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Aim: China’s Grain for Green Program (GFGP) is the largest reforestation program in the world and has been operating since 1999. The GFGP has promoted the establishment of tree plantations over the restoration of diverse native forests. In a previous study, we showed that native forests support higher species richness and abundance of birds and bees than GFGP plantations and that mixed-species GFGP plantations support a higher level of bird diversity than other GFGP monocultures. Here, we use metabarcoding of arthropod diversity to test the generality of these results. Location: Sichuan, China Methods: We sampled arthropod communities using pan traps in the land-cover types concerned under the GFGP. These land-use types include croplands, native forests, and the dominant GFGP reforestation outcomes: monoculture and mixed-species plantations. We used COI-amplicon sequencing (‘metabarcoding’) of the arthropod samples to quantify and assess the arthropod community profiles associated with each land-cover type. Results: Native forests support the highest levels of arthropod species diversity, followed by mixed-species plantations, followed by bamboo and other monocultures. Also, the arthropod community in native forests shares more species with mixed-species plantations than it does with any of the monocultures. Together, these results broadly corroborate our previous conclusions on birds and bees but show a higher arthropod biodiversity value of mixed-species plantations than previously indicated by bees alone. Main conclusion: In our previous study, we recommended that GFGP should prioritize the conservation and restoration of native forests, and where plantations are to be used, we recommended promote mixed-species arrangements over monocultures. Both these recommendations should result in more effective protection of terrestrial biodiversity, which is an important objective of China’s land-sustainability spending. The results of this study strengthen these recommendations because our policy prescriptions are now also based on a dataset that includes over 500 species-resolution taxa, ranging across the Arthropoda.
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The Chihuahuan Desert includes many endemic angiosperm species, some having very restricted geographic ranges. One of these species is Oreocarya crassipes (I. M. Johnst.) Hasenstab & M. G. Simpson, an endangered distylous gypsophile from the Trans-Pecos region in southern Brewster County, Texas, USA. The species is known from 10 populations, and this small number of populations, human development in the area, a distylous breeding system, and edaphic requirements threaten the long-term viability of the species. Using both hundreds of single nucleotide polymorphisms identified via tunable genotyping-by-sequencing (tGBS) and 10 microsatellite loci, patterns of genetic diversity, demography, selection, and migration were examined for 192 individuals from four populations of O. crassipes. From the sampled individuals, two populations (clusters) were identified via multiple methodologies and with both types of data. With SNP data, population substructure was further resolved among one of these populations to identify two distinct groups of individuals. Multiple individuals recognized as having mixed ancestry, along with Fst values and AMOVA results, provide evidence of genetic exchange among populations, which is less common for gypsophiles than non-gypsophiles, and the rate of migration among populations has been increasing recently. The Fst values for O. crassipes are more similar to those of other rare species than to other gypsophiles. Additionally, while distyly specifically does not necessarily impact the population genetics of the species, allogamy, which is facilitated by distyly, seems to have played a role in the genetic structure of O. crassipes.
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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.
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  • Tabular Data
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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).
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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.
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Carotenoid coloration is widely recognized as a signal of individual condition in various animals, but despite decades of study, the mechanisms that link carotenoid coloration to condition remain unresolved. Most birds with red feathers convert yellow dietary carotenoids to red carotenoids in an oxidation process requiring the gene encoding the putative cytochrome P450 enzyme CYP2J19. Here, we tested the hypothesis that the process of carotenoid oxidation and feather pigmentation is functionally linked to mitochondrial performance. Consistent with this hypothesis, we observed high levels of red ketolated carotenoids associated with the hepatic mitochondria of molting wild house finches (Haemorhous mexicanus), and upon fractionation, we found the highest concentration of ketolated carotenoids in the inner mitochondrial membrane. We further found that the redness of growing feathers was positively related to the performance of liver mitochondria. Structural modeling of CYP2J19 supports a direct role of this protein in carotenoid ketolation that may be functionally linked to cellular respiration. These observations suggest that feather coloration serves as a signal of core functionality through inexorable links to cellular respiration in the mitochondria.
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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.
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  • Software/Code
  • Tabular Data
  • Document
Predator-prey interactions play a key role in the evolution of species traits through antagonistic coevolutionary arms-races. The evolution of beak morphology in the Darwin’s finches in response to competition for seed resources is a classic example of evolution by natural selection. The seeds of Tribulus cistoides are an important food source for the largest ground finch species (Geospiza fortis, G. magnirostris, and G. conirostris) in dry months, and the hard spiny morphology of the fruits are a potent agent of selection that drives contemporary evolutionary change in finch beak morphology. Although the effects of these interaction on finches are well known, how seed predation affects the ecology and evolution of the plants is poorly understood. Here we examine whether seed predation by Darwin’s finches affects the ecology and evolution of T. cistoides. We ask whether the intensity of seed predation and the strength of natural selection by finches on fruit defense traits varies among populations, islands, years, or with varying finch community composition (i.e., the presence/absence of the largest beaked species, which feed on T. cistoides most easily). We then further test whether T. cistoides fruit defenses have diverged among islands in response to spatial variation in finch communities. We addressed these questions by examining seed predation by finches in 30 populations of T. cistoides over three years. Our study reveals three key results. First, Darwin’s finches strongly influence T. cistoides seed survival, whereby seed predation varies with differences in finch community composition among islands and in response to inter-annual fluctuations in precipitation. Second, finches impose phenotypic selection on T. cistoides fruit morphology, whereby smaller and harder fruits with longer or more spines exhibited higher seed survival. Variation in finch community composition and precipitation also explains variation in phenotypic selection on fruit defense traits. Third, variation in the number of spines on fruits among islands is consistent with divergent phenotypic selection imposed by variation in finch community composition among islands. These results suggest that Darwin’s finches and T. cistoides are experiencing an ongoing coevolutionary arms-race, and that the strength of this coevolution varies in space and time.
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Animal personality traits are often heritable and plastic at the same time. Indeed, behaviors that reflect an individual's personality can respond to environmental factors or change with age. To date, little is known regarding personality changes during a wild animals' lifetime and even less about stability in heritability of behavior across ages. In this study, we investigated age‐related changes in the mean and in the additive genetic variance of exploratory behavior, a commonly used measure of animal personality, in a wild population of great tits. Heritability of exploration is reduced in adults compared to juveniles, with a low genetic correlation across these age classes. A random regression animal model confirmed the occurrence of genotype–age interactions (G×A) in exploration, causing a decrease in additive genetic variance before individuals become 1 year old, and a decline in cross‐age genetic correlations between young and increasingly old individuals. Of the few studies investigating G×A in behaviors, this study provides rare evidence for this phenomenon in an extensively studied behavior. We indeed demonstrate that heritability and cross‐age genetic correlations in this behavior are not stable over an individual's lifetime, which can affect its potential response to selection. Because G×A is likely to be common in behaviors and have consequences for our understanding of the evolution of animal personality, more attention should be turned to this phenomenon in the future work.
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  • Software/Code
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Biological invasions are a primary threat to global biodiversity, supporting mounting calls for the development of early-warning systems to manage existing and emerging invaders. Here, we evaluated the geographical pattern of invasion risks of currently established and potentially emerging nonnative freshwater fishes in China by jointly considering the threats of introduction and establishment under climate change. Introduction threats were estimated according to proxies of human activities and propagule pressure for two primary pathways (aquaculture or ornamental). Establishment threats for 51 current and 64 potential invaders (based on whether having established or not self-sustaining populations) were assessed using an ensemble of species distribution models under current (1960-1990) and future [2041-2060 (2050s) and 2061-2080 (2070s)] climate scenarios. Geographical patterns of invasion risk were then assessed by overlaying the threats of introduction and establishment for each species group both in present-day and in the future. We found that eastern China displayed the highest threat of introduction. In contrast, southeastern and northwestern regions were identified as the most suitable for the establishment of both current and potential future invaders. Under a changing climate, 83 out of 115 species displayed an increase in habitat suitability, resulting in an overall increase of 4.8% by 2050s and 7.1% by 2070s in the extent of suitable habitat for nonnative freshwater fishes. Taken together, invasion risk was found to be highest in southeastern China and lowest in the Tibet Plateau. Our research highlights the importance of assessing invasion risk by integrating the threats associated with the introduction and establishment stages. In particular, our findings revealed convergent patterns of invasion risk between current and potential nonnative freshwater fishes under climate change. Geographic patterns in hotspots of existing and emerging invasions provide critical insights to guide the allocation of resources to monitor and control existing and emerging invasions in China.
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