title: Invasive European rats in Britain and New Zealand: same species, different outcomes

authors: King, Carolyn M.

subjects: Rattus rattus

abstract: Two species of European commensal murids, the Norway rat norvegicus and the ship rat Rattus rattus, have colonized two island archipelagos of comparable size and temperate climate but in opposite hemispheres and with opposite outcomes. Ship rats were common commensals in Britain until replaced by Norway rats; Norway rats were hugely abundant in native forests throughout New Zealand until widely replaced by ship rats. Interference explains the first case, as ship rats are smaller than Norway rats and are always vulnerable to aggressive competition from them, but some other explanation is needed for the second case. We used the marginal value theorem to investigate exploitation competition between these two species in arboreal habitats. We observed the climbing behaviour and ‘giving-up time’ of captive rats of both species searching for food at different heights above the ground. Our data confirmed that the smaller size and greater agility of R. rattus give it a competitive advantage in foraging for scattered small food items above ground. We propose that (1) the outcomes of the interactions between the two rat species in any given place depend on the distribution of food resources in structurally complex habitat, moderated by winter temperatures; (2) the different outcomes of invasions by the two species can be explained in Britain by interference competition, and in New Zealand by exploitation competition and by the absence of specialist arboreal rodents (squirrels).

text: Invasive European rats in Britain and New Zealand: same species, different outcomes Two species of European commensal murids, the Norway rat norvegicus and the ship rat Rattus rattus, have colonized two island archipelagos of comparable size and temperate climate but in opposite hemispheres and with opposite outcomes. Ship rats were common commensals in Britain until replaced by Norway rats; Norway rats were hugely abundant in native forests throughout New Zealand until widely replaced by ship rats. Interference explains the first case, as ship rats are smaller than Norway rats and are always vulnerable to aggressive competition from them, but some other explanation is needed for the second case. We used the marginal value theorem to investigate exploitation competition between these two species in arboreal habitats. We observed the climbing behaviour and ‘giving-up time’ of captive rats of both species searching for food at different heights above the ground. Our data confirmed that the smaller size and greater agility of R. rattus give it a competitive advantage in foraging for scattered small food items above ground. We propose that (1) the outcomes of the interactions between the two rat species in any given place depend on the distribution of food resources in structurally complex habitat, moderated by winter temperatures; (2) the different outcomes of invasions by the two species can be explained in Britain by interference competition, and in New Zealand by exploitation competition and by the absence of specialist arboreal rodents (squirrels).

year: 2011

title: Intra-species genomic variations in hydrogen-oxidising bacteria is delineated by horizontal gene flow

authors: Cabria, Gamaliel Lysander

subjects: Bacterial speciation

abstract: Species are the fundamental unit of ecology and evolutionary biology. However, there is no universal definition of a species that spans all domains of life. Eukaryotic species are traditionally defined through reproductive isolation, where reproductive barriers result in adaptive traits being shared only within the isolated population. Therefore, discontinuities in gene flow in eukaryotes generally result in the formation of an ecologically and genotypically cohesive unit. In contrast, delineating asexual bacterial species is often hampered by extensive horizontal gene flow and is further confounded by the difficulty of identifying a bacteria’s ecological niche. Therefore, the working definition of a prokaryotic species is based on arbitrary standards of relatedness and often lacks a cohesive ecological niche. To address this problem, the ecological population theory, which defines bacterial ‘species’ as ecologically distinct populations delineated through discontinuities in total gene flow, was proposed. It postulates that, rather than a hindrance, the prevalence of horizontal gene flow, primarily through homologous recombination, plays a significant role in bacterial speciation. Horizontal gene flow allows gene-specific sweeps in bacterial populations, where adaptive genes are shared preferentially between recombining bacteria independent of their genomic background. Thus, discontinuities in horizontal gene flow can be utilised to demarcate a genotypically and ecologically cohesive bacterial species. 
Previous studies have demonstrated that ecological populations exist in heterotrophic bacteria. However, examining the generalisability of the ecological population theory requires understanding the role of horizontal gene flow in delineating populations from extreme bacterial communities, especially bacteria with limited metabolic redundancy due to their higher impact of deleterious consequences (e.g., pathway dysregulation by recombination of a maladaptive gene) during horizontal gene flow. Therefore, in this work, I utilised the chemolithoautotrophic hydrogen-oxidising Aquificota bacteria from natural populations as a model system to test the generalisability of the ecological population theory. Utilising a novel high-throughput isolation method, I isolated co-habiting Aquificota bacteria with minimal enrichment from geothermal springs. Sequencing and comparative analysis of the Aquificota genomes reveal intra-species genomic variations driven by varying degrees of horizontal gene flow and a population structure composed of co-occurring clonal lineages and recombinogenic bacteria. To examine whether these Aquificota populations exhibit ecological and evolutionary patterns akin to eukaryotic species, I investigated the changes in their population structure across four additional time points (1 year). Analysis of recent horizontal gene flow and mutations in Aquificota populations show that clonal lineages remain clonal across time, with minimal changes in their genomic background diversity. In contrast, recombining populations experience variation in intra-population diversity and a shift in the dominant genomic background across time—implying an intra-population turnover. Lastly, I also investigated the role of both non-homologous and homologous recombination in maintaining ecological populations in Aquificota by analysing the presence and function of mobile genetic elements (MGEs) in its different populations. The lack of spatial and functional overlap between MGEs and horizontally swept regions confirms that homologous recombination drives horizontal gene flow in Aquificota populations.
This work demonstrated that ecological populations in Aquificota can be delineated through discontinuities in horizontal gene flow driven primarily by homologous recombination. Thus, ecological population theory can be a generalisable model for speciation and evolution in bacteria.

text: Intra-species genomic variations in hydrogen-oxidising bacteria is delineated by horizontal gene flow Species are the fundamental unit of ecology and evolutionary biology. However, there is no universal definition of a species that spans all domains of life. Eukaryotic species are traditionally defined through reproductive isolation, where reproductive barriers result in adaptive traits being shared only within the isolated population. Therefore, discontinuities in gene flow in eukaryotes generally result in the formation of an ecologically and genotypically cohesive unit. In contrast, delineating asexual bacterial species is often hampered by extensive horizontal gene flow and is further confounded by the difficulty of identifying a bacteria’s ecological niche. Therefore, the working definition of a prokaryotic species is based on arbitrary standards of relatedness and often lacks a cohesive ecological niche. To address this problem, the ecological population theory, which defines bacterial ‘species’ as ecologically distinct populations delineated through discontinuities in total gene flow, was proposed. It postulates that, rather than a hindrance, the prevalence of horizontal gene flow, primarily through homologous recombination, plays a significant role in bacterial speciation. Horizontal gene flow allows gene-specific sweeps in bacterial populations, where adaptive genes are shared preferentially between recombining bacteria independent of their genomic background. Thus, discontinuities in horizontal gene flow can be utilised to demarcate a genotypically and ecologically cohesive bacterial species. 
Previous studies have demonstrated that ecological populations exist in heterotrophic bacteria. However, examining the generalisability of the ecological population theory requires understanding the role of horizontal gene flow in delineating populations from extreme bacterial communities, especially bacteria with limited metabolic redundancy due to their higher impact of deleterious consequences (e.g., pathway dysregulation by recombination of a maladaptive gene) during horizontal gene flow. Therefore, in this work, I utilised the chemolithoautotrophic hydrogen-oxidising Aquificota bacteria from natural populations as a model system to test the generalisability of the ecological population theory. Utilising a novel high-throughput isolation method, I isolated co-habiting Aquificota bacteria with minimal enrichment from geothermal springs. Sequencing and comparative analysis of the Aquificota genomes reveal intra-species genomic variations driven by varying degrees of horizontal gene flow and a population structure composed of co-occurring clonal lineages and recombinogenic bacteria. To examine whether these Aquificota populations exhibit ecological and evolutionary patterns akin to eukaryotic species, I investigated the changes in their population structure across four additional time points (1 year). Analysis of recent horizontal gene flow and mutations in Aquificota populations show that clonal lineages remain clonal across time, with minimal changes in their genomic background diversity. In contrast, recombining populations experience variation in intra-population diversity and a shift in the dominant genomic background across time—implying an intra-population turnover. Lastly, I also investigated the role of both non-homologous and homologous recombination in maintaining ecological populations in Aquificota by analysing the presence and function of mobile genetic elements (MGEs) in its different populations. The lack of spatial and functional overlap between MGEs and horizontally swept regions confirms that homologous recombination drives horizontal gene flow in Aquificota populations.
This work demonstrated that ecological populations in Aquificota can be delineated through discontinuities in horizontal gene flow driven primarily by homologous recombination. Thus, ecological population theory can be a generalisable model for speciation and evolution in bacteria.

year: 2024

title: Creating culturally-safe schools for Māori students

authors: Macfarlane, Angus

subjects: education

abstract: In order to better understand the present trends in New Zealand’s schooling contexts, there is a clarion call for educators to develop sensitivity and sensibility towards the cultural backgrounds and experiences of Māori students. This paper reports on the work of four scholars who share research that has been undertaken in educational settings with high numbers of Māori students, and discusses the importance of creating culturally-safe schools – places that allow and enable students to be who and what they are. The theoretical frameworks drawn on are based on both a life partnership analogy as well as on a socio-cultural perspective on human development and learning. The Māori worldview presented in this paper is connected to the Treaty of Waitangi, The Educultural Wheel and the Hikairo Rationale. Data were collected from two ethnographic case studies and analysed through these frameworks. Practical suggestions are then made for using restorative practices and creating reciprocal relationships in classrooms within an environment of care. The paper reports on an evidence-based approach to creating culturally-safe schools for Māori students.

text: Creating culturally-safe schools for Māori students In order to better understand the present trends in New Zealand’s schooling contexts, there is a clarion call for educators to develop sensitivity and sensibility towards the cultural backgrounds and experiences of Māori students. This paper reports on the work of four scholars who share research that has been undertaken in educational settings with high numbers of Māori students, and discusses the importance of creating culturally-safe schools – places that allow and enable students to be who and what they are. The theoretical frameworks drawn on are based on both a life partnership analogy as well as on a socio-cultural perspective on human development and learning. The Māori worldview presented in this paper is connected to the Treaty of Waitangi, The Educultural Wheel and the Hikairo Rationale. Data were collected from two ethnographic case studies and analysed through these frameworks. Practical suggestions are then made for using restorative practices and creating reciprocal relationships in classrooms within an environment of care. The paper reports on an evidence-based approach to creating culturally-safe schools for Māori students.

year: 2007