Killer whale genomes reveal a complex history of recurrent admixture and vicariance Supplementary Materials, bioRxiv, 2019-01-16

Reconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species' range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

biorxiv evolutionary-biology 100-200-users 2019

Ecological causes of uneven diversification and richness in the mammal tree of life, bioRxiv, 2019-01-05

AbstractThe uneven distribution of species in the tree of life is rooted in unequal speciation and extinction among groups. Yet the causes of differential diversification are little known despite their relevance for sustaining biodiversity into the future. Here we investigate rates of species diversification across extant Mammalia, a compelling system that includes our own closest relatives. We develop a new phylogeny of nearly all ∼6000 species using a 31-gene supermatrix and fossil node- and tip-dating approaches to establish a robust evolutionary timescale for mammals. Our findings link the causes of uneven modern species richness with ecologically-driven variation in rates of speciation andor extinction, including 24 detected shifts in net diversification. Speciation rates are a stronger predictor of among-clade richness than clade age, countering claims of clock-like speciation in large phylogenies. Surprisingly, speciation rate heterogeneity in recent radiations shows limited association with latitude, despite the well-known increase in species richness toward the equator. Instead, we find a deeper-time association where clades of high-latitude species have the highest speciation rates, suggesting that species durations are shorter (turnover is higher) outside than inside the tropics. At shallower timescales (i.e., young clades), diurnality and low vagility are both linked to greater speciation rates and extant richness. We suggest that high turnover among small-ranged allopatric species has erased the signal of vagility in older clades, while diurnality has adaptively promoted lineage persistence. These findings highlight the underappreciated joint roles of ephemeral (turnover-based) and adaptive (persistence-based) processes of diversification, which manifest in recent and more ancient evolutionary radiations of mammals to explain modern diversity.Author SummaryThe over 6000 living species in the mammalian tree of life are distributed unevenly among branches so that similarly aged groups sometimes differ many fold in species richness (e.g., ∼2500 rodent species versus 8 pangolins). Why differential bursts of species diversification occur, and how long they persist, has implications for sustaining biodiversity. Here we develop a robust evolutionary timescale for most extant species, recovering signatures of rate-variable diversification linked to ecological factors. Mammals with low dispersal or that are day-active show the fastest recent speciation rates, consistent with mechanisms of allopatric isolation and ecological opportunity, respectively. Speciation is surprisingly faster in extra-tropical than tropical lineages, suggesting that longer species durations for tropical lineages underpin the latitudinal diversity gradient in mammal.

biorxiv evolutionary-biology 200-500-users 2019

 

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