Museomics illuminate the history of an extinct, paleoendemic plant lineage (Hesperelaea, Oleaceae) known from an 1875 collection from Guadalupe Island, Mexico

Abstract

Museum collections are essential for understanding biodiversity and next-generation sequencing methods (NGS) offer new opportunities to generate genomic data on specimens of extinct species for phylogenetic and other studies. Hesperelaea is a monotypic Oleaceae genus that was collected only once, 140 years ago on Guadalupe Island, Mexico. This lineage is almost certainly extinct, and has been considered an insular paleoendemic of unknown relationship within subtribe Oleinae. Here, a genome skimming approach was attempted on the H. palmeri specimen to generate genomic data in order to interpret the biogeographic history of Hesperelaea in a phylogenetic framework. Despite highly degraded DNA, we obtained the complete plastome, the nuclear ribosomal DNA cluster (nrDNA), and partial sequences of low-copy genes. Six plastid regions and nrDNA internal transcribed spacers were used for phylogenetic estimations of subtribe Oleinae, including data from previous studies. Bayesian and maximum likelihood phylogenies strongly place Hesperelaea within an American lineage that includes Forestiera and Priogymnanthus. Molecular dating suggests an Early Miocene divergence between Hesperelaea and its closest relatives. Our study thus confirms that Hesperelaea was a paleoendemic lineage that likely predates Guadalupe Island, and provides a notable example of the high potential of NGS for analyzing historical herbarium specimens and revolutionizing systematics.

Herbarium genomics: skimming and plastomics from archival specimens

“…herbarium specimen was sequenced (at 12 × average coverage) by Staats et al (2013), using reference mapping. More herbarium genomics studies were undertaken and they contributed importantly to testing historical biological hypotheses: for instance, genomes were sequenced from type specimens and rare or extinct species stored in herbaria by Zedane et al (2015) and Van de Paer et al (2016). enormously, from a modest 65 Mb (parasitic Genlisea, Lentibulariaceae) up to a staggering 150,000 Mb in octaploid Paris japonica, Melianthaceae.…”

The quest to resolve recent radiations: Plastid phylogenomics of extinct and endangered Hawaiian endemic mints (Lamiaceae)

“…Most paleogenomic studies to date have focused on large vertebrates that inhabit cold or temperate areas or the close relatives of crop plants that have abundant genomic information available (Allaby et al, 2015;JaenickeDespres et al, 2003), although genome-scale sequencing approaches of herbarium material are increasingly being applied (Bakker et al, 2015;Beck and Semple, 2015;Besnard et al, 2014;Staats et al, 2013;Zedane et al, 2015). The ability to sequence herbarium specimens, which may represent the only samples available for rare, endangered, or extinct taxa, provides great promise towards understanding important issues from biogeographic history to domestication, taxonomy, and conservation.…”

The time has come for Natural History Collections to claim co‐authorship of research articles

“…Technical barriers imposed by low-quality, degraded DNAs found in poorly dried or very old specimens have in many instances been overcome by next-generation sequencing (NGS) technologies. Consequently, an additional wealth of genetic and phylogenetic data derived from NHC became available beginning in the 2000s (Wandeler & al., 2007;Millar & al., 2008;Staats & al., 2013;Andreasen & al., 2014;Buerki & Baker, 2015;Parks & al., 2015;Suchan & al., 2016;Zedane & al., 2016;Silva & al., 2017). Other novel applications applied to NHC include, but are not limited to, isotopic and other chemical element analyses (Gritcan & al., 2016;Körner & al., 2016).…”