Historical Demographic Processes Dominate Genetic Variation in Ancient Atlantic Cod Mitogenomes

Ancient DNA (aDNA) approaches have been successfully used to infer the long-term impacts of climate change, domestication, and human exploitation in a range of terrestrial species. Nonetheless, studies investigating such impacts using aDNA in marine species are rare. Atlantic cod (Gadus morhua), is an economically important species that has experienced dramatic census population declines during the last century. Here, we investigated 48 ancient mitogenomes from historical specimens obtained from a range of archeological excavations in northern Europe dated up to 6,500 BCE. We compare these mitogenomes to those of 496 modern conspecifics sampled across the North Atlantic Ocean and adjacent seas. Our results confirm earlier observations of high levels of mitogenomic variation and a lack of mutation-drift equilibrium—suggestive of population expansion. Furthermore, our temporal comparison yields no evidence of measurable mitogenomic changes through time. Instead, our results indicate that mitogenomic variation in Atlantic cod reflects past demographic processes driven by major historical events (such as oscillations in sea level) and subsequent gene flow rather than contemporary fluctuations in stock abundance. Our results indicate that historical and contemporaneous anthropogenic pressures such as commercial fisheries have had little impact on mitogenomic diversity in a wide-spread marine species with high gene flow such as Atlantic cod. These observations do not contradict evidence that overfishing has had negative consequences for the abundance of Atlantic cod and the importance of genetic variation in implementing conservation strategies. Instead, these observations imply that any measures toward the demographic recovery of Atlantic cod in the eastern Atlantic, will not be constrained by recent loss of historical mitogenomic variation.</jats:p

Winter temperature and forest cover have shaped red deer distribution in Europe and the Ural Mountains since the Late Pleistocene

Aim: The Expansion-Contraction model has been used to explain the responses of species to climatic changes. During periods of unfavourable climatic conditions, species retreat to refugia from where they may later expand. This paper focuses on the palaeoecology of red deer over the past 54 ka across Europe and the Urals, to reveal patterns of change in their range and explore the role of environmental conditions in determining their distribution. Location: Europe and western Asia to 63°E. Taxon: Red deer (Cervus elaphus). Methods: We collected 984 records of radiocarbon-dated red deer subfossils from the Late Pleistocene and the Holocene, including 93 original dates. For each deer sample we compiled climatic and biome type data for the corresponding time intervals. Results: During the last 54 ka changes in red deer range in Europe and the Urals were asynchronous and differed between western and eastern Europe and western Asia due to different environmental conditions in those regions. The range of suitable areas for deer during the Last Glacial Maximum (LGM) was larger than previously thought and covered vast regions not only in southern but also in western and eastern Europe. Throughout the period investigated the majority of specimens inhabited forests in the temperate climatic zone. The contribution of forests in deer localities significantly decreased during the last 4 ka, due to deforestation of Europe caused by humans. Mean January temperature was the main limiting factor for species distribution. Over 90% of the samples were found in areas where mean January temperature was above −10°C. Main conclusions: Red deer response to climatic oscillations are in agreement with the Expansion-Contraction model but in contradiction to the statement of only the southernmost LGM refugia of the species. During the last 54 ka red deer occurred mostly in forests of the temperate climatic zone. © 2020 John Wiley & Sons Ltd.European Social Fund, Grant/Award Number: UDA-POKL.04.01.01-00-072/09-00; University of Wroclaw, Grant/Award Number: 0410/2990/18; Institute of Environmental Biology, University of Wrocław, Grant/Award Number: 0410/2990/18; Mammal Research Institute Polish Academy of Sciences; Narodowe Centrum Nauki , Grant/Award Number: DEC-2013/11/B/NZ8/00888 and UMO-2016/23/B/HS3/00387; Romanian National Authority for Scientific Research, UEFISCDI, Grant/Award Number: PN-IIIP4-ID-PCE-2016-0676; National Centre for Atmospheric Science and the Centre for Environmental Data Analysis, UK; Faunal Database of the Stage Three Project; Leverhulme Trust, Grant/Award Number: F00568W

Winter Temperature and Forest Cover Have Shaped Red Deer Distribution in Europe and the Ural Mountains Since the Late Pleistocene

Aim: The Expansion-Contraction model has been used to explain the responses of species to climatic changes. During periods of unfavourable climatic conditions, species retreat to refugia from where they may later expand. This paper focuses on the palaeoecology of red deer over the past 54 ka across Europe and the Urals, to reveal patterns of change in their range and explore the role of environmental conditions in determining their distribution. Location: Europe and western Asia to 63°E. Taxon: Red deer (Cervus elaphus). Methods: We collected 984 records of radiocarbon-dated red deer subfossils from the Late Pleistocene and the Holocene, including 93 original dates. For each deer sample we compiled climatic and biome type data for the corresponding time intervals. Results: During the last 54 ka changes in red deer range in Europe and the Urals were asynchronous and differed between western and eastern Europe and western Asia due to different environmental conditions in those regions. The range of suitable areas for deer during the Last Glacial Maximum (LGM) was larger than previously thought and covered vast regions not only in southern but also in western and eastern Europe. Throughout the period investigated the majority of specimens inhabited forests in the temperate climatic zone. The contribution of forests in deer localities significantly decreased during the last 4 ka, due to deforestation of Europe caused by humans. Mean January temperature was the main limiting factor for species distribution. Over 90% of the samples were found in areas where mean January temperature was above −10°C. Main conclusions: Red deer response to climatic oscillations are in agreement with the Expansion-Contraction model but in contradiction to the statement of only the southernmost LGM refugia of the species. During the last 54 ka red deer occurred mostly in forests of the temperate climatic zone. © 2020 John Wiley & Sons Ltd.European Social Fund, Grant/Award Number: UDA-POKL.04.01.01-00-072/09-00; University of Wroclaw, Grant/Award Number: 0410/2990/18; Institute of Environmental Biology, University of Wrocław, Grant/Award Number: 0410/2990/18; Mammal Research Institute Polish Academy of Sciences; Narodowe Centrum Nauki , Grant/Award Number: DEC-2013/11/B/NZ8/00888 and UMO-2016/23/B/HS3/00387; Romanian National Authority for Scientific Research, UEFISCDI, Grant/Award Number: PN-IIIP4-ID-PCE-2016-0676; National Centre for Atmospheric Science and the Centre for Environmental Data Analysis, UK; Faunal Database of the Stage Three Project; Leverhulme Trust, Grant/Award Number: F00568W