Recent publications in Science and Engineering

College of Science and Engineering Recent publications in Science and Engineering

Miller, Mark G.R., Silva, Fabiola R.O., Machovsky-Capuska, Gabriel E., and Congdon, Bradley C. (2018) Sexual segregation in tropical seabirds: drivers of sex-specific foraging in the Brown Booby Sula leucogaster. Journal of Ornithology. (In Press)
Sexual segregation in the behaviour, morphology or physiology of breeding seabirds can be related to divergent parental roles, foraging niche partitioning or sex-specific nutritional requirements. Here we combine GPS tracking, dietary and nutritional analysis to investigate sex-specific foraging of Brown Boobies breeding on Raine Island, Great Barrier Reef, Australia. We observed sex-specific segregation in: a) foraging location: females undertook longer trips, foraging at more distant locations than males; b) foraging time: male activity and foraging occurred throughout the day, while female activity and foraging increased from midday to an afternoon peak; and c) prey type, females mostly consumed flying fish, whereas males consumed equal proportions of flying fish and squid. Brown Booby diets contained five tropical prey species that significantly differed in their nutritional composition (Protein, Lipid and Water, wet mass). Despite this variation we found no differences in the overall nutritional content of prey caught by each sex. The observed sex-specific differences in prey type, location and time of capture are likely driven by a combination of a division of labour, risk partitioning and competition. However, Brown Boobies breeding on Raine Island, and other populations, might flexibly partition foraging niche by sex in response to varying competitive and environmental pressures. In light of such potential foraging dynamism, our inconclusive exploration of nutritional segregation between sexes warrants further investigation in the species.

Jayasinghe, Nandana Chana, Ginger, John D., Henderson, David J., and Walker, George R. (2018) Distribution of wind loads in metal-clad roofing structures. Journal of Structural Engineering, 144 (4).
The roof is the part that experiences the largest wind load and is usually the most vulnerable part of a house. However, data on how the wind loads are transferred through the roof structure are scarce. The fluctuating nature and variable spatial distribution of wind loads combined with the structural response can cause significant challenges for assessing the distribution or sharing of loads in a roof. Such studies are required to obtain more reliable estimates on vulnerability assessment to windstorms. This paper describes the transmission of wind loads from the pressure on the cladding through the cladding-to-batten connections to the batten-to-truss connections on a roofing system typical of that in many contemporary houses constructed in cyclonic regions of Australia. The study found that the use of normal design practices can significantly underestimate connection loads when highly correlated large-scale wind pressures act on these roof systems.

Parackal, Korah, Ginger, John, and Henderson, David J. (2018) Wind load fluctuations on roof batten to rafter/truss connections. Journal of Wind Engineering and Industrial Aerodynamics, 175. pp. 193-201.
Batten to rafter connections in light framed housing can be vulnerable to progressive or cascading failures where a localised failure can cause the loss of a large section of the roof envelope. The synchrony of loads at neighbouring connections may affect the initiation of such failures. A 1/50 length scale wind tunnel model study was performed on a gable roof house to record spatial and temporal pressure fluctuations on the roof surface and data were studied to determine the flow separation mechanisms causing different loading patterns on batten to rafter connections. The cross correlation between load time histories was used to give a measure of synchrony between loads experienced at neighbouring connections and indicate the direction that fluctuations move across the roof. Orthogonal wind directions result in 2-dimensional flow separation that produce more synchronous loads at batten to rafter connections than cornering wind directions, where conical vortices produce high uplift forces on connections. The patterns of loading and their correlations give a means of identifying which parts of the roof and which approach wind directions may result in the initiation of a progressive failure of batten to rafter connections.

Neilly, Heather, Nordberg, Eric J., VanDerWal, Jeremy, and Schwarzkopf, Lin (2018) Arboreality increases reptile community resistance to disturbance from livestock grazing. Journal of Applied Ecology, 55 (2). pp. 786-799.
1. Domestic livestock grazing directly alters ground-level habitat but its effects on arboreal habitat are poorly known. Similarly, the response to grazing of ground-dwelling fauna has been examined, but there are few studies of arboreal fauna. Globally, grazing has been implicated in the decline of vertebrate fauna species, but some species appear resistant to the effects of grazing, either benefiting from the structural changes at ground level or avoiding them, as may be the case with arboreal species. Here we examine arboreal and terrestrial habitat responses and reptile community responses to grazing, to determine whether arboreal reptile species are more resistant than terrestrial reptile species. 2. We conducted arboreal and terrestrial reptile surveys on four different grazing treatments, at a 19-year experimental grazing trial in northern Australia. To compare the grazing response of arboreal and terrestrial reptile assemblages, we used community, functional group and individual species-level analyses. Species responses were modelled in relation to landscape-scale and microhabitat variables. 3. Arboreal reptile species were resistant to the impact of grazing, whereas terrestrial reptiles were negatively affected by heavy grazing. Terrestrial reptiles were positively associated with complex ground structures, which were greatly reduced in heavily grazed areas. Arboreal lizards responded positively to microhabitat features such as tree hollows. 4. Synthesis and applications. Arboreal and terrestrial reptiles have different responses to the impact of livestock grazing. This has implications for rangeland management, particularly if management objectives include goals relating to conserving certain species or functional groups. Arboreal reptiles showed resistance in a landscape that is grazed, but where trees have not been cleared. We highlight the importance of retaining trees in rangelands for both terrestrial and arboreal microhabitats.

Campbell, Mason, Alamgir, Mohammed, and Laurance, William (2018) Optimizing roads to limit environmental damage and maximize societal development in the Asia-Pacific. HOPE e-news bulletin, March. p. 6.
[Extract] When thinking of threats to the environment roads are probably not at the top of many people's list. They should be. Road expansion is occurring at a frightening pace across the globe with projections by the International Energy Agency estimating more than 25 million kilometers of paved roads alone will be built by 2050. That is enough to encircle the entire planet more than 600 times! Approximately 90% of these roads will be built in developing tropical and subtropical regions; the epicenter of global biodiversity and the host of some of the planets most critical ecosystems. In the developing nations of Asia, for instance, in the next three years the total length of paved roads will double according to estimates by the Asian Development Bank. Part of this expansion will be as direct result of China's planned trillion dollars 'Belt and Road' and '21st Century Maritime Silk Road' projects which are expected to span more than 70 nations.

Nordberg, Eric J. (2018) The impacts of cattle grazing on arboreal reptiles. PhD thesis, James Cook University.
Habitat disturbances, such as grazing by livestock, can have major direct and indirect impacts on the structure and complexity of both vegetation and faunal communities. Changes to habitat structure and resource availability often lead to changes in biodiversity. While the impacts of livestock grazing has been well studied in vegetation communities, fewer studies have focused on wildlife. Further, terrestrial (ground-dwelling) communities have generally been the focal group of interest, whereas the impacts of grazing on arboreal systems have often been overlooked. Arboreal reptiles are generally difficult to capture due to their cryptic nature and tendency to flee when encountered. Further, they often shelter under loose, peeling tree bark, or in hollows, making them difficult to capture without damaging their microhabitat. I implemented and used arboreal cover boards (ACBs) as "artificial bark" made from closed-cell foam cover boards to try and increase the capture rate of arboreal lizards. I tested the difference in capture success using standard visual encounter surveys (VES) and the use of arboreal cover boards as survey methods to sample small, cryptic arboreal lizards. Diurnal and nocturnal (spotlight) VES resulted in lower capture success compared to ACB surveys. While nocturnal VES showed a bias towards adult geckos, the use of ACBs captured individuals from all age classes. Further, ACBs were successful in monitoring non-target species, and even broad taxonomic groups. The use of ACBs extends beyond just a useful survey technique, but also provides the potential for long-term monitoring and restoring damaged or degraded microhabitats. Domestic livestock alter ground-level vegetation structure due to grazing, but little is known about the effects on arboreal habitats. Similarly, the effects grazing has on ground-dwelling wildlife populations has been examined to some extent, yet the potential impacts to arboreal groups have received little attention. I examined the responses of arboreal and terrestrial reptile communities and their respective habitats to domestic livestock grazing. Terrestrial reptiles were generally negatively associated with heavy grazing, as their primary habitat (ground-level) was heavily impacted. Terrestrial reptiles were strongly associated with ground-level habitat complexity, which was greatly reduced in areas with heavy grazing. Alternatively, arboreal reptiles were generally resistant to the impacts of even heavy grazing, and were positively associated with arboreal tree structures, such as peeling bark and tree hollows. While terrestrial and arboreal reptiles showed opposing trends (negative and positive association with grazing, respectively), individual species within these groups showed varied responses. I highlight the importance of retaining trees in rangelands as an overarching management guideline, as trees provide primary habitat for arboreal species, but also provide shade, leaf litter, and woody debris for terrestrial species. Two species that showed resistance (i.e., no negative effects, or showed positive effects to livestock grazing) were a diurnal skink, the inland snake-eyed skink (Cryptoblepharus australis) and a nocturnal gecko, the Australian native house gecko (Gehyra dubia). Snake-eyed skinks showed no effect of livestock grazing on their abundance, while native house geckos were more abundant in sites with heavier stocking rates. I tested whether food availability was a driving mechanism that allowed these species to persist in areas with high levels of grazing. I quantified the invertebrate prey community available to both lizards using ACBs and light trapping. The invertebrate prey community composition was not significantly different among the four grazing regimes or habitat types. While both lizard species are habitat generalists, they were fairly selective in their diets, consuming prey disproportionally to their availability. Both snake-eyed skinks and native house geckos showed strong selection for beetles, spiders, and scorpions, resulting in high dietary niche overlap. While native house geckos and snake-eyed skinks both occupy similar microhabitats and consume similar prey items, they are temporally segregated by activity time (native house geckos = nocturnal; snake-eyed skinks = diurnal). Although not significantly different, the heavily grazed sites showed the greatest abundance of the most preferred prey items (beetles, spiders, scorpions), which may contribute to the high abundances of native house geckos in these sites. Predator–prey dynamics play a vital role in shaping population structure and community assemblages. Predator–prey interactions have been of interest to biologists for hundreds of years, yet most studies focus on the perspective of the predator (examining functional and numerical responses), or from the perspective of the prey (examining direct mortality or non-consumptive effects). Few studies have measured predation risk in relation to the abundance of both predators and prey. I tested two competing hypotheses regarding predation risk: i) predation risk is predator-density dependent (i.e., more predators result in greater predation risk); and ii) predation risk follows the alternative prey hypothesis (e.g., predation risk is dependent on alternative prey availability). I used a combination of surveys (for predators, alternative prey (invertebrates), and lizards) and physical models (n = 800) to estimate predation risk on lizards. Predation risk on lizards was greatest in the dry season, when predator abundance and alternative prey populations were lowest. Alternatively, predation risk on lizards was lowest during the wet season, when predator abundance and alternative prey availability was greatest. This suggests that predation risk to lizards is not predator-density dependent, as predation risk was lowest when predator abundance was highest, and vice – versa. Our data also indicates that predation risk follows the alternative prey hypothesis, as predation risk to lizards was greatest when alternative prey populations (invertebrates) were lowest, and vice – versa. Although predator–prey dynamics are important in shaping wildlife community composition, predation events are rarely observed. In many cases, our perception of what constitutes "predators" or "prey" may be biased towards anecdotal observations or studies that have documented predation events. In many ecosystems, vertebrates constitute a majority of what we consider "predators", but large invertebrates exist across much of the world, especially in tropical regions, that may be formidable predators to small vertebrate groups. I conducted 500 man-hours of visual searches, compiling observations of in situ predation events, and deployed 800 model lizards to measure attack frequency and identify potential predators. Observing a predation event in situ was rare: I observed 9 predation events in total (4 instances of vertebrates eating another vertebrate; and 5 instances of invertebrates eating a vertebrate). This suggests that while observing any predation event is rare, invertebrate predators (e.g., large spiders, mantids) may contribute to similar levels of predation to more traditional vertebrate predators (e.g., snakes, birds). Further, large invertebrates (predominantly huntsman spiders) contributed to up to 23% of attacks on model lizards. I highlight the potential importance of large predatory invertebrates as predators to small vertebrates, especially herpetofauna, in comparison to more "traditional" predator groups, such as birds and snakes. Predatory invertebrates have largely been overlooked in the literature as potential predators, with exception to anecdotal observations. Their importance as predators in shaping community assemblages should be reconsidered. Environments with greater habitat complexity support high biodiversity because they have abundant and diverse resources, which may reduce competition among species. Habitat disturbances, such as livestock grazing, often reduce habitat complexity and structure, resulting in a simplified, or homogenized environment. I tested if reduced competition, as a result of a homogenization from livestock grazing, acted as a mechanism that allowed native house geckos to thrive in heavily grazed environments. I compared the habitat utilization of three co-occurring arboreal geckos, native house geckos (G. dubia), northern velvet geckos (Oedura castelnaui), and eastern spiny-tailed geckos (Strophurus willsiamsi). All geckos displayed resource partitioning among tree species and tree structural characteristics. I found evidence of interspecific competition between geckos, in which native house geckos shifted their preferred habitat of dead trees, to Silver-leaf ironbark trees (Eucalyptus melanophloia) and complex trees with peeling bark in the presence of velvet geckos. Native house geckos were more resistant to the negative effects of grazing (low habitat complexity) than either velvet or spiny-tailed geckos. Native house geckos were more abundant in heavily grazed areas. In contrast, velvet and spiny-tailed geckos were rarely found in heavily grazed sites, and were more abundant in areas with lower grazing pressure. My data suggests that grazing by livestock homogenized the environment, and in turn, homogenized the arboreal reptile community. A lack of competition allowed native house geckos, a microhabitat generalist, to persist and even increase in abundance, where microhabitat specialists, such as velvet and spiny-tailed geckos, declined. Habitat disturbances, such as livestock grazing, have detrimental effects on plant and animal communities. While many studies focus on species that decline in response to disturbance, it is just as important to understand how and why some species respond positively. This thesis is focused around the positive response of an arboreal lizard, G. dubia, to try and understand what mechanisms were responsible in allowing them to persist in environments where other species declined. I tested a series of potential mechanisms, including food availability, habitat availability, predation pressure, and competition, to try and identify their effects on native house gecko populations. While my data indicates that a reduction in competition as a result of habitat simplification is a major contributor, it is likely that no stand-alone mechanism is responsible. Rather, a combination of these mechanisms contribute to their success in heavily grazed environments.

Zhang, Lijuan, Xiang, Wei, and Tan, Xiaohu (2018) An efficient bit-detecting protocol for continuous tag recognition in mobile RFID systems. IEEE Transactions on Mobile Computing, 17 (3). pp. 503-516.
In a mobile RFID system, a large number of tags move in and out of the system continuously, so that the reader has very limited time to recognize all the tags. As a result, the effective and efficient identification of tags in mobile environments is a more challenging problem compared to conventional static RFID systems. In this paper, we propose an efficient bit-detecting (EBD) protocol to accelerate the reading process of large-scale mobile RFID systems. In these systems, some previously recognized tags, i.e., known tags, may stay in the reader's reading range for two consecutive reading cycles, and some unknown tags may newly participate in the current reading cycle. In the proposed EBD protocol, a new bit monitoring method is proposed to detect the presence of known tags using a small number of slots, and to retrieve their IDs from the back-end database. Next, an M -ary bit-detecting tree recognition method is proposed to rapidly recognize unknown tags without generating any idle slots. This new protocol is shown to perform better than existing methods reported in the literature. Both theoretic and simulation results are present to demonstrate that the proposed protocol is superior to existing protocols in terms of lower time cost.

Hays, Graeme C., Alcoverro, Teresa, Christianen, Marjolijn J.A., Duarte, Carlos M., Hamann, Mark, Macreadie, Peter I., Marsh, Helene D., Rasheed, Michael A., Thums, Michele, Unsworth, Richard K.F., York, Paul H., and Esteban, Nicole (2018) New tools to identify the location of seagrass meadows: marine grazers as habitat indicators. Frontiers in Marine Science, 5.
Seagrasses are hugely valuable to human life, but the global extent of seagrass meadows remains unclear. As evidence of their value, a United Nations program exists ( to try and assess their distribution and there has been a call from 122 scientists across 28 countries for more work to manage, protect and monitor seagrass meadows ( Emerging from the 12th International Seagrass Biology Workshop, held in October 2016 has been the view that grazing marine megafauna may play a useful role in helping to identify previously unknown seagrass habitats. Here we describe this concept, showing how detailed information on the distribution of both dugongs (Dugong dugon) and green sea turtles (Chelonia mydas) obtained, for example, by aerial surveys and satellite tracking, can reveal new information on the location of seagrass meadows. We show examples of how marine megaherbivores have been effective habitat indicators, revealing major, new, deep-water seagrass meadows and offering the potential for more informed estimates of seagrass extent in tropical and sub-tropical regions where current information is often lacking.

Brazenor, Alexander K., Saunders, Richard J., Miller, Terrance L., and Hutson, Kate S. (2018) Morphological variation in the cosmopolitan fish parasite Neobenedenia girellae (Capsalidae: Monogenea). International Journal for Parasitology, 48 (2). pp. 125-134.
Intra-species morphological variation presents a considerable problem for species identification and can result in taxonomic confusion. This is particularly pertinent for species of Neobenedenia which are harmful agents in captive fish populations and have historically been identified almost entirely based on morphological characters. This study aimed to understand how the morphology of Neobenedenia girellae varies with host fish species and the environment. Standard morphological features of genetically indistinct parasites from various host fish species were measured under controlled temperatures and salinities. An initial field-based investigation found that parasite morphology significantly differed between genetically indistinct parasites infecting various host fish species. The majority of the morphological variation observed (60%) was attributed to features that assist in parasite attachment to the host (i.e. the posterior and anterior attachment organs and their accessory hooks) which are important characters in monogenean taxonomy. We then experimentally examined the effects of the interaction between host fish species and environmental factors (temperature and salinity) on the morphology of isogenic parasites derived from a single, isolated hermaphroditic N. girellae infecting barramundi, Lates calcarifer. Experimental infection of L. calcarifer and cobia, Rachycentron canadum, under controlled laboratory conditions did not confer host-mediated phenotypic plasticity in N. girellae, suggesting that measured morphological differences could be adaptive and only occur over multiple parasite generations. Subsequent experimental infection of a single host species, L. calcarifer, at various temperatures (22, 30 and 32 °C) and salinities (35 and 40‰) showed that in the cooler environments (22 °C) N. girellae body proportions were significantly smaller compared with warmer temperatures (30 and 32 °C; P < 0.0001), whereas salinity had no effect. This is evidence that temperature can drive phenotypic plasticity in key taxonomic characters of N. girellae under certain environmental conditions.

Infante Villamil, Sandra, Huerlimann, Roger, Morianos, Christina, Sarnyai, Zoltan, and Maes, Gregory E. (2018) Adverse effect of early life high-fat/high-carbohydrate ('Western') diet on bacterial community in the distal bowel of mice. Nutrition Research, 50. pp. 25-36.
Obesity and other lifestyle diseases in modern society can be related to historical dietary changes from diets balanced in omega-6 and omega-3 to the unbalanced "Western-type" diet. It is recognized that diet influences the murine and human gut microbiome, and most research indicates that microbial diversity and composition are altered by high-fat diets (HFDs). However, good knowledge about the effects of early exposure to HFD on the maturation and structure of the bacterial community is limited. Using mice as model, we hypothesized that an HFD alters the early dynamic of the gut bacterial community toward an unstable/unhealthy state. By sequencing the V3 and V4 regions of the 16S ribosomal ribonucleic acid gene, we investigated the bacterial community in fecal samples of mice fed a control diet and an HFD at weaning (sampling time 1) and after 8 weeks of dietary intervention (11 weeks of age; sampling time 2). Natural temporal microbiome maturation was evidenced by a general increase in microbial diversity and shifts in microbial community between sampling times 1 and 2 toward a mature community. However, the HFD led to significant structural segregation of the microbiome compared with controls; the HFD diet repressed health-enhancing bacteria (eg, Bifidobacterium and Akkermansia) and promoted health-detracting bacteria (ie, those associated with gut disorders, eg, Dorea). We suggest that early-life consumption of HFD negatively impacts the natural gut bacterial community maturation leading toward a potentially persistent unhealthy stage.

Alamgir, Mohammed, Campbell, Mason J., Sloan, Sean, Phin, Wong Ee, and Laurance, William F. (2018) Road risks and environmental impact assessments in Malaysian road infrastructure projects. Jurutera, February 2018. pp. 13-16.
Roads can promote economic growth and social integration but they can also initiate environmental, economic and socio-political harms. In many cases, these harms can be considerably minimised and the road benefits maximised through proactive planning by road engineers and effective Environmental Impact Assessments (EIAs).

Eurich, J.G., McCormick, M.I., and Jones, G.P. (2018) Habitat selection and aggression as determinants of fine-scale partitioning of coral reef zones in a guild of territorial damselfishes. Marine Ecology Progress Series, 587. pp. 201-215.
A major goal of ecology is to explain the mechanisms that drive species distributions and ecological partitioning along gradients in the natural environment. The distributions of ecologically similar animals may depend on the degree of habitat specialization and behavioural interactions within and among species. The extent of ecological partitioning in guilds of coral reef fishes has been a matter of debate, but the roles of habitat selectivity and agonistic interactions have received little attention. Here these effects were examined by investigating fine-scale species distributions, microhabitat use, and aggression in a guild of 7 territorial damselfish species in Kimbe Bay, Papua New Guinea. We documented patterns of habitat partitioning across the 3 reef zones—reef flat, reef crest, and reef slope—with distinct patterns of distribution within these zones at extremely fine scales (1-2 m). Distinct differences between neighbouring species in the substrata selected were also observed. We hypothesized that fine-scale differences in distribution and microhabitat use could be maintained by aggressive interactions. To test this, we employed a ‘bottle’ experiment, where stimulus fish were introduced into a resident’s territory, and aggression was recorded. Aggression elicited by neighbouring species was significantly higher for all species, compared with non-adjacent species. Levels of aggression differed among species, with the most aggressive species dominating the reef crest where the most distributional overlap occurred. This study revealed a fine level of spatial partitioning among reef zones and microhabitats in this guild of damselfish, which is likely to be maintained by agonistic interactions among neighbouring species. We demonstrate that when exploring coexistence in reef fish communities, the more traditional niche mechanisms operate alongside competitive dynamics, and within highly diverse systems these ecological processes are magnified.

Niroshan, Naguleswaran, Yin, Ling, Sivakugan, Nagaratnam, and Veenstra, Ryan Llewellyn (2018) Relevance of SEM to long-term mechanical properties of cemented paste backfill. Geotechnical and Geological Engineering. (In Press)
This paper is an attempt to relate the microstructure to long-term mechanical properties of the cemented paste backfill produced from a hard rock mine tailing from North Queensland in Australia bound with flyash-based geopolymer (geopolymer), flyash-blended cement (FBC), and general purpose cement (GPC). A relatively high slump (260 mm) paste backfill mix with 74 wt% solids has been used to prepare cylindrical paste backfill samples with a diameter of 50 mm and a height of 100 mm. The uniaxial compressive strength tests were conducted on all samples after curing for 112 days to obtain their strength, failure strain and Young's modulus. Fractured samples were examined under scanning electron microscope to understand the failure mechanisms at the microstructural scale. The results show that binders significantly affected the mechanical properties of paste backfills (ANOVA, p\0.05). The paste backfill bound with geopolymer gave the lowest strength and Young's modulus, while the paste backfills bounded with FBC and GPC showed comparable higher strength and modulus values. This was attributed to the relatively well-packed paste backfills with less cracks and smaller pore sizes in these paste backfills bound with FBC and GPC binders. In particular, needle-shaped particles, which were originally identified in GPC, highly influenced the mechanical property of paste backfills. These results indicate that fly ash can be used to partially replace the cement as a binder for paste backfills to achieve economic and environmental benefits.

Gomes, Vitor H.F., Ijff, Stéphanie D., Raes, Niels, Amaral, Iêda Leão, Salamão, Rafael P., Coelho, Luiz de Souza, De Almeida Matos, Francisca, Castilho, Carolina V., Limo Filho, Diogenes de Andrade, López, Dairon Cárdenas, Guevara, Juan Ernesto, Magnusson, William E., Phillips, Oliver L., Wittmann, Florian, Veiga Carim, Marcelo de Jesus, Martins, Maria Pires, Irume, Mariana Victória, Sabatier, Daniel, Molino, Jean-François, Bánki, Olaf S., da Silva Guimarães, José Renan, Pitman, Nigel C.A., Fernandez Piedade, Maria Teresa, Mendoza, Abel Monteagudo, Luize, Bruno Garcia, Venticinque, Eduardo Martins, de Leão Novo, Evlyn Márcia Moraes, Vargas, Percy Núñez, Silva, Thiago Sanna Freire, Manzatoo, Angelo Gilberto, Terborgh, John, Reis, Neidiane Farias Costa, Montero, Juan Carlos, Casula, Katia Regina, Marimon, Beatriz S., Marimon-junior, Ben-Hur, Honorio Coronado, N., Feldpausch, Ted R., Duque, Alvaro, Zartman, Charles Eugene, Arboleda, Nicolás Castaño, Killeen, Timothy J., Mostacedo, Bonifacio, Vásquez, Rodolfo, Schöngart, Jochen, Assis, Rafael L., Medeiros, Marcelo Brilhante, Simon, Marcelo Fragomeni, Andrade, Ana, Laurance, William F., Camargo, José Luís, Demarchi, Layon O., Laurance, Susan G.W., de Sousa Farias, Emanuelle, Nascimento, Henrique Eduardo Mendonça, Revilla, Juan David Cardenas, Quaresma, Adriano, Costa, Flavia R.C., Vieira, Ima Célia Guimarães, Cintra, Bruno Barçante Ladvocat, Castellanos, Hernán, Brienan, Roel, Stevenson, Pablo R., Feitosa, Yuri, Duivenvoorden, Joost F., Aymard C., Gerardo A., Mogollón, Hugo F., Targhetta, Natalia, Comiskey, James A., Vicentini, Alberto, Lopes, Aline, Damasco, Gabriel, Dávila, Nállarett, Garcia-Villacorta, Roosevelt, Levis, Carolina, Schietti, Juliana, Souza, Priscilla, Emilio, Thaise, Alonso, Alfonso, Neill, David, Dallmeier, Francisco, Ferreira, Leandro Valle, Araujo-Murakami, Alejandro, Praia, Daniel, do Amaral, Dário Dantas, Carvalho, Fernanda Antunes, de Souza, Fernanda Coelho, Feeley, Kenneth, Arroyo, Luzmila, Pansonato, Marcelo Petratti, Gribel, Rogerio, Villa, Boris, Licona, Juan Carlos, Fine, Paul V.A., Cerón, Carlos, Baraloto, Chris, Jiménez, Eliana M., Stropp, Juliana, Engel, Julien, Silveira, Marcos, Mora, Maria Cristina Peñuela, Petronelli, Pascal, Maas, Paul, Thomas-Caesar, Raquel, Henkel, Terry W., Daly, Doug, Paredes, Marcos Rios, Baker, Tim R., Fuentes, Alfredo, Peres, Carlos A., Chave, Jerome, Pena, Jose Luis Marcelo, Dexter, Kyle G., Silman, Miles R., Jørgensen, Peter Møller, Pennington, Toby, De Fiore, Anthony, Valverde, Fernando Cornejo, Phillips, Juan Fernando, Rivas-Torres, Gonzalo, von Hildebrand, Patricio, van Andel, Tinde R., Ruschel, Ademir R., Prieto, Adriana, Rudas, Agustín, Hoffman, Bruce, Vela, César I.A., Barbosa, Edelcilio Marques, Zent, Egleé L., Gonzales, George Pepe Gallardo, Doza, Hilda Paulette Dávila, Miranda, Irs Paula de Andrade, Guillaumet, Jean-Louis, Pinto, Linder Felipe Mozombite, Bonates, Luiz Carlos de Matos, Silva, Natalino, Gómez, Ricardo Zárate, Zent, Stanford, Gonzales, Therany, Vos, Vincent A., Malhi, Yadvinder, Oliveira, Alexandre A., Cano, Angela, Albuquerque, Bianca Weiss, Vriesendorp, Corine, Correa, Diego Felipe, Torre, Emilio Vilanova, Van Der Heijden, Geertje, Ramírez-Angulo, Hirma, Ramos, José Ferreira, Young, Kenneth R., Rocha, Maira, Nascimento, Marcelo Trindade, Medina, Maria Natalia Umaña, Tirado, Milton, Wang, Ophelia, Sierra, Rodrigo, Torres-Lezama, Armando, Mendoza, Casimiro, Ferreira, Cid, Baider, Cláudia, Villarroel, Daniel, Balslev, Henrik, Mesones, Italo, Giraldo, Ligia Estela Urrego, Casas, Luisa Fernanda, Reategui, Manuel Augusto Ahuite, Linares-Palomino, Reynaldo, Zagt, Roderick, Cárdenas, Sasha, Farfan-Rios, William, Sampaio, Adeilza Felipe, Pauletto, Daniela, Sandoval, Elvis H. Valderrama, Arevalo, Freddy Ramirez, Huamantupa-Chuquimaco, Isau, Garcia-Cabrera, Karina, Hernandez, Lionel, Gamarra, Luis Valenzuela, Alexiades, Miguel N., Pansini, Susamar, Cuenca, Walter Palacios, Milliken, William, Ricardo, Joana, López-González, Gabriela, Pos, Edwin, and ter Steege, Hans (2018) Species distribution modelling: contrasting presence-only models with plot abundance data. Scientific Reports, 8.
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model, based on a large plot dataset for Amazonian tree species, using inverse distance weighting (IDW). We also propose a new pipeline to deal with inconsistencies in NHCs and to limit the area of occupancy of the species. We found a significant but weak positive relationship between the distribution of NHCs and IDW for 66% of the species. The relationship between SDMs and IDW was also significant but weakly positive for 95% of the species, and sensitivity for both analyses was high. Furthermore, the pipeline removed half of the NHCs records. Presence-only SDM applications should consider this limitation, especially for large biodiversity assessments projects, when they are automatically generated without subsequent checking. Our pipeline provides a conservative estimate of a species’ area of occupancy, within an area slightly larger than its extent of occurrence, compatible to e.g. IUCN red list assessments.

Saiz, Gus, Goodrick, Iain, Wurster, Chris, Nelson, Paul, Wynn, Jonathan, and Bird, Michael (2018) Preferential production and transport of grass-derived pyrogenic carbon in NE-Australian savanna ecosystems. Frontiers in Earth Science, 5.
Understanding the main factors driving fire regimes in grasslands and savannas is critical to better manage their biodiversity and functions. Moreover, improving our knowledge on pyrogenic carbon (PyC) dynamics, including formation, transport and deposition, is fundamental to better understand a significant slow-cycling component of the global carbon cycle, particularly as these ecosystems account for a substantial proportion of the area globally burnt. However, a thorough assessment of past fire regimes in grass-dominated ecosystems is problematic due to challenges in interpreting the charcoal record of sediments. It is therefore critical to adopt appropriate sampling and analytical methods to allow the acquisition of reliable data and information on savanna fire dynamics. This study uses hydrogen pyrolysis (HyPy) to quantify PyC abundance and stable isotope composition (δ13C) in recent sediments across 38 micro-catchments covering a wide range of mixed C3/C4 vegetation in north Queensland, Australia. We exploited the contrasting δ13C values of grasses (i.e., C4; δ13C >−15‰) and woody vegetation (i.e., C3; δ13C <−24‰) to assess the preferential production and transport of grass-derived PyC in savanna ecosystems. Analyses were conducted on bulk and size-fractionated samples to determine the fractions into which PyC preferentially accumulates. Our data show that the δ13C value of PyC in the sediments is decoupled from the δ13C value of total organic carbon, which suggests that a significant component of PyC may be derived from incomplete grass combustion, even when the proportion of C4 grass biomass in the catchment was relatively small. Furthermore, we conducted 16 experimental burns that indicate that there is a comminution of PyC produced in-situ to smaller particles, which facilitates the transport of this material, potentially affecting its preservation potential. Savanna fires preferentially burn the grass understory rather than large trees, leading to a bias toward the finer C4-derived PyC in the sedimentary record. This in turn, provides further evidence for the preferential production and transport of C4-derived PyC in mixed ecosystems where grass and woody vegetation coexist. Moreover, our isotopic approach provides independent validation of findings derived from conventional charcoal counting techniques concerning the appropriateness of adopting a relatively small particle size threshold (i.e., ~50 μm) to reconstruct savanna fire regimes using sedimentary records. This work allows for a more nuanced understanding of the savanna isotope disequilibrium effect, which has significant implications for global 13C isotopic disequilibria calculations and for the interpretation of δ13C values of PyC preserved in sedimentary records.

Miller, Mark G.R., Carlile, Nicholas, Phillips, Joe Scutt, McDuie, Fiona, and Congdon, Bradley C. (2018) The importance of tropical tuna for seabirds foraging over a marine productivity gradient. Marine Ecology Progress Series, 586. pp. 233-249.
Foraging with tuna is a well-documented seabird strategy, referred to as facilitated foraging. However, despite this behaviour being considered almost obligatory in nutrient-poor tropical waters, little data exist on its relative importance to individual colonies. Therefore, to examine facilitated foraging under different patterns of nutrient availability we tracked Wedge-tailed Shearwaters Ardenna pacifica from two colonies, one tropical and one subtropical, situated in waters of contrasting productivity. Shearwater foraging behaviour was assessed relative to oceanographic covariates and predicted distributions for multiple tropical tuna species and age-classes, simulated by an existing ecosystem model (SEAPODYM). Shearwaters from both colonies undertook long-trips to deep, pelagic waters close to seamounts and foraged most often at fronts and eddies. Micronektonic and adult tuna age-classes were highly correlated in space. Predation between these tuna age-classes represents a likely source of facilitated foraging opportunities for shearwaters. At broad-scales, shearwaters consistently foraged in areas with higher predicted adult skipjack and micronektonic tuna densities and avoided adult bigeye tuna. At finer-scales, dynamic ocean features aggregated tuna of all sizes. Enhanced tuna density at these locations increased the likelihood of shearwater foraging activity. Long-trips in the tropics targeted oligotrophic waters with higher tuna densities. Long-trips in the subtropics targeted enhanced productivity, but in some years shifted to target the same oligotrophic, tuna-dense waters used by tropical conspecifics. We conclude that facilitated foraging with tuna is consistently important to the tropical breeding population and becomes increasingly important to the subtropical population in years of low marine productivity.

Long, Xiaowen, Wu, Xugan, Zhao, Lei, Ye, Haihui, Cheng, Yongxu, and Zeng, Chaoshu (2018) Physiological responses and ovarian development of female Chinese mitten crab Eriocheir sinensis subjected to different salinity conditions. Frontiers in Physiology, 8.
Salinity plays a key role affecting ovarian development, osmoregulation and metabolism of female Chinese mitten crab, Eriocheir sinensis during reproductive migration. In this study, female E. sinensis after their puberty molt were subjected to four salinities of 0, 6, 12, and 18% for 40 days to investigate the salinity effects on their ovarian development as well as a range of important physiological parameters. Elevated salinity accelerated the ovarian development with ovigerous crabs found at salinity treatments of 12 and 18% despite no copulation had occurred. Meanwhile the survival rate of female crabs showed a decreasing trend with increasing salinity. Higher salinity also led to increased hemolymph Na+, K+, Ca2+, Cl-, and Mg2+ concentrations. The 6% treatment had the highest contents of hemolymph total and major free amino acids while the Na+/K+ -ATPase activity in the posterior gills was the lowest among treatments. Total n-3 polyunsaturated fatty acids (Sigma n-3PUFA) and n-3/n-6 PUFA ratio in the anterior gills showed a decreasing trend with salinity while 18% had the highest Sigma PUFA and Sigma n-6PUFA. The Sigma n-3PUFA content and n-3/n-6 PUFA ratio of the posterior gills showed a fluctuating pattern and the highest value was detected at 0%, while an increasing trend was found for the Sigma n-6PUFA with increasing salinity. The hemolymph glucose showed a decreasing trend with increasing salinity and the highest total cholesterol in hemolymph was detected at 12%. The 18% treatment had the highest levels of hemolymph gamma-glutamyltransferase, alkaline phosphatase and acid phosphatase, as well as glucose, urea and acid phosphatase in hepatopancreas while the highest hemolymph superoxide dismutase and malondialdehyde were detected at 0%. Overall, the results showed that salinity increase from freshwater to brackish conditions led to lower metabolism, accelerated ovarian development, and the appearance of ovigerous crabs without copulation in female E. sinensis post puberty molt.

de Oliveira Roque, Fabio, Menezes, Jorge F.S., Northfield, Tobin, Ochoa-Quintero, Jose, Campbell, Mason J., and Laurance, William F. (2018) Warning signals of biodiversity collapse across gradients of tropical forest loss. Scientific Reports, 8.
We evaluate potential warning signals that may aid in identifying the proximity of ecological communities to biodiversity thresholds from habitat loss—often termed “tipping points”—in tropical forests. We used datasets from studies of Neotropical mammal, frog, bird, and insect communities. Our findings provide only limited evidence that an increase in the variance (heteroskedasticity) of biodiversity-related parameters can provide a general warning signal of impending threshold changes in communities, as forest loss increases. However, such an apparent effect was evident for amphibians in the Brazilian Atlantic Forest and Amazonian mammal and bird communities, suggesting that impending changes in some species assemblages might be predictable. We consider the potential of such warning signs to help forecast drastic changes in biodiversity.

Salas-Saavedra, Marcos, Dechnik, Belinda, Webb, Gregory E., Webster, Jody M., Zhao, Jian-xin, Nothdurft, Luke D., Clark, Tara R., Graham, Trevor, and Duce, Stephanie (2018) Holocene reef growth over irregular Pleistocene karst confirms major influence of hydrodynamic factors on Holocene reef development. Quaternary Science Reviews, 180. pp. 157-176.
Many factors govern reef growth through time, but their relative contributions are commonly poorly known. A prime example is the degree to which modern reef morphology is controlled by contemporary hydrodynamic settings or antecedent topography. Fortunately, reefs record essential information for interpreting palaeoclimate and palaeoenvironment within their structure as they accrete in response to environmental change. Five new cores recovered from the margin of Heron Reef, southern Great Barrier Reef (GBR), provide new insights into Holocene reef development and relationships between Holocene reefs and Pleistocene antecedent topography, suggesting much more irregular underlying topography than expected based on the configuration of the overlying modern reef margin. Cores were recovered to depths of 30 m and 94 new 230Th ages document growth between 8408 ± 24 and 2222 ± 16 yrs. BP. One core penetrated Pleistocene basement at ∼15.3 m with Holocene reef growth initiated by ∼8.4 ka BP. However, 1.83 km west along the same smooth margin, four cores failed to penetrate Pleistocene basement at depths between 20 and 30 m, suggesting that the margin at this location overlies a karst valley, or alternatively, the antecedent platform does not extend there. A 48 m-long margin-perpendicular transect of three cores documents the filling of this topographic low, at least 30 m beneath the current reef top, with seaward lateral accretion at a rate of 34.3 m/ka. Cores indicate steady vertical and lateral accretion between 3.2 and 1.8 ka BP with no evidence of the hiatus in reef flat progradation seen in most other offshore reefs of the GBR at that time. These cores suggest that the relative protection afforded by the valley allowed for unconsolidated sediment to accumulate, enabling continuous progradation even when other areas of the reef flat appear to have ‘turned off’. Additionally, the cores suggest that although reefs in the southern GBR clearly owe their location to Pleistocene antecedent topography, modern reef morphology at sea level primarily reflects the interaction of Holocene reef communities with contemporary hydrodynamics.

Jaskowiak, Pablo A., Costa, Ivan G., and Campello, Ricardo J.G.B. (2018) Clustering of RNA-Seq samples: comparison study on cancer data. Methods, 132. pp. 42-49.
RNA-Seq is becoming the standard technology for large-scale gene expression level measurements, as it offers a number of advantages over microarrays. Standards for RNA-Seq data analysis are, however, in its infancy when compared to those of microarrays. Clustering, which is essential for understanding gene expression data, has been widely investigated w.r.t. microarrays. In what concerns the clustering of RNA-Seq data, however, a number of questions remain open, resulting in a lack of guidelines to practitioners. Here we evaluate computational steps relevant for clustering cancer samples via an empirical analysis of 15 mRNA-seq datasets. Our evaluation considers strategies regarding expression estimates, number of genes after non-specific filtering and data transformations. We evaluate the performance of four clustering algorithms and twelve distance measures, which are commonly used for gene expression analysis. Results support that clustering cancer samples based on a gene quantification should be preferred. The use of non-specific filtering leading to a small number of features (1,000) presents, in general, superior results. Data should be log-transformed previously to cluster analysis. Regarding the choice of clustering algorithms, Average-Linkage and k-medoids provide, in general, superior recoveries. Although specific cases can benefit from a careful selection of a distance measure, Symmetric Rank-Magnitude correlation provides consistent and sound results in different scenarios

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