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1

Annear, Christopher M., and Peter R. Waylen. "Socializing the rain: human adaptation to ecological variability in a fishery, Mweru-Luapula, Zambia." Journal of Political Ecology 26, no. 1 (January 4, 2019): 224. http://dx.doi.org/10.2458/v26i1.23246.

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<p><strong>Abstract </strong></p><p>Rainfall drives fishery fertility in Mweru-Luapula, thus rainfall variability contributes to frequent changes in fishing catches. Fishers and traders have adapted their institutions to this variable ecology in a variety of ways, including learning to read the fishery for productive periods and practicing multiple modes of income procurement. By accurately identifying inter-annual, inter-decadal, and longer spans of rainfall trends, future high and low yields can be forecast. This article presents and analyzes annual rainfall in the fishery from 1916-1992 and quantitative fish market data comprised of observed fish catch numbers by species in three markets from September 2004 to September 2005. It uses political ecology to better understand fish production, trade, and subsistence in this South-Central African freshwater fishery. We combine qualitative analysis of fisher and marketer perceptions of the fishery and knowledge of rainfall patterns to show how human behavior is not "tragically" driven, but instead based on the state of the ecological, sociocultural, and socioeconomic environment at a given time.</p><p><strong>Keywords</strong>: African freshwater fisheries, rainfall modeling, political ecology, Mweru-Luapula, Zambia, climate change</p>
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2

Simulundu, Edgar, Akihiro Ishii, Manabu Igarashi, Aaron S. Mweene, Yuka Suzuki, Bernard M. Hang’ombe, Boniface Namangala, et al. "Characterization of influenza A viruses isolated from wild waterfowl in Zambia." Journal of General Virology 92, no. 6 (June 1, 2011): 1416–27. http://dx.doi.org/10.1099/vir.0.030403-0.

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Although the quest to clarify the role of wild birds in the spread of the highly pathogenic H5N1 avian influenza virus (AIV) has yielded considerable data on AIVs in wild birds worldwide, information regarding the ecology and epidemiology of AIVs in African wild birds is still very limited. During AIV surveillance in Zambia (2008–2009), 12 viruses of distinct subtypes (H3N8, H4N6, H6N2, H9N1 and H11N9) were isolated from wild waterfowl. Phylogenetic analyses demonstrated that all the isolates were of the Eurasian lineage. Whilst some genes were closely related to those of AIVs isolated from wild and domestic birds in South Africa, intimating possible AIV exchange between wild birds and poultry in southern Africa, some gene segments were closely related to those of AIVs isolated in Europe and Asia, thus confirming the inter-regional AIV gene flow among these continents. Analysis of the deduced amino acid sequences of internal proteins revealed that several isolates harboured particular residues predominantly observed in human influenza viruses. Interestingly, the isolates with human-associated residues exhibited higher levels of virus replication in the lungs of infected mice and caused more morbidity as measured by weight loss than an isolate lacking such residues. This study stresses the need for continued monitoring of AIVs in wild and domestic birds in southern Africa to gain a better understanding of the emergence of strains with the potential to infect mammals.
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Ormerod, W. E., and L. R. Rickman. "Sleeping sickness control—how wildlife and man could benefit." Oryx 22, no. 1 (January 1988): 36–40. http://dx.doi.org/10.1017/s003060530002737x.

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Tsetse eradication and control programmes are often carried out in order that cattle can be introduced into the cleared area. The resultant destruction to habitats and wildlife can be considerable, and the majority of Africa's human population does not benefit from increased beef production. The authors say that we need a different approach, one that would concentrate on controlling sleeping sickness in humans, and on conserving the indigenous vegetation and fauna. They illustrate their approach by describing what could be done in a part of northern Zambia where sleeping sickness is endemic.
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4

Bwalya Umar, Bridget, and Julius Kapembwa. "Economic Benefits, Local Participation, and Conservation Ethic in a Game Management Area: Evidence From Mambwe, Zambia." Tropical Conservation Science 13 (January 2020): 194008292097175. http://dx.doi.org/10.1177/1940082920971754.

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This study examines views on economic benefits, local participation in wildlife management and conservation ethic among 267 residents of three chiefdoms in Mambwe district, Eastern Zambia. Results show that 68% of the residents who live in the Lupande Game Management Area are not in any way involved in community wildlife management. For those involved, the main reason advanced for participating was economic benefit (79%). Only a small minority of 17% of the residents participated due to motivations to conserve wildlife. Human-wildlife conflicts induced by wild animal crop raiding, property destruction, and loss of human life, and perceived low or non-existent economic benefits seemingly precluded the development of a conservation ethic among residents. The local chiefs asserted wildlife ownership, lamented low wildlife benefits and justified its illegal uptake. Proponents of community conservation projects could encourage pro conservation attitudes among residents by addressing human-wildlife conflicts and raising awareness on intrinsic values of wildlife.
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5

Sprengelmeyer, Quentin D., Suzan Mansourian, Jeremy D. Lange, Daniel R. Matute, Brandon S. Cooper, Erling V. Jirle, Marcus C. Stensmyr, and John E. Pool. "Recurrent Collection of Drosophila melanogaster from Wild African Environments and Genomic Insights into Species History." Molecular Biology and Evolution 37, no. 3 (November 15, 2019): 627–38. http://dx.doi.org/10.1093/molbev/msz271.

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Abstract A long-standing enigma concerns the geographic and ecological origins of the intensively studied vinegar fly, Drosophila melanogaster. This globally distributed human commensal is thought to originate from sub-Saharan Africa, yet until recently, it had never been reported from undisturbed wilderness environments that could reflect its precommensal niche. Here, we document the collection of 288 D. melanogaster individuals from multiple African wilderness areas in Zambia, Zimbabwe, and Namibia. The presence of D. melanogaster in these remote woodland environments is consistent with an ancestral range in southern-central Africa, as opposed to equatorial regions. After sequencing the genomes of 17 wilderness-collected flies collected from Kafue National Park in Zambia, we found reduced genetic diversity relative to town populations, elevated chromosomal inversion frequencies, and strong differences at specific genes including known insecticide targets. Combining these genomes with existing data, we probed the history of this species’ geographic expansion. Demographic estimates indicated that expansion from southern-central Africa began ∼13,000 years ago, with a Saharan crossing soon after, but expansion from the Middle East into Europe did not begin until roughly 1,800 years ago. This improved model of demographic history will provide an important resource for future evolutionary and genomic studies of this key model organism. Our findings add context to the history of D. melanogaster, while opening the door for future studies on the biological basis of adaptation to human environments.
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6

Gillett, Rhonda M., and Phillip V. Tobias. "Human growth in southern Zambia: a first study of Tonga children predating the Kariba dam (1957-1958)." American Journal of Human Biology 14, no. 1 (December 27, 2001): 50–60. http://dx.doi.org/10.1002/ajhb.10019.

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7

Tripathi, Hemant G., Tiwonge I. Mzumara, Rowan O. Martin, Catherine L. Parr, Chaona Phiri, and Casey M. Ryan. "Dissimilar effects of human and elephant disturbance on woodland structure and functional bird diversity in the mopane woodlands of Zambia." Landscape Ecology 34, no. 2 (February 2019): 357–71. http://dx.doi.org/10.1007/s10980-019-00774-2.

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8

Bullock, Eric L., Sean P. Healey, Zhiqiang Yang, Phoebe Oduor, Noel Gorelick, Steve Omondi, Edward Ouko, and Warren B. Cohen. "Three Decades of Land Cover Change in East Africa." Land 10, no. 2 (February 3, 2021): 150. http://dx.doi.org/10.3390/land10020150.

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Population growth rates in Sub-Saharan East Africa are among the highest in the world, creating increasing pressure for land cover conversion. To date, however, there has been no comprehensive assessment of regional land cover change, and most long-term trends have not yet been quantified. Using a designed sample of satellite-based observations of historical land cover change, we estimate the areas and trends in nine land cover classes from 1998 to 2017 in Ethiopia, Kenya, Uganda, Malawi, Rwanda, Tanzania, and Zambia. Our analysis found an 18,154,000 (±1,580,000) ha, or 34.8%, increase in the area of cropland in East Africa. Conversion occurred primarily from Open Grasslands, Wooded Grasslands, and Open Forests, causing a large-scale reduction in woody vegetation classes. We observed far more conversion (by approximately 20 million hectares) of woody classes to less-woody classes than succession in the direction of increasing trees and shrubs. Spatial patterns within our sample highlight regional land cover conversion hotspots, such as the Central Zambezian Miombo Woodlands, as potential areas of concern related to the conservation of natural ecosystems. Our findings reflect a rapidly growing population that is moving into new areas, with a 43.5% increase in the area of Settlements over the three-decade period. Our results show the areas and ecoregions most impacted by three decades of human development, both spatially and statistically.
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9

Estes, L. D., T. Searchinger, M. Spiegel, D. Tian, S. Sichinga, M. Mwale, L. Kehoe, et al. "Reconciling agriculture, carbon and biodiversity in a savannah transformation frontier." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1703 (September 19, 2016): 20150316. http://dx.doi.org/10.1098/rstb.2015.0316.

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Rapidly rising populations and likely increases in incomes in sub-Saharan Africa make tens of millions of hectares of cropland expansion nearly inevitable, even with large increases in crop yields. Much of that expansion is likely to occur in higher rainfall savannas, with substantial costs to biodiversity and carbon storage. Zambia presents an acute example of this challenge, with an expected tripling of population by 2050, good potential to expand maize and soya bean production, and large areas of relatively undisturbed miombo woodland and associated habitat types of high biodiversity value. Here, we present a new model designed to explore the potential for targeting agricultural expansion in ways that achieve quantitatively optimal trade-offs between competing economic and environmental objectives: total converted land area (the reciprocal of potential yield); carbon loss, biodiversity loss and transportation costs. To allow different interests to find potential compromises, users can apply varying weights to examine the effects of their subjective preferences on the spatial allocation of new cropland and its costs. We find that small compromises from the objective to convert the highest yielding areas permit large savings in transportation costs, and the carbon and biodiversity impacts resulting from savannah conversion. For example, transferring just 30% of weight from a yield-maximizing objective equally between carbon and biodiversity protection objectives would increase total cropland area by just 2.7%, but result in avoided costs of 27–47% for carbon, biodiversity and transportation. Compromise solutions tend to focus agricultural expansion along existing transportation corridors and in already disturbed areas. Used appropriately, this type of model could help countries find agricultural expansion alternatives and related infrastructure and land use policies that help achieve production targets while helping to conserve Africa's rapidly transforming savannahs. This article is part of the themed issue ‘Tropical grassy biomes: linking ecology, human use and conservation’.
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10

Matsuno, Keita, Carla Weisend, Masahiro Kajihara, Colette Matysiak, Brandi N. Williamson, Martin Simuunza, Aaron S. Mweene, Ayato Takada, Robert B. Tesh, and Hideki Ebihara. "Comprehensive Molecular Detection of Tick-Borne Phleboviruses Leads to the Retrospective Identification of Taxonomically Unassigned Bunyaviruses and the Discovery of a Novel Member of the Genus Phlebovirus." Journal of Virology 89, no. 1 (October 22, 2014): 594–604. http://dx.doi.org/10.1128/jvi.02704-14.

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ABSTRACTUntil the recent emergence of two human-pathogenic tick-borne phleboviruses (TBPVs) (severe fever with thrombocytopenia syndrome virus [SFTSV] and Heartland virus), TBPVs have been neglected as causative agents of human disease. In particular, no studies have addressed the global distribution of TBPVs, and consequently, our understanding of the mechanism(s) underlying their evolution and emergence remains poor. In order to provide a useful tool for the ecological and epidemiological study of TBPVs, we have established a simple system that can detect all known TBPVs, based on conventional reverse transcription-PCR (RT-PCR) with degenerate primer sets targeting conserved regions of the viral L genome segment. Using this system, we have determined that several viruses that had been isolated from ticks decades ago but had not been taxonomically identified are novel TBPVs. Full-genome sequencing of these viruses revealed a novel fourth TBPV cluster distinct from the three known TBPV clusters (i.e., the SFTS, Bhanja, and Uukuniemi groups) and from the mosquito/sandfly-borne phleboviruses. Furthermore, by using tick samples collected in Zambia, we confirmed that our system had enough sensitivity to detect a new TBPV in a single tick homogenate. This virus, tentatively designated Shibuyunji virus after the region of tick collection, grouped into a novel fourth TBPV cluster. These results indicate that our system can be used as a first-line screening approach for TBPVs and that this kind of work will undoubtedly lead to the discovery of additional novel tick viruses and will expand our knowledge of the evolution and epidemiology of TBPVs.IMPORTANCETick-borne phleboviruses (TBPVs) have been largely neglected until the recent emergence of two virulent viruses, severe fever with thrombocytopenia syndrome virus and Heartland virus. Little is known about the global distribution of TBPVs or how these viruses evolved and emerged. A major hurdle to study the distribution of TBPVs is the lack of tools to detect these genetically divergent phleboviruses. In order to address this issue, we have developed a simple, rapid, and cheap RT-PCR system that can detect all known TBPVs and which led to the identification of several novel phleboviruses from previously uncharacterized tick-associated virus isolates. Our system can detect virus in a single tick sample and novel TBPVs that are genetically distinct from any of the known TBPVs. These results indicate that our system will be a useful tool for the surveillance of TBPVs and will facilitate understanding of the ecology of TBPVs.
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11

Changula, Katendi, Edgar Simulundu, Boniface Pongombo Lombe, Eri Nakayama, Hiroko Miyamoto, Yuji Takahashi, Hirofumi Sawa, Chuma Simukonda, Bernard M. Hang’ombe, and Ayato Takada. "Serological Evidence of Filovirus Infection in Nonhuman Primates in Zambia." Viruses 13, no. 7 (June 30, 2021): 1283. http://dx.doi.org/10.3390/v13071283.

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Ebolaviruses and marburgviruses are filoviruses that are known to cause severe hemorrhagic fever in humans and nonhuman primates (NHPs). While some bat species are suspected to be natural reservoirs of these filoviruses, wild NHPs often act as intermediate hosts for viral transmission to humans. Using an enzyme-linked immunosorbent assay, we screened two NHP species, wild baboons and vervet monkeys captured in Zambia, for their serum IgG antibodies specific to the envelope glycoproteins of filoviruses. From 243 samples tested, 39 NHPs (16%) were found to be seropositive either for ebolaviruses or marburgviruses with endpoint antibody titers ranging from 100 to 25,600. Interestingly, antibodies reactive to Reston virus, which is found only in Asia, were detected in both NHP species. There was a significant difference in the seropositivity for the marburgvirus antigen between the two NHP species, with baboons having a higher positive rate. These results suggest that wild NHPs in Zambia might be nonlethally exposed to these filoviruses, and this emphasizes the need for continuous monitoring of filovirus infection in wild animals to better understand the ecology of filoviruses and to assess potential risks of outbreaks in humans in previously nonendemic countries.
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12

Pagán-Jiménez, Jaime R., and Julio C. Lazcano-Lara. "Toponymic Data Helps to Reveal the Occurrence of Previously Unknown Populations of Wild Zamia pumila L. on Volcanic Substrates in South Central Puerto Rico." Ethnobiology Letters 4 (March 8, 2013): 52–58. http://dx.doi.org/10.14237/ebl.4.2013.9.

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This is the first report of the occurrence of wild Zamia pumila L. Zamiaceae populations on various volcanic substrates in the piedmont area of south central Puerto Rico. Data acquisition and its field confirmation were possible after the identification of toponymic names in old and current maps, and historic documents of the island in which one of the indigenous names for the genus (marunguey [marungüey] or marungueyes) has been used for naming some localities. These preliminary data have deep implications for paleo- and neoethnobotanical research, and for population ecology of the species in Puerto Rico, because they expand the traditionally accepted range for the species on the island. Zamia has been described as one of the main food plants among pre- and post-Columbian inhabitants in two islands of the Greater Antilles, Hispaniola and Puerto Rico, where the most sophisticated pre-Columbian society of the Antilles, the Taínos, emerged. Our findings suggest that Zamia might have been more available to humans, as a food source, than previously thought.
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13

Malama, Sydney, John Muma, Musso Munyeme, Grace Mbulo, Adrian Muwonge, Isdore Chola Shamputa, Berit Djønne, Jacques Godfroid, and Tone Bjordal Johansen. "Isolation and Molecular Characterization of Mycobacterium tuberculosis from Humans and Cattle in Namwala District, Zambia." EcoHealth 11, no. 4 (May 21, 2014): 564–70. http://dx.doi.org/10.1007/s10393-014-0940-0.

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14

WARBURTON, LOUISE S., and MICHAEL R. PERRIN. "Conservation implications of the drinking habits of Black-cheeked Lovebirds Agapornis nigrigenis in Zambia." Bird Conservation International 15, no. 4 (December 2005): 383–96. http://dx.doi.org/10.1017/s0959270905000614.

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Since 1950, the annual rainfall in the habitat of Black-cheeked Lovebirds Agapornis nigrigenis has decreased, increasing dependence on artificial water supplies. In this study, the seasonal water requirements and drinking behaviour of the lovebirds in their natural habitat were investigated. During the dry season, lovebirds drank at the same water-point in the early morning and late afternoon. Flock sizes of birds at drinking sites ranged from 1 to 175 individuals. Birds from one locale all drank at the same waterhole. Black-cheeked Lovebirds were vigilant and highly cautious drinkers that did not drink at waterholes when disturbed by humans or livestock. The implications for conservation of the species are discussed. Since water availability is a limiting factor for the Black-cheeked Lovebird, gradual desiccation of its habitat has caused the reduction of its small distributional range. Because of increasing dependence on artificial water supplies in a highly localized distribution the priority for conservation management of the species must be creating and maintaining water resources with minimal external disturbance.
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15

Nyirenda, Vincent R., Sudden Sakala, Matamyo Simwanda, Darius Phiri, Yuji Murayama, and Manjula Ranagalage. "Effects of environmental factors on the behaviour and nest group sizes of Smith's bush squirrels, Paraxerus cepapi, in a Zambezian bioregion." Mammalian Biology 101, no. 5 (July 20, 2021): 555–66. http://dx.doi.org/10.1007/s42991-021-00159-6.

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AbstractThe responses of wildlife to environmental factors are of conservation importance. However, the absence of relevant information due to inadequate studies, and lack of understanding of the influences of environmental factors on wildlife, particularly in the Zambezian bioregion, remain a conservation concern. For instance, there is a shortage of knowledge on the relationship between fixed effects of environmental factors and behaviour as well as nest group sizes of Smith’s bush squirrels, Paraxerus cepapi Smith, 1836. Our study examined the relationship between fixed effects of several environmental factors (i.e., with focus on ecological factors) and the behaviour as well as nest group sizes of the bush squirrels in and around Zambia’s Chembe Bird Sanctuary (CBS). Flight initiation distances (FIDs) as an index of bush squirrel behaviour, and nest group sizes were simultaneously surveyed to understand the drivers of biological and population responses, respectively. The results revealed that higher tree height (m) and larger canopy coverage (%) could increase FIDs for bush squirrels. The nest group sizes of bush squirrels could also increase with canopy coverage (%) and presence of termite mounds. By focusing on the two different squirrels' responses, the results of this study highlight the most important environmental factors to consider in minimizing the impacts of human activities on bush squirrels, especially in conservation planning and management by taking into consideration the bush squirrels’ natural history, habitat protection and safe distance between humans and bush squirrels.
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16

Youldon, David A., Jackie Abell, Joanne S. Briffitt, Lackson Chama, Michaela D. Channings, Anastasia Kilundo, Christine K. Larsen, Dabwiso Sakala, and Bruce A. Schulte. "Patch-occupancy survey of elephant (Loxodonta africana) surrounding Livingstone, Zambia." Koedoe 59, no. 1 (January 30, 2017). http://dx.doi.org/10.4102/koedoe.v59i1.1372.

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Wild elephants represent the biggest human–wildlife conflict issue in Livingstone, Zambia. However, little is known about their movements. This survey investigated elephants’ habitat use outside a core protected and fenced zone that forms part of Mosi-oa-Tunya National Park, Zambia. Using ‘patch-occupancy’ methodology, indications of elephant presence (feeding behaviour, dung and tracks) were surveyed. The survey aimed to assist proposed future monitoring exercises by defining the geographical extent that should be considered to improve accuracy in species abundance estimates. Results were supplemented using collected indications of elephant presence from prior monitoring exercises, and during this survey. Elephant presence was confirmed up to 8 km from the boundary of the protected core habitat, focussed in: (1) an unfenced zone of the national park, (2) along a road leading from the national park to the Dambwa Forest to the north and (3) along two rivers located to the west (Sinde River) and east (Maramba River) of the core area. Detection probability of elephant presence was high using these methods, and we recommend regular sampling to determine changes in habitat use by elephants, as humans continue to modify land-use patterns.Conservation implications: Identification of elephant ranging behaviour up to 8 km outside of the Mosi-oa-Tunya National Park in southern Zambia will assist in managing human– elephant conflict in the area, as well as in assessing this seasonal population’s abundance.
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17

Nyirenda, Vincent R., Felistus C. Chewe, Exildah Chisha-Kasumu, and Peter A. Lindsey. "Nest sites selection by sympatric cavity-nesting birds in miombo woodlands." Koedoe 58, no. 1 (March 31, 2016). http://dx.doi.org/10.4102/koedoe.v58i1.1359.

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Deforestation and habitat fragmentation have long been known as drivers of wildlife depletion but information on their specific impacts on cavity-nesting birds in the miombo woodlands has been lacking. A comparative study of disturbed and undisturbed sites was conducted in miombo woodlands of Zambia to assess impacts of environmental stressors on birds. Foot patrols were employed to locate, identify and count host trees and cavities for cavity-nesting birds on twenty 200 m × 200 m sample plots. Undisturbed forests had three times more cavities (the nesting sites for birds), while there were 24.6% fewer abandoned cavities in undisturbed forests than in disturbed forests. The rate of cavity abandonment was about twice as high in human-dominated forests compared to undisturbed forests (61.3% c.f. 31.9%). Cavity-nesting birds preferred larger (> 36.0 cm diameter at breast height) and taller (> 5.0 m) trees for nest placement, especially in human-dominated forests. A number of cavity-nesting birds preferred Brachystegia spiciformis (zebrawood), Julbernadia paniculata (munsa), Parinari curatellifolia (mobola-plum) and Uapaca kirkiana (mahobohobo) as host trees to 14 other miombo tree species. Arnot’s Chat (Myrmecocichla arnoti) had a wider selection of host trees for cavity-nesting than the other 40 cavity-nesting birds in the study areas. Anthropogenic activities such as uncontrolled firewood collection, wild fires, logging, and land clearing for agriculture negatively influenced wood abundance and diversity, with potential implications for persistence of cavity-nesting birds. The negative impacts of anthropogenic activities could be counteracted by conservation strategies such as implementation of sound forest policies, integrative land use practices, sustainable livelihood security and stakeholders’ awareness of the need to safeguard forest-dependent avifauna.Conservation implications: This comparative study unravels specific anthropogenic impacts on the cavity-nesting birds in the miombo woodlands, which would be relevant for designing and implementing targeted biodiversity conservation interventions against negative local environmental values and attitudes that support rural development on the expense of conservation of biodiversity such as birds.
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Snyman, Susan. "Assessment of the main factors impacting community members’ attitudes towards tourism and protected areas in six southern African countries." Koedoe 56, no. 2 (June 24, 2014). http://dx.doi.org/10.4102/koedoe.v56i2.1139.

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In southern Africa, many early conservation efforts from the late 1800s and early 1900s either displaced local communities or restricted their access to natural resources. This naturally affected community attitudes towards protected areas and efforts were later made to rectify growing tensions. In the last few decades of the 20th century, these efforts led to conservation and ecotourism models that increasingly included communities in the decision-making and benefit-sharing process in order to garner their support. Although the results of these policies were mixed, it is clear that the future success of conservation and, consequently, ecotourism in many areas will depend on the attitudes and behaviour of communities living in or adjacent to protected areas. Managing and understanding community expectations and attitudes under varying socio-economic circumstances will lead to more efficient, equitable and sustainable community-based conservation and ecotourism models. This study was based on 1400 community interview schedules conducted in Botswana, Malawi, Namibia, South Africa, Zambia and Zimbabwe, allowing for an accurate comparison of attitudes across countries, protected areas and communities. The results highlighted important demographic and socio-economic factors to consider in terms of understanding the attitudes of those living in and around protected areas. Suggestions were put forward for managing community relationships and garnering long-term support for protected areas and ecotourism. Conservation implications: It was observed that, in general, community members living in or adjacent to conservation areas in southern Africa have an understanding and appreciation of the importance of conservation. Formal education was found to positively impact attitudes and human–wildlife conflict negatively impacted attitudes, highlighting important policy focus areas.
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Farrer, Rhys A., Miwha Chang, Michael J. Davis, Lucy van Dorp, Dong-Hoon Yang, Terrance Shea, Thomas R. Sewell, et al. "A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands." mBio 10, no. 6 (November 12, 2019). http://dx.doi.org/10.1128/mbio.02306-19.

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ABSTRACT We discovered a new lineage of the globally important fungal pathogen Cryptococcus gattii on the basis of analysis of six isolates collected from three locations spanning the Central Miombo Woodlands of Zambia, Africa. All isolates were from environments (middens and tree holes) that are associated with a small mammal, the African hyrax. Phylogenetic and population genetic analyses confirmed that these isolates form a distinct, deeply divergent lineage, which we name VGV. VGV comprises two subclades (A and B) that are capable of causing mild lung infection with negligible neurotropism in mice. Comparing the VGV genome to previously identified lineages of C. gattii revealed a unique suite of genes together with gene loss and inversion events. However, standard URA5 restriction fragment length polymorphism (RFLP) analysis could not distinguish between VGV and VGIV isolates. We therefore developed a new URA5 RFLP method that can reliably identify the newly described lineage. Our work highlights how sampling understudied ecological regions alongside genomic and functional characterization can broaden our understanding of the evolution and ecology of major global pathogens. IMPORTANCE Cryptococcus gattii is an environmental pathogen that causes severe systemic infection in immunocompetent individuals more often than in immunocompromised humans. Over the past 2 decades, researchers have shown that C. gattii falls within four genetically distinct major lineages. By combining field work from an understudied ecological region (the Central Miombo Woodlands of Zambia, Africa), genome sequencing and assemblies, phylogenetic and population genetic analyses, and phenotypic characterization (morphology, histopathological, drug-sensitivity, survival experiments), we discovered a hitherto unknown lineage, which we name VGV (variety gattii five). The discovery of a new lineage from an understudied ecological region has far-reaching implications for the study and understanding of fungal pathogens and diseases they cause.
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Ryan, John C., Danielle Brady, and Christopher Kueh. "Where Fanny Balbuk Walked: Re-imagining Perth’s Wetlands." M/C Journal 18, no. 6 (March 7, 2016). http://dx.doi.org/10.5204/mcj.1038.

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Special Care Notice This article contains images of deceased people that might cause sadness or distress to Aboriginal and Torres Strait Islander readers. Introduction Like many cities, Perth was founded on wetlands that have been integral to its history and culture (Seddon 226–32). However, in order to promote a settlement agenda, early mapmakers sought to erase the city’s wetlands from cartographic depictions (Giblett, Cities). Since the colonial era, inner-Perth’s swamps and lakes have been drained, filled, significantly reduced in size, or otherwise reclaimed for urban expansion (Bekle). Not only have the swamps and lakes physically disappeared, the memories of their presence and influence on the city’s development over time are also largely forgotten. What was the site of Perth, specifically its wetlands, like before British settlement? In 2014, an interdisciplinary team at Edith Cowan University developed a digital visualisation process to re-imagine Perth prior to colonisation. This was based on early maps of the Swan River Colony and a range of archival information. The images depicted the city’s topography, hydrology, and vegetation and became the centerpiece of a physical exhibition entitled Re-imagining Perth’s Lost Wetlands and a virtual exhibition hosted by the Western Australian Museum. Alongside historic maps, paintings, photographs, and writings, the visual reconstruction of Perth aimed to foster appreciation of the pre-settlement environment—the homeland of the Whadjuck Nyoongar, or Bibbulmun, people (Carter and Nutter). The exhibition included the narrative of Fanny Balbuk, a Nyoongar woman who voiced her indignation over the “usurping of her beloved home ground” (Bates, The Passing 69) by flouting property lines and walking through private residences to reach places of cultural significance. Beginning with Balbuk’s story and the digital tracing of her walking route through colonial Perth, this article discusses the project in the context of contemporary pressures on the city’s extant wetlands. The re-imagining of Perth through historically, culturally, and geographically-grounded digital visualisation approaches can inspire the conservation of its wetlands heritage. Balbuk’s Walk through the City For many who grew up in Perth, Fanny Balbuk’s perambulations have achieved legendary status in the collective cultural imagination. In his memoir, David Whish-Wilson mentions Balbuk’s defiant walks and the lighting up of the city for astronaut John Glenn in 1962 as the two stories that had the most impact on his Perth childhood. From Gordon Stephenson House, Whish-Wilson visualises her journey in his mind’s eye, past Government House on St Georges Terrace (the main thoroughfare through the city centre), then north on Barrack Street towards the railway station, the site of Lake Kingsford where Balbuk once gathered bush tucker (4). He considers the footpaths “beneath the geometric frame of the modern city […] worn smooth over millennia that snake up through the sheoak and marri woodland and into the city’s heart” (Whish-Wilson 4). Balbuk’s story embodies the intertwined culture and nature of Perth—a city of wetlands. Born in 1840 on Heirisson Island, Balbuk (also known as Yooreel) (Figure 1) had ancestral bonds to the urban landscape. According to Daisy Bates, writing in the early 1900s, the Nyoongar term Matagarup, or “leg deep,” denotes the passage of shallow water near Heirisson Island where Balbuk would have forded the Swan River (“Oldest” 16). Yoonderup was recorded as the Nyoongar name for Heirisson Island (Bates, “Oldest” 16) and the birthplace of Balbuk’s mother (Bates, “Aboriginal”). In the suburb of Shenton Park near present-day Lake Jualbup, her father bequeathed to her a red ochre (or wilgi) pit that she guarded fervently throughout her life (Bates, “Aboriginal”).Figure 1. Group of Aboriginal Women at Perth, including Fanny Balbuk (far right) (c. 1900). Image Credit: State Library of Western Australia (Image Number: 44c). Balbuk’s grandparents were culturally linked to the site. At his favourite camp beside the freshwater spring near Kings Park on Mounts Bay Road, her grandfather witnessed the arrival of Lieutenant-Colonel Frederick Irwin, cousin of James Stirling (Bates, “Fanny”). In 1879, colonial entrepreneurs established the Swan Brewery at this significant locale (Welborn). Her grandmother’s gravesite later became Government House (Bates, “Fanny”) and she protested vociferously outside “the stone gates guarded by a sentry [that] enclosed her grandmother’s burial ground” (Bates, The Passing 70). Balbuk’s other grandmother was buried beneath Bishop’s Grove, the residence of the city’s first archibishop, now Terrace Hotel (Bates, “Aboriginal”). Historian Bob Reece observes that Balbuk was “the last full-descent woman of Kar’gatta (Karrakatta), the Bibbulmun name for the Mount Eliza [Kings Park] area of Perth” (134). According to accounts drawn from Bates, her home ground traversed the area between Heirisson Island and Perth’s north-western limits. In Kings Park, one of her relatives was buried near a large, hollow tree used by Nyoongar people like a cistern to capture water and which later became the site of the Queen Victoria Statue (Bates, “Aboriginal”). On the slopes of Mount Eliza, the highest point of Kings Park, at the western end of St Georges Terrace, she harvested plant foods, including zamia fruits (Macrozamia riedlei) (Bates, “Fanny”). Fanny Balbuk’s knowledge contributed to the native title claim lodged by Nyoongar people in 2006 as Bennell v. State of Western Australia—the first of its kind to acknowledge Aboriginal land rights in a capital city and part of the larger Single Nyoongar Claim (South West Aboriginal Land and Sea Council et al.). Perth’s colonial administration perceived the city’s wetlands as impediments to progress and as insalubrious environments to be eradicated through reclamation practices. For Balbuk and other Nyoongar people, however, wetlands were “nourishing terrains” (Rose) that afforded sustenance seasonally and meaning perpetually (O’Connor, Quartermaine, and Bodney). Mary Graham, a Kombu-merri elder from Queensland, articulates the connection between land and culture, “because land is sacred and must be looked after, the relation between people and land becomes the template for society and social relations. Therefore all meaning comes from land.” Traditional, embodied reliance on Perth’s wetlands is evident in Bates’ documentation. For instance, Boojoormeup was a “big swamp full of all kinds of food, now turned into Palmerston and Lake streets” (Bates, “Aboriginal”). Considering her cultural values, Balbuk’s determination to maintain pathways through the increasingly colonial Perth environment is unsurprising (Figure 2). From Heirisson Island: a straight track had led to the place where once she had gathered jilgies [crayfish] and vegetable food with the women, in the swamp where Perth railway station now stands. Through fences and over them, Balbuk took the straight track to the end. When a house was built in the way, she broke its fence-palings with her digging stick and charged up the steps and through the rooms. (Bates, The Passing 70) One obstacle was Hooper’s Fence, which Balbuk broke repeatedly on her trips to areas between Kings Park and the railway station (Bates, “Hooper’s”). Her tenacious commitment to walking ancestral routes signifies the friction between settlement infrastructure and traditional Nyoongar livelihood during an era of rapid change. Figure 2. Determination of Fanny Balbuk’s Journey between Yoonderup (Heirisson Island) and Lake Kingsford, traversing what is now the central business district of Perth on the Swan River (2014). Image background prepared by Dimitri Fotev. Track interpolation by Jeff Murray. Project Background and Approach Inspired by Fanny Balbuk’s story, Re-imagining Perth’s Lost Wetlands began as an Australian response to the Mannahatta Project. Founded in 1999, that project used spatial analysis techniques and mapping software to visualise New York’s urbanised Manhattan Island—or Mannahatta as it was called by indigenous people—in the early 1600s (Sanderson). Based on research into the island’s original biogeography and the ecological practices of Native Americans, Mannahatta enabled the public to “peel back” the city’s strata, revealing the original composition of the New York site. The layers of visuals included rich details about the island’s landforms, water systems, and vegetation. Mannahatta compelled Rod Giblett, a cultural researcher at Edith Cowan University, to develop an analogous model for visualising Perth circa 1829. The idea attracted support from the City of Perth, Landgate, and the University. Using stories, artefacts, and maps, the team—comprising a cartographer, designer, three-dimensional modelling expert, and historical researchers—set out to generate visualisations of the landscape at the time of British colonisation. Nyoongar elder Noel Nannup approved culturally sensitive material and contributed his perspective on Aboriginal content to include in the exhibition. The initiative’s context remains pressing. In many ways, Perth has become a template for development in the metropolitan area (Weller). While not unusual for a capital, the rate of transformation is perhaps unexpected in a city less than 200 years old (Forster). There also remains a persistent view of existing wetlands as obstructions to progress that, once removed, are soon forgotten (Urban Bushland Council). Digital visualisation can contribute to appreciating environments prior to colonisation but also to re-imagining possibilities for future human interactions with land, water, and space. Despite the rapid pace of change, many Perth area residents have memories of wetlands lost during their lifetimes (for example, Giblett, Forrestdale). However, as the clearing and drainage of the inner city occurred early in settlement, recollections of urban wetlands exist exclusively in historical records. In 1935, a local correspondent using the name “Sandgroper” reminisced about swamps, connecting them to Perth’s colonial heritage: But the Swamps were very real in fact, and in name in the [eighteen-] Nineties, and the Perth of my youth cannot be visualised without them. They were, of course, drying up apace, but they were swamps for all that, and they linked us directly with the earliest days of the Colony when our great-grandparents had founded this City of Perth on a sort of hog's-back, of which Hay-street was the ridge, and from which a succession of streamlets ran down its southern slope to the river, while land locked to the north of it lay a series of lakes which have long since been filled to and built over so that the only evidence that they have ever existed lies in the original street plans of Perth prepared by Roe and Hillman in the early eighteen-thirties. A salient consequence of the loss of ecological memory is the tendency to repeat the miscues of the past, especially the blatant disregard for natural and cultural heritage, as suburbanisation engulfs the area. While the swamps of inner Perth remain only in the names of streets, existing wetlands in the metropolitan area are still being threatened, as the Roe Highway (Roe 8) Campaign demonstrates. To re-imagine Perth’s lost landscape, we used several colonial survey maps to plot the location of the original lakes and swamps. At this time, a series of interconnecting waterbodies, known as the Perth Great Lakes, spread across the north of the city (Bekle and Gentilli). This phase required the earliest cartographic sources (Figure 3) because, by 1855, city maps no longer depicted wetlands. We synthesised contextual information, such as well depths, geological and botanical maps, settlers’ accounts, Nyoongar oral histories, and colonial-era artists’ impressions, to produce renderings of Perth. This diverse collection of primary and secondary materials served as the basis for creating new images of the city. Team member Jeff Murray interpolated Balbuk’s route using historical mappings and accounts, topographical data, court records, and cartographic common sense. He determined that Balbuk would have camped on the high ground of the southern part of Lake Kingsford rather than the more inundated northern part (Figure 2). Furthermore, she would have followed a reasonably direct course north of St Georges Terrace (contrary to David Whish-Wilson’s imaginings) because she was barred from Government House for protesting. This easier route would have also avoided the springs and gullies that appear on early maps of Perth. Figure 3. Townsite of Perth in Western Australia by Colonial Draftsman A. Hillman and John Septimus Roe (1838). This map of Perth depicts the wetlands that existed overlaid by the geomentric grid of the new city. Image Credit: State Library of Western Australia (Image Number: BA1961/14). Additionally, we produced an animated display based on aerial photographs to show the historical extent of change. Prompted by the build up to World War II, the earliest aerial photography of Perth dates from the late 1930s (Dixon 148–54). As “Sandgroper” noted, by this time, most of the urban wetlands had been drained or substantially modified. The animation revealed considerable alterations to the formerly swampy Swan River shoreline. Most prominent was the transformation of the Matagarup shallows across the Swan River, originally consisting of small islands. Now traversed by a causeway, this area was transformed into a single island, Heirisson—the general site of Balbuk’s birth. The animation and accompanying materials (maps, images, and writings) enabled viewers to apprehend the changes in real time and to imagine what the city was once like. Re-imagining Perth’s Urban Heart The physical environment of inner Perth includes virtually no trace of its wetland origins. Consequently, we considered whether a representation of Perth, as it existed previously, could enhance public understanding of natural heritage and thereby increase its value. For this reason, interpretive materials were exhibited centrally at Perth Town Hall. Built partly by convicts between 1867 and 1870, the venue is close to the site of the 1829 Foundation of Perth, depicted in George Pitt Morrison’s painting. Balbuk’s grandfather “camped somewhere in the city of Perth, not far from the Town Hall” (Bates, “Fanny”). The building lies one block from the site of the railway station on the site of Lake Kingsford, the subsistence grounds of Balbuk and her forebears: The old swamp which is now the Perth railway yards had been a favourite jilgi ground; a spring near the Town Hall had been a camping place of Maiago […] and others of her fathers' folk; and all around and about city and suburbs she had gathered roots and fished for crayfish in the days gone by. (Bates, “Derelicts” 55) Beginning in 1848, the draining of Lake Kingsford reached completion during the construction of the Town Hall. While the swamps of the city were not appreciated by many residents, some organisations, such as the Perth Town Trust, vigorously opposed the reclamation of the lake, alluding to its hydrological role: That, the soil being sand, it is not to be supposed that Lake Kingsford has in itself any material effect on the wells of Perth; but that, from this same reason of the sandy soil, it would be impossible to keep the lake dry without, by so doing, withdrawing the water from at least the adjacent parts of the townsite to the same depth. (Independent Journal of Politics and News 3) At the time of our exhibition, the Lake Kingsford site was again being reworked to sink the railway line and build Yagan Square, a public space named after a colonial-era Nyoongar leader. The project required specialised construction techniques due to the high water table—the remnants of the lake. People travelling to the exhibition by train in October 2014 could have seen the lake reasserting itself in partly-filled depressions, flush with winter rain (Figure 4).Figure 4. Rise of the Repressed (2014). Water Rising in the former site of Lake Kingsford/Irwin during construction, corner of Roe and Fitzgerald Streets, Northbridge, WA. Image Credit: Nandi Chinna (2014). The exhibition was situated in the Town Hall’s enclosed undercroft designed for markets and more recently for shops. While some visited after peering curiously through the glass walls of the undercroft, others hailed from local and state government organisations. Guest comments applauded the alternative view of Perth we presented. The content invited the public to re-imagine Perth as a city of wetlands that were both environmentally and culturally important. A display panel described how the city’s infrastructure presented a hindrance for Balbuk as she attempted to negotiate the once-familiar route between Yoonderup and Lake Kingsford (Figure 2). Perth’s growth “restricted Balbuk’s wanderings; towns, trains, and farms came through her ‘line of march’; old landmarks were thus swept away, and year after year saw her less confident of the locality of one-time familiar spots” (Bates, “Fanny”). Conserving Wetlands: From Re-Claiming to Re-Valuing? Imagination, for philosopher Roger Scruton, involves “thinking of, and attending to, a present object (by thinking of it, or perceiving it, in terms of something absent)” (155). According to Scruton, the feelings aroused through imagination can prompt creative, transformative experiences. While environmental conservation tends to rely on data-driven empirical approaches, it appeals to imagination less commonly. We have found, however, that attending to the present object (the city) in terms of something absent (its wetlands) through evocative visual material can complement traditional conservation agendas focused on habitats and species. The actual extent of wetlands loss in the Swan Coastal Plain—the flat and sandy region extending from Jurien Bay south to Cape Naturaliste, including Perth—is contested. However, estimates suggest that 80 per cent of wetlands have been lost, with remaining habitats threatened by climate change, suburban development, agriculture, and industry (Department of Environment and Conservation). As with the swamps and lakes of the inner city, many regional wetlands were cleared, drained, or filled before they could be properly documented. Additionally, the seasonal fluctuations of swampy places have never been easily translatable to two-dimensional records. As Giblett notes, the creation of cartographic representations and the assignment of English names were attempts to fix the dynamic boundaries of wetlands, at least in the minds of settlers and administrators (Postmodern 72–73). Moreover, European colonists found the Western Australian landscape, including its wetlands, generally discomfiting. In a letter from 1833, metaphors failed George Fletcher Moore, the effusive colonial commentator, “I cannot compare these swamps to any marshes with which you are familiar” (220). The intermediate nature of wetlands—as neither land nor lake—is perhaps one reason for their cultural marginalisation (Giblett, Postmodern 39). The conviction that unsanitary, miasmic wetlands should be converted to more useful purposes largely prevailed (Giblett, Black 105–22). Felicity Morel-EdnieBrown’s research into land ownership records in colonial Perth demonstrated that town lots on swampland were often preferred. By layering records using geographic information systems (GIS), she revealed modifications to town plans to accommodate swampland frontages. The decline of wetlands in the region appears to have been driven initially by their exploitation for water and later for fertile soil. Northern market gardens supplied the needs of the early city. It is likely that the depletion of Nyoongar bush foods predated the flourishing of these gardens (Carter and Nutter). Engaging with the history of Perth’s swamps raises questions about the appreciation of wetlands today. In an era where numerous conservation strategies and alternatives have been developed (for example, Bobbink et al. 93–220), the exploitation of wetlands in service to population growth persists. On Perth’s north side, wetlands have long been subdued by controlling their water levels and landscaping their boundaries, as the suburban examples of Lake Monger and Hyde Park (formerly Third Swamp Reserve) reveal. Largely unmodified wetlands, such as Forrestdale Lake, exist south of Perth, but they too are in danger (Giblett, Black Swan). The Beeliar Wetlands near the suburb of Bibra Lake comprise an interconnected series of lakes and swamps that are vulnerable to a highway extension project first proposed in the 1950s. Just as the Perth Town Trust debated Lake Kingsford’s draining, local councils and the public are fiercely contesting the construction of the Roe Highway, which will bisect Beeliar Wetlands, destroying Roe Swamp (Chinna). The conservation value of wetlands still struggles to compete with traffic planning underpinned by a modernist ideology that associates cars and freeways with progress (Gregory). Outside of archives, the debate about Lake Kingsford is almost entirely forgotten and its physical presence has been erased. Despite the magnitude of loss, re-imagining the city’s swamplands, in the way that we have, calls attention to past indiscretions while invigorating future possibilities. We hope that the re-imagining of Perth’s wetlands stimulates public respect for ancestral tracks and songlines like Balbuk’s. Despite the accretions of settler history and colonial discourse, songlines endure as a fundamental cultural heritage. Nyoongar elder Noel Nannup states, “as people, if we can get out there on our songlines, even though there may be farms or roads overlaying them, fences, whatever it is that might impede us from travelling directly upon them, if we can get close proximity, we can still keep our culture alive. That is why it is so important for us to have our songlines.” Just as Fanny Balbuk plied her songlines between Yoonderup and Lake Kingsford, the traditional custodians of Beeliar and other wetlands around Perth walk the landscape as an act of resistance and solidarity, keeping the stories of place alive. Acknowledgments The authors wish to acknowledge Rod Giblett (ECU), Nandi Chinna (ECU), Susanna Iuliano (ECU), Jeff Murray (Kareff Consulting), Dimitri Fotev (City of Perth), and Brendan McAtee (Landgate) for their contributions to this project. The authors also acknowledge the traditional custodians of the lands upon which this paper was researched and written. 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Melbourne: Bloomings Books, 2004.South West Aboriginal Land and Sea Council and John Host with Chris Owen. “It’s Still in My Heart, This is My Country:” The Single Noongar Claim History. Crawley: U of Western Australia P, 2009.Urban Bushland Council. “Bushland Issues.” 2015. 29 Sep. 2015 ‹http://www.bushlandperth.org.au/bushland-issues›.Welborn, Suzanne. Swan: The History of a Brewery. Crawley: U of Western Australia P, 1987.Weller, Richard. Boomtown 2050: Scenarios for a Rapidly Growing City. Crawley: U of Western Australia P, 2009. Whish-Wilson, David. Perth. Sydney: NewSouth Publishing, 2013.
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