Expansion and evolution of the R programming language.

Languages change over time, driven by creation of new words and cultural pressure to optimize communication. Programming languages resemble written language but communicate primarily with computer hardware rather than a human audience. I tested whether there were detectable changes over time in use of R, a mature, open-source programming language used for scientific computing. Across 393 142 GitHub repositories published between 2014 and 2021, I extracted 143 409 288 R functions, programming 'verbs', pairing linguistic and ecological analyses to detect change to diversity and composition of functions used over time. I found the number of R functions in use increased and underwent substantial change, driven primarily by the popularity of the 'tidyverse' collection of community-written extensions. I provide evidence that users can change the nature of programming languages, with patterns that match known processes from natural languages and genetic evolution. In R, there appear to be selective pressures for increased analytic complexity and R functions in decline that are not yet extinct (extinction debts). R's evolution towards the tidyverse may also represent the start of a division into two distinct dialects, which may impact the readability and continuity of analytic and scientific inquiries codified in R, as well as the language's future.

Sound garden: How snakes respond to airborne and groundborne sounds.

Evidence suggests that snakes can hear, but how snakes naturally respond to sound is still unclear. We conducted 304 controlled experiment trials on 19 snakes across five genera in a sound-proof room (4.9 x 4.9 m) at 27ºC, observing the effects of three sounds on individual snake behavior, compared to controls. We quantified eight snake behaviors (body movement, body freezing, head-flicks, tongue-flicks, hissing, periscoping, head fixation, lower jaw drop) in response to three sounds, which were filtered pink-noise within the following frequency ranges: 0-150Hz (sound 1, which produced ground vibrations, as measured by an accelerometer), 150-300Hz (sound 2, which did not produced ground vibrations), 300-450Hz (sound 3, which did not produced ground vibrations). All snake responses were strongly genus dependent. Only one genus (Aspidites, Woma Pythons) significantly increased their probability of movement in response to sound, but three other genera (Acanthophis (Death Adders), Oxyuranus (Taipans), and Pseudonaja (Brown Snakes)) were more likely to move away from sound, signaling potential avoidance behavior. Taipans significantly increased their likelihood of displaying defensive and cautious behaviors in response to sound, but three of the five genera exhibited significantly different types of behaviors in sound trials compared to the control. Our results highlight potential heritable behavioral responses of snakes to sound, clustered within genera. Our study illustrates the behavioral variability among different snake genera, and across sound frequencies, which contributes to our limited understanding of hearing and behavior in snakes.

Emergence patterns of locally novel plant communities driven by past climate change and modern anthropogenic impacts.

Anthropogenic disturbance and climate change can result in dramatic increases in the emergence of new, ecologically novel, communities of organisms. We used a standardised framework to detect local novel communities in 2135 pollen time series over the last 25,000 years. Eight thousand years of post-glacial warming coincided with a threefold increase in local novel community emergence relative to glacial estimates. Novel communities emerged predominantly at high latitudes and were linked to global and local temperature change across multi-millennial time intervals. In contrast, emergence of locally novel communities in the last 200 years, although already on par with glacial retreat estimates, occurred at midlatitudes and near high human population densities. Anthropogenic warming does not appear to be strongly associated with modern local novel communities, but may drive widespread emergence in the future, with legacy effects for millennia after warming abates.

Drivers of Acacia and Eucalyptus growth rate differ in strength and direction in restoration plantings across Australia.

Functional traits are proxies for a species' ecology and physiology and are often correlated with plant vital rates. As such they have the potential to guide species selection for restoration projects. However, predictive trait-based models often only explain a small proportion of plant performance, suggesting that commonly measured traits do not capture all important ecological differences between species. Some residual variation in vital rates may be evolutionarily conserved and captured using taxonomic groupings alongside common functional traits. We tested this hypothesis using growth rate data for 17,299 trees and shrubs from 80 species of Eucalyptus and 43 species of Acacia, two hyper-diverse and co-occurring genera, collected from 497 neighborhood plots in 137 Australian mixed-species revegetation plantings. We modeled relative growth rates of individual plants as a function of environmental conditions, species-mean functional traits, and neighbor density and diversity, across a moisture availability gradient. We then assessed whether the strength and direction of these relationships differed between the two genera. We found that the inclusion of genus-specific relationships offered a significant but modest improvement to model fit (1.6%-1.7% greater R2 than simpler models). More importantly, almost all correlates of growth rate differed between Eucalyptus and Acacia in strength, direction, or how they changed along the moisture gradient. These differences mapped onto physiological differences between the genera that were not captured solely by measured functional traits. Our findings suggest taxonomic groupings can capture or mediate variation in plant performance missed by common functional traits. The inclusion of taxonomy can provide a more nuanced understanding of how functional traits interact with abiotic and biotic conditions to drive plant performance, which may be important for constructing trait-based frameworks to improve restoration outcomes.

Reef accumulation is decoupled from recent degradation in the central and southern Red Sea.

Reefs are biogenic structures that result in three-dimensional accumulations of calcium carbonate. Over geological timescales, a positive balance between the production and accumulation of calcium carbonate versus erosional and off-reef transport processes maintains positive net accretion on reefs. Yet, how ecological processes occurring over decadal timescales translate to the accumulation of geological structures is poorly understood, in part due to a lack of studies with detailed time-constrained chronologies of reef accretion over decades to centuries. Here, we combined ecological surveys of living reefs with palaeoecological reconstructions and high-precision radiometric (U-Th) age-dating of fossil reefs represented in both reef sediment cores and surficial dead in situ corals, to reconstruct the history of community composition and carbonate accumulation across the central and southern Saudi Arabian Red Sea throughout the late Holocene. We found that reefs were primarily comprised of thermally tolerant massive Porites colonies, creating a consolidated coral framework, with unconsolidated branching coral rubble accumulating among massive corals on shallow (5-8 m depth) exposed (windward), and gently sloping reef slopes. These unconsolidated reef rubble fields were formed primarily from ex situ Acropora and Pocillopora coral fragments, infilled post deposition within a sedimentary matrix. Bayesian age-depth models revealed a process of punctuated deposition of post-mortem coral fragments transported from adjacent reef environments. That a large portion of Saudi Arabian Red Sea reef slopes is driven by allochthonous deposition (transportation) has important implications for modeling carbonate budgets and reef growth. In addition, a multi-decadal lag exists between the time of death for branching in situ coral and incorporation into the unconsolidated reef rubble. This indicates that recent climate related degradation in the 21st century has not had an immediately negative effect on reef building processes affecting a large portion of the reef area in the Saudi Arabian Red Sea.

Increased extinction in the emergence of novel ecological communities.

Environmental change is transforming ecological assemblages into new configurations, resulting in novel communities. We developed a robust methodology to detect novel communities, examine patterns of emergence, and quantify probabilities of local demographic turnover in transitions to and from novel communities. Using a global dataset of Cenozoic marine plankton communities, we found that the probability of local extinction, origination, and emigration during transitions to a novel community increased two to four times that of background community changes. Although rare, novel communities were five times more likely than chance to shift into another novel state. For marine plankton communities at a 100,000-year time grain, novel communities were sensitive to further extinctions and substantial community change.

Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA.

Marine environments face acute pressures from human impacts, often resulting in substantial changes in community structure. On the inshore Great Barrier Reef (GBR), palaeoecological studies show the collapse of the previously dominant coral Acropora from the impacts of degraded water quality associated with European colonization. Even more dramatic impacts can result in the replacement of corals by fleshy macroalgae on modern reefs, but their past distribution is unknown because they leave no fossil record. Here, we apply DNA metabarcoding and high-throughput sequencing of the 18S rDNA gene on palaeoenvironmental DNA (aeDNA) derived from sediment cores at two sites on Pandora Reef (GBR), to enhance palaeoecological studies by incorporating key soft-bodied taxa, including macroalgae. We compared temporal trends in this aeDNA record with those of coral genera derived from macrofossils. Multivariate analysis of 12 eukaryotic groups from the aeDNA community showed wide variability over the past 750 years. The occurrence of brown macroalgae was negatively correlated only with the dominant coral at both sites. The occurrence of coralline and green macroalgae was positively correlated with only the dominant coral at one of the sites, where we also observed a significant association between the whole coral community and the occurrence of each of the three macroalgae groups. Our results demonstrate that reef sediments can provide a valuable archive for understanding the past distribution and occurrence of important soft-bodied reef dwellers. Combining information from fossils and aeDNA provides an enhanced understanding of temporal changes of reefs ecosystems at decadal to millennial timescales.