Assessing ex situ genetic and ecogeographic conservation in a threatened but widespread oak after range-wide collecting effort.

Although the genetic diversity and structure of in situ populations has been investigated in thousands of studies, the genetic composition of ex situ plant populations has rarely been studied. A better understanding of how much genetic diversity is conserved ex situ, how it is distributed among locations (e.g., botanic gardens), and what minimum sample sizes are needed is necessary to improve conservation outcomes. Here we address these issues in a threatened desert oak species, Quercus havardii Rydb. We assess the genetic, geographic, and ecological representation of 290 plants from eight ex situ locations, relative to 667 wild individuals from 35 in situ locations. We also leverage a recent dataset of >3000 samples from 11 other threatened plants to directly compare the degree of genetic conservation for species that differ in geographic range size. We found that a majority of Q. havardii genetic diversity is conserved; one of its geographic regions is significantly better conserved than the other; genetic diversity conservation of this widespread species is lower than documented for the 11 rarer taxa; genetic diversity within each garden is strongly correlated to the number of plants and number of source populations; and measures of geographic and ecological conservation (i.e., percent area and percent of ecoregions represented) were typically lower than the direct assessment of genetic diversity (i.e., percent alleles). This information will inform future seed sampling expeditions to ensure that the intraspecific diversity of threatened plants can be effectively conserved.

The genomic basis of the plant island syndrome in Darwin's giant daisies.

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the 'plant island syndrome', include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin's giant daisies.

The Radiation of Darwin's Giant Daisies in the Galápagos Islands.

Evolutionary radiations on oceanic islands have fascinated biologists since Darwin's exploration of the Galápagos archipelago [1, 2]. Island radiations can provide key insights for understanding rapid speciation, including evolutionary patterns and the processes behind them. However, lack of resolution of species relationships has historically hindered their investigation, particularly in the plant kingdom [3-5]. Here, we report a time-calibrated phylogenomic analysis based on genotyping-by-sequencing data [6] of the 15 species of Scalesia (Darwin's giant daisies), an iconic and understudied plant radiation endemic to the Galápagos Islands and considered the plant counterpart to Darwin's finches [1, 7-9]. Results support a Pliocene to early Pleistocene divergence between Scalesia and the closest South American relatives, and rapid diversification of extant Scalesia species from a common ancestor dated to the Middle Pleistocene. Major evolutionary patterns in Scalesia include the following: (1) lack of compliance with the "progression rule" hypothesis, in which earlier diverging lineages are expected to occupy older islands; (2) a predominance of within-island speciation over between-island speciation; and (3) repeated convergent evolution of potentially adaptive traits and habitat preferences on different islands during the course of diversification. Massive sequencing provided the essential framework for investigating evolutionary and ecological processes in the complex natural laboratory of the Galápagos, thereby advancing our understanding of island plant radiations.

Isolation, characterization and cross-amplification of polymorphic microsatellite loci in Laelia speciosa (Orchidaceae).

Laelia speciosa is an endangered epiphytic orchid endemic to central Mexico. Here, we report on the development of 14 perfect and imperfect microsatellite repeat loci for this species. Numbers of alleles ranged from two to 16 and levels of observed heterozygosities among the 14 loci ranged from 0.28 to 1.00 across two widely divergent populations. All loci were also tested for cross-amplification in four other Laelia species and other selected genera of the subtribe Laeliinae.

Isolation, characterization, and cross-amplification of polymorphic microsatellite loci in Guaiacum coulteri (Zygophyllaceae).

Guaiacum coulteri is a dry forest hardwood species of conservation concern endemic to the Pacific coast of Mexico. Fifteen microsatellite markers were developed which show high levels of polymorphism across two populations with the number of alleles ranging from four to 21. Most loci additionally exhibited consistent multiple banding patterns, indicating the likely polyploidy of this species. All loci were tested for cross-amplification with most found to amplify well across the genus Guaiacum, although amplification in other related genera of the Zygophyllaceae was limited.

Isolation and characterization of microsatellite loci in Coccoloba cereifera (Polygonaceae), an endangered species endemic to the Serra do Cipó, Brazil.

Microsatellite primers were isolated from the microendemic and threatened species Coccoloba cereifera, a shrub known only from a small region in the Serra do Cipó, Brazil. Thirteen primer pairs amplifying perfect and imperfect microsatellite regions were tested in 40 individuals from the one known occurrence of the species. Number of alleles ranged from two to six and levels of observed heterozygosities ranged from 0.21 to 0.95. These markers will be useful for the analysis of questions concerning population genetic structure and will assist in providing information for future conservation management programmes.