Genetic continuity and change among the Indigenous peoples of California.

Before the colonial period, California harboured more language variation than all of Europe, and linguistic and archaeological analyses have led to many hypotheses to explain this diversity1. We report genome-wide data from 79 ancient individuals from California and 40 ancient individuals from Northern Mexico dating to 7,400-200 years before present (BP). Our analyses document long-term genetic continuity between people living on the Northern Channel Islands of California and the adjacent Santa Barbara mainland coast from 7,400 years BP to modern Chumash groups represented by individuals who lived around 200 years BP. The distinctive genetic lineages that characterize present-day and ancient people from Northwest Mexico increased in frequency in Southern and Central California by 5,200 years BP, providing evidence for northward migrations that are candidates for spreading Uto-Aztecan languages before the dispersal of maize agriculture from Mexico2-4. Individuals from Baja California share more alleles with the earliest individual from Central California in the dataset than with later individuals from Central California, potentially reflecting an earlier linguistic substrate, whose impact on local ancestry was diluted by later migrations from inland regions1,5. After 1,600 years BP, ancient individuals from the Channel Islands lived in communities with effective sizes similar to those in pre-agricultural Caribbean and Patagonia, and smaller than those on the California mainland and in sampled regions of Mexico.

A genetic history of the pre-contact Caribbean.

Humans settled the Caribbean about 6,000 years ago, and ceramic use and intensified agriculture mark a shift from the Archaic to the Ceramic Age at around 2,500 years ago1-3. Here we report genome-wide data from 174 ancient individuals from The Bahamas, Haiti and the Dominican Republic (collectively, Hispaniola), Puerto Rico, Curaçao and Venezuela, which we co-analysed with 89 previously published ancient individuals. Stone-tool-using Caribbean people, who first entered the Caribbean during the Archaic Age, derive from a deeply divergent population that is closest to Central and northern South American individuals; contrary to previous work4, we find no support for ancestry contributed by a population related to North American individuals. Archaic-related lineages were >98% replaced by a genetically homogeneous ceramic-using population related to speakers of languages in the Arawak family from northeast South America; these people moved through the Lesser Antilles and into the Greater Antilles at least 1,700 years ago, introducing ancestry that is still present. Ancient Caribbean people avoided close kin unions despite limited mate pools that reflect small effective population sizes, which we estimate to be a minimum of 500-1,500 and a maximum of 1,530-8,150 individuals on the combined islands of Puerto Rico and Hispaniola in the dozens of generations before the individuals who we analysed lived. Census sizes are unlikely to be more than tenfold larger than effective population sizes, so previous pan-Caribbean estimates of hundreds of thousands of people are too large5,6. Confirming a small and interconnected Ceramic Age population7, we detect 19 pairs of cross-island cousins, close relatives buried around 75 km apart in Hispaniola and low genetic differentiation across islands. Genetic continuity across transitions in pottery styles reveals that cultural changes during the Ceramic Age were not driven by migration of genetically differentiated groups from the mainland, but instead reflected interactions within an interconnected Caribbean world1,8.

Adaptations to nitrogen availability drive ecological divergence of chemosynthetic symbionts.

Bacterial symbionts, with their shorter generation times and capacity for horizontal gene transfer (HGT), play a critical role in allowing marine organisms to cope with environmental change. The closure of the Isthmus of Panama created distinct environmental conditions in the Tropical Eastern Pacific (TEP) and Caribbean, offering a "natural experiment" for studying how closely related animals evolve and adapt under environmental change. However, the role of bacterial symbionts in this process is often overlooked. We sequenced the genomes of endosymbiotic bacteria in two sets of sister species of chemosymbiotic bivalves from the genera Codakia and Ctena (family Lucinidae) collected on either side of the Isthmus, to investigate how differing environmental conditions have influenced the selection of symbionts and their metabolic capabilities. The lucinid sister species hosted different Candidatus Thiodiazotropha symbionts and only those from the Caribbean had the genetic potential for nitrogen fixation, while those from the TEP did not. Interestingly, this nitrogen-fixing ability did not correspond to symbiont phylogeny, suggesting convergent evolution of nitrogen fixation potential under nutrient-poor conditions. Reconstructing the evolutionary history of the nifHDKT operon by including other lucinid symbiont genomes from around the world further revealed that the last common ancestor (LCA) of Ca. Thiodiazotropha lacked nif genes, and populations in oligotrophic habitats later re-acquired the nif operon through HGT from the Sedimenticola symbiont lineage. Our study suggests that HGT of the nif operon has facilitated niche diversification of the globally distributed Ca. Thiodiazotropha endolucinida species clade. It highlights the importance of nitrogen availability in driving the ecological diversification of chemosynthetic symbiont species and the role that bacterial symbionts may play in the adaptation of marine organisms to changing environmental conditions.

Changes in parrot diversity after human arrival to the Caribbean.

Humans did not arrive on most of the world's islands until relatively recently, making islands favorable places for disentangling the timing and magnitude of natural and anthropogenic impacts on species diversity and distributions. Here, we focus on Amazona parrots in the Caribbean, which have close relationships with humans (e.g., as pets as well as sources of meat and colorful feathers). Caribbean parrots also have substantial fossil and archaeological records that span the Holocene. We leverage this exemplary record to showcase how combining ancient and modern DNA, along with radiometric dating, can shed light on diversification and extinction dynamics and answer long-standing questions about the magnitude of human impacts in the region. Our results reveal a striking loss of parrot diversity, much of which took place during human occupation of the islands. The most widespread species, the Cuban Parrot, exhibits interisland divergences throughout the Pleistocene. Within this radiation, we identified an extinct, genetically distinct lineage that survived on the Turks and Caicos until Indigenous human settlement of the islands. We also found that the narrowly distributed Hispaniolan Parrot had a natural range that once included The Bahamas; it thus became "endemic" to Hispaniola during the late Holocene. The Hispaniolan Parrot also likely was introduced by Indigenous people to Grand Turk and Montserrat, two islands where it is now also extirpated. Our research demonstrates that genetic information spanning paleontological, archaeological, and modern contexts is essential to understand the role of humans in altering the diversity and distribution of biota.

Evolution and environment of Caribbean coastal ecosystems.

Isolation of the Caribbean Sea from the tropical Eastern Pacific by uplift of the Isthmus of Panama in the late Pliocene was associated with major, taxonomically variable, shifts in Caribbean biotic composition, and extinction, but inferred causes of these biological changes have remained elusive. We addressed this through falsifiable hypotheses about how independently determined historical changes in oceanographic conditions may have been responsible. The most striking environmental change was a sharp decline in upwelling intensity as measured from decreases in intra-annual fluctuations in temperature and consequently in planktonic productivity. We then hypothesized three general categories of biological response based upon observed differences in natural history between the oceans today. These include changes in feeding ecology, life histories, and habitats. As expected, suspension feeders and predators became rarer as upwelling declined. However, predicted increases in benthic productivity by reef corals, and benthic algae were drawn out over more than 1 Myr as seagrass and coral reef habitats proliferated; a shift that was itself driven by declining upwelling. Similar time lags occurred for predicted shifts in reproductive life history characteristics of bivalves, gastropods, and bryozoans. Examination of the spatial variability of biotic change helps to understand the time lags. Many older species characteristic of times before environmental conditions had changed tended to hang on in progressively smaller proportions of locations until they became extinct as expected from metapopulation theory and the concept of extinction debt. Faunal turnover may not occur until a million or more years after the environmental changes ultimately responsible.

Sea urchin mass mortalities 40 y apart further threaten Caribbean coral reefs.

In 1983 to 1984, a mass mortality event caused a Caribbean-wide, >95% population reduction of the echinoid grazer, Diadema antillarum. This led to blooms of algae contributing to the devastation of scleractinian coral populations. Since then, D. antillarum exhibited only limited and patchy population recovery in shallow water, and in 2022 was struck by a second mass mortality reported over many reef localities in the Caribbean. Half-a-century time-series analyses of populations of this sea urchin from St. John, US Virgin Islands, reveal that the 2022 event has reduced population densities by 98.00% compared to 2021, and by 99.96% compared to 1983. In 2021, coral cover throughout the Caribbean was approaching the lowest values recorded in modern times. However, prior to 2022, locations with small aggregations of D. antillarum produced grazing halos in which weedy corals were able to successfully recruit and become the dominant coral taxa. The 2022 mortality has eliminated these algal-free halos on St. John and perhaps many other regions, thereby increasing the risk that these reefs will further transition into coral-free communities.

The role of tropical rainfall in driving range dynamics for a long-distance migratory bird.

Predicting how the range dynamics of migratory species will respond to climate change requires a mechanistic understanding of the factors that operate across the annual cycle to control the distribution and abundance of a species. Here, we use multiple lines of evidence to reveal that environmental conditions during the nonbreeding season influence range dynamics across the life cycle of a migratory songbird, the American redstart (Setophaga ruticilla). Using long-term data from the nonbreeding grounds and breeding origins estimated from stable hydrogen isotopes in tail feathers, we found that the relationship between annual survival and migration distance is mediated by precipitation, but only during dry years. A long-term drying trend throughout the Caribbean is associated with higher mortality for individuals from the northern portion of the species' breeding range, resulting in an approximate 500 km southward shift in breeding origins of this Jamaican population over the past 30 y. This shift in connectivity is mirrored by changes in the redstart's breeding distribution and abundance. These results demonstrate that the climatic effects on demographic processes originating during the tropical nonbreeding season are actively shaping range dynamics in a migratory bird.

General and abdominal adiposity and hypertension in eight world regions: a pooled analysis of 837 population-based studies with 7·5 million participants.

BACKGROUND: Adiposity can be measured using BMI (which is based on weight and height) as well as indices of abdominal adiposity. We examined the association between BMI and waist-to-height ratio (WHtR) within and across populations of different world regions and quantified how well these two metrics discriminate between people with and without hypertension. METHODS: We used data from studies carried out from 1990 to 2023 on BMI, WHtR and hypertension in people aged 20-64 years in representative samples of the general population in eight world regions. We graphically compared the regional distributions of BMI and WHtR, and calculated Pearson's correlation coefficients between BMI and WHtR within each region. We used mixed-effects linear regression to estimate the extent to which WHtR varies across regions at the same BMI. We graphically examined the prevalence of hypertension and the distribution of people who have hypertension both in relation to BMI and WHtR, and we assessed how closely BMI and WHtR discriminate between participants with and without hypertension using C-statistic and net reclassification improvement (NRI). FINDINGS: The correlation between BMI and WHtR ranged from 0·76 to 0·89 within different regions. After adjusting for age and BMI, mean WHtR was highest in south Asia for both sexes, followed by Latin America and the Caribbean and the region of central Asia, Middle East and north Africa. Mean WHtR was lowest in central and eastern Europe for both sexes, in the high-income western region for women, and in Oceania for men. Conversely, to achieve an equivalent WHtR, the BMI of the population of south Asia would need to be, on average, 2·79 kg/m2 (95% CI 2·31-3·28) lower for women and 1·28 kg/m2 (1·02-1·54) lower for men than in the high-income western region. In every region, hypertension prevalence increased with both BMI and WHtR. Models with either of these two adiposity metrics had virtually identical C-statistics and NRIs for every region and sex, with C-statistics ranging from 0·72 to 0·81 and NRIs ranging from 0·34 to 0·57 in different region and sex combinations. When both BMI and WHtR were used, performance improved only slightly compared with using either adiposity measure alone. INTERPRETATION: BMI can distinguish young and middle-aged adults with higher versus lower amounts of abdominal adiposity with moderate-to-high accuracy, and both BMI and WHtR distinguish people with or without hypertension. However, at the same BMI level, people in south Asia, Latin America and the Caribbean, and the region of central Asia, Middle East and north Africa, have higher WHtR than in the other regions. FUNDING: UK Medical Research Council and UK Research and Innovation (Innovate UK).

Topology Testing and Demographic Modeling Illuminate a Novel Speciation Pathway in the Greater Caribbean Sea Following the Formation of the Isthmus of Panama.

Recent genomic analyses have highlighted the prevalence of speciation with gene flow in many taxa and have underscored the importance of accounting for these reticulate evolutionary processes when constructing species trees and generating parameter estimates. This is especially important for deepening our understanding of speciation in the sea where fast-moving ocean currents, expanses of deep water, and periodic episodes of sea level rise and fall act as soft and temporary allopatric barriers that facilitate both divergence and secondary contact. Under these conditions, gene flow is not expected to cease completely while contemporary distributions are expected to differ from historical ones. Here, we conduct range-wide sampling for Pederson's cleaner shrimp (Ancylomenes pedersoni), a species complex from the Greater Caribbean that contains three clearly delimited mitochondrial lineages with both allopatric and sympatric distributions. Using mtDNA barcodes and a genomic ddRADseq approach, we combine classic phylogenetic analyses with extensive topology testing and demographic modeling (10 site frequency replicates × 45 evolutionary models × 50 model simulations/replicate = 22,500 simulations) to test species boundaries and reconstruct the evolutionary history of what was expected to be a simple case study. Instead, our results indicate a history of allopatric divergence, secondary contact, introgression, and endemic hybrid speciation that we hypothesize was driven by the final closure of the Isthmus of Panama and the strengthening of the Gulf Stream Current ~3.5 Ma. The history of this species complex recovered by model-based methods that allow reticulation differs from that recovered by standard phylogenetic analyses and is unexpected given contemporary distributions. The geologically and biologically meaningful insights gained by our model selection analyses illuminate what is likely a novel pathway of species formation not previously documented that resulted from one of the most biogeographically significant events in Earth's history.

Adaptive Radiation Without Independent Stages of Trait Evolution in a Group of Caribbean Anoles.

Adaptive radiation involves diversification along multiple trait axes, producing phenotypically diverse, species-rich lineages. Theory generally predicts that multi-trait evolution occurs via a "stages" model, with some traits saturating early in a lineage's history, and others diversifying later. Despite its multidimensional nature, however, we know surprisingly little about how different suites of traits evolve during adaptive radiation. Here, we investigated the rate, pattern, and timing of morphological and physiological evolution in the anole lizard adaptive radiation from the Caribbean island of Hispaniola. Rates and patterns of morphological and physiological diversity are largely unaligned, corresponding to independent selective pressures associated with structural and thermal niches. Cold tolerance evolution reflects parapatric divergence across elevation, rather than niche partitioning within communities. Heat tolerance evolution and the preferred temperature evolve more slowly than cold tolerance, reflecting behavioral buffering, particularly in edge-habitat species (a pattern associated with the Bogert effect). In contrast to the nearby island of Puerto Rico, closely related anoles on Hispaniola do not sympatrically partition thermal niche space. Instead, allopatric and parapatric separation across biogeographic and environmental boundaries serves to keep morphologically similar close relatives apart. The phenotypic diversity of this island's adaptive radiation accumulated largely as a by-product of time, with surprisingly few exceptional pulses of trait evolution. A better understanding of the processes that guide multidimensional trait evolution (and nuance therein) will prove key in determining whether the stages model should be considered a common theme of adaptive radiation.

Evidence for adaptive morphological plasticity in the Caribbean coral, Acropora cervicornis.

Genotype-by-environment interactions (GxE) indicate that variation in organismal traits cannot be explained by fixed effects of genetics or site-specific plastic responses alone. For tropical coral reefs experiencing dramatic environmental change, identifying the contributions of genotype, environment, and GxE on coral performance will be vital for both predicting persistence and developing restoration strategies. We quantified the impacts of G, E, and GxE on the morphology and survival of the endangered coral, Acropora cervicornis, through an in situ transplant experiment exposing common garden (nursery)-raised clones of ten genotypes to nine reef sites in the Florida Keys. By fate-tracking outplants over one year with colony-level 3D photogrammetry, we uncovered significant GxE on coral size, shape, and survivorship, indicating that no universal winner exists in terms of colony performance. Rather than differences in mean trait values, we found that individual-level morphological plasticity is adaptive in that the most plastic individuals also exhibited the fastest growth and highest survival. This indicates that adaptive morphological plasticity may continue to evolve, influencing the success of A. cervicornis and resulting reef communities in a changing climate. As focal reefs are active restoration sites, the knowledge that variation in phenotype is an important predictor of performance can be directly applied to restoration planning. Taken together, these results establish A. cervicornis as a system for studying the ecoevolutionary dynamics of phenotypic plasticity that also can inform genetic- and environment-based strategies for coral restoration.

Rapid radiation in a highly diverse marine environment.

Rapid diversification is often observed when founding species invade isolated or newly formed habitats that provide ecological opportunity for adaptive radiation. However, most of the Earth's diversity arose in diverse environments where ecological opportunities appear to be more constrained. Here, we present a striking example of a rapid radiation in a highly diverse marine habitat. The hamlets, a group of reef fishes from the wider Caribbean, have radiated into a stunning diversity of color patterns but show low divergence across other ecological axes. Although the hamlet lineage is ∼26 My old, the radiation appears to have occurred within the last 10,000 generations in a burst of diversification that ranks among the fastest in fishes. As such, the hamlets provide a compelling backdrop to uncover the genomic elements associated with phenotypic diversification and an excellent opportunity to build a broader comparative framework for understanding the drivers of adaptive radiation. The analysis of 170 genomes suggests that color pattern diversity is generated by different combinations of alleles at a few large-effect loci. Such a modular genomic architecture of diversification has been documented before in Heliconius butterflies, capuchino finches, and munia finches, three other tropical radiations that took place in highly diverse and complex environments. The hamlet radiation also occurred in a context of high effective population size, which is typical of marine populations. This allows for the accumulation of new variants through mutation and the retention of ancestral genetic variation, both of which appear to be important in this radiation.

Protecting Caribbean patients diagnosed with cancer from compounding disasters.

Caribbean small island developing states are becoming increasingly vulnerable to compounding disasters, prominently featuring climate-related hazards and pandemic diseases, which exacerbate existing barriers to cancer control in the region. We describe the complexities of cancer prevention and control efforts throughout the Caribbean small island developing states, including the unique challenges of people diagnosed with cancer in the region. We highlight potential solutions and strategies that concurrently address disaster adaptation and cancer control. Because Caribbean small island developing states are affected first and worst by the hazards of compounding disasters, the innovative solutions developed in the region are relevant for climate mitigation, disaster adaptation, and cancer control efforts globally. In the age of complex and cascading disaster scenarios, developing strategies to mitigate their effect on the cancer control continuum, and protecting the health and safety of people diagnosed with cancer from extreme events become increasingly urgent. The equitable development of such strategies relies on collaborative efforts among professionals whose diverse expertise from complementary fields infuses the local community perspective while focusing on implementing solutions.

Annotated genome and transcriptome of the endangered Caribbean mountainous star coral (Orbicella faveolata) using PacBio long-read sequencing.

Long-read sequencing is revolutionizing de-novo genome assemblies, with continued advancements making it more readily available for previously understudied, non-model organisms. Stony corals are one such example, with long-read de-novo genome assemblies now starting to be publicly available, opening the door for a wide array of 'omics-based research. Here we present a new de-novo genome assembly for the endangered Caribbean star coral, Orbicella faveolata, using PacBio circular consensus reads. Our genome assembly improved the contiguity (51 versus 1,933 contigs) and complete and single copy BUSCO orthologs (93.6% versus 85.3%, database metazoa_odb10), compared to the currently available reference genome generated using short-read methodologies. Our new de-novo assembled genome also showed comparable quality metrics to other coral long-read genomes. Telomeric repeat analysis identified putative chromosomes in our scaffolded assembly, with these repeats at either one, or both ends, of scaffolded contigs. We identified 32,172 protein coding genes in our assembly through use of long-read RNA sequencing (ISO-seq) of additional O. faveolata fragments exposed to a range of abiotic and biotic treatments, and publicly available short-read RNA-seq data. With anthropogenic influences heavily affecting O. faveolata, as well as its increasing incorporation into reef restoration activities, this updated genome resource can be used for population genomics and other 'omics analyses to aid in the conservation of this species.

Assessment of barriers to cancer screening and interventions implemented to overcome these barriers in 27 Latin American and Caribbean countries.

There is a gap in the understanding of the barriers to cancer screening participation and complying with downstream management in the Community of Latin American and Caribbean states (CELAC). Our study aimed to assess barriers across the cancer screening pathway from the health system perspective, and interventions in place to improve screening in CELAC. A standardized tool was used to collect information on the barriers across the screening pathway through engagement with the health authorities of 27 member states of CELAC. Barriers were organized in a framework adapted from the Tanahashi conceptual model and consisted of the following dimensions: availability of services, access (covering accessibility and affordability), acceptability, user-provider interaction, and effectiveness of services (which includes governance, protocols and guidelines, information system, and quality assurance). The tool also collected information of interventions in place, categorized in user-directed interventions to increase demand, user-directed interventions to increase access, provider-directed interventions, and policy and system-level interventions. All countries prioritized barriers related to the information systems, such as the population register not being accurate or complete (N = 19; 70.4%). All countries implemented some kind of intervention to improve cancer screening, group education being the most reported (N = 23; 85.2%). Training on screening delivery was the most referred provider-directed intervention (N = 19; 70.4%). The study has identified several barriers to the implementation of cancer screening in the region and interventions in place to overcome some of the barriers. Further analysis is required to evaluate the effectiveness of these interventions in achieving their objectives.

Overall and metastasis-free survival of Afro-Caribbean patients with biochemical recurrence after radical prostatectomy.

INTRODUCTION: Early salvage radiotherapy is indicated for patients with biochemical recurrence after radical prostatectomy. However, for various reasons, certain patients do not benefit from this treatment (OBS) or only at a late stage (LSR). There are few studies on this subject and none on a "high-risk" population, such as patients of African descent. Our objective was to estimate the metastasis-free (MFS) and overall survival (OS) of patients who did not receive salvage radiotherapy, and to identify risk factors of disease progression. PATIENTS AND METHODS: This was a single-center retrospective study that included 154 patients, 99 in the OBS group and 55 in the LSR group. All were treated by total prostatectomy for localized prostate cancer between January 2000 and December 2020 and none received early salvage radiotherapy after biochemical recurrence. RESULTS: Baseline characteristics were similar between groups, except for the time to biochemical recurrence. The median follow-up was 10.0 and 11.8 years for the OBS and LSR groups, respectively. The median time from surgery to LSR was 5.1 years. The two groups did not show a significant difference in MFS: 90.6% at 10 years for the OBS group and 93.3% for the LSR group. The median MFS was 19.8 and 19.6 years for the OBS and LSR groups respectively. OS for the OBS group was significantly higher than that for the LSR group (HR: 2.14 [1.07-4.29]; p = 0.03), with 10-year OS of 95.9% for the OBS group and 76.1% for the LSR group. Median OS was 16 and 15.6 years for the OBS and LSR groups, respectively. CONCLUSION: In this study, we observed satisfactory metastasis-free and OS rates relative to those reported in the scientific literature. The challenge is not to question the benefit of early salvage radiotherapy, but to improve the identification of patients at risk of progression through the development of molecular and genomic tests for more highly personalized medicine.

Assembly, Persistence, and Disassembly Dynamics of Quaternary Caribbean Frugivore Communities.

AbstractHow communities assemble and restructure is of critical importance to ecological theory, evolutionary theory, and conservation, but long-term perspectives on the patterns and processes of community assembly are rarely integrated into traditional community ecology, and the utility of communities as an ecological concept has been repeatedly questioned in part because of a lack of temporal perspective. Through a synthesis of paleontological and neontological data, I reconstruct Caribbean frugivore communities over the Quaternary (2.58 million years ago to present). Numerous Caribbean frugivore lineages arise during periods coincident with the global origins of plant-frugivore mutualisms. The persistence of many of these lineages into the Quaternary is indicative of long-term community stability, but an analysis of Quaternary extinctions reveals a nonrandom loss of large-bodied mammalian and reptilian frugivores. Anthropogenic impacts, including human niche construction, underlie the recent reorganization of frugivore communities, setting the stage for continued declines and evolutionary responses in plants that have lost mutualistic partners. These impacts also support ongoing and future introductions of invader complexes: introduced plants and frugivores that further exacerbate native biodiversity loss by interacting more strongly with one another than with native plants or frugivores. This work illustrates the importance of paleontological data and perspectives in conceptualizing ecological communities, which are dynamic and important entities.

Genetic diversity of the banana Fusarium wilt pathogen in Cuba and across Latin America and the Caribbean.

Fusarium wilt of bananas (FWB) is a severe plant disease that leads to substantial losses in banana production worldwide. It remains a major concern for Cuban banana cultivation. The disease is caused by members of the soil-borne Fusarium oxysporum species complex. However, the genetic diversity among Fusarium species infecting bananas in Cuba has remained largely unexplored. In our comprehensive survey, we examined symptomatic banana plants across all production zones in the country, collecting 170 Fusarium isolates. Leveraging genotyping-by-sequencing and whole-genome comparisons, we investigated the genetic diversity within these isolates and compared it with a global Fusarium panel. Notably, typical FWB symptoms were observed in Bluggoe cooking bananas and Pisang Awak subgroups across 14 provinces. Our phylogenetic analysis revealed that F. purpurascens, F. phialophorum, and F. tardichlamydosporum are responsible for FWB in Cuba, with F. tardichlamydosporum dominating the population. Furthermore, we identified between five and seven distinct genetic clusters, with F. tardichlamydosporum isolates forming at least two subgroups. This finding underscores the high genetic diversity of Fusarium spp. contributing to FWB in the Americas. Our study sheds light on the population genetic structure and diversity of the FWB pathogen in Cuba and the broader Latin American and Caribbean regions.

Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning.

Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative pathogens. An example is white band disease (WBD), which has killed up to 95% of the now-endangered Caribbean Acropora corals since 1979, yet the pathogen is still unknown. The 16S rRNA gene surveys have identified hundreds of WBD-associated bacterial amplicon sequencing variants (ASVs) from at least nine bacterial families with little consensus across studies. We conducted a multi-year, multi-site 16S rRNA gene sequencing comparison of 269 healthy and 143 WBD-infected Acropora cervicornis and used machine learning modelling to accurately predict disease outcomes and identify the top ASVs contributing to disease. Our ensemble ML models accurately predicted disease with greater than 97% accuracy and identified 19 disease-associated ASVs and five healthy-associated ASVs that were consistently differentially abundant across sampling periods. Using a tank-based transmission experiment, we tested whether the 19 disease-associated ASVs met the assumption of a pathogen and identified two pathogenic candidate ASVs-ASV25 Cysteiniphilum litorale and ASV8 Vibrio sp. to target for future isolation, cultivation, and confirmation of Henle-Koch's postulate via transmission assays.

A deep-sea isopod that consumes Sargassum sinking from the ocean's surface.

Most deep-ocean life relies on organic carbon from the surface ocean. While settling primary production rapidly attenuates in the water column, pulses of organic material can be quickly transported to depth in the form of food falls. One example of fresh material that can reach great depths across the tropical Atlantic Ocean and Caribbean Sea is the pelagic macroalgae Sargassum. However, little is known about the deep-ocean organisms able to use this food source. Here, we encountered the isopod Bathyopsurus nybelini at depths 5002-6288 m in the Puerto Rico Trench and Mid-Cayman Spreading Center using the Deep Submergence Vehicle Alvin. In most of the 32 observations, the isopods carried fronds of Sargassum. Through an integrative suite of morphological, DNA sequencing, and microbiological approaches, we show that this species is adapted to feed on Sargassum by using a specialized swimming stroke, having serrated and grinding mouthparts, and containing a gut microbiome that provides a dietary contribution through the degradation of macroalgal polysaccharides and fixing nitrogen. The isopod's physiological, morphological, and ecological adaptations demonstrate that vertical deposition of Sargassum is a direct trophic link between the surface and deep ocean and that some deep-sea organisms are poised to use this material.