Phylogenomics indicates the “living fossil” Isoetes diversified in the Cenozoic

Abstract

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.

Conservation implications of genetic structure in the narrowest endemic quillwort from the Eastern Amazon

“…Isoëtes (popularly known as "quillworts" or "Merlin's grass") is a cosmopolitan genus of lycophytes with about 250 species found in lakes, wetlands (swamps, marshes), and terrestrial habitats (Troia, 2016a). The group is the only extant genus of the Isoetaceae and the single representative of Isoetales, which is a lineage of vascular plants that diverged from its living sister group Selaginella Willk in the Devonian (Pigg, 2001), with the diversification of extant species occurring in the Cenozoic (Wood, 2020). This lycopod lineage's ancient origin and its morphology make this genus a key group to understand vascular plants' evolutionary pathways (Hetherington et al, 2016).…”

“…In addition, thousands of markers such as SNPs can bring more information about evolutionary processes, and more accurate estimates of demographic parameters, fundamental to optimize conservation biology efforts (Morin et al, 2009;Helyar et al, 2011;Torkamaneh et al, 2018). Few studies on Isoëtes applied high-throughput sequencing technology to acquire genomic data, most of them were focusing on phylogenomics (Wood et al, 2020), phylogeography (Wood et al, 2018), local adaptation (Yang & Liu, 2016), or species delimitation (Nunes et al, 2018).…”

Revealing the evolutionary history of a reticulate polyploid complex in the genusIsoëtes

“…In fact, early Isoetologist W. N. Clute (1905) lamented, "the marks by which the species [of Isoëtes] are distinguished are so obscure as to be puzzling to all but the select few, and in consequence the species have been largely taken upon by faith." In addition, recent work demonstrates that low molecular divergence further compounds the difficulties of circumscribing species within this genus (Pereira et al, 2017;Wood et al, 2020). Fig.…”

“…This genus has been described as a “living fossil” as it is the last remaining lineage of the ancient Isoetalean lycopsids—a clade that dates back to the middle Devonian (~400mya; Pigg, 1992). However, most of the extant diversity is relatively young (<60mya; Wood et al , 2020) and a product of recent diversification where hybridization and polyploidization are thought to play an important role in species generation (Taylor & Hickey, 1992; Hoot et al , 2004; Dai et al , 2020). Isoëtes is an ideal study system for investigating the evolutionary implications of hybridization and polyploidization within vascular plants because of its unique evolutionary dynamics (i.e., an old clade with recent diversification), high species richness, pervasiveness of polyploids, and complex biogeographical patterns.…”

“…Although there is great potential for investigating reticulate evolution within Isoëtes , discerning species relationships in the genus has historically proven difficult due to the conserved body plan with limited morphological characters and character states (Pfeiffer, 1922; Hickey et al , 1989). In fact, early Isoetologist W. N. Clute (1905) lamented, “the marks by which the species [of Isoëtes ] are distinguished are so obscure as to be puzzling to all but the select few, and in consequence the species have been largely taken upon by faith.” In addition, recent work demonstrates that low molecular divergence further compounds the difficulties of circumscribing species within this genus (Pereira et al , 2017; Wood et al , 2020).…”