On log concavity for order-preserving and order-non-reversing maps of partial orders

Stanley used the Aleksandrov-Fenchel inequalities from the theory of nixed volumes to prove the following result. Let P be a partially ordered set with n elements, and let x ∊ P. If Ni* is the number of linear extensions , ⋋ : P + (1 , 2,...,n) satisfying ⋋ (x) = i, then the sequence N*1,…,N*n is log concave (and therefore unimodal). Here the analogous results for both order-preserving and order-non-reversing maps are proved using an explicit injection. Further, if vc is the number of order-preserving maps of P into a chain of length c, then vc is shown to be 1-og concave, and the corresponding result is established for order-non-reversing maps

Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum

Plasmids drive genomic diversity in bacteria via horizontal gene transfer [1 and 2]; nevertheless, explaining their survival in bacterial populations is challenging [3]. Theory predicts that irrespective of their net fitness effects, plasmids should be lost: when parasitic (costs outweigh benefits), plasmids should decline due to purifying selection [4, 5 and 6], yet under mutualism (benefits outweigh costs), selection favors the capture of beneficial accessory genes by the chromosome and loss of the costly plasmid backbone [4]. While compensatory evolution can enhance plasmid stability within populations [7, 8, 9, 10, 11, 12, 13, 14 and 15], the propensity for this to occur across the parasitism-mutualism continuum is unknown. We experimentally evolved Pseudomonas fluorescens and its mercury resistance mega-plasmid, pQBR103 [ 16], across an environment-mediated parasitism-mutualism continuum. Compensatory evolution stabilized plasmids by rapidly ameliorating the cost of plasmid carriage in all environments. Genomic analysis revealed that, in both parasitic and mutualistic treatments, evolution repeatedly targeted the gacA/gacS bacterial two-component global regulatory system while leaving the plasmid sequence intact. Deletion of either gacA or gacS was sufficient to completely ameliorate the cost of plasmid carriage. Mutation of gacA/gacS downregulated the expression of ∼17% of chromosomal and plasmid genes and appears to have relieved the translational demand imposed by the plasmid. Chromosomal capture of mercury resistance accompanied by plasmid loss occurred throughout the experiment but very rarely invaded to high frequency, suggesting that rapid compensatory evolution can limit this process. Compensatory evolution can explain the widespread occurrence of plasmids and allows bacteria to retain horizontally acquired plasmids even in environments where their accessory genes are not immediately useful

Rapid compensatory evolution promotes the survival of conjugative plasmids

Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome

Establishment of restoration monitoring at Tārerekautuku Yarrs Lagoon: Conservation Biology (ECOL609) project reports

Ninety percent of New Zealand’s wetlands have been lost along with the endemic plants, fish, birds, and invertebrates. Those that remain are threatened by choking weeds, suffocating sediment, pollution from livestock and continued drainage and clearance (Hansford, 2010). Therefore, all remaining wetlands, regardless of their ecological state, are precious and need to be restored and managed to maximise the biodiversity within. Tārerekautuku Yarrs Lagoon is a 76.9 ha reserve located along the Ararira/LII River between Lincoln and Te Waihora/Lake Ellesmere. Tārerekautuku is administered by the Selwyn District Council (SDC) who have recognised the wetland’s intrinsic value. The lagoon area was known as a significant mahinga kai (food gathering) site for Ngāi Tahu, and particularly the local hapū of Ngāi Te Ruahikihiki based at Taumutu. Mahinga kai species being gathered at this site include tuna (eel), koareare (the edible rhizome of raupō/bullrush), koukoupara (bullies), mawehe (kōaro), pārera (grey duck), pūtakitaki (paradise duck), pākura (pukeko), whio (blue duck), kaaha (shag) and aruhe (bracken fern root) (Taiaroa 1880). The cultural and biodiversity values of Tārerekautuku are significant and ecological restoration of the lagoon has a huge potential to enhance these (Boffa Miskell, 2017). Selwyn District Council, with the support of the Department of Conservation (mainly Robin Smith), received approximately $800,000 from Ministry for the Environment ‘Freshwater Improvement Fund’ towards achieving five objectives: 1. To control willows and other weeds across approximately 87 ha in the Tārerekautuku Yarrs Lagoon Wetland. 2. To undertake predator control within the wetland and surrounding catchment to target mustelids, rats, and possums 3. To reduce sediment loads through instream works (up to five sediment traps or equivalent) and waterways re-battering work (approximately 2,000 m), including installing two bridges for site access. 4. To plant at least 12,516 native plants and trees across eight ha of Tārerekautuku wetland and connecting waterways. 5. To establish a monitoring programme at the Tārerekautuku wetland for Mātauranga Māori to measure ecological change over time. With Lincoln University’s proximity and MOU (pending) between them and SDC, this project provides a win-win scenario for students to help monitor ecological changes over time (objective 5). The project summaries that follow are an integral part of the ECOL609 (Conservation Biology) course that is undertaken in the first semester of 2022 where students chose a conservation area to monitor. Vegetation quadrat monitoring intended to replicate Stammer (2010); however, access to the site was deemed unsafe to proceed. This work has been added as an Appendix in this report to allow future comparisons

Geological control on dinosaurs’ rise to dominance: Late Triassic ecosystem stress by relative sea level change

The Late Triassic is enigmatic in terms of how terrestrial life evolved: it was the time when new groups arose, such as dinosaurs, lizards, crocodiles and mammals. Also, it witnessed a prolonged period of extinctions, distinguishing it from other great mass extinction events, while the gradual rise of the dinosaurs during the Carnian to Norian remains unexplained. Here we show that key extinctions during the early Norian might have been triggered by major sea-level changes across the largest delta plain in Earth's history situated in the Triassic Boreal Ocean, northern Pangea. Fossil and rock records display extensive marine inundations with floral turnover, demonstrating how susceptible widespread low-gradient delta plains were to transgressions. Landward shoreline translocation implies decrease in important coastal regions and ecological stress on the dominant Archosauria, thriving in these habitats, and we argue that these unique geological factors played an important role in dinosaurs gradual rise to dominance.publishedVersio

Bacteriophages limit the existence conditions for conjugative plasmids

Bacteriophages are a major cause of bacterial mortality and impose strong selection on natural bacterial populations, yet their effects on the dynamics of conjugative plasmids have rarely been tested. We combined experimental evolution, mathematical modeling, and individual-based simulations to explain how the ecological and population genetics effects of bacteriophages upon bacteria interact to determine the dynamics of conjugative plasmids and their persistence. The ecological effects of bacteriophages on bacteria are predicted to limit the existence conditions for conjugative plasmids, preventing persistence under weak selection for plasmid accessory traits. Experiments showed that phages drove faster extinction of plasmids in environments where the plasmid conferred no benefit, but they also revealed more complex effects of phages on plasmid dynamics under these conditions, specifically, the temporary maintenance of plasmids at fixation followed by rapid loss. We hypothesized that the population genetic effects of bacteriophages, specifically, selection for phage resistance mutations, may have caused this. Further mathematical modeling and individual-based simulations supported our hypothesis, showing that conjugative plasmids may hitchhike with phage resistance mutations in the bacterial chromosome

Fishspear: a priority queue algorithm

The Fishspear priority queue algorithm is presented and analyzed. Fishspear is comparable to the usual heap algorithm in its worst-case running time, and its relative performance is much better in many common situations. Fishspear also differs from the heap method in that it can be implemented efficiently using sequential storage such as stacks or tapes, making it potentially attractive for implementation of very large queues on paged memory systems

Plasmid carriage can limit bacteria–phage coevolution

Coevolution with bacteriophages is a major selective force shaping bacterial populations and communities. A variety of both environmental and genetic factors has been shown to influence the mode and tempo of bacteria–phage coevolution. Here, we test the effects that carriage of a large conjugative plasmid, pQBR103, had on antagonistic coevolution between the bacterium Pseudomonas fluorescens and its phage, SBW25ϕ2. Plasmid carriage limited bacteria–phage coevolution; bacteria evolved lower phage-resistance and phages evolved lower infectivity in plasmid-carrying compared with plasmid-free populations. These differences were not explained by effects of plasmid carriage on the costs of phage resistance mutations. Surprisingly, in the presence of phages, plasmid carriage resulted in the evolution of high frequencies of mucoid bacterial colonies. Mucoidy can provide weak partial resistance against SBW25ϕ2, which may have limited selection for qualitative resistance mutations in our experiments. Taken together, our results suggest that plasmids can have evolutionary consequences for bacteria that go beyond the direct phenotypic effects of their accessory gene cargo