Biology subjects

Palumbi, S. R.

Publications and source records attributed to Palumbi, S. R..

8 recordsLinked to original sources

bioRxiv2026

Spatial inference of ancestor locations suggests northern refugia for canopy-forming kelps in the Northeast Pacific

O_LIPockets of the formerly glaciated Pacific coastline of North America likely remained ice-free throughout the Last Glacial Maximum (LGM). These areas may have served as refugia for terrestrial species, but less is known about their role in the persistence of coastal marine species. C_LIO_LIWe examined genetic diversity from >1,000 newly and previously sequenced whole genomes of canopy-forming kelps of the genera Nereocystis and Macrocystis, and built simple ecological niche models. We then reconstructed ancestral recombination graphs and modelled the geographic locations of genetic ancestors through time. C_LIO_LIWe detected high genetic diversity in both species in north-central British Columbia, in a region where suitable LGM habitat is plausible. Ancestor locations spatially converged backward in time toward this region, with multiple refugia inferred between northern Vancouver Island and southern Haida Gwaii. An expanded set of global samples for Macrocystis confirmed pre-LGM divergence with California but hinted at the possibility of subsequent gene flow. C_LIO_LIKelp forests survived in northern refugia and have continuously occupied portions of the northern Pacific coastline since the LGM. One implication of these results is their support for the Kelp Highway Hypothesis of the peopling of the Americas by a coastal route. C_LI

evolutionary biology↗

bioRxiv2025

Population Genomics of P. miniata along the Pacific Coastline Reveal Subtly Diverging Genomics Along an Extensive Range Gap

Many marine species exhibit range gaps, patchy distributions, or genetic disjunctions throughout their ranges. These discontinuities can result from various interacting mechanisms, though directly linking ecological and historical factors to observed distributions or genetic disjunctions often proves challenging. Intriguingly, substantial research has demonstrated that these spatial and genetic discontinuities frequently occur in species with long-lived planktonic larvae, which possess the capacity for extensive oceanic dispersal. This study investigates the population genetics of one such species, the bat star Patiria miniata. Despite its long-lived planktonic larval stage of six to ten weeks, P. miniata maintains both a range gap and a, geographically separate, strong genetic disjunction throughout its distribution from Alaska to Baja California. Utilizing low-coverage whole-genome sequencing of over 200 individuals collected throughout P. miniatas range between the early 2000s and 2023, we corroborate previous findings of a significant genetic disjunction across Queen Charlotte Sound, north of Vancouver Island. Additionally, we present new evidence of strong divergence at several genomic loci across an extensive range gap in Washington and Oregon, despite subtle genetic population structure at most loci here. Such differences may reflect more recent ecological or oceanographic barriers, rather than historical processes. Our results demonstrate that while marine invertebrate populations may appear panmictic based on genome-wide metrics of population structure alone, strong local selection for specific gene segments may be maintained in some populations. This research contributes to our understanding of the complex interplay between dispersal potential and local adaptation in marine ecosystems and highlights the importance of considering both genetic structure and finer-scale adaptation in coastal marine populations.

evolutionary biology↗

bioRxiv2024

Marine spatial planning to enhance coral adaptive potential

Ocean warming interacts with local stressors to negatively affect coral reefs. The adaptive capacity of reefs to survive these stressors is driven by ecological and evolutionary processes occurring at multiple spatial scales. Marine protected area (MPA) networks are one solution that can address both local and regional threats, yet the impacts of MPA network design on adaptive processes remains unclear. In this paper, we used an eco-evolutionary model to simulate hypothetical MPA configurations in the Caribbean, Southwest Pacific and Coral Triangle under projected warming. We found that protecting thermal refugia (i.e., cooler reefs) largely benefited corals inside the refugia while other reefs declined. In contrast, protecting a diverse habitat portfolio led to increased coral cover both inside and outside of the MPA network. We then quantified the thermal habitat and connectivity representations of reefs both inside and outside existing MPA networks across each region. Most strikingly, reefs in current MPA networks in the Southwest Pacific and Coral Triangle are approximately 2 {degrees}C cooler than reefs outside the MPA networks, while the Caribbeans MPA network is approximately 1 {degrees}C warmer than reefs outside the network, based on mean temperatures from 2008-2018. These results suggest that the Caribbean MPA network is poised to protect sources of warm-adapted larvae but not destinations, and the opposite is true of the Southwest Pacific and Coral Triangle. Our results suggest that 1) by protecting sites with particular temperature and connectivity characteristics, marine spatial planning may alter eco-evolutionary processes to enhance or inhibit the adaptive capacity of a reef network and 2) the distribution, extent, and effectiveness of local interventions have the potential to affect regional distributions of coral cover beyond what would be expected from local benefits alone, due to the potentially wide-reaching effects of larval dispersal and gene flow.

ecology↗

bioRxiv2022

Persistence of phenotypic responses to short-term heat stress in the tabletop coral Acropora hyacinthus

Widespread mapping of coral thermal resilience is essential for developing effective management strategies and requires replicable and rapid multi-location assays of heat resistance and recovery. One- or two-day short-term heat stress experiments have been previously employed to assess heat resistance, followed by single assays of bleaching condition. We tested the reliability of short-term heat stress resistance, and linked resistance and recovery assays, by monitoring the post short-term heat stress phenotypic response of fragments from 101 Acropora hyacinthus colonies located in Palau (Micronesia). Following short-term heat stress, bleaching and mortality were recorded after 16 hours, daily for seven days, and after months one and two into recovery. To follow corals over time, we utilized a qualitative, non-destructive visual bleaching score metric that correlated with standard symbiont retention assays. The bleaching state of coral nubbins 16 hours post-heat stress was highly indicative of their state over the next 7 days, suggesting that symbiont population sizes within corals may quickly stabilize post-heat stress. Bleaching 16 hours post-heat stress predicted likelihood of mortality over the subsequent 3-5 days, after which there was little additional mortality. Together, bleaching and mortality suggested that rapid assays of the phenotypic response following short-term heat stress were good metrics of the total heat treatment effect. Additionally, our data confirm geographic patterns of intraspecific variation in Palau and show that bleaching severity among colonies was highly correlated with mortality over the first week post-stress. We found high survival (98%) and visible recoverability (100%) two months after heat stress among coral nubbins that survived the first week post-stress. These findings help simplify rapid, widespread surveys of heat sensitivity in Acropora hyacinthus by showing that standardized short-term experiments can be confidently assayed after 16 hours, and that bleaching sensitivity may be linked to subsequent survival using experimental assessments.

ecology↗

bioRxiv2021

Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia

Understanding the mechanisms driving phenotypic variation in traits facing intensified selection from climate change is a crucial step in developing effective conservation and restoration initiatives. This is particularly true for reef-building corals, which are among the most vulnerable to climate change and are in dramatic decline globally. At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterising the mechanisms that control phenotypic responses to different environments. We combined whole genome re-sequencing, common garden heat stress experiments, transcriptome-wide gene expression analyses, and symbiont metabarcoding to explore the mechanisms that facilitate survival in contrasting habitat conditions. Our data show that, despite high gene flow between habitats, spatially varying selection drives subtle shifts in allele frequencies at hundreds of loci. These changes were concentrated into several islands of divergence spanning hundreds of SNPs that showed strong linkage disequilibrium and were associated with a coordinated increase in minor allele frequencies in corals taken from the lagoon habitat, where the range of environmental conditions is greatest. Common garden heat stress assays showed individuals from the lagoon exhibited higher bleaching resistance than colonies from the reef slope, and RNAseq identified pronounced physiological differences between the corals from the two habitats, primarily associated with molecular pathways including cell signalling, ion transport and metabolism. Despite the pronounced physioloigical and environmental differences between habitats, metabarcoding of the Symbiodiniaceae ITS2 region revealed all colonies to be associated exclusively with the genus Cladocopium, with no detectable differences between habitats. This study contributes to the growing number of studies documenting the complex mechanisms that facilitate coral survival in extreme environments, and showcases the utility of combining multiple sequencing techniques to unravel complex climate-related traits.

genomics↗

bioRxiv2021

Mutations in coral soma and sperm imply lifelong stem cell differentiation

In many animals, the germline differentiates early in embryogenesis, so only mutations that accumulate in germ cells are inherited by offspring1. Exceptions to this developmental process may indicate that other mechanisms have evolved to limit the effects of deleterious mutation accumulation2. Stony corals are animals that can live for hundreds of years3 and have long been thought to produce gametes from somatic tissue4. To clarify conflicting evidence about germline-soma distinction in corals, we sequenced high coverage, full genomes with technical replicates for parent coral branches and their sperm pools. We identified post-embryonic single nucleotide variants (SNVs) unique to each parent branch, then checked if each SNV was shared by the respective sperm pool: 26% of post-embryonic SNVs were shared by the sperm but 74% were not. We also identified germline SNVs, those that were present in the sperm but not in the parent. These data suggest that self-renewing stem cells in corals differentiate into germ and soma throughout the adult life of the colony, with SNV rates and patterns differing markedly in stem, soma, and germ lineages. In addition to informing the important place in the evolutionary spectrum from non-Weismannian to Weismmanian animals that corals occupy, these insights inform how corals may generate adaptive diversity necessary in the face of global climate change.

genetics↗

bioRxiv2021

Evolution and connectivity influence the persistence and recovery of coral reefs under climate change in the Caribbean, Southwest Pacific, and Coral Triangle

Corals are experiencing unprecedented decline from climate change-induced mass bleaching events. Dispersal not only contributes to coral reef persistence through demographic rescue but can also hinder or facilitate evolutionary adaptation. Locations of reefs that are likely to survive future warming therefore remain largely unknown, particularly within the context of both ecological and evolutionary processes across complex seascapes that differ in temperature range, strength of connectivity, network size, and other characteristics. Here, we used eco-evolutionary simulations to examine coral adaptation to warming across reef networks in the Caribbean, the Southwest Pacific, and the Coral Triangle. We assessed the factors associated with coral persistence in multiple reef systems to understand which results are general and which are sensitive to particular geographic contexts. We found that evolution can be critical in preventing extinction and facilitating the long-term recovery of coral communities in all regions. Furthermore, the strength of immigration to a reef (destination strength) and current sea surface temperature robustly predicted reef persistence across all reef networks and across temperature projections. However, we found higher initial coral cover, slower recovery, and more evolutionary lag in the Coral Triangle, which has a greater number of reefs and more larval settlement than the other regions. We also found the lowest projected future coral cover in the Caribbean. These findings suggest that coral reef persistence depends on ecology, evolution, and habitat network characteristics, and that, under an emissions stabilization scenario (RCP 4.5), recovery may be possible over multiple centuries.

ecology↗

bioRxiv2019

Somatic mutations and genome stability maintenance in clonal coral colonies

One challenge for multicellular organisms is maintaining genome stability in the face of mutagens across long life spans. Imperfect genome maintenance leads to mutation accumulation in somatic cells, which is associated with tumors and senescence in vertebrates. Colonial reef-building corals are often large, can live for hundreds of years, rarely develop recognizable tumors, and are thought to convert somatic cells into gamete producers, so they are a pivotal group in which to understand long-term genome maintenance. To measure rates and patterns of somatic mutations, we analyzed transcriptomes from 17-22 branches from each of four Acropora hyacinthus colonies, determined putative single nucleotide variants, and verified them with Sanger resequencing. Unlike for human skin carcinomas, there is no signature of mutations caused by UV damage, indicating either higher efficiency of repair than in vertebrates, or strong sunscreen protection in these shallow water tropical animals. The somatic mutation frequency per nucleotide in A. hyacinthus is on the same order of magnitude (10-7) as noncancerous human somatic cells, and accumulation of mutations with age is similar. Unlike mammals, loss of heterozygosity variants outnumber gain of heterozygosity mutations about 2:1. Although the mutation frequency is similar in mammals and corals, the preponderance of loss of heterozygosity changes and potential selection may reduce the frequency of deleterious mutations in colonial animals like corals. This may limit the deleterious effects of somatic mutations on the coral organism as well as potential offspring.

evolutionary biology↗