Biology subjects

Komoroske, L. M.

Publications and source records attributed to Komoroske, L. M..

11 recordsLinked to original sources

bioRxiv2026

A GENOMIC BASIS FOR TRANS-OCEANIC SEA TURTLE MIGRATION

Long-distance migration has evolved repeatedly across the animal kingdom, yet the underlying processes giving rise to and maintaining these complex eco-behavioral phenotypes remain poorly understood. Here, we present the first evidence of genomic determinants of migratory phenotypes in sea turtles, using whole genome resequencing to demonstrate that complex genomic architecture underlies divergent migratory destinations and reproductive timing in the critically endangered western Pacific leatherback turtle (Dermochelys coriacea). Individuals from this admixed population that navigate to foraging grounds on opposite sides of the Pacific Ocean have a putative inversion on chromosome 2 encompassing one gene, potentially conferring pleiotropic physiological effects and supporting magnetoreception. Genomic architecture underlying divergent reproductive timing is more dispersed, aligned with reduced gene flow, and is associated with genes that may influence reproductive success. Genes underlying both traits suggest a role for neurodevelopment and memory. Our study adds to the increasing evidence of at least partial genomic control of migratory traits in wild populations, with important potential implications for conservation measures such as translocation and genetic rescue. Our results align with a growing body of work describing complex genomic architecture and structural variants underlying key eco-behavioral traits, advancing the understanding of evolution of long-distance migration across taxa.

ecology↗

bioRxiv2026

Phenological plasticity provides limited resilience to climate warming in a sea turtle species with temperature-dependent sex determination

Anthropogenic climate change is threatening global biodiversity, with sea turtles particularly vulnerable as offspring sex and developmental success are strongly influenced by incubation temperature. Behavioral plasticity, including the seasonal distribution of reproductive output, may provide short-term mechanisms for mitigating these impacts. Here, we investigated season-wide hatchling sex ratios and emergence success in a small population of green turtles (Chelonia mydas), tracking individual females across their nesting seasons. Sex ratios varied markedly through the nesting season, with later nests producing a greater proportion of male hatchlings. Moreover, sex ratios were relatively consistent among nests laid by individual females. Overall, females producing more nests over a season also produced more male offspring, suggesting that both nesting phenology and reproductive output influence individual contributions to future population demographics. Mechanistic models indicate that hatchling sex ratios have trended towards female-biased ratios (>80% female) over the past 50 years, and are projected to approach complete feminization by 2100 under continued warming. Although emergence success currently remains high (>85%), it is predicted to decline sharply after mid-century, with viable hatchling production falling to [~]30% by the end of the century. Models further show that maintaining contemporary sex ratios and emergence success will require unrealistically large delays in nesting phenology, and that even extreme shifts in phenology become ineffective by 2100. Together, these findings demonstrate that individual females can increase male hatchling production by nesting later and producing more nests, but behavioral plasticity alone is unlikely to offset the accelerating impacts of climate change on this population.

ecology↗

bioRxiv2026

Genomic indicators of risk and resilience in global leatherback turtle populations

Understanding the drivers of genomic health and their consequences for population viability is often overlooked but potentially important to effective conservation amidst the biodiversity crisis of the Anthropocene. Leatherback turtle (Dermochelys coriacea) populations have declined globally due to anthropogenic factors, with some populations losing over 90% of their abundance over the past 30-50 years. While conservation efforts have been successful in stabilizing some populations, others continue to decline, and the reasons for these differential trajectories remain unclear. To assess how recent demographic factors, such as population size and decline, influence population genomic health, we combined population monitoring information with medium depth whole-genome and reduced representation resequencing data from globally representative populations. We found that small-stable populations have lower genomic diversity and higher inbreeding than large declining populations, reflecting prolonged small population sizes and limited gene flow. Yet, small-stable populations also show evidence of deleterious allele purging, suggesting genetic resilience. This, combined with lack of detectable genomic erosion over the study period, provides hope for potential recovery of healthy leatherback populations provided that anthropogenic threats are effectively mitigated. However, potential time lags and possible recent increases in inbreeding among close relatives in recently declined populations warrant continued monitoring and assessment. Genomic and abundance-based metrics were less aligned following rapid population declines, emphasizing the different timescales of the evolutionary and demographic processes they reflect, respectively, and the strength in their complementary, integrative use for extinction risk assessments. This also supports that it is not too late to turn the tide for recently declined leatherback populations and that continued investment in conservation efforts and threat reductions are warranted. Collectively, our results highlight how recent and historical demography shapes current genomic health and recovery potential in leatherback turtles, aids understanding of current risks and informs future conservation and management strategies.

ecology↗

bioRxiv2026

Assessing climate adaptation among Canada lynx (Lynx canadensis) populations at the trailing edge

Species must acclimate, shift their distributions, or adapt in place in response to anthropogenic climate change. Populations at low-latitude trailing edges of species distributions typically experience thermal conditions closest to the upper limit of their thermoregulatory capacity. Landscape and functional genomic approaches provide quantitative measures of risk and adaptive capacity which can inform and prioritize conservation actions. Using low-coverage whole genomes from Canada lynx (Lynx canadensis), we characterized population genomic structure and identified putatively adaptive loci using genotype-environment association analyses across the eastern extent of their distribution. We detected genetic breaks across two previously identified biogeographical barriers, the St. Lawrence River and the Strait of Belle Isle, and found relatively high genome-wide diversity in the Maine population at the southern trailing edge, suggesting a reservoir of warm-adapted variation. We identified 759 loci from 329 genes as putatively adaptive, many associated with temperature during warm and dry periods, and functionally enriched in photoreception, circadian entrainment, and temperature regulation. We identified ten putatively adaptive genes linked to epilepsy, presenting candidate genes underlying reports of idiopathic epilepsy in captive populations of closely related lynx species (L. lynx and L. pardinus). Genetic offset showed lynx in Western Newfoundland, and the Gaspe Peninsula in Quebec are at the greatest risk of maladaptation under future conditions. If gene flow allows, introgression of climate-adapted loci from the trailing-edge may benefit regional populations under future climates. Together, these findings demonstrate the conservation value of locally adapted range-edge populations.

genomics↗

bioRxiv2026

DNA methylation reveals evolved buffering responses to climate-driven sex ratio skew in sea turtles

Species with temperature-dependent sex determination (TSD), including all sea turtles which produce females at warmer temperatures, face projections of demographic collapse under climate-driven sex ratio skews. However, the accuracy of such predictions remains uncertain, as current models rely heavily on indirect sex ratio proxies due to the lack of a scalable, non-invasive method for sexing hatchlings. Through whole methylome sequencing, we identified 777 sex-associated DNA methylation markers from blood samples of sex-verified loggerhead turtle (Caretta caretta) hatchlings incubated at three controlled temperatures. Applying these markers to a large-scale field experiment showed that classic nest temperature-based models overestimated female production by an average of up to 60.2%, suggesting the presence of evolved buffering mechanisms against thermal effects on sex determination. Our findings highlight the need to revise climate-driven sex ratio forecasts with empirical field data, such as methylation-based assessments, to better understand and safeguard the hidden resilience of vulnerable TSD species.

zoology↗

bioRxiv2025

Adaptation to warm environments with a fast pace of life in a marine predatory snail

Understanding how latitudinal temperature variation shapes local adaptation of life history strategies is crucial for predicting future responses to warming. Contrasting predictive frameworks explain how growth and other life history traits may respond to differing selective pressures across latitude. However, these frameworks have rarely been explored within the context of fluctuating environmental temperatures across longer (i.e., seasonal) time scales experienced in nature. Furthermore, consequences of growth differences for other aspects of fitness, including reproductive output, remain unclear. Here, we conducted a long-term (17-month) simulated reciprocal transplant experiment to examine local adaptation in two populations of the predatory marine snail Urosalpinx cinerea separated by 8.6{degrees} latitude (1000 km). We reared F1 offspring under two seasonally fluctuating temperature regimes ("warm" and "cold", simulating field thermal conditions experienced by low and high latitude populations, respectively), quantifying temporal patterns in growth, maturation, and reproductive output. We identified striking divergence in life-history strategies between populations in the warm regime, with offspring from the low latitude population achieving greater growth in their first year, and high reproductive output coupled with reduced growth in their second year. In contrast, the high latitude population grew slower in their first year, but eventually attained larger sizes in their second year, at the expense of reduced reproductive output. Responses were consistent with this in the cold regime, although growth and reproductive output was reduced in both populations. Our data provides support for adaptive divergence across latitude consistent with the Pace-of-Life hypothesis, with the low latitude population selected for a fast-paced life characterized by rapid development and early reproduction. In contrast, the high latitude population exhibited slower growth and delayed maturation. Our results highlight the potential limitations of short-term comparisons of growth without considering processes over longer time scales that may exhibit seasonal temperature variation and ontogenetic shifts in energy allocation and imply a radical reshaping of physiological performance and life history traits across populations under climate change.

ecology↗

bioRxiv2025

Fast and slow-paced reproductive life history across native and invasive populations of a predatory marine snail

Populations across a species range may be locally adapted, and failure to recognize this variation can lead to inaccurate predictions of their resilience or vulnerability to climate change. Because life history traits are directly linked to fitness, life history theory can serve as a useful framework for evaluating how populations within species may respond to rapid environmental change. However, relatively few studies quantify multiple life history traits and their tradeoffs across many populations, especially in marine taxa. Here, we used a 10-month laboratory experiment to quantify a suite of reproductive traits in populations spanning the strongest latitudinal temperature gradient in the worlds coastal oceans. We examined reproductive traits in wild-captured adults exposed to simulated local conditions for 7 native Atlantic and 4 introduced Pacific populations of the marine predatory gastropod Urosalpinx cinerea. Our data reveals that reproductive season length, the number of reproductive attempts, and annual fecundity unimodally peaked at mid-latitude populations, the species range-center. Introduced populations had comparably few spawning attempts and low fecundity despite a longer reproductive period in a less seasonal environment. We then conducted a second experiment quantifying thermal tolerance of developing embryos from 3 native populations, which revealed high sensitivity to temperature at early life stages but weak population differentiation. Taken together, our data reveal stark differences in reproduction that appear to reflect "fast" and "slow" paced lifestyles, which may maximize fitness by spreading the risk of reproductive failure over a single season or lifetime. Our results indicate that warm range-edge populations are highly vulnerable to warming, as low embryonic thermal tolerance may shorten the spawning season and warming is likely to reduce fecundity. This study highlights heterogeneity in life history traits across marine populations that may underlie differential vulnerability to climate warming. Open research statementAll data and code will be publicly available via Figshare and the NSF Biological and Chemical Oceanography Data Management Office (BCO-DMO).

ecology↗

bioRxiv2025

Haplotype-resolved reference genomes of the sea turtle clade unveil ultra-syntenic genomes with hotspots of divergence

BackgroundReference genomes for the entire sea turtle clade have the potential to reveal the genetic basis of traits driving the ecological and phenotypic diversity in these ancient and iconic marine species. Furthermore, these genomic resources can support conservation efforts and deepen our understanding of their unique evolution. ResultsWe present haplotype-resolved, chromosome-level reference genomes and high-quality gene annotations for five sea turtle species. This completes the catalog of reference genomes of the entire sea turtle clade when combined with our previously published reference genomes. Our analysis reveals remarkable genome synteny and collinearity across all species, despite the clades origin dating back more than 60 million years. Regions of high interspecific genetic distance and intraspecific genetic diversity are consistently clustered in genomic hotspots, which are enriched with genes coding for immune response proteins, olfactory receptors, zinc fingers, and G-protein-coupled receptors. These hotspot regions may offer insights into the genetic mechanisms driving phenotypic divergence among species, and represent areas of significant adaptive potential. Ancient demographic analysis revealed a synchronous population expansion among sea turtle species during the Pleistocene, with varying magnitudes of demographic change, likely shaped by their diverse ecological adaptations, and biogeographic contexts. ConclusionsOur work provides genomic resources for exploring genetic diversity, evolutionary adaptations, and demographic histories of sea turtles. We outline genomic regions with increased diversity, linked to immune response, sensory evolution, and adaptation to varying environments that have historically been subject to strong diversifying selection, and likely will underpin sea turtles responses to future environmental change. These reference genomes can assist conservation by providing insights into the demographic and evolutionary processes that sustain and threaten these iconic species.

genomics↗

bioRxiv2023

Accounting for population growth, intermittent breeding, and aging error in close-kin mark-recapture assessments

Obtaining robust estimates of population abundance is a central challenge hindering the conservation and management of many threatened and exploited species. Close-kin mark-recapture (CKMR) is a genetics-based approach that has strong potential to improve monitoring of data-limited species by enabling estimates of abundance, survival, and other parameters for populations that are challenging to assess. However, CKMR models have received limited sensitivity testing under realistic population dynamics and sampling scenarios, impeding application of the method in population monitoring programs and stock assessments. Here, we use individual-based simulation to examine how unmodeled population dynamics and aging uncertainty affect the accuracy and precision of CKMR parameter estimates under different sampling strategies. We then present adapted models that correct the biases that arise from model misspecification. Our results demonstrate that a simple base-case CKMR model produces robust estimates of population abundance with stable populations that breed annually; however, if a population trend or non-annual breeding dynamics are present, or if year-specific estimates of abundance are desired, a more complex CKMR model must be constructed. In addition, we show that CKMR can generate reliable abundance estimates for adults from a variety of sampling strategies, including juvenile-focused sampling where adults are never directly observed (and aging error is minimal). Finally, we apply a CKMR model that has been adapted for population growth and intermittent breeding to two decades of genetic data from juvenile lemon sharks (Negaprion brevirostris) in Bimini, Bahamas, to demonstrate how application of CKMR to samples drawn solely from juveniles can contribute to monitoring efforts for highly mobile populations. Overall, this study expands our understanding of the biological factors and sampling decisions that cause bias in CKMR models, identifies key areas for future inquiry, and provides recommendations that can aid biologists in planning and implementing an effective CKMR study, particularly for long-lived data-limited species.

ecology↗

bioRxiv2021

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all [~]70,000 extant vertebrate species.

genomics↗

bioRxiv2018

A Versatile Rapture (RAD-Capture) Platform for Genotyping Marine Turtles

Advances in high-throughput sequencing (HTS) technologies coupled with increased interdisciplinary collaboration is rapidly expanding capacity in the scope and scale of wildlife genetic studies. While existing HTS methods can be directly applied to address some evolutionary and ecological questions, certain research goals necessitate tailoring methods to specific study organisms, such as high-throughput genotyping of the same loci that are comparable over large spatial and temporal scales. These needs are particularly common for studies of highly mobile species of conservation concern like marine turtles, where life history traits, limited financial resources and other constraints require affordable, adaptable methods for HTS genotyping to meet a variety of study goals. Here, we present a versatile marine turtle HTS targeted enrichment platform adapted from the recently developed Rapture (RAD-Capture) method specifically designed to meet these research needs. Our results demonstrate consistent enrichment of targeted regions throughout the genome and discovery of candidate variants in all species examined for use in various conservation genetics applications. Accurate species identification confirmed the ability of our platform to genotype over 1,000 multiplexed samples, and identified areas for future methodological improvement such as optimization for low initial concentration samples. Finally, analyses within green turtles supported the ability of this platform to identify informative SNPs for stock structure, population assignment and other applications over a broad geographic range of interest to management. This platform provides an additional tool for marine turtle genetic studies and broadens capacity for future large-scale initiatives such as collaborative global marine turtle genetic databases.

genomics↗