ORCID Profile
0000-0002-1578-8473
Current Organisations
UNSW Sydney
,
University of Melbourne Faculty of Science
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Publisher: Authorea, Inc.
Date: 02-06-2023
DOI: 10.22541/AU.168569955.57431501/V1
Abstract: The Australian range of little penguins, Eudyptula minor, extends around southern Australia, with range-edge sites near the large cities of Perth (west) and Sydney (east). Both range-edges are closer to the equator than the range-core, being likely to experience similar heating with climate change. As a result, movement to one range-edge is not an option for little penguins, unlike in many other species. Therefore, adaptation at the range edge might be very important for little penguins. Capacity for future adaptation depends upon the variability each site holds, and the amount of exchange between sites. In peripheral sites, incoming dispersal might either forestall demographic collapse and replenish genetic variation (good), or overcome local adaptation and increase disease transmission (bad). We aimed to establish the genetic variability in each site, and the exchange (dispersal) of in iduals between sites. Genetic markers included biparentally-inherited microsatellites, and maternally-inherited mitochondrial DNA sequence. For microsatellites, no site appeared to have critically low variation, including the peripheral sites, however there was a significant but slight trend of increased variation from east to west. In contrast, mitochondrial DNA showed a pattern of significantly reduced variation at the two range-edges, possibly indicating differential dispersal patterns in males and females. There appear to be two main genetically distinct groups, in the west and the east, but analysis of lifetime dispersal patterns across the Australian range also suggests complex dispersal, sometimes with high dispersal or similarity between locations that are not adjacent. Our work suggests that despite some differentiation, little penguin sites are interdependent due to complex dispersal patterns, and all have valuable genetic variation. In particular, the peripheral sites are not depauperate of variation, and are moderately connected to the remainder of the distribution, so possibly may be able to adapt in response to climate warming.
Publisher: Springer Science and Business Media LLC
Date: 03-11-2022
DOI: 10.1038/S42003-022-04038-9
Abstract: The evolutionarily unique platypus ( Ornithorhynchus anatinus ) has experienced major declines and extinctions from a range of historical and recent interacting human-mediated threats. Although spending most of their time in the water, platypuses can move over land. Nevertheless, uncertainties remain whether dams are barriers to movement, thus limiting gene flow and dispersal, essential to evolution and ecology. Here we examined disruption of gene flow between platypus groups below and above five major dams, matched to four adjacent rivers without major dams. Genetic differentiation ( F ST ) across dams was 4- to 20-fold higher than along similar stretches of adjacent undammed rivers F ST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent major barriers for platypus movements. Furthermore, F ST between groups was correlated with the year in which the dam was built, increasing by 0.011 every generation, reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when groups are fragmented by major dams. Mitigation strategies, such as building of by-pass structures and translocation between upstream and downstream of the dam, should be considered in conservation and management planning.
Publisher: Proceedings of the National Academy of Sciences
Date: 29-08-2022
Abstract: Efforts to understand human social evolution rely largely on comparisons with nonhuman primates. However, a population of bottlenose dolphins in Shark Bay, Western Australia, combines a chimpanzee-like fission-fusion grouping pattern, mating system, and life history with the only nonhuman ex le of strategic multilevel male alliances. Unrelated male dolphins form three alliance levels, or “orders”, in competition over females: both within-group alliances (i.e., first- and second-order) and between-group alliances (third-order), based on cooperation between two or more second-order alliances against other groups. Both sexes navigate an open society with a continuous mosaic of overlapping home ranges. Here, we use comprehensive association and consortship data to examine fine-scale alliance relationships among 121 adult males. This analysis reveals the largest nonhuman alliance network known, with highly differentiated relationships among in iduals. Each male is connected, directly or indirectly, to every other male, including direct connections with adult males outside of their three-level alliance network. We further show that the duration with which males consort females is dependent upon being well connected with third-order allies, independently of the effect of their second-order alliance connections, i.e., alliances between groups increase access to a contested resource, thereby increasing reproductive success. Models of human social evolution traditionally link intergroup alliances to other ergent human traits, such as pair bonds, but our study reveals that intergroup male alliances can arise directly from a chimpanzee-like, promiscuous mating system without one-male units, pair bonds, or male parental care.
Publisher: Cold Spring Harbor Laboratory
Date: 23-08-2021
DOI: 10.1101/2021.08.22.457241
Abstract: 1. During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species’ ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species’ invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris, to identify parallel and ergent evolutionary change between contemporary native and invasive range s les and their common ancestral population. To do this, we use reduced-representation sequencing of native s les collected recently in north-western Europe and invasive s les from Australia, together with museum specimens s led in the UK during the mid-19 th Century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants (e.g. TCDD) and food carbohydrate content. We also identified ergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary s les. Our results demonstrate the value of including historical s les in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.
Publisher: Wiley
Date: 05-05-2020
DOI: 10.1002/ECE3.6288
Publisher: Authorea, Inc.
Date: 06-05-2021
DOI: 10.22541/AU.162031847.75356972/V1
Abstract: New sequencing technologies have opened the door to many new research opportunities, but these advances in data collection are not always compatible with some important methods for data analysis. Fis has been a staple calculation in the field of population genetics. Fis can be used to measure either a departure from random mating, or measure underlying selective pressures for or against heterozygote genotypes. However, when using Next Generation Sequencing (NGS) technology on multi-locus gene families it is often impossible to discern which allelic variants are present at each locus. Some important multi-locus gene families are: the major histocompatibility complex (MHC) in animals homeobox genes in fungi or the self-incompatibility genes in plants. This in turn makes it impossible to calculate either locus-specific expected heterozygosity, or observed heterozygosity, both of which are required to calculate Fis. Without the ability to calculate Fis from NGS of multi-locus gene families, we need a new multi-locus measure that will allow us to detect the underlining mating, and selective patterns present in such multi-locus genes. This paper provides such a novel multi-locus measure, called 1His. We demonstrate the accuracy of the 1His equation using simulated data, and two datasets taken from natural populations of dolphins and penguins. The introduction of this new measure is particularly important because of the great interest in mating patterns and selection of multi-locus gene families, such as MHC.
Publisher: Wiley
Date: 09-2022
DOI: 10.1002/ECE3.9176
Abstract: Geographic genetic differentiation measures are used for purposes such as assessing genetic ersity and connectivity, and searching for signals of selection. Confirmation by unrelated measures can minimize false positives. A popular differentiation measure, Bray‐Curtis, has been used increasingly in molecular ecology, renamed AFD (hereafter called BCAFD ). Critically, BCAFD is expected to be partially independent of the commonly used Hill “Q‐profile” measures. BCAFD needs scrutiny for potential biases, by examining limits on its value, and comparing simulations against expectations. BCAFD has two dependencies on within‐population (alpha) variation, undesirable for a between‐population (beta) measure. The first dependency is derived from similarity to and . The second dependency is that BCAFD cannot be larger than the highest allele proportion in either location (alpha variation), which can be overcome by data‐filtering or by a modified statistic A A or “Adjusted AFD”. The first dependency does not forestall applications such as assessing connectivity or selection, if we know the measure's null behavior under selective neutrality with specified conditions—which is shown in this article for A A , for equilibrium, and nonequilibrium, for the commonly used data type of single‐nucleotide‐polymorphisms (SNPs) in two locations. Thus, A A can be used in tandem with mathematically contrasting differentiation measures, with the aim of reducing false inferences. For detecting adaptive loci, the relative performance of A A and other measures was evaluated, showing that it is best to use two mathematically different measures simultaneously, and that A A is in one of the best such pairwise criteria. For any application, using A A , rather than BCAFD, avoids the counterintuitive limitation by maximum allele proportion within localities.
Publisher: Cold Spring Harbor Laboratory
Date: 19-05-2021
DOI: 10.1101/2021.05.19.442026
Abstract: A species’ success during the invasion of new areas hinges on an interplay between demographic processes and the outcome of localized selection. Invasive European Starlings ( Sturnus vulgaris ) established populations in Australia and North America in the 19 th century. Here, we compare whole-genome sequences among native and independently introduced European Starling populations from three continents to determine how demographic processes interact with rapid adaptive evolution to generate similar genetic patterns in these recent and replicated invasions. Our results confirm that a post-bottleneck expansion may in fact support local adaptation. We find that specific genomic regions have differentiated even on this short evolutionary timescale, and suggest that selection best explains differentiation in at least two of these regions. This infamous and highly mobile invader adapted to novel selection (e.g., extrinsic factors), perhaps in part due to the demographic boom intrinsic to many invasions.
Publisher: CSIRO Publishing
Date: 10-07-2023
DOI: 10.1071/WR22128
Publisher: Cold Spring Harbor Laboratory
Date: 04-07-2022
DOI: 10.1101/2022.07.04.498653
Abstract: Adaptive ergence is a fundamental process that shapes genetic ersity within and across species. Structural variants (SVs) are large-scale genetic differences (insertion, deletions, and rearrangements) within a species or population. SVs can cause important functional differences in the in idual’s phenotype. Characterising SVs across invasive species will help fill knowledge gaps regarding how patterns of genetic ersity and genetic architecture shape rapid adaptation in response to new selection regimes. In this project we seek to understand patterns in genetic ersity within the globally invasive European starling, Sturnus vulgaris . We use whole genome sequencing of eight native United Kingdom (UK), eight invasive North America (NA), and 33 invasive Australian (AU) starlings to examine patterns in genome-wide SNPs and SVs between populations and within Australia. The findings of our research demonstrate that even within recently erged lineages or populations, there may be high amounts of structural variation. Further, patterns of genetic ersity estimated from SVs do not necessarily reflect relative patterns from SNP data, either when considering patterns of ersity along the length of the organism’s chromosomes (owing to enrichment of SVs in sub telomeric repeat regions), or interpopulation ersity patterns (possibly a result of altered selection regimes or introduction history). Finally, we find that levels of balancing selection within the native range differ across SNP and SV of different classes and outlier classifications. Overall, our results demonstrate that the processes that shape allelic ersity within populations is complex and supports the need for further investigation of SVs across a range of taxa to better understand correlations between oft well studied SNP ersity and that of SVs.
Publisher: Research Square Platform LLC
Date: 14-04-2022
DOI: 10.21203/RS.3.RS-1406456/V1
Abstract: Populations of the evolutionarily unique platypus ( Ornithorhynchus anatinus ) have experienced major declines and local extinctions from a range of historical and recent interacting threats, including fur trade, land clearing, water resource developments (dams and extractions), invasive species, fire, pollution, and urbanisation. Although spending most of their time in the water, platypuses can move over land. Nevertheless, significant uncertainties remain whether major dams across the platypus’ distribution pose barriers to movement, limiting gene flow and dispersal, which are essential evolutionary and ecological processes. Here we examined disruption of gene flow between platypus groups below and above major dams (wall height 10 m). Platypuses were surveyed above and below five major dams, matched to four adjacent rivers without major dams. Genetic differentiation ( F ST ) across dams was 4- to 20- fold higher than along similar stretches of adjacent undammed rivers F ST across dams was similar to differentiation between adjacent river systems. This indicates that major dams represent significant barriers for platypus movements. Furthermore, F ST between populations was significantly correlated with the year in which the dam was built, increasing by 0.011 every generation (7.9 years), reflecting the effects of these barriers on platypus genetics. This study provides evidence of gene flow restriction, which jeopardises the long-term viability of platypus populations when populations are fragmented by major dams. Alternatives to large dam construction, such as building of by-pass structures and translocation between upstream and downstream populations, should be considered in water conservation and management planning.
Publisher: Wiley
Date: 06-02-2022
DOI: 10.1111/MEC.16353
Abstract: During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline and global climate change. Concurrently, greater globalization is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species’ ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species’ invasion success or persistence informs invasive species management, assists with native species preservation and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling, Sturnus vulgaris , to identify parallel and ergent evolutionary change between contemporary native and invasive range s les and their common ancestral population. To do this, we use reduced‐representation sequencing of native s les collected recently in northwestern Europe and invasive s les from Australia, together with museum specimens s led in the UK during the mid‐19th century. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants. We also identified ergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary s les. Our results demonstrate the value of including historical s les in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.
Publisher: Wiley
Date: 08-06-2020
DOI: 10.1111/GEB.13117
Abstract: Tropical species are thought to be more susceptible to climate warming than are higher latitude species. This prediction is largely based on the assumption that tropical species can tolerate a narrower range of temperatures. While this prediction holds for some animal taxa, we do not yet know the latitudinal trends in temperature tolerance for plants. We aim to address this knowledge gap and establish if there is a global trend in plant warming risk. Global. Present–2070. Plants. We used 9,737 records for 1,312 species from the Kew Gardens’ global germination database to quantify global patterns in germination temperature. We found no evidence for a latitudinal gradient in the breadth of temperatures at which plant species can germinate. However, tropical plants are predicted to face the greatest risk from climate warming, because they experience temperatures closer to their upper germination limits. By 2070, over half (79/142) of tropical plant species are predicted to experience temperatures exceeding their optimum germination temperatures, with some even exceeding their maximum germination temperature (41/190). Conversely, 95% of species at latitudes above 45° are predicted to benefit from warming, with environmental temperatures shifting closer to the species’ optimal germination temperatures. The prediction that tropical plant species would be most at risk under future climate warming was supported by our data, but through a different mechanism to that generally assumed.
Publisher: Authorea, Inc.
Date: 10-06-2022
DOI: 10.22541/AU.165485737.71827018/V1
Abstract: Potential sub ision events in populations can have a wide range of causes: from natural disasters like bushfires that isolate communities, to anthropogenic disturbances like infrastructure projects cutting through a population’s habitat. Due to the unpredictability inherent in events like bushfires, or even for predictable events such as property development, populations affected by these potential sub isions are often not studied until after the event, making it extremely hard to assess negative conservation impacts without the benefit of prior data. This paper aims to apply population genetics methods to assess whether it is possible to accurately assess the impact a potential sub ision event can have on the genetic makeup of a population, especially when one has no data prior to such an event. Differentiation measures, such as Fst, might be used for detecting whether a population has been sub ided. However, these measures often take dozens of generations to show a significant change from zero (i.e., no differentiation), especially in larger populations. In this paper we present a more sensitive method, which is suitable for detecting sub ision effects within a few generations of the event and which can be applied without prior data. We test this method using both simulated data, and genetic data from a population of koalas impacted by a railroad infrastructure development.
Publisher: Wiley
Date: 18-07-2022
Abstract: The European starling, Sturnus vulgaris , is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long‐read transcriptome of an Australian‐sourced European starling ( S. vulgaris vAU), and a second, North American, short‐read genome assembly ( S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked‐reads, low‐coverage Nanopore sequencing, and PacBio Iso‐Seq full‐length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high‐quality zebra finch ( Taeniopygia guttata ) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species‐specific transcript mapping and gene annotation revealed good gene‐level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso‐Seq transcript data and complementary homology‐based annotation of sequential assembly steps (assessed using a new tool, saaga ) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base‐calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.
Publisher: Cold Spring Harbor Laboratory
Date: 08-04-2021
DOI: 10.1101/2021.04.07.438753
Abstract: The European starling, Sturnus vulgaris , is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling ( S. vulgaris vAU), and a second North American genome ( S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterisation. S. vulgaris vAU combined 10x Genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 1,628 scaffolds (72.5 Mb scaffold N50). Species-specific transcript mapping and gene annotation revealed high structural and functional completeness (94.6% BUSCO completeness). Further scaffolding against the high-quality zebra finch ( Taeniopygia guttata ) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Rapid, recent advances in sequencing technologies and bioinformatics software have highlighted the need for evidence-based assessment of assembly decisions on a case-by-case basis. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, SAAGA) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counter-intuitive behaviour in traditional BUSCO metrics, and present B uscomp , a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. Finally, we present a second starling assembly, S. vulgaris vNA, to facilitate comparative analysis and global genomic research on this ecologically important species.
Publisher: MDPI AG
Date: 15-08-2019
DOI: 10.3390/E21080794
Abstract: In ecology and evolution, entropic methods are now used widely and increasingly frequently. Their use can be traced back to Ramon Margalef’s first attempt 70 years ago to use log-series to quantify ecological ersity, including searching for ecologically meaningful groupings within a large assemblage, which we now call the gamma level. The same year, Shannon and Weaver published a generally accessible form of Shannon’s work on information theory, including the measure that we now call Shannon–Wiener entropy. Margalef seized on that measure and soon proposed that ecologists should use the Shannon–Weiner index to evaluate ersity, including assessing local (alpha) ersity and differentiation between localities (beta). He also discussed relating this measure to environmental variables and ecosystem processes such as succession. Over the subsequent decades, he enthusiastically expanded upon his initial suggestions. Finally, 2019 also would have been Margalef’s 100th birthday.
Publisher: Springer Science and Business Media LLC
Date: 05-08-2023
DOI: 10.1007/S10841-023-00499-3
Abstract: The wildfires of Australia’s Black Summer in 2019/2020 caused a massive loss of wildlife and habitats, but the effects of the fire on invertebrate species post-burn are unknown. We hypothesised that the fires would negatively affect the genetic ersity of invertebrate species by impeding movement between populations due to habitat loss. We studied the genetic ersity of a flightless dung beetle, Amphistomus primonactus Matthews 1974, to determine the impact of the wildfires on this species. We examined 90 SNPs from 193 in iduals across seven localities impacted by the wildfires in north-eastern New South Wales. We used STRUCTURE to determine the overall population structure of the seven localities. We calculated four within-locality genetic ersity measures (observed heterozygosity ( H o ), unbiased expected heterozygosity (u H e ), Shannon’s Information ( 1 H ), and the inbreeding coefficient ( F IS ). We calculated three between-locality genetic ersity measures (Fixation Index ( F ST ), Hedrick’s G” ST , and Shannon’s Mutual Information ( I ). We used partial Mantel tests to compare the between-locality genetic ersity measures with the mean fire intensity along each pairwise linear transect, while accounting for genetic variation due to geographic distance. We compared the within-locality genetic ersity measures to the mean fire intensity at each site. STRUCTURE showed a large degree of intermixing between localities. We found no significant effect of fire on any within-locality genetic ersity measure, or on any between-locality genetic ersity measure. We suggest that the genetic ersity of A. primonactus was not significantly affected by the Black Summer wildfires. Implications for insect conservation: Our results show that the 2019/2020 wildfires had a negligible impact on the genetic structure of A. primonactus . This offers a promising outlook for the species in its recovery from the fires.
Publisher: Wiley
Date: 29-09-2021
DOI: 10.1111/MEC.15601
Abstract: A detailed understanding of population genetics in invasive populations helps us to identify drivers of successful alien introductions. Here, we investigate putative signals of selection in Australian populations of invasive common starlings, Sturnus vulgaris , and seek to understand how these have been influenced by introduction history. We used reduced representation sequencing to determine population structure, and identify Single Nucleotide Polymorphisms (SNPs) that are putatively under selection. We found that since their introduction into Australia, starling populations have become genetically differentiated despite the potential for high levels of dispersal, and that starlings have responded to selective pressures imposed by a wide range of environmental conditions across their geographic range. Isolation by distance appears to have played a strong role in determining genetic substructure across the starling's Australian range. Analyses of candidate SNPs that are putatively under selection indicated that aridity, precipitation and temperature may be important factors driving adaptive variation across the starling's invasive range in Australia. However, we also noted that the historic introduction regime may leave footprints on sites flagged as being under adaptive selection, and encourage critical interpretation of selection analyses in non‐native populations.
Publisher: Wiley
Date: 13-03-2023
DOI: 10.1111/MEC.16877
Abstract: The genetic consequences of the sub ision of populations are regarded as significant to long‐term evolution, and research has shown that the scale and speed at which this is now occurring is critically reducing the adaptive potential of most species which inhabit human‐impacted landscapes. Here, we provide a rare and, to our knowledge, the first analysis of this process while it is happening and demonstrate a method of evaluating the effect of mitigation measures such as fauna crossings. We did this by using an extensive genetic data set collected from a koala population which was intensely monitored during the construction of linear transport infrastructure which resulted in the sub ision of their population. First, we found that both allelic richness and effective population size decreased through the process of population sub ision. Second, we predicted the extent to which genetic drift could impact genetic ersity over time and showed that after only 10 generations the resulting two sub ided populations could experience between 12% and 69% loss in genetic ersity. Lastly, using forward simulations we estimated that a minimum of eight koalas would need to disperse from each side of the sub ision per generation to maintain genetic connectivity close to zero but that 16 koalas would ensure that both genetic connectivity and ersity remained unchanged. These results have important consequences for the genetic management of species in human‐impacted landscapes by showing which genetic metrics are best to identify immediate loss in genetic ersity and how to evaluate the effectiveness of any mitigation measures.
Publisher: Authorea, Inc.
Date: 21-03-2022
DOI: 10.22541/AU.164787523.38878185/V1
Abstract: Linear infrastructure stands as one of the main culprits of anthropogenically caused bio ersity decline. As it fragments landscapes, it ultimately results in a myriad of direct and indirect ecological consequences for wildlife. As transportation networks will continue to grow under increasing human population growth, bio ersity will continue to decline making the need to understand and mitigate their impact on species an urgent need for conservation worldwide. The implementation of mitigation measures to alleviate the barrier effect produced by linear transport infrastructure on local fauna is not new, and research has shown that their effectiveness has been shown to be influenced by their design, their placement and the biology of the impacted species. Our understanding of their effectiveness in preventing the longer-term impacts of linear transport infrastructure on habitat connectivity via gene flow, however, remains poorly understood. Here, we used a pre- and post-habitat fragmentation genetic dataset collected as part of an extensive Koala Management Program to ask questions about the immediate and predicted longer-term genetic consequences of linear transport infrastructure on the impacted species. Importantly, using forward migration simulations, we show that to preserve connectivity would need to result in around 20% of the population mixing to avoid long-term genetic drift. These results have important consequences for the management of species at the forefront of linear infrastructure. In particular, the study shows the importance of considering gene flow in our assessment of the effectiveness of fauna crossings.
Publisher: Authorea, Inc.
Date: 16-06-2023
DOI: 10.22541/AU.168691541.17899618/V1
Abstract: 1. The fixation index, FIS has been a staple measure to detect selection or departures from random mating in populations. However, current Next Generation Sequencing (NGS) cannot easily estimate Fis, in multi-locus gene families, which contain multiple loci having similar or identical arrays of variant sequences of ≥1 kilobase, which differ at multiple positions. In these families, high-quality short-read NGS data typically identify variants, but not the genomic location, which is required to calculate Fis (based on locus-specific observed and expected heterozygosity). Thus, to assess assortative mating, or selection on heterozygotes, from NGS of multi-locus gene families, we need a method that does not require knowledge of which variants are allelic at which locus in the genome. 2. We developed such a method. Like Fis, our novel measure, 1His, is based on the principle that positive assortative mating, or selection against heterozygotes, reduces within-in idual variability relative to the population. 3. We demonstrate high accuracy of 1His on a wide-range of simulated scenarios, and two datasets from natural populations of penguins and dolphins. 4. 1His is important because multi-locus gene families are often involved in assortative mating, or selection on heterozygotes. 1His is particularly useful for multi-locus gene families such as toll-like receptors, the major-histocompatibility-complex in animals, homeobox genes in fungi and self-incompatibility genes in plants.
No related grants have been discovered for William B Sherwin.