Biology subjects

O'Dea, A.

Publications and source records attributed to O'Dea, A..

12 recordsLinked to original sources

bioRxiv2026

Can the Z:A ratio serve as a genomic index of sexual selection? An assessment across space and time in a genus of lekking birds

Understanding the role of sexual selection in shaping evolutionary trajectories is a key goal of biology, and thus developing a genomic measure of sexual selection strength is desirable. In systems with ZW sex determination, the ratio of nucleotide diversity ({pi}) on the male-biased Z chromosome to that on the autosomes (the Z:A ratio) is expected to decline as male effective population size decreases under strong sexual selection, offering one such measure. However, non-equilibrium processes other than sexual selection (e.g., hybridization, changes in population size) can influence levels of Z-linked diversity relative to the rest of the genome, complicating interpretation of this metric and necessitating a systematic evaluation of how Z:A ratios vary across known demographic and selective circumstances. We leveraged longitudinal sampling over a [~]25-year period in Manacus manakin populations in western Panama, spanning a mainland transect (including M. candei, M. vitellinus, and their hybrid zone) and insular populations of the Bocas del Toro Archipelago. On the mainland, Z:A ratios were temporally stable within populations, but varied across populations: (1) Z:A ratios were lower in M. vitellinus than M. candei, likely due to stronger sexual selection in the former; and (2) Z:A ratios increased at the hybrid zone center, likely due to fast-Z effects in parentals inflating Z:A ratios in recent hybrids. Island populations exhibited significantly lower Z:A ratios than mainland populations, consistent with theoretical expectations of Z:A reductions following population contractions as the islands became isolated. Insular Z:A ratios increased with proximity to other landmasses, suggesting gene flow mitigates these effects in this system. While the Z:A ratio behaved predictably in relation to known non-equilibrium processes, our results demonstrate the potentially strong effects of demographic history and admixture on Z-linked diversity, which should be considered in studies aiming to use the Z:A ratio as a measure of sexual selection.

evolutionary biology↗

bioRxiv2026

Geomorphic evolution of a Caribbean biological hotspot

Continental shelf archipelagos offer rare opportunities to test island biogeography in a time-resolved, non-equilibrium setting because postglacial sea-level rise drives datable changes in both island area and isolation. Yet most near-shore systems still lack reconstructions that integrate spatial changes in island configuration with duration-weighted histories of fragmentation. Such information is essential for interpreting modern genomic and biodiversity patterns and for evaluating responses to fragmentation such as extinction debt, immigration lag and adaptive responses over time. Here we reconstruct the land-sea geomorphic history of the Bocas del Toro Archipelago, Panama, combining high-resolution bathymetry and topography with a sea-level model corrected for sedimentation and tectonic movement. From this, we quantify multi-scale isolation, historical fragmentation dynamics, and composite metrics that integrate space and time. We show that present-day islands became isolated sequentially from 9.5 to 2.9 ka, with post-isolation area contraction rates varying 20-fold among islands. Over the same interval, shallow marine habitat (0-10 m depth) expanded ninefold as shelf flooding created space for reefs, seagrass, and mangroves. Extending the analyses through the Pleistocene reveals the modern archipelago is atypical and for much of the last million years, the region existed as continuous coastal lowland rather than discrete islands. Projections under moderate emissions scenarios predict [~]5% terrestrial habitat loss but [~]50% expansion of shallow marine habitat by 2150, though whether degraded Caribbean reefs can exploit this expansion remains uncertain. Exploratory correlations between species richness of terrestrial vertebrate groups and geomorphometric predictors reveal that island area, maximum elevation, and cumulative habitat availability since isolation are the strongest correlates of diversity, whilst buffer-zone isolation indices are confounded by covariation between island size and surrounding landmass in this continental shelf context. Overall, Bocas del Toro provides a time-calibrated natural experiment for testing how dynamic connectivity and isolation shaped island and coastal biodiversity.

evolutionary biology↗

bioRxiv2024

Dietary resilience of coral reef fishes to habitat degradation

The ability of consumers to adjust their diet in response to resource shifts is a key mechanism allowing the persistence of populations and underlying species adaptive capacity. Yet on coral reefs, one of the marine habitats most vulnerable to global change, the extent to which species alter their diet remains poorly understood. Here, we integrated DNA-based gut content analyses (metabarcoding), otolith analysis, body condition, and field surveys to test how diet can mediate effects of habitat degradation on two invertivorous fishes: Chaetodon capistratus, a browser, and Hypoplectrus puella, an active predator. Metabarcoding revealed significant dietary variation in both species across a habitat gradient. However, the response was more pronounced in the browser, whose diet was anthozoan-dominated on healthy reefs, whereas annelid-dominated on degraded reefs. We found reduced growth and body condition on degraded reefs in the browser but not the active predator. Our results reveal that dietary versatility can serve as a mechanism to cope with degraded environments, but that species differ as to whether these changes are sufficient to buffer from changes in habitat. We detected intraspecific dietary variation across sites that suggests food webs and energy flow differ at relatively small scales between healthy and degraded reefs.

ecology↗

bioRxiv2023

Lunulite bryozoan biogeography - a convergent global success with a distinct Western Australian twist

Lunulites are a polyphyletic group of marine bryozoans that have been a conspicuous element of marine shelf faunas since the Late Cretaceous into the present day. They are easily recognizable by their domed colony form and free-living mode of life on sea floor sediments. Here we explore the waxing and waning of the major lunulitiform groups and their unique morphology and mode of life from the Cretaceous to the present day. Because relatively few and simple modifications are needed to transition from an encrusting form into this highly specialized lifestyle, shared colonial features are rampant and we find examples of both convergent and iterative evolution across several unrelated clades, although detailed phylogenetic relationship remain largely unresolved. The early chapter of the lunulite story is focused on the Late Cretaceous European Chalk Sea, which appears to have been a crucible for the evolution of lunulites. At least six, and likely more, cheilostome groups independently evolved the free-living mode of life in this tropical shelf area. To what extent any of these free-living clades gave rise to post-Cretaceous groups remains unclear. The Cenozoic chapter is more complex, comprising at least three independently evolved major clades, two of which are extant; (1) the Lunulitidae s. str., a North American/European cluster, comprising the classic Lunulites, which became extinct in the late Neogene, (2) the Cupuladriidae, which reached circum-global tropical and sub-tropical distribution in the Miocene, and (3) the Austral lunulite cluster, which is almost certainly polyphyletic and through most of its history confined to Australia and New Zealand, bar a comparatively brief colonization of the southern part of South America, with the earliest representatives from NW Western Australia.

evolutionary biology↗

bioRxiv2022

Simulated green turtle grazing reduces seagrass productivity and alters benthic community structure while triggering further disturbance by feeding stingrays

While green turtles (Chelonia mydas) were once abundant throughout the Caribbean, overexploitation has dramatically reduced their numbers. We conducted a 168-day simulated grazing experiment to determine how loss of this once-abundant mega-herbivore could have affected the productivity and community composition of Thalassia testudinum-dominated seagrass beds in Bocas del Toro, Panama. Simulated grazing reduced both percent cover and productivity of T. testudinum. High runoff and local pollution from industrial farming may limit light availability and reduce seagrass photosynthetic performance to replace biomass lost to simulated grazing. Other seagrass species and algae failed to colonize space opened by reductions in T. testudinum percent cover. Many plots subjected to simulated grazing were also bioturbated by stingrays. Relevance of these findings to balancing sea turtle and seagrass conservation efforts are discussed.

ecology↗

bioRxiv2021

Millennial-scale change on a Caribbean reef system that experiences hypoxia

Coastal hypoxia has become an increasingly acknowledged threat to coral reefs that is potentially intensifying because of increased input of anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a semi-enclosed system that experiences hypoxia in deeper waters which occasionally expand into shallow coral reefs, suffocating most aerobic benthic life. To explore the long-term history of reefs in the bay we extracted reef matrix cores from two reefs that today experience contrasting patterns of oxygenation. We constructed a 1800-year-long record of gastropod assemblages and isotope compositions from six U-Th chronologically-constrained reef matrix cores. We extracted two cores from each reef at 3 m water depth and two additional cores from a deeper part (4.8 m) of the hypoxia-exposed reef. Results show that the deeper part of the hypoxic reef slowed in growth and stopped accreting approximately 1500 years BP while the shallow part of the reef continued to accrete to the present day, in agreement with a model of expanding hypoxia at this time. Our proxy-based approach suggests that differences among these palaeoindicators in the two reefs may have been driven by an increase in hypoxia via eutrophication caused by either natural changes or human impacts. Similar patterns of increasing herbivores and decreasing carbon isotope values occurred in the shallow part of the hypoxic reef during the last few decades. This suggests that hypoxia may be expanding to depths as shallow as 3 m and that shallow reefs are experiencing greater risk due to increased human activity.

paleontology↗

bioRxiv2021

Convergent evolution of resistance pathways during early stage breast cancer treatment with combination cell cycle (CDK) and endocrine inhibitors

Combining cyclin-dependent kinase (CDK) inhibitors with endocrine therapy improves outcomes for metastatic estrogen receptor positive (ER+), HER2 negative, breast cancer patients. However, the value of this combination in potentially curable earlier stage patients is not clear. Using single cell transcriptomic profiling, we examined the evolutionary trajectories of early stage breast cancer tumors using serial tumor biopsies from a clinical trial of preoperative endocrine therapy (letrozole) alone or in combination with the cell cycle inhibitor ribociclib. Applying hierarchical regression and Gaussian process mathematical modelling, we classified each tumor by whether it shrinks or persists with therapy and determined cancer phenotypes related to evolution of resistance and cell cycle transcriptional rewiring. We found that all patients tumors undergo subclonal evolution during therapy, irrespective of the clinical response. However, tumors subjected to endocrine therapy alone showed reduced diversity over time, while those facing combination therapy exhibited increased diversity. Despite different subclonal diversity, single nuclei RNA sequencing uncovered common phenotypic changes in tumor cells that persist following treatment. In these tumors, cancer cells with accelerated loss of estrogen signaling have convergent up-regulation of the JNK pathway, while cells that maintain estrogen signaling during therapy show potentiation of CDK4/6 activation consistent with ERBB4 and ERK signaling up-regulation. These convergent phenotypes were associated with growing tumors resistant to combination therapy. Cell cycle reconstruction identified that these tumors can rebound during combination therapy treatment, indicating stronger selection and promotion of a proliferative state. These results indicate that combination therapy in early stage ER+ breast cancers with ER and CDK inhibition drives rapid evolution of resistance via a shift from estrogen signaling to alternative growth factor receptor mediated proliferation and JNK signaling activation, concordant with a bypass in the G1 checkpoint.

cancer biology↗

bioRxiv2021

Reconstructing tumor trajectories during therapy through integration of multiple measurement modalities.

BackgroundAccurately determining changes in tumor size during therapy is essential to evaluating response or progression. However, individual imaging methodologies often poorly reflect pathologic response and long-term treatment efficacy in patients with estrogen receptor positive (ER+) early-stage breast cancer. Mathematical models that measure tumor progression over time by integrating diverse imaging and tumor measurement modalities are not currently used but could increase accuracy in measuring response and provide biological insights into cancer evolution. MethodsFor ER+ breast cancer patients enrolled on a neoadjuvant clinical trial, we reconstructed their tumor size trajectories during therapy by combining all available information on tumor size, including different imaging modalities, physical examinations and pathological assessment data. Tumor trajectories during six months of treatment were generated, using a Gaussian process and the most probable trajectories were evaluated, based on clinical data, using measurement models that account for biases and differences in precision between tumor measurement methods, such as MRI, ultrasound and mammograms. ResultsReconstruction of tumor trajectories during treatment identified five distinct patterns of tumor size changes, including rebound growth not evident from any single modality. These results increase specificity to distinguish innate or acquired resistance compared to using any single measurement alone. The speed of therapeutic response and extent of subsequent rebound tumor growth quantify sensitivity or resistance in this patient population. ConclusionsTumor trajectory reconstruction integrating multiple modalities of tumor measurement accurately describes tumor progression on therapy and reveals various patterns of patient responses. Mathematical models can integrate diverse response assessments and account for biases in tumor measurement, thereby providing insights into the timing and rate at which resistance emerges.

systems biology↗

bioRxiv2020

Modern, archaeological, and paleontological DNA analysis of a human-harvested marine gastropod (Strombus pugilis) from Caribbean Panama

Although protocols exist for the recovery of ancient DNA from land snail and marine bivalve shells, marine conch shells have yet to be studied from a paleogenomic perspective. We first present reference assemblies for both a 623.7 Mbp nuclear genome and a 15.4 kbp mitochondrial genome for Strombus pugilis, the West Indian fighting conch. We next detail a method to extract and sequence DNA from conch shells and apply it to conch from Bocas del Toro, Panama across three time periods: recently-eaten and discarded (n=3), Late Holocene (984-1258 BP) archaeological midden (n=5), and a mid-Holocene (5711-7187 BP) paleontological fossil coral reef (n=5). These results are compared to control DNA extracted from live-caught tissue and fresh shells (n=5). Using high-throughput sequencing, we were able to obtain S. pugilis nuclear sequence reads from shells across all age periods: up to 92.5 thousand filtered reads per sample in live-caught shell material, 4.57 thousand for modern discarded shells, 12.1 thousand reads for archaeological shells, and 114 reads in paleontological shells. We confirmed authenticity of the ancient DNA recovered from the archaeological and paleontological shells based on 5.7x higher average frequency of deamination-driven misincorporations and 15% shorter average read lengths compared to the modern shells. Reads also mapped to the S. pugilis mitochondrial genome for all but the paleontological shells, with consistent ratios of mitochondrial to nuclear mapped reads across sample types. Our methods can be applied to diverse archaeological sites to facilitate reconstructions of the long-term impacts of human behavior on mollusc evolutionary biology.

evolutionary biology↗

bioRxiv2019

The Panama Canal after a century of human impacts

Large tropical river dam projects are set to accelerate over the forthcoming decades to satisfy growing demand for energy, irrigation and flood control. When tropical rivers are dammed, the immediate impacts are well studied, but the long-term (decades-centuries) consequences of impoundment remain poorly known. Here, we gather historical and paleoecological data from Gatun Lake, formed by the building of the Gatun Dam (Panama Canal, Panama) over 100 years ago, to reconstruct the limnological evolution of the system in response to individual and linked stressors (river damming, forest flooding, deforestation, invasive species, pollution and hydro-climate). We found that after a century of dam construction parallels associated with the natural hydrological functioning of river floodplains persist. Hence, hydrology remains the most important temporal structural factor positively stimulating primary productivity, deposition of new minerals, and reduction of water transparency during wet periods. During dry periods, clear water and aerobic conditions prevail and nutrients transform into available forms in the detrital-rich reductive sediments. We highlight the importance of climate change as an ultimate rather than proximate anthropogenic factor for sustainable management options of tropical dams.

ecology↗

bioRxiv2019

Defining variation in pre-human ecosystems can guide conservation: An example from a Caribbean coral reef

There is a consensus that Caribbean coral reefs are a pale shadow of what they once were, yet a reef’s pre-human state is typically assumed or estimated using space-for-time substitution approaches. These approaches may fail to account for past variation before human impact which could mislead conservation priorities and actions. In this study we use a suite of fossilised mid-Holocene (7.2-5.6 ka) fringing reefs in Caribbean Panama to define the Historical Range of Variation (HRV) in coral community structure before human-impact to provide context for the states of modern reefs in the same area. Using the abundances of coral taxa to quantify communities, we found that most of the modern coral communities exist in novel ecosystem states with no fossil precedence. We do however identify one modern reef that is indistinguishable in coral community structure from the mid-Holocene reefs. Reef-matrix cores show that the community on this reef has remained in a stable state for over 760 years, suggesting long-term resistance to the region-wide shift to novel states. Without historical context this robust and stable reef would be overlooked since it does not fulfil expectations of what a “pristine” coral reef should look like. This example illustrates how defining past variation using the fossil record can place modern degradation in historical context and improve conservation recommendations.View Full Text

paleontology↗

bioRxiv2019

The flickering connectivity system of the north Andean paramos

ABSTRACT AND KEYWORDSO_ST_ABSAimC_ST_ABSTo quantify the effect of Pleistocene climate fluctuations on habitat connectivity across paramos in the Neotropics.\n\nLocationThe Northern Andes\n\nMethodsThe unique paramos habitat underwent dynamic shifts in elevation in response to changing climate conditions during the Pleistocene. The lower boundary of the paramos is defined by the upper forest line, which is known to be highly responsive to temperature. Here we reconstruct the extent and connectivity of paramos over the last 1 million years (Myr) by reconstructing the UFL from the long fossil pollen record of Funza09, Colombia, and applying it to spatial mapping on modern topographies across the Northern Andes for 752 time slices. Data provide an estimate of how often and for how long different elevations were occupied by paramos and estimates their connectivity to provide insights into the role of topography in biogeographic patterns of paramos.\n\nResultsOur findings show that connectivity amongst paramos of the Northern Andes was highly dynamic, both within and across mountain ranges. Connectivity amongst paramos peaked during extreme glacial periods but intermediate cool stadials and mild interstadials dominated the climate system. These variable degrees of connectivity through time result in what we term the flickering connectivity system. We provide a visualization (video) to showcase this phenomenon. Patterns of connectivity in the Northern Andes contradict patterns observed in other mountain ranges of differing topographies.\n\nMain conclusionsPleistocene climate change was the driver of significant elevational and spatial shifts in paramos causing dynamic changes in habitat connectivity across and within all mountain ranges. Some generalities emerge, including the fact that connectivity was greatest during the most ephemeral of times. However, the timing, duration and degree of connectivity varied substantially among mountain ranges depending on their topographic configuration. The flickering connectivity system of the paramos uncovers the dynamic settings in which evolutionary radiations shaped the most diverse alpine biome on Earth.

ecology↗