Macroevolution of desiccation‐related morphology in plethodontid salamanders as inferred from a novel surface area to volume ratio estimation approach

Evolutionary biologists have long been interested in the macroevolutionary consequences of various selection pressures, yet physiological responses to selection across deep time are not well understood. In this paper, we investigate how a physiologically-relevant morphological trait, surface area to volume ratio (SA:V) of lungless salamanders, has evolved across broad regional and climatic variation. SA:V directly impacts an organisms’ ability to retain water, leading to the expectation that smaller SA:Vs would be advantageous in arid, water-limited environments. To explore the macroevolutionary patterns of SA:V, we first develop an accurate method for estimating SA:V from linear measurements. Next, we investigate the macroevolutionary patterns of SA:V across 257 salamander species, revealing that higher SA:Vs phylogenetically correlate with warmer, wetter climates. We also observe higher SA:V disparity and rate of evolution in tropical species, mirrored by higher climatic disparity in available and occupied tropical habitats. Taken together, these results suggest that the tropics have provided a wider range of warmer, wetter climates for salamanders to exploit, thereby relaxing desiccation pressures on SA:V. Overall, this paper provides an accurate, efficient method for quantifying salamander SA:V, allowing us to demonstrate the power of physiological selection pressures in influencing the macroevolution of morphology

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements

Assessing environmental variables across Plethodontid salamanders

The majority of the 700 extant salamander species inhabit moist environments, such as under rocks, logs, and in leaf litter on the forest floor, or in aquatic habitats. Yet surprisingly, nearly 100 species have adopted an arboreal lifestyle. Life in trees can be ecologically challenging due to increased oxygen demands, mechanics of climbing, and the more variable temperature and humidity found in the canopy compared to on or under the forest floor. These difficulties are particularly salient for salamanders of the family Plethodontidae, as they lack lungs and are completely dependent upon cutaneous respiration. Yet, we have found that plethodontids have transitioned from terrestrial life to arboreal life in at least six independent lineages. Although morphology has responded to these changes in microhabitat, a distinct arboreal phenotype does not exist as it does in other vertebrate lineages It must be so that other influences are in play to explain the unequal distribution of diversity across North, Central, and South America, especially in the tropics. We suggest that climate may facilitate large clade dispersal and may explain some of the variation in terms of microhabitat use. We use ecological niche modeling to investigate specifically (1) if arboreal species live in different climatic niches compared to terrestrial species and (2) if these climatic variables sufficiently explain the distribution of arboreality across North America informing our larger question of how climate shapes microhabitat use in Plethodontid salamanders

Assessing environmental variables across Plethodontid salamanders

The majority of the 700 extant salamander species inhabit moist environments, such as under rocks, logs, and in leaf litter on the forest floor, or in aquatic habitats. Yet surprisingly, nearly 100 species have adopted an arboreal lifestyle. Life in trees can be ecologically challenging due to increased oxygen demands, mechanics of climbing, and the more variable temperature and humidity found in the canopy compared to on or under the forest floor. These difficulties are particularly salient for salamanders of the family Plethodontidae, as they lack lungs and are completely dependent upon cutaneous respiration. Yet, we have found that plethodontids have transitioned from terrestrial life to arboreal life in at least six independent lineages. Although morphology has responded to these changes in microhabitat, a distinct arboreal phenotype does not exist as it does in other vertebrate lineages It must be so that other influences are in play to explain the unequal distribution of diversity across North, Central, and South America, especially in the tropics. We suggest that climate may facilitate large clade dispersal and may explain some of the variation in terms of microhabitat use. We use ecological niche modeling to investigate specifically (1) if arboreal species live in different climatic niches compared to terrestrial species and (2) if these climatic variables sufficiently explain the distribution of arboreality across North America informing our larger question of how climate shapes microhabitat use in Plethodontid salamanders.</p

Is salamander arboreality limited by broad-scale climatic conditions?

Identifying the historical processes that drive microhabitat transitions across deep time is of great interest to evolutionary biologists. Morphological variation can often reveal such mechanisms, but in clades with high microhabitat diversity and no concomitant morphological specialization, the factors influencing animal transitions across microhabitats are more difficult to identify. Lungless salamanders (family: Plethodontidae) have transitioned into and out of the arboreal microhabitat many times throughout their evolutionary history without substantial morphological specialization. In this study, we explore the relationship between microhabitat use and broad-scale climatic patterns across species’ ranges to test the role of climate in determining the availability of the arboreal microhabitat. Using phylogenetic comparative methods, we reveal that arboreal species live in warmer, lower elevation regions than terrestrial species. We also employ ecological niche modeling as a complementary approach, quantifying species-level pairwise comparisons of niche overlap. The results of this approach demonstrate that arboreal species on average display more niche overlap with other arboreal species than with terrestrial species after accounting for non-independence of niche model pairs caused by geographic and phylogenetic distances. Our results suggest that occupation of the arboreal microhabitat by salamanders may only be possible in sufficiently warm, low elevation conditions. More broadly, this study indicates that the impact of micro-environmental conditions on temporary microhabitat use, as demonstrated by small-scale ecological studies, may scale up dramatically to shape macroevolutionary patterns.This article is published as Baken EK, Mellenthin LE, Adams DC (2021) Is salamander arboreality limited by broadscale climatic conditions? PLoS ONE 16(8):e0255393. https://doi.org/10.1371/journal.pone.0255393. Posted with permission. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Macroevolution of desiccation‐related morphology in plethodontid salamanders as inferred from a novel surface area to volume ratio estimation approach

Evolutionary biologists have long been interested in the macroevolutionary consequences of various selection pressures, yet physiological responses to selection across deep time are not well understood. In this paper, we investigate how a physiologically-relevant morphological trait, surface area to volume ratio (SA:V) of lungless salamanders, has evolved across broad regional and climatic variation. SA:V directly impacts an organisms’ ability to retain water, leading to the expectation that smaller SA:Vs would be advantageous in arid, water-limited environments. To explore the macroevolutionary patterns of SA:V, we first develop an accurate method for estimating SA:V from linear measurements. Next, we investigate the macroevolutionary patterns of SA:V across 257 salamander species, revealing that higher SA:Vs phylogenetically correlate with warmer, wetter climates. We also observe higher SA:V disparity and rate of evolution in tropical species, mirrored by higher climatic disparity in available and occupied tropical habitats. Taken together, these results suggest that the tropics have provided a wider range of warmer, wetter climates for salamanders to exploit, thereby relaxing desiccation pressures on SA:V. Overall, this paper provides an accurate, efficient method for quantifying salamander SA:V, allowing us to demonstrate the power of physiological selection pressures in influencing the macroevolution of morphology.This is a manuscript of an article published as Baken, Erica K., Lauren E. Mellenthin, and Dean C. Adams. "Macroevolution of desiccation‐related morphology in plethodontid salamanders as inferred from a novel surface area to volume ratio estimation approach." Evolution (2019). doi: 10.1111/evo.13898. Posted with permission.</p

Data from: Genomic signatures of convergent shifts to plunge-diving behavior in birds

Understanding the genetic basis of convergence at broad phylogenetic scales remains a key challenge in biology. Kingfishers (Aves: Alcedinidae) are a cosmopolitan avian radiation with diverse colors, diets, and feeding behaviors—including the archetypal plunge-dive into water. Transitioning from air to water poses major sensory and locomotor challenges that might affect the evolution of both sensory genes and morphological structures involved in these functions. Kingfishers therefore offer a powerful opportunity to explore the effects of convergent behaviors on the evolution of genomes and phenotypes, as well as direct comparisons between continental and island lineages. Here, we use whole-genome sequencing of 31 diverse kingfisher species to identify the genomic signatures associated with convergent feeding behaviors. We show that species with smaller ranges (i.e., on islands) have experienced stronger demographic fluctuations than those on continents, and that these differences have influenced the dynamics of molecular evolution. Comparative genomic analyses reveal positive selection and genomic convergence in brain and dietary genes in plunge-divers. These findings enhance our understanding of the connections between genotype and phenotype in a diverse avian radiation.Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: EP 2112468Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: EP 2112467Funding provided by: National Science FoundationCrossref Funder Registry ID: http://dx.doi.org/10.13039/100000001Award Number: DEB 1557051Funding provided by: Iridian Genomes*Crossref Funder Registry ID: Award Number: IRGEN_RG_2021-134

Video S1 from Rheology of marine sponges reveals anisotropic mechanics and tuned dynamics

Time-lapse video of different sponge species reacting to 1 mL of commercial bleach solution. The specimens in each well are identied in Fig. S6. Note the disparate chemistries

Supplementary Information from Rheology of marine sponges reveals anisotropic mechanics and tuned dynamics

Sponges are animals that inhabit many aquatic environments while filtering small particles and ejecting metabolic wastes. They are composed of cells in a bulk extracellular matrix, often with an embedded scaffolding of stiff, siliceous spicules. We hypothesize that the mechanical response of this heterogeneous tissue to hydrodynamic flow influences cell proliferation in a manner that generates the body of a sponge. Towards a more complete picture of the emergence of sponge morphology, we dissected a set of species and subjected discs of living tissue to physiological shear and uniaxial deformations on a rheometer. Various species exhibited rheological properties such as anisotropic elasticity, shear softening and compression stiffening, negative normal stress, and non-monotonic dissipation as a function of both shear strain and frequency. Erect sponges possessed aligned, spicule-reinforced fibres which endowed three times greater stiffness axially compared with orthogonally. By contrast, tissue taken from shorter sponges was more isotropic but time-dependent, suggesting higher flow sensitivity in these compared with erect forms. We explore ecological and physiological implications of our results and speculate about flow-induced mechanical signalling in sponge cells

Video S3 from Rheology of marine sponges reveals anisotropic mechanics and tuned dynamics

Video of semi-dry compression (ε >−50% at end) of an un-identied sponge collected from Pompano Beach, FL. Contraction of the material upon compression confirms that negative values of νij can be directly observed in these animals, supporting the conclusion that some sponge species are likely auxetic