This thesis examines the effects of species, rainfall and soil type on tree biomass regressions, as well as the effects of stand dominance and structure on stand biomass regressions in north-east Australian woodlands. This was achieved by examining tree characteristics and biomass relationships for a series of woodland monitoring sites throughout the study area. This study utilised a modified data set from this permanent monitoring site network to provide structural attributes for trees and communities of varying composition in the grazed woodlands. These data were supplemented with environmental data and tree harvest data sets. Initially, the research reported in this thesis developed allometric and stand biomass regressions for Callitris glaucophylla communities. This research also demonstrated that changes in tree-form were not reflected in changes in the environment, nor did such changes reflect changes in tree biomass regressions for three eucalypt species. As a result, a common regression provides a robust estimate of total aboveground biomass of eucalypt trees in the study area. Thus expensive destructive harvesting can generally be avoided for minor eucalypt species. Finally, this study demonstrated a successful methodology that described the stand structure of all the grazed woodland sites based on tree heights. This methodology was developed to allow the expansion of a single stand regression to estimate stand biomass across the entire north-east Australian woodlands. The findings demonstrated in this study, combined with the long-term data from the permanent monitoring network sites, should enhance the estimation of carbon flux within eucalypt communities of north-east Australia’s grazed woodlands.

(1) Rate of increase was measured for feral donkey populations in parts of northern Australia as the average exponential rate of increase, r, in a population subjected to substantial reduction. (2) The annual rate of increase was estimated to be r = 0.21. This estimate was compared with the exponential rate of increase in another recovering donkey population and found to be in close agreement. (3) Ultimate and proximate factors regulating the abundance of feral donkey populations were examined by monitoring and sampling two populations; one at or close to equilibrium density, the other below equilibrium density and recovering from reduction. (4) The size of the population at equilibrium density remained stable over the 12 months of monitoring while the size of the recovering population increased by 20 percent (r = 0.18/yr). (5) Growth and body condition were significantly depressed in the population at equilibrium density suggesting that donkey populations are limited by the food resources available to them. (6) Breeding occured over a discrete season, with births occurring between September and February. 11 (7) Fecundity was high, with more than 75 percent of mature females breeding in each year, and was independent of population density. (8) Adult and juvenile mortality were density dependent, with mortality over the first six months of life the most important demographic factor influencing rate of increase in donkey populations, and hence population abundance. (9) Implications of the estimated rate of population increase for the cost of long-term control of feral donkey populations were examined by constructing numerical models predicting the relative cost of ongoing control. (10) These models were constructed using functions to describe density dependent variation in population productivity and the cost per donkey removed. (11) The cost of removing donkeys at various population densities was estimated using predator-prey theory. The cost, measured in hours of helicopter time per removal, was found theoretically and empirically to take the form of an inverted functional response curve, with cost saturated at high donkey densities. (12) The utility of models predicting the cost of continuing pest control is illustrated by comparing the relative costs of two potential strategies for feral donkey control.

This study provides one of the first accounts of the relationships between termites, termitaria and the pedolith, towards developing their application as a biogeochemical sampling medium for mineral exploration. Mapping regolith–landforms, termitaria, and the associated termitaria biogeochemistry show that termites are an integral control on the organisation of trace metals in the landscapes of northern Australia. In particular, termites are important for transporting geochemical signatures from depth, through the pedolith and to the ground surface. This occurs by way of bioturbative and constructional activities of the mound-building termites, which in this study included Nasutitermes triodiae, Amitermes vitiosus, Drepanotermes rubriceps, Tumulitermes hastilis and T. pastinator. Termitaria from these species are mappable regolith– landform attributes at the local scale; this highlights their specific preferences for colony sites, such as access to vegetation, drainage, and the availability of construction materials. The mound-building termites featured in this study are also soil modifiers, altering the pedolith terms of both structure and chemistry. Developing an understanding of these processes has helped to refine a model for pedolith development through biotic processes, which is applicable to subtropical and tropical climatic regions, where termites act as important ecosystem engineers. This research project fills a niche for new scientific investigation of deeper regolith profiles and associated terrains; it moves away from theories of shallow soil development overlying an abiotic deep regolith, towards understanding pedolith development as wholly biotically driven. For mineral explorers this means that ore-related elements, such as Au, As and Zn, are re-organised and moved towards the land surface in settings such as buried Au-deposits and mineralisation in the Tanami region, and Pine Creek Orogen. A key finding within the study of the application of this technique is that the fine, silt-clay (>79 μm) from termitaria is capable of accurately delineating the surficial expression of buried Au mineralisation. Termitaria can therefore provide an accessible surficial biogeochemical sampling media that can be used in mineral exploration programs / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1369217 / Thesis (Ph.D.) - University of Adelaide, School of Earth and Environmental Sciences, 2009

This thesis presents the results of an archaeological investigation of shell matrix sites, and in particular, shell mounds sites that occur around the shores of Albatross Bay, near Weipa on the north western Cape York Peninsula, northern Australia. It is the contention of this thesis that earlier approaches to the investigation of shell mound sites in northern Australia have tended to place too much emphasis on developing long-term explanatory models that gloss over explanations for the specific roles of these unique sites in past economic systems. While long-term explanations represent important contributions, it is argued here that short-term decadal scale modelling of the production systems associated with shell mound formation and use are required in order to fully understand the significance of the mid- to late Holocene emergence of these types of sites. A focus on production – defined in a substantive economic sense – is a suitable avenue through which archaeologists can expand our understanding of the role of these features in past gatherer-hunter societies, and their broader importance on longer-term time scales The thesis thus develops a detailed model of the production strategies associated with the formation of shell mound sites that occur around Albatross Bay, while also considering the broader significance of this model, particularly within the context of Cape York Peninsula. It presents the results of field surveys and excavations carried out around Albatross Bay by the author, as well as a detailed review and analysis of work carried out by others. It is argued that shell mounds are the result of relatively specialised production activities focussing on a very specific resource base: mudflat shellfish species. Shell mounds offered a range of unique benefits for people engaged in these specialised activities, including as camp sites and as specialised activity areas. These events were inherently flexible in size and in terms of timing, reflecting the dynamic nature of the resource base itself; yet the flexible nature of this production strategy also enabled more regular small scale social gatherings, along with a range of social and economic benefits to participants, than would have been otherwise possible. It is proposed that these types of strategies may represent an important characteristic of the production systems employed by gatherer-hunter peoples in late Holocene Cape York. Overall, this thesis makes a significant contribution to both our understanding of late Holocene lifeways at Albatross Bay as well as to our understanding of the broader significance of the emergence of shell mound sites in Cape York. Furthermore, it highlights the range of insights that can come from a focus on short-term modelling of gatherer-hunter lifeways alongside approaches oriented toward longer-term explanations of economic, social and environmental change.

This study provides one of the first accounts of the relationships between termites, termitaria and the pedolith, towards developing their application as a biogeochemical sampling medium for mineral exploration. Mapping regolith–landforms, termitaria, and the associated termitaria biogeochemistry show that termites are an integral control on the organisation of trace metals in the landscapes of northern Australia. In particular, termites are important for transporting geochemical signatures from depth, through the pedolith and to the ground surface. This occurs by way of bioturbative and constructional activities of the mound-building termites, which in this study included Nasutitermes triodiae, Amitermes vitiosus, Drepanotermes rubriceps, Tumulitermes hastilis and T. pastinator. Termitaria from these species are mappable regolith– landform attributes at the local scale; this highlights their specific preferences for colony sites, such as access to vegetation, drainage, and the availability of construction materials. The mound-building termites featured in this study are also soil modifiers, altering the pedolith terms of both structure and chemistry. Developing an understanding of these processes has helped to refine a model for pedolith development through biotic processes, which is applicable to subtropical and tropical climatic regions, where termites act as important ecosystem engineers. This research project fills a niche for new scientific investigation of deeper regolith profiles and associated terrains; it moves away from theories of shallow soil development overlying an abiotic deep regolith, towards understanding pedolith development as wholly biotically driven. For mineral explorers this means that ore-related elements, such as Au, As and Zn, are re-organised and moved towards the land surface in settings such as buried Au-deposits and mineralisation in the Tanami region, and Pine Creek Orogen. A key finding within the study of the application of this technique is that the fine, silt-clay (>79 μm) from termitaria is capable of accurately delineating the surficial expression of buried Au mineralisation. Termitaria can therefore provide an accessible surficial biogeochemical sampling media that can be used in mineral exploration programs / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1369217 / Thesis (Ph.D.) - University of Adelaide, School of Earth and Environmental Sciences, 2009

It is often hypothesised that marine species with mobile planktonic phases are capable of widespread dispersal and may therefore be genetically homogenous throughout their distribution. Studies that have demonstrated positive correlation between duration of plankton phase and levels of gene flow reinforce the prediction that life history characteristics of marine species determine the potential extent of genetic and demographic connectivity throughout their distributions. This prediction has however been challenged by studies that have employed genetic markers highly sensitive to both historical and contemporary demographic changes. Disparities between dispersal potential and measured levels of gene flow have been demonstrated both among historically disconnected ocean basins and within semi-enclosed areas of strong hydraulic connectivity. These studies and others highlight a need for greater focus on factors that may influence population structure and distribution for marine species. In this thesis, I have examined genetic structure within and among populations of an estuarine species of mud crab Scylla serrata (Forskal, 1775) using a number of genetic markers and methods. The species is widely distributed throughout mangrove and estuarine habitats of the Indo - West Pacific (IWP); it is generally assumed that life-history characteristics of S. serrata promote high levels of population admixture and gene flow throughout its distribution. Alternatively, factors that have promoted population genetic structure for a variety of IWP marine species may also have affected S. serrata populations. By investigating genetic structure at several spatial scales of sampling, I was able to address a variety of hypotheses concerning the species distribution, dispersal, and genetic structure. Episodic changes to marine habitat and conditions experienced within the IWP during the Pleistocene may have affected genetic structure for a broad variety of marine taxa. The relative strength of this hypothesis may be assayed by comparative genetic studies of widespread IWP taxa with high dispersal capacity. In order to ascertain levels of historical and contemporary gene flow for S. serrata, I investigated the phylogeographic distribution of mitochondrial DNA haplotypes sampled throughout the species range. Adults were sampled from three west Indian ocean locations (N=21), six west Pacific sites (N=68), and two sites from northern eastern Australia (N=35). Temperature gradient gel electrophoresis and sequencing of 549 base pairs of the mitochondrial cytochrome oxidase I (COI) coding gene identified 18 distinct haplotypes. Apart from that seen in northern Australia, haplotype diversity was low (h < 0.36) at each of the locations. Total nucleotide diversity in the entire sample (excluding northern Australian locations) was also low (p = 0.09). Haplotypes clustered into two clades separated by approximately 2% sequence divergence. One clade was widespread throughout the IWP (clade 1) whereas the other was strictly confined to northern Australia (clade 2). Genealogical assessment of sequenced haplotypes relative to their distributions suggested that a historical radiation of clade 1 S. serrata throughout the IWP occurred rapidly and recently (<1Myr bp) from a west Pacific origin. The evidence of fixed unique haplotypes at the majority of locations suggested that contemporary maternal gene flow between trans-oceanic sites was limited. Contrary to reports for other widespread species of IWP taxa, there was no evidence of lengthy periods of regional separation between Indian from Pacific Ocean populations. However, results may indicate a separation of northern Australian crabs from other locations before and during the IWP radiation. I speculated that this isolation might have resulted in the formation of a new species of Scylla. Additional sampling of mud crabs from the Australian coastline allowed an examination of the diversity and distribution of clade 1 and 2 haplotypes among recently formed shelf-connected coastal locations, and across a historical bio-geographic barrier. Over 300 individuals were sampled from multiple locations within coastal regions (western, northern and eastern) of Australia and analysed for mutational differences at the COI gene. Analysis of molecular variance partitioned by sampling scale (Among regions, within regions, and within all locations) indicated mitochondrial haplotypes were structured regionally (P < 0.001), which contrasted with evidence of genetic panmixia within regions. Regional genetic structure broadly correlated with hydrological circulation, supporting the contention that release and transport of propagules away from the estuary may allow genetic connectivity among widespread shelf-connected S. serrata populations. That similar patterns of maternal gene flow were absent among trans-oceanic populations may indicate that the spatial scale of effective dispersal for this species is generally limited to areas of coastal shelf. The two clades of haplotypes were geographically separated either side of the Torres Strait, a narrow sea channel connecting the northern and eastern regions of coastal Australia. This pattern of historical genetic separation was concordant with a number of other marine species across northern Australia, and might indicate a shared history of vicariance induced by eustasy. Alternatively, differences in diversity and distribution of the clades may be evidence of two independent expansions of clade 1 and 2 crab populations into Australian regions following post-glacial estuary formation. Overall, despite evidence of genetic panmixia within extensive sections of the Australian distribution, there was also evidence of significant barriers to maternal gene flow with both shallow and deep regional phylogeographic assortment of mtDNA haplotypes. The presence of these barriers indicated both historical and contemporary factors have imposed limits to effective dispersal by this species among coastal habitats. A subset of the Australian sample (8 locations, N = 188) was also examined for variation at five microsatellite loci developed specifically here for S. serrata. I examined variation among samples at each of the loci to: a) independently verify regional structure among crab populations previously detected using the mtDNA analysis; b) test for evidence of co-distributed non-interbreeding stocks of S. serrata within Australian waters by examining samples for segregation of alleles within microsatellite loci concordant with the two mtDNA clades. The frequency and distribution of alleles for each of the highly polymorphic microsatellites were homogenous at all levels of sample partitioning and contrasted sharply with the instances of both weak and strong regional phylogeographic assortment of mtDNA haplotypes. These contrasting results between different genomic markers were examined in relation to the species life history, and to differences in mutational rate and inheritance of the genetic markers. Several hypotheses may explain the disparity, however it is most likely that rampant homoplasy and high rates of mutation at the microsatellite in conjunction with large Ne at locations may be concerted to delay equilibrium between genetic drift and migration among populations at these highly polymorphic nuclear markers. There was also no evidence that alleles at microsatellite loci were co-segregated with mtDNA clades and therefore no evidence of segregated breeding between the clades of crabs. Whether or not this result was also driven by homoplasy at the microsatellites remains unknown. Recently established mud crab populations (~ 3-4 years old) observed in a number of southwest Australian estuaries are almost 1000 kilometres south of their previously recorded distribution on the Western Australian coast. Colonisation of the southwest region may have occurred either by a natural range expansion from northwest Australian mud crab populations or by means of translocation from any number of mud crab sources within the Indo - West Pacific. I used mtDNA analysis to verify the species and determine the potential source population(s) of the colonists, by comparing sampled genetic material from the southwest (N = 32) against that previously described for the genus. I also compared levels of diversity at mtDNA and two microsatellite loci between the colonist and suspected source population(s) to qualitatively determine if the southwest populations experienced reductions in genetic diversity as a result of the colonisation process. All colonist samples had S. serrata mtDNA COI sequences identical to one previously described as both prevalent and endemic to northwest Australia. High levels of genetic diversity among source and colonist populations at two microsatellite loci contrasted to the mitochondrial locus which displayed an absence of variation among colonists compared to moderately diverse source populations. I argued that the southwest was recently colonised by large numbers of S. serrata propagules derived from the northwest of Australia, possibly due to an enhanced recruitment event coinciding with the reported strengthening of the Leeuwin Current during 1999. Contrasting levels of diversity among nuclear and mitochondrial loci may be attributed to a difference in response by the two genomes to the colonisation process. I predict that such differences may be generally prevalent among plankton-dispersed species. Finally, I discuss aspects of the species distribution and biogeography obtained as a composite of the various results and ideas expressed in this thesis. I propose that S. serrata populations in the IWP may have experienced several cycles of extinction and population retraction from temperate areas followed by subsequent periods of colonisation and rapid coastal expansion in response to the effects of glacial episodes on coastal habitats in the IWP. I propose that persistence of this species as remnant populations of clade 1 and 2 crabs at equatorial locations during low sea level stands provided source populations for later expansions by the species into a variety of coastal areas throughout the IWP. Further analysis is required to determine if mtDNA clade 1 and 2 crabs are non-interbreeding species of mud crab.