Phenotype and gene flow in a marsupial (Antechinus flavipes) in contrasting habitats

Ecological factors are important drivers of phenotypic divergence, which may lead to incipient speciation. A variety of habitats should be preserved to maintain evolutionary potential. We used the marsupial, the yellow-footed antechinus ( Antechinus flavipes ) as a model species for investigating phenotypic differentiation between animals inhabiting two habitat types in south-eastern Australia: flood-plain river red gum and box–ironbark forests. All tested phenotypic characteristics varied between years at the same sites and therefore were not useful for investigating morphological specialization that may lead to speciation. Males generally were significantly heavier when antechinus densities were lower, but exceptions were found, possibly related to food availability. Teat-number variation recently has been shown to be associated with habitat specialization and incipient speciation within Antechinus agilis . We investigated genetic differentiation associated with this trait in A. flavipes . Population genetic analyses of microsatellite genotypes and mitochondrial DNA haplotypes revealed that sympatric 12-, 13- and 14-teat females in Chiltern forest were part of one freely interbreeding population. Our parentage analyses found two cases where 13-teat mothers produced 12-teat daughters. This suggests either plasticity or paternal genetic influence on the offspring's teat-number phenotype. Laboratory matings may be required to resolve the extent to which teat number is heritable in A. flavipes .  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 303–314.     

Isolated remnant or recent introduction? Estimating the provenance of Yellingbo Leadbeater's possums by genetic analysis and bottleneck simulation

Effective conservation management requires that genetically divergent populations potentially harbouring important local adaptations be identified and maintained as separate management units. In the case of the endangered Australian Leadbeater's possum (Gymnobelideus leadbeateri), an arboreal marsupial endemic to Victoria, uncertainty over the evolutionary origin of a potentially important extant wild population recently discovered in atypical habitat (lowland swamp) at Yellingbo is hampering such efforts. The population is rumoured to be a recent introduction. Microsatellite allele frequencies at Yellingbo differed substantially from those in sampled populations in montane ash forest (F_ST between 0.23 and 0.36), and Bayesian clustering analyses of genotypes strongly separated them (K = 2). We conducted a suite of bottlenecking tests which all indicated that Yellingbo had undergone a recent reduction in size. The extent to which the distinctiveness of Yellingbo animals might be expected solely through bottlenecking associated with a recent introduction, was tested by simulating population–history scenarios seeded with genotypes from candidate wild and captive sources. No bottleneck scenario reproduced anything approaching the genetic distinction of the Yellingbo population, with all structure analyses placing Yellingbo in a separate cluster to simulated populations (K = 2, minimum F_ST = 0.13). These results suggest that Yellingbo does not share recent ancestry with other extant populations and instead may be a remnant of an otherwise extinct gene pool. Importantly, this may include genes involved in adaptation to a lowland swamp environment, substantially adding to the conservation importance of this population, and suggesting that separate management may be prudent until evidence suggests otherwise.     

Linking the occurrence of brook trout with isolation and extinction in small Boreal Shield lakes

1. We surveyed 62 Canadian Shield lakes (<50 ha) to determine the relationship between factors related to isolation and extinction and the occurrence of brook trout (BT) (Salvelinus fontinalis), for which local extinctions have been documented over the last century in half of the lakes. 2. Logistic regression and information–theoretic model selection were used to determine the importance for the occupancy of BT of (i) isolation factors (degree of lake connectivity and the proximity of source populations of BT in neighbouring bodies of water) and (ii) extinction factors (lake morphometry and trophic status, as proxies of the risk of lake anoxia; predation and competition; and flooding caused by beaver (Castor canadensis) dams, which could potentially increase the risk of anoxia). 3. Isolation factors were the best predictors of the absence of BT in these lakes. Among extinction factors, only the impact of beaver dams (as measured by an index of increased water level and mortality of shrubs and trees in the littoral zone) improved model fits. Beaver dams were present at the outlets of all study lakes, but extensive mortality of riparian trees and shrubs was more common in lakes where BT populations were extinct. 4. Taken together, these results suggest that recolonization is a major factor determining the occurrence of BT while flooding caused by beaver dams might contribute to BT extinction by increasing the likelihood of winterkill in these small lakes.     

Biomass of primary and secondary vegetation in Rondônia, Western Brazilian Amazon

Biomass estimates of primary and different ages of secondary vegetation are reported for a tropical forest region in Rondônia, Western Brazilian Amazon. The estimates are based on published allometric equations, and on vegetation composition and allometric data collected in areas of primary forest and secondary vegetation of ages 2, 3, 5, 9, 11, 16 and 18 years. Primary forest biomass estimates varied from 290 to 495 t ha^–1. Secondary vegetation biomass estimates accounted for 40–60% of the primary forest biomass after 18 years of abandonment. Secondary growth rates in lightly used areas are estimated to have varied from 6.6 to 8.7 t ha^–1 y^–1 between the third and the eighteenth years after abandonment. CO₂ sequestration by regrowing vegetation is discussed for two scenarios of land abandonment.     

Semiparametric regression estimation in the presence of dependent censoring

We propose a semiparametric estimation procedure for estimatingthe regression of an outcome Y, measured at the end of a fixedfollow-up period, on baseline explanatory variables X, measuredprior to start of follow-up, in the presence of dependent censoringgiven X. The proposed estimators are consistent when the dataare ‘missing at random’ but not ‘missing completelyat random’ (Rubin, 1976), and do not require full specificationof the complete data likelihood. Specifically, we assume thatthe probability of censoring at time t is independent of theoutcome Y conditional on the recorded history up to t of a vectorof time-dependent covariates that are correlated with Y. Ourestimators can be used to adjust for dependent censoring andnonrandom noncompliance in randomised trials studying the effectof a treatment on the mean of a response variable of interest.Even with independent censoring, our methods allow the investigatorto increase efficiency by exploiting the correlation of theoutcome with a vector of time-dependent covariates.     

Geographical variation in floral traits of the tree tobacco in relation to its hummingbird pollinator fauna

Nicotiana glauca , a hummingbird pollinated plant, exhibits geographical variation in several floral traits. We examined whether geographical differentiation occurred for different flower characters and if this differentiation could be explained, at least in part, by the existence or abundance of different hummingbird species in the respective pollinator assemblages. The comparison between five populations showed significant variation in six floral traits and two female fitness measures. The traits that better discriminated between populations were corolla length and corolla width. There were metric correlations between corolla length and style length in all populations studied and, in four of the five populations, both corolla length and width were also correlated. Among plants in each population, seed weight was correlated positively and significantly with style exertion, suggesting that fruit quality is dependent on the degree of cross pollination. Assemblages of hummingbirds differed between populations in species composition, visitation frequencies, and bill length. Linear regression involving bill length of the more frequent hummingbird pollinators and corolla length yielded positive and significant relationships. Thus, there appears to be an adjustment between pollinators and flowers traits that have high incidence in the among population variation.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 657–667.     

Effects of resources and mortality on the growth and reproduction of Nile perch in Lake Victoria

1. A collapse of Nile perch stocks of Lake Victoria could affect up to 30 million people. Furthermore, changes in Nile perch population size‐structure and stocks make the threat of collapse imminent. However, whether eutrophication or fishing will be the bane of Nile perch is still debated. 2. Here, we attempt to unravel how changes in food resources, a side effect of eutrophication, and fishing mortality determine fish population growth and size structures. We parameterised a physiologically structured model to Nile perch, analysed the influence of ontogenetic diet shifts and relative resource abundances on existence boundaries of Nile perch and described the populations on either side of these boundaries. 3. Our results showed that ignoring ontogenetic diet shifts can lead to over‐estimating the maximum sustainable mortality of a fish population. Size distributions can be indicators of processes driving population dynamics. However, the vulnerability of stocks to fishing mortality is dependent on its environment and is not always reflected in size distributions. 4. We suggest that the ecosystem, instead of populations, should be used to monitor long‐term effects of human impact.