title: The genetic structure of New Zealand's coastal benthos: using the estuarine clam Austrovenus stutchburyi, to determine rates of gene flow and population connectivity

authors: Ross, Philip M.

subjects: cockle

abstract: For many benthic marine taxa, dispersal over large distances is dependent on a pelagic larval phase. It is through the dispersal process that benthic taxa can found new populations, colonise disturbed or degraded habitats and achieve genetic exchange between geographically separated subpopulations. While it is widely accepted that the dispersal process is important in determining the dynamics of many marine communities, difficulties associated with the direct measurement of larval dispersal mean that detailed knowledge of the mechanisms controlling larval transport has been elusive. Consequently, indirect methods, such as population genetics, have been used to estimate dispersal pathways. This thesis examines the population genetic structure of New Zealand’s coastal benthos with the aim of enhancing our understanding of population connectivity, as well as identifying physical and biological processes that might influence population genetic structure.

The population genetic structure of New Zealand’s coastal benthos was examined in a quantitative literature review. Divergence between northern and southern populations was identified as the most frequently reported population genetic structure, with the divergence most often located in central New Zealand. Additional population structure although rare, was reported for a number of taxa, particularly those restricted to estuaries and with life history traits indicative of limited dispersal potential. A significant negative correlation between pelagic larval duration (PLD) and genetic divergence suggests that PLD may be a useful proxy for a species’ dispersal ability. However, variation in estimates of divergence for taxa with limited PLDs suggests that other factors may also influence dispersal potential. 
To determine whether populations of an estuarine organism with life history traits indicative of widespread dispersal are genetically subdivided, I examined the population genetic structure of the clam Austrovenus stutchburyi using the mitochondrial gene cytochrome oxidase c subunit I (COI). Analyses indicated that dispersal was limited and that gene flow was mostly occurring among estuaries in close proximity. Genetic boundaries were detected in central New Zealand, about the East and North Capes and in the south of the South Island. Similar boundaries have been reported for estuarine taxa lacking a dispersive larval phase suggesting that distribution and habitat requirements may influence patterns of gene flow. 
To further investigate gene flow among estuaries, I conducted a multi-scale genetic analysis of A. stutchburyi populations on New Zealand’s west coast Analyses of COI and microsatellite loci showed populations to be well connected within estuaries and at the regional sampling scale (≤ 156 km) although not at a national scale (≤ 1226 km). Distance among populations explained much of the observed genetic variation as did distance between estuaries. Long stretches of open coast appear to act as barriers to dispersal among A. stutchburyi populations. However, as long stretches of open coast also coincide with putative hydrodynamic dispersal barriers there is some uncertainty about the roles of barriers versus inter-estuary distance in generating the observed divergences. Within-estuary genetic differences were evident from COI analyses, but may result from local adaptation to within-estuary environmental gradients. 
I conclude that genetic connectivity among populations of New Zealand’s estuarine taxa is generally low relative to coastal species. The data presented here also suggest that migration among patchily distributed habitats, such as estuaries, will be dependent on the spatial arrangement of habitats. Consequently, patchily distributed taxa may experience low rates of ecologically meaningful connectivity, requiring relatively cautious management at small spatial scales to ensure the persistence of intact biological communities in the face of persistent anthropogenic and natural disturbances.

text: The genetic structure of New Zealand's coastal benthos: using the estuarine clam Austrovenus stutchburyi, to determine rates of gene flow and population connectivity For many benthic marine taxa, dispersal over large distances is dependent on a pelagic larval phase. It is through the dispersal process that benthic taxa can found new populations, colonise disturbed or degraded habitats and achieve genetic exchange between geographically separated subpopulations. While it is widely accepted that the dispersal process is important in determining the dynamics of many marine communities, difficulties associated with the direct measurement of larval dispersal mean that detailed knowledge of the mechanisms controlling larval transport has been elusive. Consequently, indirect methods, such as population genetics, have been used to estimate dispersal pathways. This thesis examines the population genetic structure of New Zealand’s coastal benthos with the aim of enhancing our understanding of population connectivity, as well as identifying physical and biological processes that might influence population genetic structure.

The population genetic structure of New Zealand’s coastal benthos was examined in a quantitative literature review. Divergence between northern and southern populations was identified as the most frequently reported population genetic structure, with the divergence most often located in central New Zealand. Additional population structure although rare, was reported for a number of taxa, particularly those restricted to estuaries and with life history traits indicative of limited dispersal potential. A significant negative correlation between pelagic larval duration (PLD) and genetic divergence suggests that PLD may be a useful proxy for a species’ dispersal ability. However, variation in estimates of divergence for taxa with limited PLDs suggests that other factors may also influence dispersal potential. 
To determine whether populations of an estuarine organism with life history traits indicative of widespread dispersal are genetically subdivided, I examined the population genetic structure of the clam Austrovenus stutchburyi using the mitochondrial gene cytochrome oxidase c subunit I (COI). Analyses indicated that dispersal was limited and that gene flow was mostly occurring among estuaries in close proximity. Genetic boundaries were detected in central New Zealand, about the East and North Capes and in the south of the South Island. Similar boundaries have been reported for estuarine taxa lacking a dispersive larval phase suggesting that distribution and habitat requirements may influence patterns of gene flow. 
To further investigate gene flow among estuaries, I conducted a multi-scale genetic analysis of A. stutchburyi populations on New Zealand’s west coast Analyses of COI and microsatellite loci showed populations to be well connected within estuaries and at the regional sampling scale (≤ 156 km) although not at a national scale (≤ 1226 km). Distance among populations explained much of the observed genetic variation as did distance between estuaries. Long stretches of open coast appear to act as barriers to dispersal among A. stutchburyi populations. However, as long stretches of open coast also coincide with putative hydrodynamic dispersal barriers there is some uncertainty about the roles of barriers versus inter-estuary distance in generating the observed divergences. Within-estuary genetic differences were evident from COI analyses, but may result from local adaptation to within-estuary environmental gradients. 
I conclude that genetic connectivity among populations of New Zealand’s estuarine taxa is generally low relative to coastal species. The data presented here also suggest that migration among patchily distributed habitats, such as estuaries, will be dependent on the spatial arrangement of habitats. Consequently, patchily distributed taxa may experience low rates of ecologically meaningful connectivity, requiring relatively cautious management at small spatial scales to ensure the persistence of intact biological communities in the face of persistent anthropogenic and natural disturbances.

year: 2011

title: Speeding up logistic model tree induction

authors: Sumner, Marc

subjects: computer science

abstract: Logistic Model Trees have been shown to be very accurate and compact classifiers [8]. Their greatest disadvantage is the computational complexity of inducing the logistic regression models in the tree. We address this issue by using the AIC criterion [1] instead of cross-validation to prevent overfitting these models. In addition, a weight trimming heuristic is used which produces a significant speedup. We compare the training time and accuracy of the new induction process with the original one on various datasets and show that the training time often decreases while the classification accuracy diminishes only slightly.

text: Speeding up logistic model tree induction Logistic Model Trees have been shown to be very accurate and compact classifiers [8]. Their greatest disadvantage is the computational complexity of inducing the logistic regression models in the tree. We address this issue by using the AIC criterion [1] instead of cross-validation to prevent overfitting these models. In addition, a weight trimming heuristic is used which produces a significant speedup. We compare the training time and accuracy of the new induction process with the original one on various datasets and show that the training time often decreases while the classification accuracy diminishes only slightly.

year: 2005

title: From mainstream to manaaki: Indigenising our approach to immigration

authors: Kukutai, Tahu

abstract: In recent years, discontent with migration and migrants in the wealthy global north has manifested in disturbing ways: cue Brexit, xenophobia, border paranoia, far-right nationalism and its bedfellow white supremacy. On the surface, Aotearoa New Zealand appears to have escaped the uglier aspects of this nativism. Despite the grumblings of the New Zealand First Party, no serious popular or political anti-immigration movement has appeared, and racially motivated attacks against migrants are relatively rare. This is despite the fact that Aotearoa has a much higher relative foreign-born population share than the United States or United Kingdom,1 and ‘superdiverse’ Auckland – which comprises at least 40 per cent migrants – now has the ignominious claim to being the fourthleast affordable city in the world, far outstripping London and New York.

text: From mainstream to manaaki: Indigenising our approach to immigration In recent years, discontent with migration and migrants in the wealthy global north has manifested in disturbing ways: cue Brexit, xenophobia, border paranoia, far-right nationalism and its bedfellow white supremacy. On the surface, Aotearoa New Zealand appears to have escaped the uglier aspects of this nativism. Despite the grumblings of the New Zealand First Party, no serious popular or political anti-immigration movement has appeared, and racially motivated attacks against migrants are relatively rare. This is despite the fact that Aotearoa has a much higher relative foreign-born population share than the United States or United Kingdom,1 and ‘superdiverse’ Auckland – which comprises at least 40 per cent migrants – now has the ignominious claim to being the fourthleast affordable city in the world, far outstripping London and New York.

year: 2017