TY - BOOK

T1 - Ancient Genomics of Baltic seals

T2 - Insights on the past Baltic grey seal and harp seal populations

AU - Bro-Jørgensen, Maiken Hemme

PY - 2021

Y1 - 2021

N2 - This thesis aims to study and describe the ancient populations of grey and harp seals in the Baltic Sea, and to present newmethodological approaches for general use in ancient DNA studies.The dissertation is comprised of five studies: a review of the use of paleogenetics in studying ancient human-marinemammal interactions; a method paper investigating patterns of DNA preservation in ancient pinniped samples; a methodpaper presenting a genetic sex identification method for ancient pinnipeds; a population genomic study of the Baltic greyseal; and a population genomic study of the now extinct Baltic harp seal.Guidelines for ancient DNA sample selections were deduced from broad-scale statistical modelling of factors influencingDNA preservation in pinniped bones, the most significant of which included type of bone element, collagen content,and whether the bone derive from a cave context. Modern ringed seal samples with known sex were used to test analternative pinniped sex identification method using the annotated dog genome as a reference for quantification of therelative representation of X chromosome reads. Reliable sex identification was shown to require a minimum of 5,000 totalreads mapped to the reference genome. A total of 69 mitochondrial control regions were generated for Baltic grey seals,which revealed that the Mesolithic data largely represent extinct haplotypes, the main of which continued until the EarlyNeolithic. A population replacement prior to the early Bronze Age introduced mitochondrial variation resembling thatof modern Baltic greys seals. The level of genetic differentiation between the Baltic harp seal population and the threecontemporary breeding populations, suggests that the White Sea population is the most likely ancestor of the Baltic harpseal breeding population. An increase in genetic diversity, following a hiatus with no Baltic harp seals, combined with themeasures of genetic differentiation from this period, further suggests that a second colonization likely occurred from theWhite Sea during the early Bronze Age.

AB - This thesis aims to study and describe the ancient populations of grey and harp seals in the Baltic Sea, and to present newmethodological approaches for general use in ancient DNA studies.The dissertation is comprised of five studies: a review of the use of paleogenetics in studying ancient human-marinemammal interactions; a method paper investigating patterns of DNA preservation in ancient pinniped samples; a methodpaper presenting a genetic sex identification method for ancient pinnipeds; a population genomic study of the Baltic greyseal; and a population genomic study of the now extinct Baltic harp seal.Guidelines for ancient DNA sample selections were deduced from broad-scale statistical modelling of factors influencingDNA preservation in pinniped bones, the most significant of which included type of bone element, collagen content,and whether the bone derive from a cave context. Modern ringed seal samples with known sex were used to test analternative pinniped sex identification method using the annotated dog genome as a reference for quantification of therelative representation of X chromosome reads. Reliable sex identification was shown to require a minimum of 5,000 totalreads mapped to the reference genome. A total of 69 mitochondrial control regions were generated for Baltic grey seals,which revealed that the Mesolithic data largely represent extinct haplotypes, the main of which continued until the EarlyNeolithic. A population replacement prior to the early Bronze Age introduced mitochondrial variation resembling thatof modern Baltic greys seals. The level of genetic differentiation between the Baltic harp seal population and the threecontemporary breeding populations, suggests that the White Sea population is the most likely ancestor of the Baltic harpseal breeding population. An increase in genetic diversity, following a hiatus with no Baltic harp seals, combined with themeasures of genetic differentiation from this period, further suggests that a second colonization likely occurred from theWhite Sea during the early Bronze Age.

UR - https://soeg.kb.dk/permalink/45KBDK_KGL/1f0go08/cdi_swepub_primary_oai_DiVA_org_su_189293

M3 - Ph.D. thesis

BT - Ancient Genomics of Baltic seals

PB - GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen

ER -