Limited Population Structure,Genetic Drift and Bottlenecks Characterise an Endangered Bird Species in a Dynamic,Fire-Prone Ecosystem

Fire is a major disturbance process in many ecosystems world-wide, resulting in spatially and temporally dynamic landscapes. For populations occupying such environments, fire-induced landscape change is likely to influence population processes, and genetic patterns and structure among populations. The Mallee Emu-wren Stipiturus mallee is an endangered passerine whose global distribution is confined to fire-prone, semi-arid mallee shrublands in south-eastern Australia. This species, with poor capacity for dispersal, has undergone a precipitous reduction in distribution and numbers in recent decades. We used genetic analyses of 11 length-variable, nuclear loci to examine population structure and processes within this species, across its global range. Populations of the Mallee Emu-wren exhibited a low to moderate level of genetic diversity, and evidence of bottlenecks and genetic drift. Bayesian clustering methods revealed weak genetic population structure across the species'' range. The direct effects of large fires, together with associated changes in the spatial and temporal patterns of suitable habitat, have the potential to cause population bottlenecks, serial local extinctions and subsequent recolonisation, all of which may interact to erode and homogenise genetic diversity in this species. Movement among temporally and spatially shifting habitat, appears to maintain long-term genetic connectivity. A plausible explanation for the observed genetic patterns is that, following extensive fires, recolonisation exceeds in-situ survival as the primary driver of population recovery in this species. These findings suggest that dynamic, fire-dominated landscapes can drive genetic homogenisation of populations of species with low-mobility and specialised habitat that otherwise would be expected to show strongly structured populations. Such effects must be considered when formulating management actions to conserve species in fire-prone systems.     

A novel framework for evaluating in situ breeding management strategies in endangered populations

Conservation breeding management aims to reduce inbreeding and maximize the retention of genetic diversity in endangered populations. However, breeding management of wild populations is still rare, and there is a need for approaches that provide data-driven evidence of the likelihood of success of alternative in situ strategies. Here, we provide an analytical framework that uses in silico simulations to evaluate, for real wild populations, (i) the degree of population-level inbreeding avoidance, (ii) the genetic quality of mating pairs, and (iii) the potential genetic benefits of implementing two breeding management strategies. The proposed strategies aim to improve the genetic quality of breeding pairs by splitting detrimental pairs and allowing the members to re-pair in different ways. We apply the framework to the wild population of the Critically Endangered helmeted honeyeater by combining genomic data and field observations to estimate the inbreeding (i.e., pair-kinship) and genetic quality (i.e., Mate Suitability Index) of all mating pairs for seven consecutive breeding seasons. We found no evidence of population-level inbreeding avoidance and that ~91.6% of breeding pairs were detrimental to the genetic health of the population. Furthermore, the framework revealed that neither proposed management strategy would significantly improve the genetic quality or reduce inbreeding of the mating pairs in this population. Our results demonstrate the usefulness of our analytical framework for testing the efficacy of different in situ breeding management strategies and for making evidence-based management decisions.     

Lack of detectable genetic recombination on the X chromosome during the parthenogenetic production of female and male aphids

We used polymorphic microsatellite markers to look for recombination during parthenogenetic oogenesis between the X chromosomes of aphids of the tribe Macrosiphini. We examined the X chromosome because it comprises approximately 25 % of the genome and previous cytological observations of chromosome pairing and nucleolar organizer (NOR) heteromorphism suggest recombination, although the same is not true for autosomes. A total of 564 parthenogenetic females of Myzus clones with three distinct reproductive modes (cyclical parthenogenesis, obligate parthenogenesis and obligate parthenogenesis with male production) were genotyped at three informative X-linked loci. Also, parthenogenetically produced males from clones encompassing the full range of male-producing reproductive strategies were genotyped. These included 391 Myzus persicae males that were genotyped at three X-linked loci and 538 males from Sitobion clones that were genotyped at five informative X-linked loci. Our results show no departure from clonality in parthenogenetic generations of aphids of the tribe Macrosiphini: no recombinant genotypes were observed in parthenogenetically produced males or females.     

Microsatellite variation in cyclically parthenogenetic populations of Myzus persicae in south-eastern Australia

We examined the population structure of the introduced aphid, Myzus persicae collected mainly from its primary host, Prunus persica, in south-east Australia. Myzus persicae has been present in Australia since at least 1893. Samples were collected in the spring of 1998 from two mainland and three Tasmanian localities and isofemale lines were established in the laboratory. The reproductive mode (life cycle), karyotype and 17-locus microsatellite genotype of each clone were determined. All populations showed significant population differentiation (F(ST) 0.058-0.202) even over small geographic distances (<50 km). All clones were karyotypically normal except for a subset of clones from one site that was exposed to the carbamate insecticide, Pirimor, the week prior to sampling. Those clones were heterozygous for an autosomal 1,3 translocation frequently associated in M. persicae with insecticide resistance. In contrast to other loci and despite being on different chromosomes, loci myz2(A) and M55(A) showed general and significant linkage disequilibrium. These loci may be affected by epistatic selection. We discuss the observed high clonal diversity, moderate but significant population differentiation, general conformance to Hardy-Weinberg equilibria and low linkage disequilibria with particular focus on the global population biology of M. persicae.     

Highly reliable genetic identification of individual northern hairy-nosed wombats from single remotely collected hairs: a feasible censusing method

The highly endangered northern hairy-nosed wombat (Lasiorhinus krefftii) is extremely difficult to study in the wild, and its numbers correspondingly difficult to estimate. Disturbance to the animals caused by trapping and radio-tracking may not only constitute an excessive risk to the population's viability, but may also yield biased data. The results of a pilot study are presented, which clearly show noninvasive genotyping to be a highly feasible and reliable alternative censusing method for L. krefftii. The protocol can identify individual wombats from single hairs collected remotely at burrow entrances, using: (i) a panel of microsatellite markers giving individual-specific genotypes; and (ii) a Y-linked sexing marker in combination with a single-copy X-linked amplification control. Using just the eight most variable microsatellites (of 20 available), only one in 200 pairs of full-sibs are predicted to share the same genotype. From 12 wombat hair samples collected on tape suspended over burrow entrances, three known female, two known male and an unknown wombat of each sex were identified. The approach will allow censusing of individuals that evade capture, and will also reveal some otherwise problematic aspects of the behaviour of this elusive animal.     

Early emergence in a butterfly causally linked to anthropogenic warming

There is strong correlative evidence that human-induced climate warming is contributing to changes in the timing of natural events. Firm attribution, however, requires cause-and-effect links between observed climate change and altered phenology, together with statistical confidence that observed regional climate change is anthropogenic. We provide evidence for phenological shifts in the butterfly Heteronympha merope in response to regional warming in the southeast Australian city of Melbourne. The mean emergence date for H. merope has shifted −1.5 days per decade over a 65-year period with a concurrent increase in local air temperatures of approximately 0.16°C per decade. We used a physiologically based model of climatic influences on development, together with statistical analyses of climate data and global climate model projections, to attribute the response of H. merope to anthropogenic warming. Such mechanistic analyses of phenological responses to climate improve our ability to forecast future climate change impacts on biodiversity.     

Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus Sitobion (Hemiptera: Aphididae)

Polymerase chain reaction (PCR) products corresponding to 803 bp of the cytochrome oxidase subunits I and II region of mitochondrial DNA (mtDNA COI-II) were deduced to consist of multiple haplotypes in three Sitobion species. We investigated the molecular basis of these observations. PCR products were cloned, and six clones from one individual per species were sequenced. In each individual, one sequence was found commonly, but also two or three divergent sequences were seen. The divergent sequences were shown to be nonmitochondrial by sequencing from purified mtDNA and Southern blotting experiments. All seven nonmitochondrial clones sequenced to completion were unique. Nonmitochondrial sequences have a high proportion of unique sites, and very few characters are shared between nonmitochondrial clones to the exclusion of mtDNA. From these data, we infer that fragments of mtDNA have been transposed separately (probably into aphid chromosomes), at a frequency only known to be equalled in humans. The transposition phenomenon appears to occur infrequently or not at all in closely related genera and other aphids investigated. Patterns of nucleotide substitution in mtDNA inferred over a parsimony tree are very different from those in transposed sequences. Compared with mtDNA, nonmitochondrial sequences have less codon position bias, more even exchanges between A, G, C and T, and a higher proportion of nonsynonymous replacements. Although these data are consistent with the transposed sequences being under less constraint than mtDNA, changes in the nonmitochondrial sequences are not random: there remains significant position bias, and probable excesses of synonymous replacements and of conservative inferred amino acid replacements. We conclude that a proportion of the inferred change in the nonmitochondrial sequences occurred before transposition. We believe that Sitobion aphids (and other species exhibiting mtDNA transposition) may be important for studying the molecular evolution of mtDNA and pseudogenes. However, our data highlight the need to establish the true evolutionary relationships between sequences in comparative investigations.