120-years of ecological monitoring data shows that the risk of overhunting is increased by environmental degradation for an isolated marine mammal population: The Baltic grey seal

The Baltic Sea is home to a genetically isolated and morphologically distinct grey seal population. This population has been the subject of 120-years of careful documentation, from detailed records of bounty statistics to annual monitoring of health and abundance. It has also been exposed to a range of well-documented stressors, including hunting, pollution and climate change. To investigate the vulnerability of marine mammal populations to multiple stressors, data series relating to the Baltic grey seal population size, hunt and health were compiled, vital demographic rates were estimated, and a detailed population model was constructed. The Baltic grey seal population fell from approximately 90,000 to as few as 3000 individuals during the 1900s as the result of hunting and pollution. Subsequently, the population has recovered to approximately 55,000 individuals. Fertility levels for mature females have increased from 9% in the 1970s to 86% at present. The recovery of the population has led to demands for increased hunting, resulting in a sudden increase in annual quotas from a few hundred to 3550 in 2020. Simultaneously, environmental changes, such as warmer winters and reduced prey availability due to overfishing, are likely impacting fecundity and health. Future population development is projected for a range of hunting and environmental stress scenarios, illustrating how hunting, in combination with environmental degradation, can lead to population collapse. The current combined hunting quotas of all Baltic Nations caused a 10% population decline within three generations in 100% of simulations. To enable continued recovery of the population, combined annual quotas of less than 1900 are needed, although this quota should be re-evaluated annually as monitoring of population size and seal health continues. Sustainable management of long-lived slowly growing species requires an understanding of the drivers of population growth and the repercussions of management decisions over many decades. The case of the Baltic grey seal illustrates how long-term ecological time series are pivotal in establishing historical baselines in population abundance and demography to inform sustainable management.

Whole-genome phylogeography of the blue-faced honeyeater (Entomyzon cyanotis) and discovery and characterization of a neo-Z chromosome

Whole-genome surveys of genetic diversity and geographic variation often yield unexpected discoveries of novel structural variation, which long-read DNA sequencing can help clarify. Here, we report on whole-genome phylogeography of a bird exhibiting classic vicariant geographies across Australia and New Guinea, the blue-faced honeyeater (Entomyzon cyanotis), and the discovery and characterization of a novel neo-Z chromosome by long-read sequencing. Using short-read genome-wide SNPs, we inferred population divergence events within E. cyanotis across the Carpentarian and other biogeographic barriers during the Pleistocene (~0.3-1.7 Ma). Evidence for introgression between nonsister populations supports a hypothesis of reticulate evolution around a triad of dynamic barriers around Pleistocene Lake Carpentaria between Australia and New Guinea. During this phylogeographic survey, we discovered a large (134 Mbp) neo-Z chromosome and we explored its diversity, divergence and introgression landscape. We show that, as in some sylvioid passerine birds, a fusion occurred between chromosome 5 and the Z chromosome to form a neo-Z chromosome; and in E. cyanotis, the ancestral pseudoautosomal region (PAR) appears nonrecombinant between Z and W, along with most of the fused chromosome 5. The added recombination-suppressed portion of the neo-Z (~37.2 Mbp) displays reduced diversity and faster population genetic differentiation compared with the ancestral-Z. Yet, the new PAR (~17.4 Mbp) shows elevated diversity and reduced differentiation compared to autosomes, potentially resulting from introgression. In our case, long-read sequencing helped clarify the genomic landscape of population divergence on autosomes and sex chromosomes in a species where prior knowledge of genome structure was still incomplete.

Multilocus phylogeography, population genetics and niche evolution of Australian brown and black-tailed treecreepers (Aves: Climacteris)

The Carpentarian barrier across north-eastern Australia is a major biogeographic barrier and a generator of biodiversity within the Australian Monsoonal Tropics. Here we present a continent-wide analysis of mitochondrial (control region) and autosomal (14 anonymous loci) sequence and indel variation and niche modelling of brown and black-tailed treecreepers (Climacteris picumnus and Climacteris melanurus), a clade with a classic distribution on either side of the Carpentarian barrier. mtDNA control region sequences exhibited reciprocal monophyly and strong differentiation (Fst = 0.91), and revealed a signature of a recent selective sweep in C. picumnus. A variety of tests support an isolation-with-migration model of divergence, albeit with low levels of gene flow across the Carpentarian barrier and a divergence time between species of ~1.7–2.8 Mya. Palaeoecological niche models show that both range size as measured by available habitat and estimated historical population sizes of both species declined in the past ~600 kyr and that the area of interspecific range overlap was never historically large, perhaps decreasing opportunities for extensive gene flow. The relatively long divergence time and low opportunity for gene flow may have facilitated speciation more so than in other co-distributed bird taxa across the Australian Monsoonal Tropics.