Nuclear DNA content correlates with depth, body size, and diversification rate in amphipod crustaceans from ancient Lake Baikal, Russia

Abstract

Lake Baikal in Russia is a large, ancient lake that has been the site of a major radiation of amphipod crustaceans. Nearly 400 named species are known in this single lake, and it is thought that many more await description. The size and depth of Lake Baikal, in particular, may have contributed to the radiation of endemic amphipods by providing a large number of microhabitats for species to invade and subsequently experience reproductive isolation. Here we investigate the possibility that large-scale genomic changes have also accompanied diversification in these crustaceans. Specifically, we report genome size estimates for 36 species of Baikal amphipods, and examine the relationship between genome size, body size, and the maximum depths at which the amphipods are found in the lake. Genome sizes ranged nearly 8-fold in this sample of amphipod species, from 2.15 to 16.63 pg, and there were significant, positive, phylogenetically corrected relationships between genome size, body size, maximum depth, and diversification rate among these species. Our results suggest that major genomic changes, including transposable element proliferation, have accompanied speciation that was driven by selection for differences in body size and habitat preference in Lake Baikal amphipods.

Transcriptome‐based phylogeny of endemic Lake Baikal amphipod species flock: fast speciation accompanied by frequent episodes of positive selection

“…The analysis of genome size in Baikal amphipods (Jeffery et al . ) indicates that genomes are larger in quickly diversifying lineages, possibly corroborating the previously discovered elevated rate of gene duplications and transposable elements insertions in quickly diversifying Great African Rift Lakes cichlid lineages (Brawand et al . ).…”

“…Likewise, our estimates of diversification rates are high in comparison with those in numerous other invertebrates (typically 0.05-0.01 per 1 Myr), but similar to those obtained for Hawaiian Drosophila or Great African Rift lakes cichlids (Coyne & Orr 2004;Table 12.1). The analysis of genome size in Baikal amphipods (Jeffery et al 2016) indicates that genomes are larger in quickly diversifying lineages, possibly corroborating the previously discovered elevated rate of gene duplications and transposable elements insertions in quickly diversifying Great African Rift Lakes cichlid lineages (Brawand et al 2014).…”

Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans

“…Contrary to the findings in amphipods species from Lake Baikal in Jeffery et al. (2016b), a phylogenetic structuring was observed for genome size variation in this study (λ ≈ 1), likely due to the use of a generalized phylogeny based on taxonomy (equal branch lengths) rather than transcriptome data (unequal branch lengths).…”

“…In some invertebrate phyla, there is a clear positive relationship between genome size and body size (Gregory, 2001;Hessen, Ventura, & Elser, 2008). This has been documented in amphipods and copepods in colder waters (Angilletta, Steury, & Sears, 2004;Atkinson, 1994;Leinaas, Jalal, Gabrielsen, & Hessen, 2016;Timofeev, 2001), and in deepwater crustaceans (Jeffery, Yampolsky, & Gregory, 2016b;Rees, Belzile, Glemet, & Dufresne, 2008;Timofeev, 2001). These findings have been attributed low temperature and low metabolic rate.…”

The genome sizes of ostracod crustaceans correlate with body size and phylogeny

“…However, the implications of these relationships at organismal and ecological levels are more complex. Body size (Gregory, Hebert and Kolasa, 2000; Jeffery, Yampolsky and Gregory, 2016; Wyngaard, et al, 2005), metabolic rate (Gregory, 2002; Vinogradov, 1995), developmental rate (Gregory, 2002; Gregory and Johnston, 2008), life history (Rees, et al, 2007; Reeves, et al, 1998), and geographic distribution (Bonnivard, et al, 2009) have been found to correlate with genome size in some animal groups, but these are far from universal, and depend on the biology of the animals in question. Sorting out the broader patterns of genome size diversity and its biological significance therefore requires studies of a wide variety of taxa.…”