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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.
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Plant traits are critical to plant form and function —including growth, survival and reproduction— and therefore shape fundamental aspects of population and ecosystem dynamics as well as ecosystem services. Here, we present a global species-level compilation of key functional traits for palms (Arecaceae), a plant family with keystone importance in tropical and subtropical ecosystems. We derived measurements of essential functional traits for all (>2500) palm species from key sources such as monographs, books, other scientific publications, as well as herbarium collections. This includes traits related to growth form, stems, armature, leaves and fruits. Although many species are still lacking trait information, the standardized and global coverage of the data set will be important for supporting future studies in tropical ecology, rainforest evolution, paleoecology, biogeography, macroecology, macroevolution, global change biology and conservation. Potential uses are comparative eco-evolutionary studies, ecological research on community dynamics, plant-animal interactions and ecosystem functioning, studies on plant-based ecosystem services, as well as conservation science concerned with the loss and restoration of functional diversity in a changing world.
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Cetaceans possess brains that rank among the largest to have ever evolved, either in terms of absolute mass or relative to body size. Cetaceans have evolved these huge brains under relatively unique environmental conditions, making them a fascinating case study to investigate the constraints and selection pressures that shape how brains evolve. Indeed, cetaceans have some unusual neuroanatomical features, including a thin but highly folded cerebrum with low cortical neuron density, as well as many structural adaptations associated with acoustic communication. Previous reports also suggest that at least some cetaceans have an expanded cerebellum, a brain structure with wide-ranging functions in adaptive filtering of sensory information, the control of motor actions, and cognition. Here, we report that, relative to the size of the rest of the brain, both the cerebrum and cerebellum are dramatically enlarged in cetaceans and show evidence of co-evolution, a pattern of brain evolution that is convergent with primates. However, we also highlight several branches where cortico-cerebellar co-evolution may be partially decoupled, suggesting these structures can respond to independent selection pressures. Across cetaceans, we find no evidence of a simple linear relationship between either cerebrum and cerebellum size and the complexity of social ecology or acoustic communication, but do find evidence that their expansion may be associated with dietary breadth. In addition, our results suggest that major increases in both cerebrum and cerebellum size occurred early in cetacean evolution, prior to the origin of the major extant clades, and predate the evolution of echolocation.
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Phenological investigation can provide valuable insights into the ecological effects of climate change. Appropriate modelling of the time distribution of phenological events is key to determining the nature of any changes, as well as the driving mechanisms behind those changes. Here we present the nlstimedist R package, a distribution function and modelling framework that describes the temporal dynamics of unimodal phenological events. The distribution function is derived from first principles and generates three biologically interpretable parameters. Using seed germination at different temperatures as an example, we show how the influence of environmental factors on a phenological process can be determined from the quantitative model parameters. The value of this model is its ability to represent various unimodal temporal processes statistically. The three intuitively meaningful parameters of the model can make useful comparisons between different time periods, geographical locations or species’ populations, in turn allowing exploration of possible causes.
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Oryctocephalid trilobites are seldom abundant and often tectonically deformed, creating problems for robust species delimitation and compromising their utility in biostratigraphic and evolutionary studies. By studying more than 140 specimens recovered from the upper portion of the Combined Metals Member (Pioche Formation, Nevada; Cambrian Stage 4, Series 2), we exploit a rare opportunity to explore how morphological variation among oryctocephalid specimens is partitioned into intraspecific variation versus interspecific disparity. Qualitative and quantitative analyses reveal that two species are represented: Oryctocephalites palmeri Sundberg and McCollum, 1997 and Oryctocephalites sp. A, the latter known from a single cranidium stratigraphically below all occurrences of the former. In contrast to the conclusions of a previous study, there is no evidence of cranidial dimorphism in O. palmeri. However, that species exhibits considerable variation in cranidial shape and pygidial spine arrangement and number. Cranidial shape variation within O. palmeri is approximately one-half of the among-species disparity within the genus. Comparison of cranidial shape between noncompacted and compacted samples reveals that compaction causes significant change in mean shape and an increase in shape variation; such changes are interpretable in terms of observed fracture patterns. Nontaphonomic variation is partitioned into ontogenetic and nonallometric components. Those components share similar structure with each other and with interspecific disparity, suggesting that ontogenetic shape change might be an important source of variation available for selection. This highlights the importance of ontogenetic and taphonomic sources of variation with respect to species delimitation, morphospace occupation, and investigation of evolutionary patterns and processes.
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1. Long-term pathogen control or eradication in wildlife is rare and represents a major challenge in conservation. Control is particularly difficult for environmentally transmitted pathogens, including some of the most conservation-critical wildlife diseases. 2. We undertook a treatment program aimed at population-scale eradication of the environmentally transmitted Sarcoptes scabiei mite (causative agent of sarcoptic mange) during an epizootic in bare-nosed wombats (Vombatus ursinus). Field trial results were used to parameterize a mechanistic host-disease model that explicitly described indirect-transmission, host behaviour, and viable disease intervention methods. 3. Model analysis shows that elimination of S. scabiei in the wild is most sensitive to the success of treatment delivery, and duration of the program. In addition, we found the frequency that wombats switch burrows was an important positive driver of mite persistence. 4. Synthesis and applications: This research emphasises the utility of applying model-guided management techniques in order to achieve practical solutions in the field. Our approach and findings have applicability to other species affected by S. scabiei (e.g., wolves, red foxes, Spanish ibex, and American black bear), as well as other conservation-critical systems involving environmental transmission (e.g., bat white-nose syndrome and amphibian chytridiomycosis).
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Aim: Understanding how landscape features affect gene flow is critical to connectivity conservation and restoration management. Here, we examined the relationship between functional connectivity (gene flow) and structural connectivity (area and spatial configuration of habitats) in three co-occurring short-range plant taxa in an ancient terrestrial island system. Location: Low altitude mountain ranges south-western Australia Methods: We analysed spatial patterns of genetic differentiation at nuclear microsatellite loci using Bayesian clustering. Circuit theory modelling was used to generate all possible pathways that connect populations as resistance distance matrices based on two surfaces for each taxon. The first surface assumes a flat terrain and tests whether genetic similarity declines only with distance – isolation by distance (IBD). The second surface is habitat suitability based on species distribution modelling (SDM), which tests whether genetic similarity is a function of connected and suitable habitat. Multiple matrix regression with randomisation was used to test the significance of the resistance distance matrices at predicting two metrics of genetic differentiation (FST and DEST). Variance explained was partitioned using redundancy analysis. Results: Genetic structure for the insect-pollinated taxa - Acacia adinophylla, and Tetratheca aphylla subsp. aphylla was at similar spatial scales. Unexpectedly, a higher level of genetic structure was found in the wind-pollinated Lepidosperma bungalbin. IBD best explained the gene flow of A. adinophylla (R2 = 0.41-0.43) with partial support provided by habitat suitability (R2 = 0.04-0.07). In contrast, connectivity by habitat suitability was highest for T. aphylla subsp. aphylla (R2 = 0.56-0.59). Drivers of L. bungalbin connectivity were inconsistent between the two measures of genetic differentiation. Main conclusions: Gene flow is facilitated by different factors for the three taxa. Habitat fragmentation would most strongly impede gene flow for T. aphylla subsp. aphylla. Geographic distance cannot be assumed as the sole or best determinant of gene flow among populations, nor can findings be generalised to coexisting taxa.
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Acer (the maple genus) is one of the diverse tree genera in the Northern Hemisphere with about152 species, most of which are in eastern Asia. There are roughly a dozen of species in Europe/western Asia and a dozen in North America. Several phylogenetic studies of Acer have been conducted since 1998, but none have provided a satisfactory resolution for basal relationships among sections of Acer. Here we report the first well-resolved phylogeny of Acer based on DNA sequences of over 500 nuclear loci generated using the anchored hybrid enrichment method and explore the implications of the robust phylogeny for Acer systematics and biogeography. Our phylogenetic results support the most recent taxonomic treatment of Acer by de Jong with some modifications; section Pentaphylla may be expanded to include section Trifoliata, and A. yangbiense may be included in section Lithocarpa. Sections Spicata, Negundo, Arguta, and Palmata form a clade sister to the rest of the genus where sections Glabra and Parviflora comprise the first clade followed by section Macrantha, sections Ginnala, Lithocarpa, Indivisa, sections Platanoidea and Macrophylla, section Rubra, section Acer, and section Pentaphylla. Monotypic sections Glabra and Macrophylla in North America are sister to the Japanese section Parviflora and Eurasian section Platanoidea, respectively. Ancestral area inferences using S-DIVA (statistical dispersal and vicariance analysis) and DEC (dispersal and extinction cladogenesis) methods suggest that Asia might be the most likely ancestral area of Acer as proposed by Wolfe and Tanai and molecular dating using BEAST (Bayesian evolutionary analysis by sampling trees) indicate that section diversifications of Acer might have completed largely in the late Eocene and the intercontinental disjunctions of Acer between eastern Asia and eastern North America formed mostly in the Miocene.
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Aim. Understanding the forces that drive range shifts in forest landscapes is imperative for predicting species distributions under anthropogenic climate and land use change. However, empirical studies exploring how these components jointly influence critical early-life stages of mountain tree species across environmental gradients are scarce. We used the high-mountain tree Polylepis australis as model species to investigate the relative importance of altitude and associated climatic conditions, land use for livestock and microsite characteristics on early-life performance. Location. Córdoba Sierras, central Argentina. Methods. We set up an extensive in situ sowing experiment with a robust split-plot design that integrated spatial scales ranging from 0.4 m2 subplots at the microsite level (associated with vegetative and micro-topographic structures), to livestock exclosure and enclosure plots of several hectares, to an altitudinal gradient of 1000 m. Components of early-life performance were monitored across two subsequent growing seasons. Results. Microsite characteristics played a fundamental role in P. australis establishment, whereby interactions with altitude and/or land use suggested alternate mechanisms: facilitation (likely reduced desiccation) dominated at low altitude while at high altitude abiotic stress (likely intensive frost and radiation) overruled any microsite effects. At mid altitude benefits of competition release prevailed over facilitation and microsite effects gained importance under livestock presence. Inconsistencies between pre- and post- emergence responses illustrated potential tradeoffs between beneficial and detrimental effects of microsite conditions upon performance throughout early life: a favorable location for seeds may abruptly turn adverse for seedlings. Main conclusions. We unravel how changes in altitude, anthropogenic disturbances and microsite characteristics jointly modulate P. australis performance across stages of early establishment. Such information is fundamental when categorizing specific microhabitats as “safe sites” for tree regeneration especially in mountain environments with high spatiotemporal heterogeneity.
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Top predators cause avoidance behaviours in competitors and prey, which can lead to niche partitioning and facilitate coexistence. We investigate changes in partitioning of the temporal niche in a mammalian community in response to both the rapid decline in abundance of a top predator and its rapid increase, produced by two concurrent natural experiments: 1) the severe decline of the Tasmanian devil due to a transmissible cancer, and 2) the introduction of Tasmanian devils to an island, with subsequent population increase. We focus on devils, two mesopredators, and three prey species, allowing us to examine niche partitioning in the context of intra- and inter-specific competition, and predator-prey interactions. The most consistent shift in temporal activity occurred in devils themselves, which were active earlier in the night at high densities, presumably because of heightened intraspecific competition. When devils were rare, their closest competitor, the spotted-tailed quoll, increased activity in the early part of the night, resulting in increased overlap with the devil’s temporal niche and suggesting release from interference competition. The invasive feral cat, another mesopredator, did not shift its temporal activity in response to either decreasing or increasing devil densities. Shifts in temporal activity of the major prey species of devils were stronger in response to rising than to falling devil densities. We infer that the costs associated with not avoiding predators when their density is rising (i.e., death) are higher than the costs of continuing to adopt avoidance behaviours as predator densities fall (i.e., loss of foraging opportunity), so rising predator densities may trigger more rapid shifts. The rapid changes in devil abundance provide a unique framework to test how the non-lethal effects of top predators affect community-wide partitioning of temporal niches, revealing that this top-predator has an important but varied influence on the diel activity of other species.
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