title: Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences.
abstract: Global climate fluctuations have significantly influenced the distribution and abundance of biodiversity. During unfavorable glacial periods, many species experienced range contraction and fragmentation, expanding again during interglacials. An understanding of the evolutionary consequences of both historical and ongoing climate changes requires knowledge of the temporal dynamics of population numbers during such climate cycles. Variation in abundance should have left clear signatures in the patterns of intraspecific genetic variation in extant species, from which historical effective population sizes (N(e)) can be estimated. We analyzed whole-genome sequences of 38 avian species in a pairwise sequentially Markovian coalescent (PSMC, [5]) framework to quantitatively reveal changes in N(e) from approximately 10 million to 10 thousand years ago. Significant fluctuations in N(e) over time were evident for most species. The most pronounced pattern observed in many species was a severe reduction in N(e) coinciding with the beginning of the last glacial period (LGP). Among species, N(e) varied by at least three orders of magnitude, exceeding 1 million in the most abundant species. Several species on the IUCN Red List of Threatened Species showed long-term reduction in population size, predating recent declines. We conclude that cycles of population expansions and contractions have been a common feature of many bird species during the Quaternary period, likely coinciding with climate cycles. Population size reduction should have increased the risk of extinction but may also have promoted speciation. Species that have experienced long-term declines may be especially vulnerable to recent anthropogenic threats.
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden. Electronic address: krystyna.nadachowska-brzyska@ebc.uu.se.
authors.forename: Krystyna
authors.initials: K
authors.lastname: Nadachowska-Brzyska
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
authors.forename: Cai
authors.initials: C
authors.lastname: Li
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Linnea
authors.initials: L
authors.lastname: Smeds
authors.affiliation: China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China; Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
authors.affiliation: Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.
authors.forename: Hans
authors.initials: H
authors.lastname: Ellegren
mesh_terms: D000818:Animals; D001717:Birds / Q000235:genetics*; D057231:Climate Change; D056727:Endangered Species; D014644:Genetic Variation; D005828:Genetics, Population; D016678:Genome; D011156:Population Density; D011157:Population Dynamics