Breeding systems,hybridization and continuing evolution in Avon Gorge Sorbus

Background and Aims

Interspecific hybridization and polyploidy are key processes in plant evolution and are responsible for ongoing genetic diversification in the genus Sorbus (Rosaceae). The Avon Gorge, Bristol, UK, is a world ‘hotspot’ for Sorbus diversity and home to diploid sexual species and polyploid apomictic species. This research investigated how mating system variation, hybridization and polyploidy interact to generate this biological diversity.

Methods

Mating systems of diploid, triploid and tetraploid Sorbus taxa were analysed using pollen tube growth and seed set assays from controlled pollinations, and parent–offspring genotyping of progeny from open and manual pollinations.

Key Results

Diploid Sorbus are outcrossing and self-incompatible (SI). Triploid taxa are pseudogamous apomicts and genetically invariable, but because they also display self-incompatibility, apomictic seed set requires pollen from other Sorbus taxa – a phenomenon which offers direct opportunities for hybridization. In contrast tetraploid taxa are pseudogamous but self-compatible, so do not have the same obligate requirement for intertaxon pollination.

Conclusions

The mating inter-relationships among Avon Gorge Sorbus taxa are complex and are the driving force for hybridization and ongoing genetic diversification. In particular, the presence of self-incompatibility in triploid pseudogamous apomicts imposes a requirement for interspecific cross-pollination, thereby facilitating continuing diversification and evolution through rare sexual hybridization events. This is the first report of naturally occurring pseudogamous apomictic SI plant populations, and we suggest that interspecific pollination, in combination with a relaxed endosperm balance requirement, is the most likely route to the persistence of these populations. We propose that Avon Gorge Sorbus represents a model system for studying the establishment and persistence of SI apomicts in natural populations.     

Accuracy of de novo assembly of DNA sequences from double‐digest libraries varies substantially among software

Advances in DNA sequencing have made it feasible to gather genomic data for non‐model organisms and large sets of individuals, often using methods for sequencing subsets of the genome. Several of these methods sequence DNA associated with endonuclease restriction sites (various RAD and GBS methods). For use in taxa without a reference genome, these methods rely on de novo assembly of fragments in the sequencing library. Many of the software options available for this application were originally developed for other assembly types and we do not know their accuracy for reduced representation libraries. To address this important knowledge gap, we simulated data from the Arabidopsis thaliana and Homo sapiens genomes and compared de novo assemblies by six software programs that are commonly used or promising for this purpose (ABySS , CD‐HIT , Stacks , Stacks2 , Velvet and VSEARCH ). We simulated different mutation rates and types of mutations, and then applied the six assemblers to the simulated data sets, varying assembly parameters. We found substantial variation in software performance across simulations and parameter settings. ABySS failed to recover any true genome fragments, and Velvet and VSEARCH performed poorly for most simulations. Stacks and Stacks2 produced accurate assemblies of simulations containing SNPs, but the addition of insertion and deletion mutations decreased their performance. CD‐HIT was the only assembler that consistently recovered a high proportion of true genome fragments. Here, we demonstrate the substantial difference in the accuracy of assemblies from different software programs and the importance of comparing assemblies that result from different parameter settings.     

Exclusion rules, bottlenecks and the evolution of stochastic phenotype switching

Stochastic phenotype switching--often considered a bet hedging or risk-reducing strategy--can enhance the probability of survival in fluctuating environments. A recent experiment provided direct evidence for an adaptive origin by showing the de novo evolution of switching in bacterial populations propagated under a selective regime that captured essential features of the host immune response. The regime involved strong frequency-dependent selection realized via dual imposition of an exclusion rule and population bottleneck. Applied at the point of transfer between environments, the phenotype common in the current environment was assigned a fitness of zero and was thus excluded from participating in the next round (the exclusion rule). In addition, also at the point of transfer, and so as to found the next bout of selection, a single phenotypically distinct type was selected at random from among the survivors (the bottleneck). Motivated by this experiment, we develop a mathematical model to explore the broader significance of key features of the selective regime. Through a combination of analytical and numerical results, we show that exclusion rules and population bottlenecks act in tandem as potent selective agents for stochastic phenotype switching, such that even when initially rare, and when switching engenders a cost in Malthusian fitness, organisms with the capacity to switch can invade non-switching populations and replace non-switching types. Simulations demonstrate the robustness of our findings to alterations in switching rate, fidelity of exclusion, bottleneck size, duration of environmental state and growth rate. We also demonstrate the relevance of our model to a range of biological scenarios such as bacterial persistence and the evolution of sex.     

Shifts in a single muscle's control potential of body dynamics are determined by mechanical feedback

Muscles are multi-functional structures that interface neural and mechanical systems. Muscle work depends on a large multi-dimensional space of stimulus (neural) and strain (mechanical) parameters. In our companion paper, we rewrote activation to individual muscles in intact, behaving cockroaches (Blaberus discoidalis L.), revealing a specific muscle's potential to control body dynamics in different behaviours. Here, we use those results to provide the biologically relevant parameters for in situ work measurements. We test four hypotheses about how muscle function changes to provide mechanisms for the observed control responses. Under isometric conditions, a graded increase in muscle stress underlies its linear actuation during standing behaviours. Despite typically absorbing energy, this muscle can recruit two separate periods of positive work when controlling running. This functional change arises from mechanical feedback filtering a linear increase in neural activation into nonlinear work output. Changing activation phase again led to positive work recruitment, but at different times, consistent with the muscle's ability to also produce a turn. Changes in muscle work required considering the natural sequence of strides and separating swing and stance contributions of work. Both in vivo control potentials and in situ work loops were necessary to discover the neuromechanical coupling enabling control.     

Axons of retinal ganglion cells are insulted in the optic nerve early in DBA/2J glaucoma

Here, we use a mouse model (DBA/2J) to readdress the location of insult(s) to retinal ganglion cells (RGCs) in glaucoma. We localize an early sign of axon damage to an astrocyte-rich region of the optic nerve just posterior to the retina, analogous to the lamina cribrosa. In this region, a network of astrocytes associates intimately with RGC axons. Using BAX-deficient DBA/2J mice, which retain all of their RGCs, we provide experimental evidence for an insult within or very close to the lamina in the optic nerve. We show that proximal axon segments attached to their cell bodies survive to the proximity of the lamina. In contrast, axon segments in the lamina and behind the eye degenerate. Finally, the Wld^s allele, which is known to protect against insults to axons, strongly protects against DBA/2J glaucoma and preserves RGC activity as measured by pattern electroretinography. These experiments provide strong evidence for a local insult to axons in the optic nerve.     

Shanidar 10: a Middle Paleolithic immature distal lower limb from Shanidar Cave, Iraqi Kurdistan

The analysis of the faunal remains from Shanidar Cave has identified an incomplete immature human distal leg and foot from the deepest levels of the Middle Paleolithic of Shanidar Cave, Iraq. The distal tibia, fibula, first metatarsal, and two tarsals, designated Shanidar 10, derive from a 1-2-year-old infant. The tibia exhibits a transverse line from a stress episode during the last quarter of its first year postnatal. The cross-sectional geometry of the tibial midshaft reveals modest cortical thickening and a level of diaphyseal robusticity similar to those of recent human infants of a similar developmental age.