Data from: Maladaptation beyond a geographic range limit driven by antagonistic and mutualistic biotic interactions across an abiotic gradient
Contributors: Benning, John William, Moeller, David
... Species’ geographic range limits often result from maladaptation to the novel environments beyond the range margin. However, we rarely know which aspects of the n-dimensional environment are driving this maladaptation. Especially of interest is the influence of abiotic versus biotic factors in delimiting species’ distributions. We conducted a two-year reciprocal transplant experiment involving manipulations of the biotic environment to explore how spatio-temporal gradients in precipitation, fatal mammalian herbivory, and pollination affected lifetime fitness within and beyond the range of the California annual plant, Clarkia xantiana ssp. xantiana. In the first, drier year of the experiment, fitness outside the range edge was limited mainly by low precipitation, and there was some evidence for local adaptation within the range. In the second, wetter year, we did not observe abiotic limitations to plant fitness outside the range; instead biotic interactions, especially herbivory, limited fitness outside the range. Together, protection from herbivory and supplementation of pollen resulted in 3-7 fold increases in lifetime fitness outside the range margin in the abiotically benign year. Overall, our work demonstrates the importance of biotic interactions, particularly as they interact with the abiotic environment, in determining fitness beyond geographic range boundaries.
Contributors: Godoy, Pedro L
... Crocodylomorpha, which includes living crocodylians and their extinct relatives, has a rich fossil record, extending back for more than 200 million years. Unlike modern semi-aquatic crocodylians, extinct crocodylomorphs exhibited more varied lifestyles, ranging from marine to fully terrestrial forms. This ecological diversity was mirrored by a remarkable morphological disparity, particularly in terms of cranial morphology, which seems to be closely associated with ecological roles in the group. Here, I use geometric morphometrics to comprehensively investigate cranial shape variation and disparity in Crocodylomorpha. I quantitatively assess the relationship between cranial shape and ecology (i.e. terrestrial, aquatic, and semi-aquatic lifestyles), as well as possible allometric shape changes. I also characterise patterns of cranial shape evolution and identify regime shifts. I found a strong link between shape and size, and a significant influence of ecology on the observed shape variation. Terrestrial taxa, particularly notosuchians, have significantly higher disparity, and shifts to more longirostrine regimes are associated with large-bodied aquatic or semi-aquatic species. This demonstrates an intricate relationship between cranial shape, body size and lifestyle in crocodylomorph evolutionary history. Additionally, disparity-through-time analyses were highly sensitive to different phylogenetic hypotheses, suggesting the description of overall patterns among distinct trees. For crocodylomorphs, most results agree in an early peak during the Early Jurassic and another in the middle of the Cretaceous, followed by nearly continuous decline until today. Since only crown-group members survived through the Cenozoic, this decrease in disparity was likely the result of habitat loss, which narrowed down the range of crocodylomorph lifestyles.
Data from: Sauropod teeth from the Middle Jurassic of Madagascar, and the oldest record of Titanosauriformes
Contributors: Bindellini, Gabriele, Dal Sasso, Cristiano
... Here we describe 31 fossil teeth, deposited in the paleontological collections of the Museo di Storia Naturale di Milano (MSNM), that come from the inland portion of the Mahajanga Basin, NW Madagascar, namely from the Sakahara Formation (classically known as Isalo IIIb subunit), which is dated back to the Middle Jurassic Bathonian stage. Based on detailed morphological characters, the eight morphotypes recognised herein are tentatively referred to four sauropod taxa: Archaeodontosaurus descouensi, ‘Bothriospondylus madagascariensis’, Lapparentosaurus madagascariensis, and an indeterminate specialised eusauropod, which may represent a new species, and the first evidence of a Bathonian diplodocoid in Madagascar. The identification of the teeth is corroborated by comparative examination of morphometric data. In this paper we provide evidence that Titanosauriformes were present in the Bathonian, on the basis of seven specimens referable to this clade. We also discuss in detail some dental characters that support the existence of a clear niche partitioning between the above mentioned taxa, that co–existed in the Malagasy Middle Jurassic terrestrial ecosystem. We finally hypothesise, for the first time, a direct correlation between the pattern drawn on the tooth crown by the enamel wrinkles and the feeding ecology of sauropod dinosaurs. The enamel wrinkles likely played a structural function: coarse wrinkles were associated to a diet composed mainly by hard foodstuff, whereas fainter wrinkles, which appeared in more derived morphologies, were associated to a diet composed by softer foodstuff.
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Contributors: Sinn, Brandon T, Barrett, Craig F
... The mitochondrial genomes (mitogenomes) of plants are known to incorporate and accumulate DNA from intra- and extracellular donors. Despite the intimate relationships formed between flowing plants (angiosperms) and fungi, lengthy fungal-like sequence has not been identified in angiosperm mitogenomes to date. Here we present multiple lines of evidence documenting horizontal gene transfer (HGT) between the mitogenomes of fungi and the ancestors of the orchids, plants that are obligate parasites of fungi during their early development. We show that the ancestor of the orchids acquired an approximately 270 bp fungal mitogenomic region containing three transfer RNA genes. We propose that the short HGT was later replaced by a second HGT event transferring more than 8 kb and 14 genes from a fungal mitogenome to that of the ancestor of the largest orchid subfamily, Epidendroideae. Our results represent the first evidence of genomic-scale HGT between fungal and angiosperm mitogenomes and demonstrate that the length intergenic spacer regions of angiosperm mitogenomes can effectively fossilize the genomic remains of ancient, non-plant organisms.
Data from: Evidence of rapid adaptive trait change to local salinity in the sperm of an invasive fish
Contributors: Green, Leon, Havenhand, Jonathan, Kvarnemo, Charlotta
... Invasive species may quickly colonize novel environments, which could be attributed to both phenotypic plasticity and an ability to locally adapt. Reproductive traits are expected to be under strong selection when the new environment limits reproductive success of the invading species. This may be especially important for external fertilizers, which release sperm and eggs into the new environment. Despite adult tolerance to high salinity, the invasive fish Neogobius melanostomus (round goby) is absent from fully marine regions of the Baltic Sea, raising the possibility that its distribution is limited by tolerance during earlier life-stages. Here, we investigate the hypothesis that the spread of N. melanostomus is limited by sperm function in novel salinities. We sampled sperm from two invasion fronts with higher and lower salinities in the Baltic Sea and tested them across a range of salinity levels. We found that sperm velocity and percentage of motile sperm declined in salinity levels higher and lower than those currently experienced by the Baltic Sea populations, with different performance curves for the two fronts. Sperm velocity also peaked closer to the home salinity conditions in each respective invasion front, with older localities showing an increased fit to local conditions. By calculating how the sperm velocity has changed over generations, we show this phenotypic shift to be in the range of other fish species under strong selection, indicating on-going local adaptation or epigenetic acclimation to their novel environment. These results show that while immigrant reproductive dysfunction appears to at least partly limit the distribution of invasive N. melanostomus in the Baltic Sea, local adaptation to novel environments could enable future spread beyond their current boundaries.
Data from: Quartet-based computations of internode certainty provide robust measures of phylogenetic incongruence
Contributors: Zhou, Xiaofan, Lutteropp, Sarah, Czech, Lucas, Stamatakis, Alexandros, von Looz, Moritz, Rokas, Antonis
... Incongruence, or topological conflict, is prevalent in genome-scale data sets. Internode Certainty (IC) and related measures were recently introduced to explicitly quantify the level of incongruence of a given internal branch among a set of phylogenetic trees and complement regular branch support measures (e.g., bootstrap, posterior probability) that instead assess the statistical confidence of inference. Since most phylogenomic studies contain data partitions (e.g., genes) with missing taxa and IC scores stem from the frequencies of bipartitions (or splits) on a set of trees, IC score calculation typically requires adjusting the frequencies of bipartitions from these partial gene trees. However, when the proportion of missing taxa is high, the scores yielded by current approaches that adjust bipartition frequencies in partial gene trees differ substantially from each other and tend to be overestimates. To overcome these issues, we developed three new IC measures based on the frequencies of quartets, which naturally apply to both complete and partial trees. Comparison of our new quartet-based measures to previous bipartition-based measures on simulated data shows that: 1) on complete data sets, both quartet-based and bipartition-based measures yield very similar IC scores; 2) IC scores of quartet-based measures on a given data set with and without missing taxa are more similar than the scores of bipartition-based measures; and 3) quartet-based measures are more robust to the absence of phylogenetic signal and errors in phylogenetic inference than bipartition-based measures. Additionally, the analysis of an empirical mammalian phylogenomic data set using our quartet-based measures reveals the presence of substantial levels of incongruence for numerous internal branches. An efficient open-source implementation of these quartet-based measures is freely available in the program QuartetScores (https://github.com/lutteropp/QuartetScores).
Data from: Disruption of the ascending arousal network in acute traumatic disorders of consciousness
Contributors: Snider, Samuel B., Bodien, Yelena G., Bianciardi, Marta, Brown, Emery N., Wu, Ona, Edlow, Brian L.
... Objective: To determine whether ascending arousal network (AAN) connectivity is reduced in patients presenting with traumatic coma. Methods: We performed high angular resolution diffusion imaging (HARDI) in 16 patients with acute severe traumatic brain injury who were comatose on admission and in 16 matched controls. We used probabilistic tractography to measure the connectivity probability (CP) of AAN axonal pathways linking the brainstem tegmentum to the hypothalamus, thalamus and basal forebrain. To assess the spatial specificity of CP differences between patients and controls, we also measured CP within four subcortical pathways outside the AAN. Results: Compared to controls, patients showed a reduction in AAN pathways connecting the brainstem tegmentum to a region of interest encompassing the hypothalamus, thalamus, and basal forebrain. Examining each pathway individually, brainstem-hypothalamus and brainstem-thalamus CPs, but not brainstem-forebrain CP, were significantly reduced in patients. Only one subcortical pathway outside the AAN showed reduced CP in patients. Conclusions: We provide initial evidence for the reduced integrity of axonal pathways linking the brainstem tegmentum to the hypothalamus and thalamus in patients presenting with traumatic coma. Our findings support current conceptual models of coma as being caused by subcortical AAN injury. AAN connectivity mapping provides an opportunity to advance the study of human coma and consciousness.
Data from: Hierarchical controls on extinction selectivity across the diplobathrid crinoid phylogeny
Contributors: Cole, Selina
... Identifying correlates of extinction risk is important for understanding the underlying mechanisms driving differential rates of extinction and variability in the temporal durations of taxa. Increasingly, it is recognized that the effects of multiple, potentially interacting variables and phylogenetic relationships should be incorporated when studying extinction selectivity to account for covariation of traits and shared evolutionary history. Here, I explore a variety of biological and ecological controls on genus longevity in the global fossil record of diplobathrid crinoids by analyzing the combined effects of species richness, habitat preference, body size, filtration fan density, and food size selectivity. I employ a suite of taxic and phylogenetic approaches to (1) quantitatively compare and rank the relative effects of multiple factors on taxonomic longevity, and (2) determine how phylogenetic comparative approaches alter interpretations of extinction selectivity. I find controls on diplobathrid genus duration are hierarchically structured, where species richness is the primary predictor of duration, habitat is the secondary predictor, and a combination of ecological and biological traits are tertiary controls. Ecology plays an important but complex role in the generation of crinoid macroevolutionary patterns. Notably, tolerance of environmental heterogeneity promotes increased genus duration across diplobathrid crinoids, and the effects of traits related to feeding ecology vary depending on habitat lithology. Finally, I find accounting for phylogeny does not consistently decrease the significance of correlations between traits and genus duration, as is commonly expected. Instead, the strength of relationships between traits and duration may increase, decrease, or remain statistically similar, and both the magnitude and direction of these shifts are generally unpredictable. However, traits with strong correlations and/or moderately large effect sizes (Cohen’s f2 > 0.15) under taxic approaches tend to remain qualitatively unchanged under phylogenetic approaches.
Contributors: Lindenmayer, David, Blanchard, Wade, Blair, David, Westgate, Martin, Scheele, Ben
... Forests globally are subject to multiple disturbances such as logging and fire that create complex temporal variation in spatial patterns of forest cover and stand age. However, investigations that quantify temporal changes in biodiversity in response to multiple forms of disturbance in space and time are relatively uncommon. Over a 10-year period, we investigated the response of bird species to spatio-temporal changes in cover associated with logging and wildfire in the Mountain Ash (Eucalyptus regnans) forests of south-eastern Australia. Specifically, we examined how bird occurrence changed with shifts in the proportion of area burnt or logged in a 4.5km radius surrounding each of 87 field survey sites. Overall species richness was greatest in older forest patches. Bird species richness declined as the amount of fire around each site increased. At the individual species level, most species were more likely to be found in old growth than younger forest. Twenty-five of 36 bird species we modeled, exhibited a negative response to the amount of fire in the surrounding landscape (while two species responded positively to fire). Only nine species exhibited signs of post-fire recovery. Ten species were more likely to be recorded as the proportion of logged forest surrounding a site increased, suggesting a possible “concentration effect” with displaced birds moving into unlogged areas following harvesting of adjacent areas. In contrast to predictions from the disturbance-congruence hypothesis, no bird species exhibited similar responses to fire and logging in the landscape surrounding our sites. Similarly, no bird life history traits were associated with burned or logged forest, although insectivorous birds were more likely to be found in old growth forests and increased over time. Birds in Mountain Ash forests are strongly associated with old growth stands and exhibit complex, time-dependent and species-specific responses to landscape disturbance. Despite logging and fire both being high-severity perturbations, species responses to one kind of landscape-scale disturbance are not readily predictable based on an understanding of the responses to another kind of (albeit superficially similar) disturbance.
Data from: New cranial fossils of the Jurassic turtle Neusticemys neuquina and phylogenetic relationships of the only thalassochelydian known from the Eastern Pacific
Contributors: González Ruiz, Pablo, de la Fuente, Marcelo, Fernandndez, Marta
... Neusticemys neuquina is a turtle from the Upper Jurassic of the Neuquén Basin, Patagonia, Argentina. Here we describe in detail a new skull, lower jaw, and a vertebra, utilizing both traditional anatomical description and computed tomography (CT). New diagnostic cranial characters of Ne. neuquina are: a round depression on the ventral surface of the basisphenoid, a relatively larger oval foramen nervi trigemini and reduced and steepened triturating surfaces on both the maxilla and dentary. The new morphological information presented in this study was included in a phylogenetic analysis, the primary result of which was recovery of Ne. neuquina within Thalassochelydia. Characters recognized as synapomorphies of this clade include (1) anterolateral recess of the anterior surface of the quadrate positioned lateral to the processus trochlearis oticum, (2) presence of a fossa on the supraoccipital-opisthotic-exoccipital contact area, (3) foramina anterius caroticus cerebralis located close together but independently perforating the basisphenoid, and (4) presence of the splenial in the mandible. Two contrasting dispersal scenarios may explain how this species of Thalassochelydia can be found outside of Europe. The presence of Ne. neuquina in the Neuquén Basin could be the consequence of an early dispersion event, for which we lack intermediate forms, or it may be the result of a later event once the clade was already established in Europe.