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Birds in Fragmented Landscapes: Genes to LandscapesFull project title funded under Australian Research Council Linkage grant scheme: How much habitat and what configuration maintain natural levels of connectivity in southeast Australian native birds?
 One of the study sites  Striated pardalote in the net  Jim banding a yellow-tufted honeyeater Participants Paul Sunnucks, Chief Investigator  Shandiya and Linda processing brown treecreeper Paul Sunnucks, Alexandra (Sasha) Pavlova, Alan Lill & Naoko Takeuchi (School of Biological Sciences, Australian Centre for Biodiversity and Monash U). Jim Radford (Deakin U, Bush Heritage Australia), Jane Melville (Museum Victoria), Graeme Newell & Matt White (ARI, DSE), Leo Joseph (ANWC). PhD students: Nevil Amos (Monash U) & Shandiya Balasubramaniam (U Melbourne with Raoul Mulder, Museum Victoria). Volunteer student: Katherine Harrisson. Honours students (completed): Linda Grootendorst (Monash U) & Rebecca (Bec) Bray (Museum Victoria). Partner OrganisationsDepartment of Sustainability & Environment, Museum Victoria, Department of Primary Industries, Parks Victoria, North-Central Catchment Management Authority, Goulburn Broken Catchment Management Authority Supporting OrganisationsBirds Australia, Australian National Wildlife Collection Project background Naoko measuring noisy miner Natural levels of movement of individuals are critical for maintaining populations in fragmented systems. Movement is necessary to recolonise empty habitat, ‘rescue’ declining populations, and prevent negative genetic impacts. Thus, movement between fragments is likely to be critical for persistence in fragmented landscapes. Population viability is enhanced by natural levels of exchange of individuals and genes between sub-populations. Although rarely tested, it is assumed that movement is closely aligned with structural connectivity (eg corridors, stepping-stones). Thus, considerable emphasis has been placed on increasing structural connection to increase population persistence. However, there is scant evidence that movement is dependent on structural connectivity. A major impediment here has been the logistic constraints associated with quantifying movement using traditional ecological techniques (eg mark-recapture, radio-tracking). The advent of a variety of powerful genetic analyses means that movement can now be feasibly assessed. Molecular information contained in the genotype provides a direct proxy for mark-recapture data but without the need for recapture. The accumulation of movement over many generations can also be resolved, to examine responses in relation to landscape change. Demographic processes and population trajectories can also be estimated. The integration of molecular data with relative abundance data from observational surveys and measures of landscape structure from GIS analyses (ie ‘landscape genetics’) generates a powerful toolkit for evaluating population-level responses to landscape change.  Shandiya releasing eastern yellow robin  Alan releasing by-catch (brown falcon) This project examines the relationship between movement of individuals, landscape structure (amount and arrangement of native vegetation) and population size, for selected bird species, building on the major landscape-scale innovative research of Radford et al. (2005) & Radford and Bennett (2007), who demonstrated that many species decrease in abundance with decrease of the size of the remaining remnants (‘decliners’) but some maintain or even increase their population density in small remnants in fragmented landscapes (‘resistant’). A fundamental difference between ‘resistant’ species and ‘decliners’ may be their ability to move through fragmented landscapes. We are employing a novel research approach that couples existing data on the incidence of bird species in landscapes with molecular techniques that quantify the extent of ‘within-landscape’ and ‘between-landscape’ movement, and population trends, or ‘trajectories’. Thus, we will assemble a unique dataset that contains information on current population size (survey data), extent of movement at several spatial and temporal scales (molecular data) and population trajectories (molecular data) for selected species in landscapes that vary in the amount and pattern of native vegetation. Our objectives are to quantify the movement and other population processes of selected bird species within and among landscapes, which will enable us to identify landscape features that promote natural population functions at patch, landscape and bioregional scales, and to compare population function and trajectories among species that have contrasting responses to landscape-level habitat loss.  Sasha extracting brown treecreeper from the net  Alan taking a blood sample  Naoko giving a yellow-tufted honeyeater a drink Field work Paul and Megan and are processing a bird The fieldwork will last 2.5 years from November 2007 to March 2010 and include mist-netting, trapping and banding birds, taking morphological measurements and collecting small blood and feather samples for genetic analyses and tests of bird health. Our study "landscapes" (801kb) are situated in the beautiful box-ironbark forests of central Victoria: eight of them have experienced different levels of habitat loss and fragmentation, and the other two contain continuous native forest. Follow these links to find out where our landscapes and sites are: Target species include resident ‘decliners’ Brown Treecreeper, Superb Fairy-wren, Grey Shrike-thrush, Eastern Yellow Robin, Spotted Pardalote, Dusky Woodswallow, Buff-rumped Thornbill, mobile ‘decliners’ Fuscus Honeyeater, Yellow-tufted Honeyeater, Brown-headed Honeyeater, sedentary ‘resistant species’ Striated Pardalote and Weebill, and mobile ‘resistant species’ White-plumed Honeyeater. Click here to look at our trapping success so far. Join in!If you love birds, enjoy working in a bush and would like to help us in the field please e-mail Naoko or Sasha on your availability. Download the schedule of our future trips (808kb) (June 2009- February 2010, the dates may slightly change). The project provides meals and accommodation to field volunteers. We are looking forward to sharing hard but fun and rewarding fieldwork with you! Take a look at our Autumn 2008, Winter 2008, Spring 2008 -Summer 2009, and Autumn-Winter 2009 newsletters. Landscape Genetic analysesGenetic analyses Agarose DNA sexing gel  DNA sexing could be done on licor gel in multiplex PCR Sasha will use nuclear microsatellite markers for genotyping all sampled individuals. About 40 of nearly 70 markers developed for other species of birds are effective in our target species. Several markers could be successfully combined in one multiplex reaction to reveal genotypes of individual birds. Analyses of genotypes will allow us to explore population structure and patterns of dispersal within and between landscapes. Also, using a small sample of DNA from blood or feather tissue, the sex of the individual birds can be identified. This is particularly useful for honeyeaters and other species that are difficult to sex in the hand. This information will be used to explore patterns of sex-biased dispersal. In addition, genetic data will help to answer other important questions about kin associations and social structures (does level of relatedness within patch increase with level of fragmentation?), mating systems (does it change in fragmented landscapes?), parentage and extra-pair paternity in fragmented landscapes. 
 Multiplex PCR: several loci amplified in the same tube Landscape permeability models Nev with crested shrike-tits Nev, Matt and Graeme are developing models of landscape permeability for a range of bird species using multiple lines of evidence (expert opinion, banding recovery data, observational surveys). It is particularly interesting to develop models of movement potential through agricultural landscapes that have multiple and varied land-uses. Nev is using the several approaches that identify multiple dispersal paths through the landscape to predict critical areas for maintaining or promoting connectivity within and between landscapes. These models will be used to predict a priori the genetic distances which the landscape genetics will measure. Landscape geneticsGenetic estimates of dispersal will be used to test and improve landscape permeability models and allow to identify the landscape features that are likely to enhance functional connectivity at inter-patch, landscape and bioregional scales. Molecular ecology data on social organisation, population dynamics, juvenile/sex-biased dispersal, species-specific patch connectivity, will be integrated into landscape context: path analyses will be performed for each of the species, impacts of habitat configuration and landscape features on bird mobility will be explored, occurrence and population persistence will be estimated. Our landscape genetic models will then be compared to Radford and Bennett species models (patterns tied to structural connectivity) which will allow us to relate structural landscape connectivity to mobility (processes underlying functional connectivity) and answer important questions such as: do decliners have lower functional connectivity than resisters under similar levels of structural connectivity? This knowledge will trigger re-evaluation of Radford et al.’s (2005) 30% vegetation cover threshold (below which population decline is observed for many woodland species) with molecular estimates (indices of population growth/decline, estimates of within-patch relatedness and inbreeding, levels of within-patch genetic variation) and estimation of “extinction debt” (time lags between habitat loss and local extinction). Thus we will test how reliable are studies based on occupancy of patches. Integration of landscape genetics and spatial modellingIntegrated data on landscape genetics and ecological permeability will be incorporated into policy-informing documents, recommendations for mitigating the impacts of habitat loss and fragmentation on species survival will be developed. Apart from these mainstream questions other exceptionally important issues that have potential to impact population persistence and the nature of human-impacted populations will be explored. Here are some examples:  Linda with sacred kingfisher Impact of habitat fragmentation on level of chronic stress in bird populationsFragmentation could lead to a significant increase in the number of natural stressors affecting a local population of animals and result in repeated and frequent stress responses and, eventually, chronic stress. Members of populations experiencing chronic stress would thus be likely to have a reduced survival probability and reproductive output, and the populations themselves therefore a greater chance of becoming extinct. Linda will compare morphometrics and blood stress indicators (such as haemoglobin, hematocrit and H/L ratio, the ratio of two types of leucocytes) across landscapes with different level of fragmentation. Immune-response analyses Bec with willie wagtail Shandiya is investigating the effects of habitat fragmentation on the genetic diversity of immune system genes (MHC class II β genes) and blood parasite infection in a co-operative living bird, the Brown Treecreeper. Level of variation in this immune-response gene complex may differ among fragmented and continuous landscapes. This will be tested by estimating genetic diversity of the MHC gene complex and comparing it to infection rates of blood parasites.  The blood of the infected Brown Treecreeper: Plasmodium gametocyte is marked with an arrow Immune-responses may differ in species with different social structure: group living birds may have higher diversity and better survival ability compared to solitary species. Bec will explore this question by comparing genetic diversity and gene expression of MHC genes across several species. Some other important questions we will explore: The interplay between immune system genes and stress levels. Contrasting stress level and acoustic activity: does habitat fragmentation induces stress and impairs aspects of reproductive performance in birds? Breeding biology: how do birds search for breeding areas at the landscape level? Population viability modelling: integration of spatially-explicit distribution data from surveys and genetically-derived parameters of pop growth and dispersal capabilities. Download our first progress update here (pdf 172kb). Citations
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