Biology subjects

Cordero, S.

Publications and source records attributed to Cordero, S..

6 recordsLinked to original sources

bioRxiv2026

Decoupling environmental suitability from realized recruitment through ontogenetic environmental filtering in a long-lived Mediterranean palm species

Long-lived plants facing anthropogenic disturbance often exhibit recruitment failure despite persistent reproductive adults, generating extinction debt masked by longevity. However, whether adult presence reliably reflects environmental suitability for recruitment remains unclear. Here, we examine ontogenetic niche differentiation and its consequences for recruitment in Jubaea chilensis, an endangered long-lived Mediterranean palm with an aging population. We assigned individuals within the largest known population to four ontogenetic stages and characterized their environmental niches using climatic, edaphic, topographic, and vegetation variables. We then applied spatial and multivariate analyses, including Random Forest models to evaluate environmental segregation and identify predictors of seedling establishment. Age classes occupied significantly different environmental niches, with the greatest differentiation between seedlings and reproductive adults. Saplings and adult differentiation reflected mainly topographic variables at landscape scale, whereas seedling establishment was primarily predicted by microhabitat conditions (vegetation cover heterogeneity, east-facing slope orientation, and soil texture). This pattern is consistent with niche reconfiguring throughout the life cycle, suggesting that adult occurrence and recruitment suitability respond to distinct environmental conditions. Over one-fifth of sampled individuals occupied high-suitability sites without recruitment, suggesting that ontogenetic niche shifts are associated with a spatial decoupling between adult persistence and recruitment, consistent with demographic collapse independent of habitat degradation. This failure is likely mediated by insufficient effective seed dispersal, as the sole disperser (Octodon degus) preys on most seeds before dispersal. Conservation strategies based solely on adult distribution may therefore overestimate effective habitat and underestimate extinction risk in long-lived species.

ecology↗

bioRxiv2024

Goliath clades and in vivo tracking of clonal dynamics show three phases of UV-induced skin carcinogenesis

While the genetic paradigm of cancer etiology has proven powerful, it remains incomplete as evidenced by the widening spectrum of non-cancer cell-autonomous "hallmarks" of cancer. Studies have demonstrated the commonplace presence of high oncogenic mutational burdens in homeostatically-stable epithelia. Hence, the presence of driver mutations alone does not result in cancer. Here, we reveal additional forces governing the eco-evolutionary dynamics of carcinogenesis. Using a UV-driven mouse model of cutaneous squamous cell carcinoma, we tested our central hypothesis that cancer initiation occurs in three phases: 1) tissue disruption and the emergence of unusually large "goliath" clades (ecological driver), 2) clonal selection within a subset of these goliaths as evidenced by the presence of areas of unusually high local densities of cells (termed "micro-lumps") with higher mutational burdens (evolutionary driver), and 3) emergence of macroscopic lesions. We tracked these tissue level ecological and evolutionary drivers of cancer initiation via in-vivo serial imaging and 3-D reconstruction of fluorescently labeled keratinocyte clades, yielding 25,085 clade measurements from 14 mice over 3 months, and 14,525 clades from 4 of these mice over 6 months. While median and mean clade sizes differed little between UV and non-UV exposure (cc. 65,000 {micro}m3), our ecological survey revealed the emergence of large goliath clades (> cc. 4.2x106 {micro}m3), almost exclusively within UV-exposed skin. Goliath clades emerged by month 2, increased dramatically in number by months 3-4, and plateaued between months 5-6. Goliath clades arose as serpentine structures, intercalating between adjacent keratinocytes. Unexpectedly, targeted DNA sequencing revealed mutations with very low variant allele frequencies within clades, but substantial differences among clades, suggesting that positive selection for these mutations is superfluous to the development of goliaths early in carcinogenesis. scRNAseq analysis of both bulk skin and sorted clades revealed epidermal de-differentiation and immune suppression as early events. By month 7, mutational burdens were significantly larger in goliath clades, particularly for those with micro-lumps. Finally, lesions began to emerge between months 6 and 7, only in UV-exposed skin. To confirm that goliath clades are orders of magnitude more likely to spawn lesions, we randomly selected 21 goliath clades at months 6-7, prior to the time of the emergence of detectable lesions, and followed them over time. Remarkably, 2 of these developed into macroscopic lesions. Our adaptation of the Drake equation estimated the probability of this to be <10-6. Taken together, our results support the presence of three phases of cancer initiation, the earliest of which presage the acquisition of driver mutations and also explains why cancers are relatively rare in relation to the degree of somatic mosaicism present in UV-exposed skin.

cancer biology↗

bioRxiv2022

Modular automated microfluidic cell culture platform reduces glycolytic stress in cerebral cortex organoids

Organ-on-a-chip systems combine microfluidics, cell biology, and tissue engineering to culture 3D organ-specific in vitro models that recapitulate the biology and physiology of their in vivo counterparts. Here, we have developed a multiplex platform that automates the culture of individual organoids in isolated microenvironments at user-defined media flow rates. Programmable workflows allow the use of multiple reagent reservoirs that may be applied to direct differentiation, study temporal variables, and grow cultures long term. Novel techniques in polydimethylsiloxane (PDMS) chip fabrication are described here that enable features on the upper and lower planes of a single PDMS substrate. RNA sequencing (RNA-seq) analysis of automated cerebral cortex organoid cultures shows benefits in reducing glycolytic and endoplasmic reticulum stress compared to conventional in vitro cell cultures.

bioengineering↗

bioRxiv2020

The best bang for the bucks: rethinking global investment on biodiversity conservation

Biodiversity loss is a central issue in conservation biology, being protected areas the primary approach to stop biodiversity loss. However, education has been identified as an important factor in this regard. Based on a database of threatened species and socio-economic features for 138 countries, we tested whether more protected areas or more education investment are associated with a lower proportion of threatened species (for different groups of vertebrates and plants). We found that education investment was negatively associated with the proportion of threatened species in 2007 and 2017, as well as with their change rates. Conversely, the percentage of protected land was significant for reptiles, but show weak relationships with other groups. Our results suggest that only increasing protected areas will not stop or reduce biodiversity loss, as the context and peoples attitudes towards wildlife also play major roles here. Therefore, investing in education, in addition to protected areas, would have a positive effect missing to achieve effective species conservation actions worldwide.

ecology↗

bioRxiv2019

Quantifying shape, integration, and ecology in avian pedal claws: comparing geometric morphometric and traditional metric approaches

Terrestrial tetrapods use their claws to interact with their environments in a plethora of ways. Birds in particular have developed a diversity of claw shapes since they are not bound to terrestrial locomotion and have heterogeneous body masses ranging several orders of magnitude. Numerous previous studies have hypothesized a connection between pedal claw shape and ecological mode in birds, but have generated conflicting results, spanning from clear ecological groupings based on claw shape to a complete overlap of ecological modes. These studies have relied on traditional morphometric arc measurements of keratinous sheaths and have variably accounted for likely confounding factors such as body mass and phylogenetic relatedness. To better address the hypothesized relationship between ecology and claw shape in birds, 580 radiographs were collected allowing visualization of the bony core and keratinous sheath shape spanning 21 avian orders. A new method was used to quantify claw shape using geometric morphometrics and was compared to results using traditional arc measurements. Neither traditional nor geometric morphometrics are capable of significantly separating bird claws into coarse ecological categories after integrating body size and phylogenetic relatedness. Further, the bony claw core and keratinous sheath are significantly integrated with one another, suggesting that they function as a single unit. Therefore, it is likely possible to compare fossil bony cores with extant keratinous sheaths after applying corrections. Finally, traditional metrics and geometric morphometric shape are significantly, yet loosely correlated, and geometric morphometric data better distinguish ecological groups in morphospace than is possible with traditional metrics. Based on these results, future workers are encouraged to use geometric morphometric approaches to study claw geometry and account for confounding factors such as body size, phylogeny, and individual variation prior to predicting ecology in fossil taxa.

evolutionary biology↗

bioRxiv2019

Keeping salamanders off the streets: An assessment of one of the first amphibian road tunnels in the United States 30 years after installation

Culverts are often installed under busy roads to help a variety of animals, from small frogs to bears, safely cross roads that bisect their habitats. One of the first roadway culvert systems designed specifically for amphibian use in the United States was installed along Henry Street in Amherst, Massachusetts in 1987 to protect spotted salamanders (Ambystoma maculatum). These salamanders cross Henry Street during their annual migration to their breeding pools. In recent years, anecdotal evidence from volunteers monitoring the site suggested that salamanders were no longer using the tunnels. To evaluate this concern we conducted salamander counts in 2016, 2017, and 2018 to quantify tunnel use. In 2016, only 11% of observed salamanders used the tunnels- a substantial decrease from 68% in 1988, one year after their installation, when the tunnels were last evaluated. Subsequently, we implemented two tunnel modifications in an effort to increase tunnel usage above the established 2016 baseline. Unfortunately, neither retrofit was successful. Previous studies have demonstrated that salamanders prefer minimum tunnel apertures of >0.4 m, so it is likely that the 0.2 m apertures here are inadequate. This may create differential light and humidity inside and outside the tunnels that is recognized by the salamanders. While many studies have evaluated amphibian tunnel use in lab and field settings, ours is one of the first studies to have examined tunnel usage data long after initial installation. These long-term data are critical for evaluating what factors are necessary for maintaining tunnels over decades-long time scales.

ecology↗