Ancient and modern DNA track temporal and spatial population dynamics in the European fallow deer since the Eemian interglacial.

Anthropogenic factors have impacted the diversity and evolutionary trajectory of various species. This can be through factors such as pressure on population size or range, habitat fragmentation, or extensive manipulation and translocation. Here we use time-calibrated data to better understand the pattern and processes of evolution in the heavily manipulated European fallow deer (Dama dama). During the Pleistocene, fallow deer had a broad distribution across Europe and were found as far north as Britain during the Eemian interglacial. The last glacial period saw fallow deer retreat to southern refugia and they did not disperse north afterwards. Their recolonisation was mediated by people and, from northern Europe and the British Isles, fallow deer were transported around the world. We use ancient and modern mitochondrial DNA (mtDNA) and mitogenomic data from Eemian Britain to assess the pattern of change in distribution and lineage structure across Europe over time. We find founder effects and mixed lineages in the northern populations, and stability over time for populations in southern Europe. The Eemian sample was most similar to a lineage currently in Italy, suggesting an early establishment of the relevant refuge. We consider the implications for the integration of anthropogenic and natural processes towards a better understanding of the evolution of fallow deer in Europe.

Evolution and dispersal of mammoths across the Northern Hemisphere.

Mammoths provide a detailed example of species origins and dispersal, but understanding has been impeded by taxonomic confusion, especially in North America. The Columbian mammoth Mammuthus columbi was thought to have evolved in North America from a more primitive Eurasian immigrant. The earliest American mammoths (1.5 million years ago), however, resemble the advanced Eurasian M. trogontherii that crossed the Bering land bridge around that time, giving rise directly to M. columbi. Woolly mammoth M. primigenius later evolved in Beringia and spread into Europe and North America, leading to a diversity of morphologies as it encountered endemic M. trogontherii and M. columbi, respectively. In North America, this included intermediates ("M. jeffersonii"), suggesting introgression of M. primigenius with M. columbi. The lineage illustrates the dynamic interplay of local adaptation, dispersal, and gene flow in the evolution of a widely distributed species complex.

The phylogenetic position of the 'giant deer' Megaloceros giganteus.

The giant deer, or 'Irish elk', has featured extensively in debates on adaptation, sexual selection, and extinction. Its huge antlers--the largest of any deer species, living or extinct--formed a focus of much past work. Yet the phylogenetic position of the giant deer has remained an enigma. On the basis of its flattened antlers, the species was previously regarded as closely related to the living fallow deer. Recent morphological studies, however, have challenged that view and placed the giant deer closer to the living red deer or wapiti. Here we present a new phylogenetic analysis encompassing morphological and DNA sequence evidence, and find that both sets of data independently support a sister-group relationship of giant and fallow deer. Our results include the successful extraction and sequencing of DNA from this extinct species, and highlight the value of a joint molecular and morphological approach.

Pleistocene to Holocene extinction dynamics in giant deer and woolly mammoth.

The extinction of the many well-known large mammals (megafauna) of the Late Pleistocene epoch has usually been attributed to 'overkill' by human hunters, climatic/vegetational changes or to a combination of both. An accurate knowledge of the geography and chronology of these extinctions is crucial for testing these hypotheses. Previous assumptions that the megafauna of northern Eurasia had disappeared by the Pleistocene/Holocene transition were first challenged a decade ago by the discovery that the latest woolly mammoths on Wrangel Island, northeastern Siberia, were contemporaneous with ancient Egyptian civilization. Here we show that another spectacular megafaunal species, the giant deer or 'Irish elk', survived to around 6,900 radiocarbon yr bp (about 7,700 yr ago) in western Siberia-more than three millennia later than its previously accepted terminal date-and therefore, that the reasons for its ultimate demise are to be sought in Holocene not Pleistocene events. Before their extinction, both giant deer and woolly mammoth underwent dramatic shifts in distribution, driven largely by climatic/vegetational changes. Their differing responses reflect major differences in ecology.

The origin and evolution of the woolly mammoth.

The mammoth lineage provides an example of rapid adaptive evolution in response to the changing environments of the Pleistocene. Using well-dated samples from across the mammoth's Eurasian range, we document geographical and chronological variation in adaptive morphology. This work illustrates an incremental (if mosaic) evolutionary sequence but also reveals a complex interplay of local morphological innovation, migration, and extirpation in the origin and evolution of a mammalian species. In particular, northeastern Siberia is identified as an area of successive allopatric innovations that apparently spread to Europe, where they contributed to a complex pattern of stasis, replacement, and transformation.

Molecular and morphological evidence on the phylogeny of the Elephantidae.

The African and Asian elephants and the mammoth diverged ca. 4-6 million years ago and their phylogenetic relationship has been controversial. Morphological studies have suggested a mammoth Asian elephant relationship, while molecular studies have produced conflicting results. We obtained cytochrome b sequences of up to 545 base pairs from five mammoths, 14 Asian and eight African elephants. A high degree of polymorphism is detected within species. With a dugong sequence used as the outgroup, parsimony and maximum-likelihood analyses support a mammoth African elephant clade. As the dugong is a very distant outgroup, we employ likelihood analysis to root the tree with a molecular clock, and use bootstrap and Bayesian analyses to quantify the relative support for different topologies. The analyses support the mammoth African elephant relationship, although other trees cannot be rejected. Ancestral polymorphisms may have resulted in gene trees differing from the species phylogeny Examination of morphological data, especially from primitive fossil members, indicates that some supposed synapomorphies between the mammoth and Asian elephant are variable, others convergent or autapomorphous. A mammoth African elephant relationship is not excluded. Our results highlight the need, in both morphological and molecular phylogenetics, for multiple markers and close attention to within-taxon variation and outgroup selection.

Kinetics of the tingible body macrophage response in mouse germinal center development and its depression with age.

Although tingible body macrophages (TBM) have been recognized in germinal centers for over 100 years, their role in the germinal center response is not clear. In this study, the kinetics of the TBM response was quantitatively assessed and correlated with the kinetics of germinal center development in young mice. The TBM response in old mice (which have an age-related depression of germinal center development; Szakal et al., 1990) was analyzed for comparison. Young and old immune mice were challenged with human serum albumin and 0, 1, 3, 5, 7, 10, and 14 days later the popliteal and axillary lymph nodes were evaluated. Germinal centers were localized histochemically in alternate serial sections using horseradish peroxidase conjugated peanut agglutinin. TBM numbers were determined per germinal center on adjacent sections by the presence of tingible bodies or histochemically by using the monoclonal antibody Mac-2. Analysis of lymph nodes from young mice showed that TBM numbers decreased with the dissociation of preexisting germinal centers. TBM reappeared 5 days after challenge and the TBM kinetics paralleled the increase in size of de novo germinal centers. In fact, a constant ratio of one TBM to every 350-450 B cells was maintained from day 5 to day 10. In old lymph nodes, TBM were generally absent throughout germinal center development. The lack of TBM prior to germinal center development and their absence in aged mice are inconsistent with the concept that TBM are required for the induction of the germinal center reaction. However, the data are consistent with a role for TBM in regulating the magnitude of the germinal center reaction.

Rapid dwarfing of red deer on Jersey in the last interglacial.

The dwarfing of large mammals on islands occurred repeatedly in the Pleistocene. Elephants, deer, hippopotami and other species became dwarfed on islands in Indonesia, the Mediterranean, the east Pacific and elsewhere. In most cases, the full-sized ancestral form can be recognized among the adjacent mainland fauna, but evolutionary rates cannot be estimated because the entry of the ancestor onto the island, and appearance of the dwarf form, are poorly dated. Here I give the first example in which the island dwarf is well dated, the full-sized ancestor is found in demonstrably older deposits on the island, and a good estimate can be made for the duration of the isolation leading to dwarfing. In the Last Interglacial, red deer on Jersey, Channel Islands, became reduced to one sixth of their body weight in less than six thousand years.