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Journal ArticleDOI

Genetic effects of habitat contraction on Lumholtz's tree-kangaroo (Dendrolagus lumholtzi) in the Australian Wet Tropics

01 Mar 2002-Conservation Genetics (Kluwer Academic Publishers)-Vol. 3, Iss: 1, pp 59-67
TL;DR: Assessment of genetic diversity in D. lumholtzi suggests the species has relatively low levels of diversity which is uniformly distributed throughout the Atherton Tablelands; a pattern congruent with data from many othervertebrates endemic to the Australian Wet Tropics.
Abstract: Lumholtz’s tree-kangaroo (Dendrolagus lumholtzi) is one of two species of tree-kangaroo resident in the tropical rainforests of north-eastern Australia The species is confined to the Wet Tropics region, with its distribution centred on the Atherton Tablelands While D lumholtzi was exposed to periodic large-scale climatic fluctuations during the Quaternary that have effectively acted as natural fragmentation events, the species is currently under pressure from anthropogenic disturbance and habitat fragmentation This study aimed to assess the level of genetic diversity in D lumholtzi by examining hypervariable microsatellite loci and the control region of mitochondrial DNA (mtDNA) in 21 individuals from a single 20 ha forest fragment, and from a further 24 animals collected throughout the Atherton Tablelands Results suggest that D lumholtzi has relatively low levels of genetic diversity which is uniformly distributed throughout the Atherton Tablelands; a pattern congruent with data from many other vertebrates endemic to the Australian Wet Tropics It is suggested that Pleistocene climatic fluctuations, which resulted in large-scale rainforest contractions, have imposed an ancient population bottleneck on the ancestral D lumholtzi population The apparent over-riding influence of these natural, historical effects on the genetic structure of D lumholtzi populations, will complicate attempts to assess the genetic impact of current anthropogenic habitat loss and fragmentation
Citations
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Journal ArticleDOI
TL;DR: The results suggest that populations of both rare and common mammals are currently losing genetic diversity and that conservation efforts focused above the population level may fail to protect the breadth of persisting genetic diversity.
Abstract: Policy aimed at conserving biodiversity has focused on species diversity. Loss of genetic diversity, however, can affect population persistence, evolutionary potential, and individual fitness. Although mammals are a well-studied taxonomic group, a comprehensive assessment of mammalian genetic diversity based on modern molecular markers is lacking. We examined published microsatellite data from populations of 108 mammalian species to evaluate background patterns of genetic variability across taxa and body masses. We tested for loss of genetic diversity at the population level by asking whether populations that experienced de- mographic threats exhibited lower levels of genetic diversity. We also evaluated the effect of ascertainment bias (a reduction in variability when microsatellite primers are transferred across species) on our assessment of genetic diversity. Heterozygosity did not vary with body mass across species ranging in size from shrews to whales. Differences across taxonomic groupings were noted at the highest level, between populations of mar- supial and placental mammals. We documented consistently lower heterozygosity, however, in populations that had experienced demographic threats across a wide range of mammalian species. We also documented a significant (p = 0.01) reduction in heterozygosity as a result of ascertainment bias. Our results suggest that populations of both rare and common mammals are currently losing genetic diversity and that conservation efforts focused above the population level may fail to protect the breadth of persisting genetic diversity. Con- servation policy makers may need to focus their efforts below the species level to stem further losses of genetic resources.

127 citations


Cites methods from "Genetic effects of habitat contract..."

  • ...Other sources included selected primer notes from Molecular Ecology, papers located through literature searches, and original papers listed in recent key articles (Goossens et al. 2001; Neff & Gross 2001; Walker et al. 2001; Bowyer et al. 2002)....

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Journal ArticleDOI
TL;DR: The genetic diversity within these two island populations of the platypus is assessed and these patterns are contrasted with genetic diversity estimates in areas from which the populations are likely to have been founded and Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.
Abstract: Genetic diversity generally underpins population resilience and persistence. Reductions in population size and absence of gene flow can lead to reductions in genetic diversity, reproductive fitness, and a limited ability to adapt to environmental change increasing the risk of extinction. Island populations are typically small and isolated, and as a result, inbreeding and reduced genetic diversity elevate their extinction risk. Two island populations of the platypus, Ornithorhynchus anatinus, exist; a naturally occurring population on King Island in Bass Strait and a recently introduced population on Kangaroo Island off the coast of South Australia. Here we assessed the genetic diversity within these two island populations and contrasted these patterns with genetic diversity estimates in areas from which the populations are likely to have been founded. On Kangaroo Island, we also modeled live capture data to determine estimates of population size. Levels of genetic diversity in King Island platypuses are perilously low, with eight of 13 microsatellite loci fixed, likely reflecting their small population size and prolonged isolation. Estimates of heterozygosity detected by microsatellites (HE= 0.032) are among the lowest level of genetic diversity recorded by this method in a naturally outbreeding vertebrate population. In contrast, estimates of genetic diversity on Kangaroo Island are somewhat higher. However, estimates of small population size and the limited founders combined with genetic isolation are likely to lead to further losses of genetic diversity through time for the Kangaroo Island platypus population. Implications for the future of these and similarly isolated or genetically depauperate populations are discussed.

94 citations


Cites background from "Genetic effects of habitat contract..."

  • ...Levels of genetic diversity in platypus populations from Tasmania and Victoria are similar to those observed in mainland populations of other Australian mammalian species (Taylor et al. 1994; Pope et al. 2000; Bowyer et al. 2002; Eldridge et al. 2004)....

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Journal ArticleDOI
TL;DR: Assessment of genetic diversity in island and remnant mainland populations of three endemic species of macropodid marsupial shows that island populations appear to retain substantially more genetic diversity than their island counterparts and therefore are more likely to contribute to the long-term persistence of their species.
Abstract: Since European settlement, mainland Australia has experienced a wave of mammal extinctions and population declines. However, some species have persisted on off-shore islands, which are now viewed as important wildlife refuges. In this study, we assessed the level of genetic diversity, at 7–11 microsatellite loci, in island and remnant mainland populations of three endemic species of macropodid marsupial; the tammar wallaby Macropus eugenii(n = 92); rufous hare-wallaby Lagorchestes hirsutus(n = 40) and black-footed rock-wallaby Petrogale lateralis(n = 164). There was a consistent pattern of significantly higher levels of microsatellite diversity in the remnant mainland population (A= 4.9–13.9; He= 0.61–0.86) of each species compared to conspecific “pristine” island populations (A= 1.2–3.7; He= 0.05–0.44). These marked differences are even apparent where island populations currently have a substantially larger census size. In addition, island populations were substantially inbred (Fe= 0.49–0.91). Although island populations have been insulated from the relatively recent threatening processes operating on the mainland, they have nevertheless been significantly impacted by increased inbreeding and the substantial erosion of genetic diversity. Despite the difficulties of ensuring the survival of remnant mainland populations, they appear to retain substantially more genetic diversity than their island counterparts and therefore are more likely to contribute to the long-term persistence of their species. These data also demonstrate that small remnant mainland populations (n < 10–20) are often capable of rapid recovery and are not necessarily genetically depauperate.

75 citations

Journal ArticleDOI
TL;DR: The results suggest that the biogeography of southern Australia is more complex than previously thought and reveal that seemingly minor landscape features can significantly impact genetic structuring in large vagile mammals.
Abstract: Large vagile mammals typically exhibit little genetic structuring across their range, particularly when their habitat is essentially continuous. We investigated the population genetic structure of a large vagile Australian macropodid, Macropus fuliginosus, which is continuously distributed across most of southern Australia, using nine highly polymorphic nuclear microsatellite loci. Five distinct genetic units were identified across the range, four on the mainland and one on Kangaroo Island. In addition to the predicted historic Nullarbor Plain Barrier, two unexpected mainland barriers to gene flow were identified. Both were associated with landscape discontinuities (Swan River, Flinders Ranges), which appear within the dispersal capabilities of M. fuliginosus. Typical of large vagile mammals, M. fuliginosus displays high genetic diversity (with the exception of an insular population) and weak genetic structuring (within genetic units). However, the expansion of M. fuliginosus from southwestern Australia during the Pleistocene has resulted in significantly reduced genetic diversity in eastern populations. No significant sex-biased dispersal was detected, although differences in habitat, densities and climatic conditions between the eastern and western regions of the range appear to influence dispersal with the effects of isolation by distance only evident in the west. These results suggest that the biogeography of southern Australia is more complex than previously thought and reveal that seemingly minor landscape features can significantly impact genetic structuring in large vagile mammals.

66 citations

Journal ArticleDOI
01 Aug 2003-Heredity
TL;DR: An analysis of mitochondiral DNA and microsatellite data is used to infer both historical and contemporary patterns of population structuring and dispersal in the eastern grey kangaroo (Macropus giganteus) in Australia.
Abstract: Genetic information has played an important role in the development of management units by focusing attention on the evolutionary properties and genetics of populations. Wildlife authorities cannot hope to manage species effectively without knowledge of geographical boundaries and demic structure. The present investigation provides an analysis of mitochondiral DNA and microsatellite data, which is used to infer both historical and contemporary patterns of population structuring and dispersal in the eastern grey kangaroo (Macropus giganteus) in Australia. The average level of genetic variation across sample locations was one of the highest observed for marsupials (h=0.95, HE=0.82). Contrary to ecological studies, both genic and genotypic analyses reveal weak genetic structure of populations, where high levels of dispersal may be inferred up to 230 km. The movement of individuals was predominantly male-biased (average Nem=22.61, average Nfm=2.73). However, neither sex showed significant isolation by distance. On a continental scale, there was strong genetic differentiation and phylogeographic distinction between southern (TAS, VIC and NSW) and northern (QLD) populations, indicating a current and/or historical restriction of gene flow. In addition, it is evident that northern populations are historically more recent, and were derived from a small number of southern founders. Phylogenetic comparisons between M. g. giganteus and M. g. tasmaniensis indicated that the current taxonomic status of these subspecies should be revised as there was a lack of genetic differentiation between the populations sampled.

59 citations


Cites background from "Genetic effects of habitat contract..."

  • ...This level is one of the highest recorded for marsupial taxa (HE range 0.05–0.86, n¼ 24; see Bowyer et al, 2002)....

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  • ...Haplotypic diversity (h7SD) across all M. giganteus individuals was also high (94.8370.66%), and again greater than most other marsupial taxa (h range 12–99%, n¼ 14; see Bowyer et al, 2002)....

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References
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Book
01 Feb 1987
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Abstract: Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.

15,840 citations


"Genetic effects of habitat contract..." refers background or methods in this paper

  • ...The average number of alleles per locus and average heterozygosity (Nei 1987) were calculated using BIOSYS-1 (Swofford and Selander 1981)....

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  • ...Haplotype diversity (h) (Nei 1987) for the mtDNA control region in 14 populations of 12 marsupial taxa...

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  • ...Microsatellite data analysis The average number of alleles per locus and average heterozygosity (Nei 1987) were calculated using BIOSYS-1 (Swofford and Selander 1981)....

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Journal ArticleDOI
TL;DR: Technique non parametrique pour la signification statistique de tables de tests utilisees dans les etudes sur l'evolution notamment.
Abstract: Technique non parametrique pour la signification statistique de tables de tests utilisees dans les etudes sur l'evolution notamment

14,666 citations


"Genetic effects of habitat contract..." refers methods in this paper

  • ...Table-wide significance criteria for each comparison were determined according to the sequential Bonferroni method of Rice (1989)....

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Journal Article
TL;DR: The technic to be given below for imparting statistical validity to the procedures already in vogue can be viewed as a generalized form of regression with possible useful application to problems arising in quite different contexts.
Abstract: The problem of identifying subtle time-space clustering of disease, as may be occurring in leukemia, is described and reviewed. Published approaches, generally associated with studies of leukemia, not dependent on knowledge of the underlying population for their validity, are directed towards identifying clustering by establishing a relationship between the temporal and the spatial separations for the n ( n - 1)/2 possible pairs which can be formed from the n observed cases of disease. Here it is proposed that statistical power can be improved by applying a reciprocal transform to these separations. While a permutational approach can give valid probability levels for any observed association, for reasons of practicability, it is suggested that the observed association be tested relative to its permutational variance. Formulas and computational procedures for doing so are given. While the distance measures between points represent symmetric relationships subject to mathematical and geometric regularities, the variance formula developed is appropriate for arbitrary relationships. Simplified procedures are given for the case of symmetric and skew-symmetric relationships. The general procedure is indicated as being potentially useful in other situations as, for example, the study of interpersonal relationships. Viewing the procedure as a regression approach, the possibility for extending it to nonlinear and multivariate situations is suggested. Other aspects of the problem and of the procedure developed are discussed. Similarly, pure temporal clustering can be identified by a study of incidence rates in periods of widespread epidemics. In point of fact, many epidemics of communicable diseases are somewhat local in nature and so these do actually constitute temporal-spatial clusters. For leukemia and similar diseases in which cases seem to arise substantially at random rather than as clear-cut epidemics, it is necessary to devise sensitive and efficient procedures for detecting any nonrandom component of disease occurrence. Various ingenious procedures which statisticians have developed for the detection of disease clustering are reviewed here. These procedures can be generalized so as to increase their statistical validity and efficiency. The technic to be given below for imparting statistical validity to the procedures already in vogue can be viewed as a generalized form of regression with possible useful application to problems arising in quite different contexts.

11,408 citations


"Genetic effects of habitat contract..." refers methods in this paper

  • ...Genetic differentiation amongst individual D. lumholtzi throughout the Atherton Tablelands was tested by calculating the correlation between genetic and geographic distance using a Mantel test (Mantel 1967)....

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  • ...lumholtzi throughout the Atherton Tablelands was tested by calculating the correlation between genetic and geographic distance using a Mantel test (Mantel 1967)....

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Journal ArticleDOI
01 Dec 1996-Genetics
TL;DR: In this article, two statistical tests for detecting a heterozygosity excess are described, and the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci.
Abstract: When a population experiences a reduction of its effective size, it generally develops a heterozygosity excess at selectively neutral loci, i.e., the heterozygosity computed from a sample of genes is larger than the heterozygosity expected from the number of alleles found in the sample if the population were at mutation drift equilibrium. The heterozygosity excess persists only a certain number of generations until a new equilibrium is established. Two statistical tests for detecting a heterozygosity excess are described. They require measurements of the number of alleles and heterozygosity at each of several loci from a population sample. The first test determines if the proportion of loci with heterozygosity excess is significantly larger than expected at equilibrium. The second test establishes if the average of standardized differences between observed and expected heterozygosities is significantly different from zero. Type I and II errors have been evaluated by computer simulations, varying sample size, number of loci, bottleneck size, time elapsed since the beginning of the bottleneck and level of variability of loci. These analyses show that the most useful markers for bottleneck detection are those evolving under the infinite allele model (IAM) and they provide guidelines for selecting sample sizes of individuals and loci. The usefulness of these tests for conservation biology is discussed.

4,106 citations