Ninua, L. | Search bioRxiv

bioRxiv2020

Cetaceans of the Black Sea: where did they survive glacial?

Three species of cetaceans, Phocoena phocoena, Delphinus delphis and Tursiops truncatus ponticus are found in the Black Sea. The Black Sea populations of all three species show morpho-ecological peculiarities that leaded to their subspecific status: P. p. relicta (PPR), D. d. ponticus (DDP), and T. t. ponticus (TTP). It is not clear how long-lasting was their isolation from the core conspecific populations that ensured the development of adaptive features of PPR, DDP, and TTP. The analysis of mitochondrial haplotypes of PPR suggests that the split time of the at least maternal lineage of the Black Sea population of harbour porpoise lasted for over 100 ky (i.e. they should survive at least the latest glacial maximum within the Black Sea). However, the analysis of multiple microsatellite genotypes leaded some authors to suggest that the isolation is much less long, since middle Holocene. We re-analysed published mitochondrial sequences of all three Black Sea cetaceans along with several tens of sequences obtained from the stranded cetaceans. Our analyses suggest that Black Sea populations of all three cetacean species have an important input of populations that survived the last (and maybe earlier) glacial maxima within the Black Sea, most likely in its south-eastern fragment, which did not freeze in winter time even during the glacial peaks. This analysis is supported by both molecular clock approach and simple population modelling based on the assumption on the effective population size range. Different from the PPR, whose Black Sea population is currently fully isolated, there is a limited migration between the Black Sea and Atlantic populations of T. truncatus and D. delphis, through the Mediterranean "bridge" population. However, the migration rates are not sufficient to overweight differential selection between the Black Sea and Mediterranean populations, and the local morpho-ecological specifics is successfully maintained.

ecology↗

bioRxiv2018

Avian influenza viruses in wild birds: virus evolution in a multi-host ecosystem

Wild ducks and gulls are the major reservoirs for avian influenza A viruses (AIVs). The mechanisms that drive AIV evolution are complex at sites where various duck and gull species from multiple flyways breed, winter or stage. The Republic of Georgia is located at the intersection of three migratory flyways: Central Asian Flyway, East Asian/East African Flyway and Black Sea/Mediterranean Flyway. For six consecutive years (2010-2016), we collected AIV samples from various duck and gull species that breed, migrate and overwinter in Georgia. We found substantial subtype diversity of viruses that varied in prevalence from year to year. Low pathogenic (LP)AIV subtypes included H1N1, H2N3, H2N5, H2N7, H3N8, H4N2, H6N2, H7N3, H7N7, H9N1, H9N3, H10N4, H10N7, H11N1, H13N2, H13N6, H13N8, H16N3, plus two H5N5 and H5N8 highly pathogenic (HP)AIVs belonging to clade 2.3.4.4. Whole genome phylogenetic trees showed significant host species lineage restriction for nearly all gene segments and significant differences for LPAIVs among different host species in observed reassortment rates, as defined by quantification of phylogenetic incongruence, and in nucleotide diversity. Hemagglutinin clade 2.3.4.4 H5N8 viruses, circulated in Eurasia during 2014-2015 did not reassort, but analysis after its subsequent dissemination during 2016-2017 revealed reassortment in all gene segments except NP and NS. Some virus lineages appeared to be unrelated to AIVs in wild bird populations in other regions with maintenance of local AIV viruses in Georgia, whereas other lineages showed considerable genetic inter-relationship with viruses circulating in other parts of Eurasia and Africa, despite relative under-sampling in the area.\n\nImportanceWaterbirds (e.g., gulls/ducks) are natural reservoirs of avian influenza viruses (AIVs) and have been shown to mediate dispersal of AIV at inter-continental scales during seasonal migration. The segmented genome of influenza viruses enables viral RNA from different lineages to mix or re-assort when two viruses infect the same host. Such reassortant viruses have been identified in most major human influenza pandemics and several poultry outbreaks. Despite their importance, we have only recently begun to understand AIV evolution and reassortment in their natural host reservoirs. This comprehensive study illustrates of AIV evolutionary dynamics within a multi-host ecosystem at a stop-over site where three major migratory flyways intersect. Our analysis of this ecosystem over a six-year period provides a snapshot of how these viruses are linked to global AIV populations. Understanding the evolution of AIVs in the natural host is imperative to both mitigating the risk of incursion into domestic poultry and potential risk to mammalian hosts including humans.

microbiology↗