, it suggests fluctuating ranges that may reflect shifting climates and/or biomes over time. Alternatively, if both taxa were simultaneously present in the same place, it may suggest a high degree of niche partitioning in mammutids. Additional accurately dated specimens will be required to resolve this question.

A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.

Interpreting spatially explicit variation in dietary proxies through species distribution modeling reveals foraging preferences of mammoth (Mammuthus) and American mastodon (Mammut americanum)

Introduction

The end Pleistocene was a time of considerable ecological upheaval. Recent work has explored the megafauna extinction’s role in altering ecosystem processes. Analyses of functional traits withing communities reveal hidden consequences of the megafauna extinction beyond declines in taxonomic diversity. Functional diversity analyses offer new insight into our understanding of past ecosystems and may even inform future rewilding efforts. However, the utility of functional diversity may be hampered by the use of discrete, taxon-level functional traits, such as dietary categories, that mask variation in functional diversity over space and time.

Methods

We present an approach in which species distribution modeling, in Maxent, provides context for interpreting variation in two widely used proxies for diet among fossil taxa: stable isotope analysis and dental microwear texture analysis. We apply this approach to two ecologically distinct taxa, the American mastodon (Mammut americanum) and mammoths (Mammuthus) and investigate their resource use over space and time from the last glacial maximum to the end Pleistocene (25–11.7 thousand years before present).

Results

Mammoth dietary behavior varies by context across their geographic distribution, despite possessing evolutionary adaptations that facilitate grazing. Mammoths exhibit a preference for grazing where species distribution modeling predicts the highest likelihood of occurrence but engage in more mixed-feeding outside of core likelihood areas. In contrast, dietary preferences for mastodon are less resolved and our analyses were unable to identify significant differences in diet across their distribution.

Discussion

The ecological roles of some species are context specific and need to be critically evaluated when planning for management of reintroductions or introducing novel species to restore lost ecological function.

The origin and evolution of open habitats in North America inferred by Bayesian deep learning models

Some of the most extensive terrestrial biomes today consist of open vegetation, including temperate grasslands and tropical savannas. These biomes originated relatively recently in Earth's history, likely replacing forested habitats in the second half of the Cenozoic. However, the timing of their origination and expansion remains disputed. Here, we present a Bayesian deep learning model that utilizes information from fossil evidence, geologic models, and paleoclimatic proxies to reconstruct paleovegetation, placing the emergence of open habitats in North America at around 23 million years ago. By the time of the onset of the Quaternary glacial cycles, open habitats were covering more than 30% of North America and were expanding at peak rates, to eventually become the most prominent natural vegetation type today. Our entirely data-driven approach demonstrates how deep learning can harness unexplored signals from complex data sets to provide insights into the evolution of Earth's biomes in time and space.

A novel approach to combatting proboscidean ivory trafficking using a multiplex High-Resolution Melt (M-HRM) assay

To support efforts in prosecuting wildlife crimes, we developed and validated a multiplex High-Resolution Melt (M-HRM) assay for the identification of proboscidean taxa commonly required to be identified or excluded in ivory seizures and forensic casework: Asian elephant (Elephas maximus), African elephant (Loxodonta spp.), mammoth (Mammuthus spp.), and mastodon (Mammut spp.). Five hundred and fifty (550) blood, tissue, and ivory samples from individuals of these 4 proboscidean taxa were used to develop and validate the 2 proboscidean-specific mitochondrial sites targeted by this assay. The 28-basepair (bp) 16S ribosomal RNA (rRNA) and 54-bp cytochrome b (Cytb) gene segments yield a combination of melt peaks that create composite melt profiles unique to each of the 4 proboscidean taxa. Wildlife forensic laboratories can use this sensitive, rapid, and cost-effective assay to assist efforts to combat the unlawful commercialization of proboscidean ivory and to stop the poaching crisis leading to the decline of these ivory-bearing species in the wild.

Overkill, glacial history, and the extinction of North America's Ice Age megafauna

The end of the Pleistocene in North America saw the extinction of 38 genera of mostly large mammals. As their disappearance seemingly coincided with the arrival of people in the Americas, their extinction is often attributed to human overkill, notwithstanding a dearth of archaeological evidence of human predation. Moreover, this period saw the extinction of other species, along with significant changes in many surviving taxa, suggesting a broader cause, notably, the ecological upheaval that occurred as Earth shifted from a glacial to an interglacial climate. But, overkill advocates ask, if extinctions were due to climate changes, why did these large mammals survive previous glacial-interglacial transitions, only to vanish at the one when human hunters were present? This question rests on two assumptions: that previous glacial-interglacial transitions were similar to the end of the Pleistocene, and that the large mammal genera survived unchanged over multiple such cycles. Neither is demonstrably correct. Resolving the cause of large mammal extinctions requires greater knowledge of individual species' histories and their adaptive tolerances, a fuller understanding of how past climatic and ecological changes impacted those animals and their biotic communities, and what changes occurred at the Pleistocene-Holocene boundary that might have led to those genera going extinct at that time. Then we will be able to ascertain whether the sole ecologically significant difference between previous glacial-interglacial transitions and the very last one was a human presence.