Ross D. E. MacPhee

Age and Paleogeographical Origin of Dominican Amber

The age and depositional history of Dominican amber-bearing deposits have not been well constrained. Resinites of different ages exist in Hispaniola, but all of the main amberiferous deposits in the Dominican Republic (including those famous for yielding biological inclusions) were formed in a single sedimentary basin during the late Early Miocene through early Middle Miocene (15 to 20 million years ago), according to available biostratigraphic and paleogeographic data. There is little evidence for extensive reworking or redeposition, in either time or space. The brevity of the depositional interval (less than 5 million years) provides a temporal benchmark that can be used to calibrate rates of molecular evolution in amber taxa.

Fifty thousand years of Arctic vegetation and megafaunal diet

Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25–15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.

Historical Mammal Extinction on Christmas Island (Indian Ocean) Correlates with Introduced Infectious Disease

It is now widely accepted that novel infectious disease can be a leading cause of serious population decline and even outright extinction in some invertebrate and vertebrate groups (e.g., amphibians). In the case of mammals, however, there are still no well-corroborated instances of such diseases having caused or significantly contributed to the complete collapse of species. A case in point is the extinction of the endemic Christmas Island rat (Rattus macleari): although it has been argued that its disappearance ca. AD 1900 may have been partly or wholly caused by a pathogenic trypanosome carried by fleas hosted on recently-introduced black rats (Rattus rattus), no decisive evidence for this scenario has ever been adduced. Using ancient DNA methods on samples from museum specimens of these rodents collected during the extinction window (AD 1888–1908), we were able to resolve unambiguously sequence evidence of murid trypanosomes in both endemic and invasive rats. Importantly, endemic rats collected prior to the introduction of black rats were devoid of trypanosome signal. Hybridization between endemic and black rats was also previously hypothesized, but we found no evidence of this in examined specimens, and conclude that hybridization cannot account for the disappearance of the endemic species. This is the first molecular evidence for a pathogen emerging in a naïve mammal species immediately prior to its final collapse.

Ancient DNA reveals late survival of mammoth and horse in interior Alaska

Causes of late Quaternary extinctions of large mammals (“megafauna”) continue to be debated, especially for continental losses, because spatial and temporal patterns of extinction are poorly known. Accurate latest appearance dates (LADs) for such taxa are critical for interpreting the process of extinction. The extinction of woolly mammoth and horse in northwestern North America is currently placed at 15,000–13,000 calendar years before present (yr BP), based on LADs from dating surveys of macrofossils (bones and teeth). Advantages of using macrofossils to estimate when a species became extinct are offset, however, by the improbability of finding and dating the remains of the last-surviving members of populations that were restricted in numbers or confined to refugia. Here we report an alternative approach to detect ‘ghost ranges’ of dwindling populations, based on recovery of ancient DNA from perennially frozen and securely dated sediments (sedaDNA). In such contexts, sedaDNA can reveal the molecular presence of species that appear absent in the macrofossil record. We show that woolly mammoth and horse persisted in interior Alaska until at least 10,500 yr BP, several thousands of years later than indicated from macrofossil surveys. These results contradict claims that Holocene survival of mammoths in Beringia was restricted to ecologically isolated high-latitude islands. More importantly, our finding that mammoth and horse overlapped with humans for several millennia in the region where people initially entered the Americas challenges theories that megafaunal extinction occurred within centuries of human arrival or were due to an extraterrestrial impact in the late Pleistocene.

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics

The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at ≈45,000 radiocarbon years before present (14C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 14C YBP, recontracted at ca. 18,000 14C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.

Domo de Zaza, an Early Miocene Vertebrate Locality in South-Central Cuba, with Notes on the Tectonic Evolution of Puerto Rico and the Mona Passage1

Abstract This report summarizes the results of paleontological and geological investigations carried out during the 1990s at Domo de Zaza, a late Early Miocene vertebrate locality in south-central Cuba. Paleontologically, the most important result of fieldwork at Zaza was the first discovery of terrestrial mammals of Tertiary age in Cuba. Three terrestrial mammal taxa are now known from this locality—a megalonychid sloth (Imagocnus zazae), an isolobodontine capromyid rodent (Zazamys veronicae), and a platyrrhine primate (Paralouatta marianae, new species). In addition to these finds, a number of selachian, chelonian, crocodylian, cetacean, and sirenian remains have been recovered. Domo de Zaza is a low hill transected by a large artificial channel, the Canal de Zaza, whose walls provide an extensive exposure of Miocene sediments attributable to the Lagunitas Formation (Fm). This formation is laterally and vertically complex, showing evidence of at least four different depositional regimes. However, the sedimentary sequence indicates that all depositional phases took place within a broader episode of transgression. Estimated Burdigalian age (16.1–21.5 Ma) for Lagunitas Fm is based on the presence of marine invertebrate taxa corresponding to the late Early Miocene Miogypsina–Soritiidae zone. The overall transgressive aspect of Lagunitas suggests rising sea level, possibly in correlation with a global onlap event. Within Burdigalian time, the most likely correlate is the eustatic rise centered on 17.5–18.5 Ma. Most of the vertebrate fossils were recovered from lagoonal and alluvial beds; those from lagoonal beds are exceptionally well preserved. The terrestrial facies displays evidence of paleosol formation, subaerial erosion, and plant life in the form of grass and palm pollen. Other evidence indicates that most of the present-day highlands of Cuba, including the Cordillera del Escambray near Zaza, have been continuously subaerial since the latter part of the Late Eocene. Although no land vertebrate fossils of this age are known from Cuba, recent discoveries elsewhere in the Greater Antilles indicate that land vertebrates could have colonized landmasses in the Caribbean Basin as early as 33–36 Ma. Recently, marine geological data have been interpreted as showing that (1) the Mona Passage began to form in the Early Oligocene, and (2) the Puerto Rico/Virgin Island block was entirely transgressed by shallow marine environments during the period between the Late Oligocene and the Early Pliocene. However, the seismic reflection profile evidence for an Early Oligocene opening of the Passage is ambiguous. Even if the separation of Puerto Rico and eastern Hispaniola occurred relatively early, it remains more probable than not that this happened in the medial Oligocene or even somewhat later (i.e., ≤30 Ma). On the other hand, the evidence is not at all ambiguous concerning the hypothesized mid-Cenozoic inundation of Puerto Rico: it did not happen. When available land and marine indicators are adequately compared, apparent contradictions in datasets can be evaluated and resolved. When examined in this way, the preponderance of evidence supports the contention that Puerto Rico has been an emergent landmass and has supported terrestrial environments continuously since the latest Eocene.

Dating of modified femora of extinct dwarf Hippopotamus from Southern Madagascar: Implications for constraining human colonization and vertebrate extinction events

Two significant events in the late Holocene history of Madagascar were (a) the arrival of people, and (b) the loss of nearly two dozen species of land vertebrates in the socalled “subfossil extinctions”. The consensus is that the faunal losses occurred shortly subsequent to human arrival, but the timing of these events is poorly constrained. The minimum age for initial human presence on the island may now be set at approximately 2000 bp, on the basis of AMS 14C dates for human-modified femora of extinct dwarf hippos from SW Madagascar. Assuming that this date also marks the beginning of deleterious human interactions with the subfossil fauna, and assuming that this fauna became completely extinct by 900 bp, the width of the anthropogenic “extinction window” may have been as long as c. 1000 a. This estimate, nearly twice the length of previous ones, is close to the unadjusted minimum for the duration of the terminal Pleistocene extinction event in the Americas. Whether or not this length of time comports with theoretical expectations of a “blitzkrieg” pattern of losses is uncertain, but greater refinement in dating the end of the subfossil extinctions is unlikely to produce radically shorter estimates of duration.

Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths

BackgroundLate Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus columbi). To date, mammoth genetic research has been entirely restricted to woolly mammoths, rendering their genetic evolution difficult to contextualize within broader Pleistocene paleoecology and biogeography. Here, we take an interspecific approach to clarifying mammoth phylogeny by targeting Columbian mammoth remains for mitogenomic sequencing.ResultsWe sequenced the first complete mitochondrial genome of a classic Columbian mammoth, as well as the first complete mitochondrial genome of a North American woolly mammoth. Somewhat contrary to conventional paleontological models, which posit that the two species were highly divergent, the M. columbi mitogenome we obtained falls securely within a subclade of endemic North American M. primigenius.ConclusionsThough limited, our data suggest that the two species interbred at some point in their evolutionary histories. One potential explanation is that woolly mammoth haplotypes entered Columbian mammoth populations via introgression at subglacial ecotones, a scenario with compelling parallels in extant elephants and consistent with certain regional paleontological observations. This highlights the need for multi-genomic data to sufficiently characterize mammoth evolutionary history. Our results demonstrate that the use of next-generation sequencing technologies holds promise in obtaining such data, even from non-cave, non-permafrost Pleistocene depositional contexts.

Pre-Wisconsinan mammals from Jamaica and models of late Quaternary extinction in the greater Antilles

Abstract The vertebrate fauna recovered from indurated conglomerates at Wallingford Roadside Cave (central Jamaica) is shown to be in excess of 100,000 yr old according to uranium series and electron spin resonance dating. The Wallingford local fauna is therefore pre-Wisconsinan in age, and Roadside Cave is now the oldest radiometrically dated locality in the West Indies containing identifiable species of land mammals. In the absence of a good radiometric record for Quaternary paleontological sites in the Caribbean, there is no satisfactory basis for determining whether most extinct Antillean mammals died out in a “blitzkrieg”-like event immediately following initial human colonization in the mid-Holocene. Fossils of Clidomys (Heptaxodontidae, Caviomorpha), the giant Wallingford rodent, have never been found in situ in sediments of demonstrably Holocene age, and its extinction may antedate the middle Holocene. This is also a possibility for the primate Xenothrix mcgregori, although its remains have been found in loose cave earth. A major, climate-driven bout of terrestrial vertebrate extinction at about 14,000–12,000 yr B.P. has been hypothesized for the West Indies by G. Pregill and S. L. Olson (Annual Review of Ecology and Systematics 12, 75–98, 1981), but at present there is nothing to connect the disappearance of Clidomys with this event either. Quaternary extinctions in the Caribbean may prove to be of critical significance for evaluating the reality of New World blitzkrieg, but not until an effort is mounted to constrain them rigorously using modern radiometric approaches.

Infectious Disease, Endangerment, and Extinction

Infectious disease, especially virulent infectious disease, is commonly regarded as a cause of fluctuation or decline in biological populations. However, it is not generally considered as a primary factor in causing the actual endangerment or extinction of species. We review here the known historical examples in which disease has, or has been assumed to have had, a major deleterious impact on animal species, including extinction, and highlight some recent cases in which disease is the chief suspect in causing the outright endangerment of particular species. We conclude that the role of disease in historical extinctions at the population or species level may have been underestimated. Recent methodological breakthroughs may lead to a better understanding of the past and present roles of infectious disease in influencing population fitness and other parameters.