From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition

Abstract

Collections of specimens held by natural history museums are invaluable material for biodiversity inventory and evolutionary studies, with specimens accumulated over 300 years readily available for sampling. Unfortunately, most museum specimens yield low-quality DNA. Recent advances in sequencing technologies, so called next-generation sequencing, are revolutionizing phylogenetic investigations at a deep level. Here, the Illumina technology (HiSeq) was used on herbarium specimens of Sartidia (subfamily Aristidoideae, Poaceae), a small African-Malagasy grass lineage (six species) characteristic of wooded savannas, which is the C3 sister group of Stipagrostis, an important C4 genus from Africa and SW Asia. Complete chloroplast and nuclear ribosomal sequences were assembled for two Sartidia species, one of which (S. perrieri) is only known from a single specimen collected in Madagascar 100 years ago. Partial sequences of a few single-copy genes encoding phosphoenolpyruvate carboxylases (ppc) and malic enzymes (nadpme) were also assembled. Based on these data, the phylogenetic position of Malagasy Sartidia in the subfamily Aristidoideae was investigated and the biogeographical history of this genus was analysed with full species sampling. The evolutionary history of two genes for C4 photosynthesis (ppc-aL1b and nadpme-IV) in the group was also investigated. The gene encoding the C4 phosphoenolpyruvate caroxylase of Stipagrostis is absent from S. dewinteri suggesting that it is not essential in C3 members of the group, which might have favoured its recruitment into a new metabolic pathway. Altogether, the inclusion of historical museum specimens in phylogenomic analyses of biodiversity opens new avenues for evolutionary studies.

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 Genus <I>Sartidia</I> (Poaceae: Aristidoideae) in Madagascar

“…Sartidia isaloensis appears to be more stout than Aristida, with a more compact inflorescence, redder vegetative parts, and generally darker in colour. Sequences of the chloroplast (rbcL, ndhF, matK, trnL-trnF, rps16 intron) and nuclear (ITS) regions are similar to those of all accessions of Sartidia analysed and consistently different from the numerous species of Aristida and Stipagrostis analysed (Besnard et al 2014). …”

“…VORONTSOVA ET AL: SARTIDIA IN MADAGASCAR 449 builds a platform for ongoing molecular phylogenomic work on herbarium specimens of Sartidia and relatives (Besnard et al 2014). …”

“…250 C 4 species (Cerros-Tlatilpa and Columbus 2009). The diversifications of Sartidia and Aristida and other grass species of Malagasy grasslands are currently under study (Vorontsova 2013;Besnard et al 2014). Our ultimate aim is to reconstruct the vegetation history of the extensive open areas on the High Plateaux and establish the presence and composition of any natural savannas, a controversial subject in Madagascar nature conservation (Bond et al 2008;Willis et al 2008;Quéméré et al 2012;Vorontsova and Rakotoarisoa 2014;Parr et al 2014).…”

First record of Langdonia aristidae (Ustilaginales) from Madagascar

“…Madagascar is home to an unusually high diversity of endemic species of Aristida and other members of the Aristidoideae (Besnard et al 2014). Recently, a taxonomic treatment of Aristida tenuissima, a grass species endemic to Madagascar, was published by Vorontsova (2013), who noted that a tuft, mounted on the isolectotype sheet (in P), was infected with a smut fungus.…”