Trophic facilitation in forest restoration: Can trees use ectomycorrhizal fungi of the pioneer shrub ?

The benefits of plant-to-plant facilitation in ecological restoration are well recognized, yet the potential for indirect trophic facilitation remains understudied. (southern beech; Nothofagaceae) is an iconic southern hemisphere tree genus that is frequently the focus of ecological restoration efforts. One aspect of ecology that may limit restoration success is the availability of appropriate ectomycorrhizal fungi.

Phylogenomics and morphology of Celmisiinae (Asteraceae: Astereae): Taxonomic and evolutionary implications.

The tribe Astereae (Asteraceae) includes 36 subtribes and 252 genera, and is distributed worldwide in temperate and tropical regions. One of the subtribes, Celmisiinae Saldivia, has been recently circumscribed to include six genera and ca. 160 species, and is restricted to eastern Australia, New Zealand, and New Guinea.

Indirect Mechanisms of Transcription Factor-Mediated Gene Regulation during Cell Fate Changes.

Transcription factors (TFs) are the master regulators of cellular identity, capable of driving cell fate transitions including differentiations, reprogramming, and transdifferentiations. Pioneer TFs recognize partial motifs exposed on nucleosomal DNA, allowing for TF-mediated activation of repressed chromatin. Moreover, there is evidence suggesting that certain TFs can repress actively expressed genes either directly through interactions with accessible regulatory elements or indirectly through mechanisms that impact the expression, activity, or localization of other regulatory factors.

Correlated evolution in an ectomycorrhizal host-symbiont system.

Mechanisms of diversification in fungi are relatively poorly known. Many ectomycorrhizal symbionts show preference for particular host genera or families, so host-symbiont selection may be an important driver of fungal diversification in ectomycorrhizal systems. However, whether ectomycorrhizal hosts and symbionts show correlated evolutionary patterns remains untested, and it is unknown whether fungal specialisation also occurs in systems dominated by hosts from the same genus.

Zeta diversity differentiates factors driving community assembly of rare and common ectomycorrhizal fungi.

A fundamental goal in community ecology is to understand what factors drive community assembly processes. The factors affecting ectomycorrhizal fungal communities are unknown in many regions, particularly in the southern hemisphere. We investigate community assembly using ITS2 metabarcoding of ectomycorrhizal fungi sampled from 3943 hyphal ingrowth bags buried in 81 Nothofagus forests across New Zealand's South Island.

Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells.

Induced pluripotent stem cells (iPSCs) can in principle differentiate into any cell of the body, and have revolutionized biomedical research and regenerative medicine. Unlike their human counterparts, mouse iPSCs (miPSCs) are reported to silence transposable elements and prevent transposable element-mediated mutagenesis. Here we apply short-read or Oxford Nanopore Technologies long-read genome sequencing to 38 bulk miPSC lines reprogrammed from 10 parental cell types, and 18 single-cell miPSC clones.

Comparative roadmaps of reprogramming and oncogenic transformation identify Bcl11b and Atoh8 as broad regulators of cellular plasticity.

Coordinated changes of cellular plasticity and identity are critical for pluripotent reprogramming and oncogenic transformation. However, the sequences of events that orchestrate these intermingled modifications have never been comparatively dissected. Here, we deconvolute the cellular trajectories of reprogramming (via Oct4/Sox2/Klf4/c-Myc) and transformation (via Ras/c-Myc) at the single-cell resolution and reveal how the two processes intersect before they bifurcate.

Diversification and trait evolution in New Zealand woody lineages across changing biomes.

Diversification of woody plant lineages in New Zealand has unfolded in complex physiographic, climatic, and environmental contexts. Many tree and shrub lineages have existed in New Zealand since the late Cenozoic when Forest was the dominant biome, subsequently diversifying (or continuing to diversify) during the Pliocene/Pleistocene as Open (below treeline) and Alpine biomes emerged. We examine the links between biomes occupied, traits, and diversification.

Transferability of correlative and process-based species distribution models revisited: A response to Booth.

Here, we respond to Booth's criticism of our paper, "Predictive ability of a process-based versus a correlative species distribution model." Booth argues that our usage of the MaxEnt model was flawed and that the conclusions of our paper are by implication flawed. We respond by clarifying that the error Booth implies we made was not made in our analysis, and we repeat statements from the original manuscript which anticipated such criticisms.

Transcriptional signature in microglia associated with Aβ plaque phagocytosis.

The role of microglia cells in Alzheimer's disease (AD) is well recognized, however their molecular and functional diversity remain unclear. Here, we isolated amyloid plaque-containing (using labelling with methoxy-XO4, XO4) and non-containing (XO4) microglia from an AD mouse model. Transcriptomics analysis identified different transcriptional trajectories in ageing and AD mice.

The effect of single biome occupancy on the estimation of biome shifts and the detection of biome conservatism.

Biome conservatism is often regarded as common in diversifying lineages, based on the detection of low biome shift rates or high phylogenetic signal. However, many studies testing biome conservatism utilise a single-biome-per-species approach, which may influence the detection of biome conservatism. Meta-analyses show that biome shift rates are significantly lower (less than a tenth), when single biome occupancy approaches are adopted.

TINC- A Method to Dissect Regulatory Complexes at Single-Locus Resolution- Reveals an Extensive Protein Complex at the Nanog Promoter.

Cellular identity is ultimately dictated by the interaction of transcription factors with regulatory elements (REs) to control gene expression. Advances in epigenome profiling techniques have significantly increased our understanding of cell-specific utilization of REs. However, it remains difficult to dissect the majority of factors that interact with these REs due to the lack of appropriate techniques.

Illicit Cannabis Usage as a Management Strategy in New Zealand Women with Endometriosis: An Online Survey.

Endometriosis affects around 10% of women worldwide. Many women with endometriosis struggle with finding adequate pain management, and data from other countries suggest that women use cannabis, either legal or illicit, to help manage their endometriosis symptoms. The aim of this study was to determine use of cannabis where endometriosis was self-identified as a condition that was being treated with cannabis, as well as the impact of cannabis use on the usage on other pharmaceuticals.

Predictive ability of a process-based versus a correlative species distribution model.

Species distribution modeling is a widely used tool in many branches of ecology and evolution. Evaluations of the transferability of species distribution models-their ability to predict the distribution of species in independent data domains-are, however, rare. In this study, we contrast the transferability of a process-based and a correlative species distribution model.

Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre.

Oligotrophic subtropical gyres are the largest continuous biomes on Earth and play a key role in global biogeochemical cycles. Microbial communities govern primary production and carbon cycling in the oligotrophic South Pacific Gyre, yet the ecological processes which underpin microbial biogeography in the region remain understudied. We investigated microbial biogeography and community assembly processes at three depths over a ~2,000-km the transect was longitudinal, so ran from 32°S, 170°W to 32°S, 152°W).

Diversification in evolutionary arenas-Assessment and synthesis.

Understanding how and why rates of evolutionary diversification vary is a key issue in evolutionary biology, ecology, and biogeography. Evolutionary rates are the net result of interacting processes summarized under concepts such as adaptive radiation and evolutionary stasis. Here, we review the central concepts in the evolutionary diversification literature and synthesize these into a simple, general framework for studying rates of diversification and quantifying their underlying dynamics, which can be applied across clades and regions, and across spatial and temporal scales.

Does Evolutionary History Correlate with Contemporary Extinction Risk by Influencing Range Size Dynamics?

Extinction threatens many species yet is predicted by few factors across the plant tree of life (ToL). Taxon age is one factor that may associate with extinction if occupancy of geographic and adaptive zones varies with time, but evidence for such an association has been equivocal. Age-dependent occupancy can also influence diversification rates and thus extinction risk where new taxa have small range and population sizes.

Production of High-Titer Lentiviral Particles for Stable Genetic Modification of Mammalian Cells.

Lentiviral gene transfer technologies exploit the natural efficiency of viral transduction to integrate exogenous genes into mammalian cells. This provides a simple research tool for inducing transgene expression or endogenous gene knockdown in both dividing and nondividing cells. This chapter describes an improved protocol for polyethylenimine (PEI)-mediated multi-plasmid transfection and polyethylene glycol (PEG) precipitation to generate and concentrate lentiviral vectors.

The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification.

There are two prominent and competing hypotheses that disagree about the effect of competition on diversification processes. The first, the bounded hypothesis, suggests that species diversity is limited (bounded) by competition between species for finite ecological niche space. The second, the unbounded hypothesis, proposes that innovations associated with evolution render competition unimportant over macroevolutionary timescales.

Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming.

Somatic cell reprogramming into induced pluripotent stem cells (iPSCs) induces changes in genome architecture reflective of the embryonic stem cell (ESC) state. However, only a small minority of cells typically transition to pluripotency, which has limited our understanding of the process. Here, we characterize the DNA regulatory landscape during reprogramming by time-course profiling of isolated sub-populations of intermediates poised to become iPSCs.

On the persistence of reproductive barriers in Eucalyptus: the bridging of mechanical barriers to zygote formation by F1 hybrids is counteracted by intrinsic post-zygotic incompatibilities.

Background And Aims: Many previous studies conclude that pre-zygotic barriers such as mechanical isolation account for most reproductive isolation between pairs of taxa. However, the inheritance and persistence of barriers such as these after the first generation of hybridization is rarely quantified, even though it is a vital consideration in understanding gene flow potential. There is an asymmetrical pre-zygotic mechanical barrier to hybridization between Eucalyptus nitens and Eucalyptus globulus, which completely prevents small-flowered E.

Transient hybridization, not homoploid hybrid speciation, between ancient and deeply divergent conifers.

Premise Of The Study: Homoploid hybrid speciation is receiving growing attention due the increasing recognition of its role in speciation. We investigate if individuals intermediate in morphology between the two species of the conifer genus Athrotaxis represent a homoploid hybrid species, A. laxifolia, or are spontaneous F1 hybrids.

Patterns of Reproductive Isolation in Eucalyptus-A Phylogenetic Perspective.

We assess phylogenetic patterns of hybridization in the speciose, ecologically and economically important genus Eucalyptus, in order to better understand the evolution of reproductive isolation. Eucalyptus globulus pollen was applied to 99 eucalypt species, mainly from the large commercially important subgenus, Symphyomyrtus. In the 64 species that produce seeds, hybrid compatibility was assessed at two stages, hybrid-production (at approximately 1 month) and hybrid-survival (at 9 months), and compared with phylogenies based on 8,350 genome-wide DArT (diversity arrays technology) markers.