Comparative Population Genetic Structure of the Endangered Southern Brown Bandicoot,Isoodon obesulus,in Fragmented Landscapes of Southern Australia

Genetic connectivity is a key factor for maintaining the persistence of populations in fragmented landscapes. In highly modified landscapes such us peri-urban areas, organisms’ dispersal among fragmented habitat patches can be reduced due to the surrounding matrix, leading to subsequent decreased gene flow and increased potential extinction risk in isolated sub-populations. However, few studies have compared within species how dispersal/gene flow varies between regions and among different forms of matrix that might be encountered. In the current study, we investigated gene flow and dispersal in an endangered marsupial, the southern brown bandicoot (Isoodon obesulus) in a heavily modified peri-urban landscape in South Australia, Australia. We used 14 microsatellite markers to genotype 254 individuals which were sampled from 15 sites. Analyses revealed significant genetic structure. Our analyses also indicated that dispersal was mostly limited to neighbouring sites. Comparisons of these results with analyses of a different population of the same species revealed that gene flow/dispersal was more limited in this peri-urban landscape than in a pine plantation landscape approximately 400 km to the south-east. These findings increase our understanding of how the nature of fragmentation can lead to profound differences in levels of genetic connectivity among populations of the same species.     

Isolation and characterization of microsatellite loci in the southern brown bandicoot (Isoodon obesulus), and their applicability to other marsupial species

The southern brown bandicoot (Isoodon obesulus) was once widely distributed throughout coastal regions of Australia, however, populations have now become fragmented and the number of individuals are declining rapidly. As a result, this species is now classified as endangered in New South Wales and requires management. We have developed eight microsatellite markers to investigate levels of genetic variation and subdivision among these isolated populations. These microsatellite markers show levels of variability ranging from four to eight alleles and observed heterozygosities of 0.353–0.938. These microsatellite markers are also suitable for similar population studies on other related marsupials.     

Random amplified polymorphic DNA analysis of southern brown bandicoot (Isoodon obesulus) populations in Western Australia reveals genetic differentiation related to environmental variables

Random amplified polymorphic DNA (RAPD) markers were used to analyse genetic variation within and between populations of Isoodon obesulus in Western Australia. Genetically controlled geographical variation in body size associated with habitat type and rainfall exists in this species, raising the question of whether local conditions may influence gene flow in I. obesulus. The RAPD markers displayed substantial genetic variation, with all animals possessing unique RAPD phenotypes over 39 polymorphic bands produced by three primers. Significant geographical subdivision was apparent (PhiST = 0.208) with southwest locations being divergent from all others, despite there being no physical barriers to gene flow. The pattern of subdivision was unrelated to physical distance between the locations, but was related to both annual rainfall and habitat type. Therefore, the most reasonable explanation for this pattern of subdivision appears to be that gene flow is restricted by selection against migrants between local populations with substantially different habitat type or rainfall. Restriction of gene flow through selection against migrants is rarely investigated, and the results of this study suggest that the importance of this process in the formation of population structure may be underestimated.     

Sex chromosome elimination,X chromosome inactivation and reactivation in the southern brown bandicoot Isoodon obesulus (Marsupialia: Peramelidae)

Cytogenetic studies have shown that bandicoots (family Peramelidae) eliminate one X chromosome in females and the Y chromosome in males from some somatic tissues at different stages during development. The discovery of a polymorphism for X-linked phosphoglycerate kinase (PGK-1) in a population of Isoodon obesulus from Mount Gambier, South Australia, has allowed us to answer a number of long standing questions relating to the parental source of the eliminated X chromosome, X chromosome inactivation and reactivation in somatic and germ cells of female bandicoots. We have found no evidence of paternal PGK-1 allele expression in a wide range of somatic tissues and cell types from known female heterozygotes. We conclude that paternal X chromosome inactivation occurs in bandicoots as in other marsupial groups and that it is the paternally derived X chromosome that is eliminated from some cell types of females. The absence of PGK-1 paternal activity in somatic cells allowed us to examine the state of X chromosome activity in germ cells. Electrophoresis of germ cells from different aged pouch young heterozygotes showed only maternal allele expression in oogonia whereas an additional paternally derived band was observed in pre-dictyate oocytes. We conclude that reactivation of the inactive X chromosome occurs around the onset of meiosis in female bandicoots. As in other mammals, late replication is a common feature of the Y chromosome in male and the inactive X chromosome in female bandicoots. The basis of sex chromosome loss is still not known; however later timing of DNA synthesis is involved. Our finding that the paternally derived X chromosome is eliminated in females suggests that late DNA replication may provide the imprint for paternal X inactivation and the elimination of sex chromosomes in bandicoots.     

Effect of season on thermoregulation, metabolism and ventilation of the southern brown bandicoot Isoodon obesulus (Marsupialia: Peramelidae)

Seasonal variation in various thermoregulatory, metabolic and ventilatory parameters was examined for southern brown bandicoots (Isoodon obesulus fusciventer) from a Mediterranean climate near Perth, Western Australia. There was significant seasonal variation over the four annual seasons at thermoneutrality (Ta=30 degrees C) in body temperature, oxygen consumption, carbon dioxide production, respiratory exchange ratio, total evaporative water loss, wet and dry thermal conductance and tidal volume but not mass, ventilatory frequency, minute volume or oxygen extraction efficiency. Only carbon dioxide production and respiratory exchange ratio showed an annual pattern that was significantly related to season, with both being significantly higher in winter, presumably as a result of greater and higher quality food availability.     

The effect of supplementary food on home range of the southern brown bandicoot,Isoodon obesulus (Marsupialia: Peramelidae)

The study investigated the relationship between home range and food abundance in a population of the southern brown bandicoot. Isoodon obesulus, in Western Australia. Home range areas were estimated seven times between 1986 and 1988 by live-trapping, spool-and-line devices and fluorescent pigment tracking. The abundance of invertebrate food was measured simultaneously by placing pitfall traps within the home ranges of individual animals, and by sampling invertebrates in topsoil and litter. Home range areas tended to be negatively correlated with food abundance, especially in the autumn and winter of 1986 and 1987. The influence of food on home range was investigated further in September 1988 by providing eight individual I. obesulus with a supplementary food mixture. Contrary to expectation, the added food caused an increase in home range area, home range overlap and displacement, as well as an influx of new individuals to food stations. In contrast, home range parameters in control (non-fed) individuals changed little during the experiment. The shuffling of home ranges due to feeding suggests that the home range system of I. obesulus is relatively flexible, with individuals monitoring and exploiting resources in an opportunistic manner. In contrast to previous studies, we found no evidence that I. obesulus was territorial. We speculate that individuals may be territorial at low population density if resources are defendable and intruder pressure is low, but occupy overlapping ranges if population density is high.     

Effects of temperature on metabolism,ventilation, and oxygen extraction in the southern brown bandicoot Isoodon obesulus (Marsupialia: Peramelidae)

The effects of ambient temperatures (T(a)) from 10 degrees to 35 degrees C on metabolism, ventilation, and oxygen extraction were examined for the southern brown bandicoot (Isoodon obesulus). Oxygen consumption (VO2) followed the pattern typical for endotherms, decreasing with increasing T(a) from 10 degrees to 25 degrees C. It did not significantly change between Ta=25 degrees and 35 degrees C (the thermoneutral zone). VO2 was approximately 2.4 times higher at Ta=10 degrees C (0.967 mL O(2) g(-1) h(-1)) compared with basal (0.410 mL O(2) g(-1) h(-1)) at Ta=30 degrees C. While the metabolic rates of the bandicoots were basal at Ta=30 degrees C, respiratory frequency (f(R)) was 24.6 breaths min(-1), tidal volume (V(T)) was 7.79 mL, minute volume (V(I)) was 191.3 mL min(-1), and oxygen extraction efficiency (EO2) was 26.8%. Increased VO2 at Ta< or =25 degrees C was associated with a large increase in V(I) due to increases in V(T) and f(R). A greater proportion of the change was due to the increase in tidal volume. EO2 was constant at approximately 26% for all T(a) up to and including 30 degrees C. At Ta=35 degrees C, EO2 decreased to 17.7%, f(R) increased to 35.6 breaths min(-1), and V(T) decreased to 7.22 mL. The metabolic and ventilatory physiology of the southern brown bandicoot are typical of an unspecialized medium-sized marsupial.     

Cone topography and spectral sensitivity in two potentially trichromatic marsupials, the quokka (Setonix brachyurus) and quenda (Isoodon obesulus)

The potential for trichromacy in mammals, thought to be unique to primates, was recently discovered in two Australian marsupials. Whether the presence of three cone types, sensitive to short- (SWS), medium- (MWS) and long- (LWS) wavelengths, occurs across all marsupials remains unknown. Here, we have investigated the presence, distribution and spectral sensitivity of cone types in two further species, the quokka (Setonix brachyurus) and quenda (Isoodon obesulus). Immunohistochemistry revealed that SWS cones in the quokka are concentrated in dorso-temporal retina, while in the quenda, two peaks were identified in naso-ventral and dorso-temporal retina. In both species, MWS/LWS cone spatial distributions matched those of retinal ganglion cells. Microspectrophotometry (MSP) confirmed that MWS and LWS cones are spectrally distinct, with mean wavelengths of maximum absorbance at 502 and 538 nm in the quokka, and at 509 and 551 nm, in the quenda. Although small SWS cone outer segments precluded MSP measurements, molecular analysis identified substitutions at key sites, accounting for a spectral shift from ultraviolet in the quenda to violet in the quokka. The presence of three cone types, along with previous findings in the fat-tailed dunnart and honey possum, suggests that three spectrally distinct cone types are a feature spanning the marsupials.     

Morphological and molecular characteristics of a species of Hepatozoon Miller, 1908 (Apicomplexa: Adeleorina) from the blood of Isoodon obesulus (Marsupialia: Peramelidae) in Western Australia

Examination of blood films as part of a study to assess the health status of the southern brown bandicoot Isoodon obesulus (Shaw) in Western Australia revealed the gamonts of a haemogregarine parasite in some samples, the first to be recognised in a bandicoot in this state. Light microscope morphological characteristics and partial sequence of the 18S rRNA gene were used to describe these organisms. Morphological characters did not differentiate the organism in the current study from previously reported Hepatozoon peramelis (Welsh & Dalyell, 1909). Phylogenetic analysis has not previously been reported for any species of Hepatozoon from Australian marsupials and consequently could not be used to confirm the identity of the organism in the current study as that described in the 1900s. If this organism is H. peramelis, then it has a wide distribution, being found in three species of bandicoot, in western and eastern Australia and the in island state of Tasmania.     

Plagiorhynchus (Prosthorhynchus) cylindraceus (Goeze, 1782) Schmidt and Kuntz, 1966, from the Australian bandicoots, Perameles gunnii Gray 1838, and Isoodon obesulus (Shaw, 1797)

Plagiorhynchus (Prosthorhynchus) cylindraceus (Goeze, 1782) Schmidt and Kuntz, 1966, usually parasitic in passerine birds, is here reported to be found encysted in the peritoneum of the bandicoot Isoodon obesulus from Tasmania. Specimens recovered from the bandicoot Perameles gunnii, also collected from Tasmania, are the first reported from the intestine of a mammal. The origin of P. cylindraceus infection in Australian hosts is discussed.     

植物种质群体遗传结构改变的测度

本文旨在探讨植物种质资源保存中由于人为和自然缘故导致遗传结构改变的评价指标和评价方法.在介绍植物种质资源保存研究一些基本概念的基础上,归纳了测度种质库(收集品)遗传潜势的6种遗传多样性统计指标,包括同一变异层次的类型数、类型分布均衡度、遗传相似性与遗传距离、遗传方差与遗传变异系数、多元变异指数以及亲本系数.指出若无遗传丰富度相伴,单有遗传离散度并未提供遗传多样性的完整测度.探讨了人为条件导致植物种质资源遗传结构改变的遗传流失、环境胁迫所致植物种质资源遗传结构改变的遗传脆弱性和种子扩繁所引发的植物种质资源遗传结构改变的遗传漂变和遗传漂移等的统计指标.文末给出了自花授粉植物和异花授粉植物群体适宜样本容量研究的个例.     

EPISTASIS AND THE EFFECT OF FOUNDER EVENTS ON THE ADDITIVE GENETIC VARIANCE

Models of founder events have focused on the reduction in the genetic variation following a founder event. However, recent work (Bryant et al., 1986; Goodnight, 1987) suggests that when there is epistatic genetic variance in a population, the total genetic variance within demes may actually increase following a founder event. Since the additive genetic variance is a statistical property of a population and can change with the level of inbreeding, some of the epistatic genetic variance may be converted to additive genetic variance during a founder event. The model presented here demonstrates that some of the additive-by-additive epistatic genetic variance is converted to additive genetic variance following a founder event. Furthermore, the amount of epistasis converted to additive genetic variance is a function of the recombination rate and the propagule size. For a single founder event of two individuals, as much as 75% of the epistatic variance in the ancestral population may become additive genetic variance following the founder event. For founder events involving two individuals with free recombination, the relative contribution of epistasis to the additive genetic variance following a founder event is equal to its proportion of the total genetic variance prior to the founder event. Traits closely related to fitness are expected to have relatively little additive genetic variance but may have substantial nonadditive genetic variance. Founder events may be important in the evolution of fitness traits, not because they lead to a reduction in the genetic variance, but rather because they lead to an increase in the additive genetic variance.     

Impact of Genetic Counseling and Connexin-26 and Connexin-30 Testing on Deaf Identity and Comprehension of Genetic Test Results in a Sample of Deaf Adults: A Prospective,Longitudinal Study

Using a prospective, longitudinal study design, this paper addresses the impact of genetic counseling and testing for deafness on deaf adults and the Deaf community. This study specifically evaluated the effect of genetic counseling and Connexin-26 and Connexin-30 genetic test results on participants'' deaf identity and understanding of their genetic test results. Connexin-26 and Connexin-30 genetic testing was offered to participants in the context of linguistically and culturally appropriate genetic counseling. Questionnaire data collected from 209 deaf adults at four time points (baseline, immediately following pre-test genetic counseling, 1-month following genetic test result disclosure, and 6-months after result disclosure) were analyzed. Four deaf identity orientations (hearing, marginal, immersion, bicultural) were evaluated using subscales of the Deaf Identity Development Scale-Revised. We found evidence that participants understood their specific genetic test results following genetic counseling, but found no evidence of change in deaf identity based on genetic counseling or their genetic test results. This study demonstrated that culturally and linguistically appropriate genetic counseling can improve deaf clients'' understanding of genetic test results, and the formation of deaf identity was not directly related to genetic counseling or Connexin-26 and Connexin-30 genetic test results.     

Genetic effects of harvest on wild animal populations

Human harvest of animals in the wild occurs in terrestrial and aquatic habitats throughout the world and is often intense. Harvest has the potential to cause three types of genetic change: alteration of population subdivision, loss of genetic variation, and selective genetic changes. To sustain the productivity of harvested populations, it is crucial to incorporate genetic considerations into management. Nevertheless, it is not necessary to disentangle genetic and environmental causes of phenotypic changes to develop management plans for individual species. We recommend recognizing that some genetic change due to harvest is inevitable. Management plans should be developed by applying basic genetic principles combined with molecular genetic monitoring to minimize harmful genetic change.     

Low genetic diversity and high genetic differentiation in the critically endangered Omphalogramma souliei (Primulaceae):implications for its conservation

Omphalogramma souliei Franch. Is an endangered perennial herb only distributed in alpine areas of SW China. ISSR markers were applied to determine the genetic variation and genetic structure of 60 individuals of three populations of O. Souliei in NW Yunnan, China. The genetic diversity at the species level is low with P= 42.5% (percentage of polymorphic bands) and Hsp=0.1762 (total genetic diversity). However, a high level of genetic differentiation among populations was detected based on different measures (Nei's genetic diversity analysis: Gst=0.6038; AMOVA analysis: Fst=0.6797). Low level of genetic diversity within populations and significant genetic differentiation among populations might be due to the mixed mating system in which xenog-amy predominated and autogamy played an assistant role in O. Souliei. The genetic drift due to small population size and limited current gene flow also resulted in significant genetic differentiation. The assessment of genetic variation and differentiation of the endangered species provides important information for conservation on a genetic basis. Conservation strategies for this rare endemic species are proposed.     

Identification of genetic networks

In this report, we propose the use of structural equations as a tool for identifying and modeling genetic networks and genetic algorithms for searching the most likely genetic networks that best fit the data. After genetic networks are identified, it is fundamental to identify those networks influencing cell phenotypes. To accomplish this task we extend the concept of differential expression of the genes, widely used in gene expression data analysis, to genetic networks. We propose a definition for the differential expression of a genetic network and use the generalized T2 statistic to measure the ability of genetic networks to distinguish different phenotypes. However, describing the differential expression of genetic networks is not enough for understanding biological systems because differences in the expression of genetic networks do not directly reflect regulatory strength between gene activities. Therefore, in this report we also introduce the concept of differentially regulated genetic networks, which has the potential to assess changes of gene regulation in response to perturbation in the environment and may provide new insights into the mechanism of diseases and biological processes. We propose five novel statistics to measure the differences in regulation of genetic networks. To illustrate the concepts and methods for reconstruction of genetic networks and identification of association of genetic networks with function, we applied the proposed models and algorithms to three data sets.