Plant population dynamics on oceanic islands during the Late Quaternary climate changes: genetic evidence from a tree species (Coffea mauritiana) in Reunion Island

Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole-genome sequencing

Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White-eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White-eye (Z. olivaceus (Linnaeus, 1766)) and the Mauritius Grey White-eye (Z. mauritianus (Gmelin, 1789)) and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long-term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species' demography and long-term population processes.

Past volcanic activity predisposes an endemic threatened seabird to negative anthropogenic impacts

Humans are regularly cited as the main driver of current biodiversity extinction, but the impact of historic volcanic activity is often overlooked. Pre-human evidence of wildlife abundance and diversity are essential for disentangling anthropogenic impacts from natural events. Réunion Island, with its intense and well-documented volcanic activity, endemic biodiversity, long history of isolation and recent human colonization, provides an opportunity to disentangle these processes. We track past demographic changes of a critically endangered seabird, the Mascarene petrel Pseudobulweria aterrima, using genome-wide SNPs. Coalescent modeling suggested that a large ancestral population underwent a substantial population decline in two distinct phases, ca. 125,000 and 37,000 years ago, coinciding with periods of major eruptions of Piton des Neiges. Subsequently, the ancestral population was fragmented into the two known colonies, ca. 1500 years ago, following eruptions of Piton de la Fournaise. In the last century, both colonies declined significantly due to anthropogenic activities, and although the species was initially considered extinct, it was rediscovered in the 1970s. Our findings suggest that the current conservation status of wildlife on volcanic islands should be firstly assessed as a legacy of historic volcanic activity, and thereafter by the increasing anthropogenic impacts, which may ultimately drive species towards extinction.

Multi-Approach Analysis Reveals Local Adaptation in a Widespread Forest Tree of Reunion Island

Detecting processes of local adaptation in forest trees and identifying environmental selective drivers are of primary importance for forest management and conservation. Transplant experiments, functional genomics and population genomics are complementary tools to efficiently characterize heritable phenotypic traits and to decipher the genetic bases of adaptive traits. Using an integrative approach combining phenotypic assessment in common garden, transcriptomics and landscape genomics, we investigated leaf adaptive traits in Coffea mauritiana, a forest tree endemic to Reunion Island. Eight populations of C. mauritiana originating from sites with contrasted environmental conditions were sampled in common garden to assess several leaf morphological traits, to analyze the leaf transcriptome and leaf cuticular wax composition. The relative alkane content of cuticular waxes was significantly correlated with major climatic gradients, paving the way for further transcriptome-based analyses. The expression pattern of cuticle biosynthetic genes was consistent with a modulation of alkane accumulation across the population studied, supporting the hypothesis that the composition of cuticular wax is involved in the local adaptation of C. mauritiana. Association tests in landscape genomics performed using RNA-seq-derived single-nucleotide polymorphisms revealed that genes associated with cell wall remodeling also likely play an adaptive role. By combining these different approaches, this study efficiently identified local adaptation processes in a non-model species. Our results provide the first evidence for local adaptation in trees endemic to Reunion Island and highlight the importance of cuticle composition for the adaptation of trees to the high evaporative demand in warm climates.

Evolutionary effects of geographic and climatic isolation between Rhododendron tsusiophyllum populations on the Izu Islands and mainland Honshu of Japan

Geographic and environmental isolations of islands and the mainland offer excellent opportunity to investigate colonization and survival dynamics of island populations. We inferred and compared evolutionary processes and the demographic history of Rhododendron tsusiophyllum, in the Izu Islands and the much larger island Honshu, treated here as the mainland, using thousands of nuclear SNPs obtained by ddRAD-seq from eight populations of R. tsusiophyllum and three populations of R. tschonoskii as an outgroup. Phylogenetic relationships and their habitats suggest that R. tsusiophyllum had evolved and migrated from cold north to warm south regions. We detected clear genetic divergence among populations in three regions of Honshu and the Izu Islands, suggesting restricted migration between them due to isolated habitats on mountains even in the mainland. The three regions have different changes in effective population size, especially, genetic diversity and population size of the Izu Islands are small compared to the others. Further, habitats of populations in the Izu Islands are warmer than those in Honshu, suggesting that they have undergone adaptive evolution. Our study provides evidences of montane rather than insular isolation on genetic divergence, survival of populations and significance of adaptive evolution for island populations with small population size and low genetic diversity, despite close proximity to mainland populations.

Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs

Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima’s D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, H_e = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (F_st from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (N_e) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of N_e over a short period, and a subsequent gradual decline in N_e to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.