Divergence population genetic analysis of hybridization between rhesus and cynomolgus macaques

The geographic ranges of rhesus ( Macaca mulatta ) and cynomolgus ( M. fascicularis ) macaques adjoin in Indochina where they appear to hybridize. We used published and newly generated DNA sequences from 19 loci spanning ~20 kb to test whether introgression has occurred between these macaque species. We studied introgression at the level of nuclear DNA and distinguished between incomplete lineage sorting of ancestral polymorphisms or interspecific gene flow. We implemented a divergence population genetics approach by fitting our data to an isolation model implemented in the software IMa. The model that posits no gene flow from the rhesus into the cynomolgus macaque was rejected ( P  = 1.99 × 10⁻⁸). Gene flow in this direction was estimated as 2 Nm ~1.2, while gene flow in the reverse direction was nonsignificantly different from zero ( P  = 0.16). The divergence time between species was estimated as ~1.3 million years. Balancing selection, a special case of incomplete sorting, was taken into consideration, as well as potential crossbreeding in captivity. Parameter estimates varied between analyses of subsets of data, although we still rejected isolation models. Geographic sampling of the data, where samples of cynomolgus macaques derived from Indochina were excluded, revealed a lost signature of gene flow, indicating that interspecific gene flow is restricted to mainland Indochina. Our results, in conjunction with those by others, justify future detailed analyses into the genetics of reproductive barriers and reticulate evolution in these two genome-enabled primates. Future studies of the natural hybridization between rhesus and cynomolgus macaques would expand the repertoire of systems available for speciation studies in primates.     

Molecular genetic data provide support for a model of transmission dynamics in an Australian reptile tick, Bothriocroton hydrosauri

Bothriocroton hydrosauri is a three-host ixodid tick that infests large reptiles in southeastern Australia, where its most common host is a large scincid lizard Tiliqua rugosa . Based on previous ecological and behavioural studies of this system, we propose a 'ripple' model of tick population dynamics, where only a few female ticks succeed in producing surviving offspring. These females then are the centres of ripples of their progeny spreading into the broader landscape. The model predicts higher relatedness among larvae than among nymphs or adults on a host, and significant spatial autocorrelation in larvae extending further than for the later life stages. The model also predicts that adult ticks are likely to encounter related partners and that this will generate inbreeding within the population. We tested those predictions using nine polymorphic microsatellite loci on a sample of 848 ticks (464 larvae, 140 nymphs and 244 adults) collected from 98 lizard hosts from near Bundey Bore Station in South Australia. Our data support the predictions and indicate that the dynamics of transmission among hosts play an important role in parasite population structure.     

Changes in soil organic carbon under biofuel crops

One potentially significant impact of growing biofuel crops will be the sequestration or release of carbon (C) in soil. Soil organic carbon (SOC) represents an important C sink in the lifecycle C balances of biofuels and strongly influences soil quality. We assembled and analyzed published estimates of SOC change following conversion of natural or agricultural land to biofuel crops of corn with residue harvest, sugarcane, Miscanthus x giganteus , switchgrass, or restored prairie. We estimated SOC losses associated with land conversion and rates of change in SOC over time by regressing net change in SOC relative to a control against age since establishment year. Conversion of uncultivated land to biofuel agriculture resulted in significant SOC losses – an effect that was most pronounced when native land was converted to sugarcane agriculture. Corn residue harvest (at 25–100% removal) consistently resulted in SOC losses averaging 3–8 Mg ha⁻¹ in the top 30 cm, whereas SOC accumulated under all four perennial grasses, with SOC accumulation rates averaging <1 Mg ha⁻¹ yr⁻¹ in the top 30 cm. More intensive harvests led to decreased C gains or increased C losses – an effect that was particularly clear for residue harvest in corn. Direct or indirect conversion of previously uncultivated land for biofuel agriculture will result in SOC losses that counteract the benefits of fossil fuel displacement. Additionally, SOC losses under corn residue harvest imply that its potential to offset C emissions may be overestimated, whereas SOC sequestration under perennial grasses represents an additional benefit that has rarely been accounted for in life cycle analyses of biofuels.     

Development and characterization of novel di‐ and tetranucleotide microsatellite markers in Pacific cod (Gadus macrocephalus)

The Pacific cod (Gadus macrocephalus) supports large commercial fisheries in the northern Pacific Ocean and the Bering Sea. Here we characterize 10 polymorphic microsatellite loci isolated from enriched genomic libraries. Loci were screened on a sample of 96 spawning adults. The average number of alleles per locus was 25.3 (range 12–44), with expected heterozygosities (H_E) ranging from 0.54 to 0.97. No significant deviations of genotypic proportions from Hardy–Weinberg equilibrium or linkage equilibrium were detected. These markers will be used in future studies of population structure and mixed stock analysis of this important gadid species.     

Fire frequency and biodiversity conservation in Australian tropical savannas: implications from the Kapalga fire experiment

Abstract Every year large proportions of northern Australia's tropical savanna landscapes are burnt, resulting in high fire frequencies and short intervals between fires. The dominant fire management paradigm in these regions is the use of low‐intensity prescribed fire early in the dry season, to reduce the incidence of higher‐intensity, more extensive wildfire later in the year. This use of frequent prescribed fire to mitigate against high‐intensity wildfire has parallels with fire management in temperate forests of southern Australia. However, unlike in southern Australia, the ecological implications of high fire frequency have received little attention in the north. CSIRO and collaborators recently completed a landscape‐scale fire experiment at Kapalga in Kakadu National Park, Northern Territory, Australia, and here we provide a synthesis of the effects of experimental fire regimes on biodiversity, with particular consideration of fire frequency and, more specifically, time‐since‐fire. Two recurring themes emerged from Kapalga. First, much of the savanna biota is remarkably resilient to fire, even of high intensity. Over the 5‐year experimental period, the abundance of most invertebrate groups remained unaffected by fire treatment, as did the abundance of most vertebrate species, and we were unable to detect any effect of fire on floristic composition of the grass‐layer. Riparian vegetation and associated stream biota, as well as small mammals, were notable exceptions to this general resilience. Second, the occurrence of fire, independent of its intensity, was often the major factor influencing fire‐sensitive species. This was especially the case for extinction‐prone small mammals, which have suffered serious population declines across northern Australia in recent decades. Results from Kapalga indicate that key components of the savanna biota of northern Australia favour habitat that has remained unburnt for at least several years. This raises a serious conservation concern, given that very little relatively long unburnt habitat currently occurs in conservation reserves, with most sites being burnt at least once every 2 years. We propose a conservation objective of increasing the area that remains relatively long unburnt. This could be achieved either by reducing the proportion of the landscape burnt each year, or by setting prescribed fires more strategically. The provision of appropriately long unburnt habitat is a conservation challenge for Australia's tropical savanna landscapes, just as it is for its temperate forests.     

Evidence that the recessive bymovirus resistance locus rym4 in barley corresponds to the eukaryotic translation initiation factor 4E gene

Recent studies have shown that resistance in several dicotyledonous plants to viruses in the genus Potyvirus is controlled by recessive alleles of the plant translation initiation factor eIF4E or eIF ( iso ) 4E genes. Here we provide evidence that the barley rym 4 gene locus, controlling immunity to viruses in the genus Bymovirus , corresponds to eIF4E . A molecular marker based on the sequence of eIF4E was developed and used to demonstrate that eIF4E and rym 4 map to the same genetic interval on chromosome 3HL in barley . Another genetic marker was developed that detects a polymorphism in the coding sequence of eIF4E and consistently distinguishes between rym 4 and susceptible barley cultivars of diverse parentage. The eIF4E gene product from barley genotypes carrying rym 4 and allelic rym 5 and rym 6 genes, originating from separate exotic germplasm, and a novel resistant allele that we identified through a reverse genetics approach all contained unique amino acid substitutions compared with the wild-type protein. Three-dimensional models of the barley eIF4E protein revealed that the polymorphic residues identified are all located at or near the mRNA cap-binding pocket, similarly to recent findings from studies on recessive potyvirus resistance in dicotyledonous plants. These new data complement our earlier observations that specific mutations in bymovirus VPg are responsible for overcoming rym 4/5-controlled resistance. Because the potyviral VPg is known to interact with eIF4E in dicotyledonous plants, it appears that monocotyledonous and dicotyledonous plants have evolved a similar strategy to combat VPg-encoding viruses in the family Potyviridae .     

Evolution of Dactylorhiza baltica (Orchidaceae) in European Russia: evidence from molecular markers and morphology

Four plastid markers, four nuclear markers and 14 morphometric characters were used in this study to investigate the evolution of Dactylorhiza baltica (Orchidaceae) in European Russia. In total, 98, 214 and 775 samples from 85, 112 and 121 populations were involved in the combined and separate molecular and morphometric analyses, respectively. In most cases, morphometric measures were done on exactly the same plants that were used for DNA studies. Dactylorhiza baltica plants from European Russia are most probably the products of several recent and mostly local hybridization events between the diploids D. fuchsii and D. incarnata , which have each been the maternal parent on different occasions. Considerable introgression into the parental diploids via the allopolyploid D. baltica is also hypothesized. Several morphological characters, such as length of the lip lateral lobe and the length of longest leaf, were found to be robust and could be useful in identification of D. baltica . This study demonstrates the advantage of 'combined' techniques, especially in the case of taxonomically complex taxa.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 147 , 257–274.     

EFFECT OF HABITAT AND FORAGING HEIGHT ON BAT ACTIVITY IN THE COASTAL PLAIN OF SOUTH CAROLINA

Abstract: We compared bat activity levels in the Coastal Plain of South Carolina among 5 habitat types: forested riparian areas, clearcuts, young pine plantations, mature pine plantations, and pine savannas. We used time-expansion radio-microphones and integrated detectors to simultaneously monitor bat activity at 3 heights (30, 10, 2 m) in each habitat type. Variation in vegetative clutter among sampling heights and among habitat types allowed us to examine the differential effect of forest vegetation on the spatial activity patterns of clutter-adapted and open-adapted bat species. Moreover, monitoring activity at 30, 10, and 2 m permitted us to also compare bat activity above and below the forest canopy. We detected calls of 5 species or species groups: eastern red/Seminole bats (Lasiurus borealis/L. seminolus), eastern pipistrelles (Pipistrellus subflavus), evening bats (Nycticeius humeralis), big brown bats (Eptesicus fuscus), and hoary bats (Lasiurus cinerius). At 2 and 10 m, bat activity was concentrated in riparian areas, whereas we detected relatively low levels of bat activity in upland habitats at those heights. Activity was more evenly distributed across the landscape at 30 m. Bat activity levels above the forest canopy were almost 3 times greater than within or below the canopy. We detected significantly greater activity levels of 2 open-adapted species (hoary and big brown bats) above rather than within or below the forest canopy. However, activity levels of 2 clutter-adapted species (eastern red/Seminole bats and eastern pipistrelles) did not differ above, within, or below the forest canopy. Despite classification as a clutter-adapted species, evening bat activity was greater above rather than within or below the forest canopy. We believe our results highlight the importance of riparian areas as foraging habitat for bats in pine-dominated landscapes in the southeastern United States. Although acoustical surveys conducted below forest canopies can provide useful information about species composition and relative activity levels of bats that forage in cluttered environments, our results showing activity above canopy suggest that such data may not accurately reflect relative activity of bats adapted to forage in more open conditions, and therefore may provide an inaccurate picture of bat community assemblage and foraging habitat use.     

GRIZZLY BEAR DEMOGRAPHICS IN AND AROUND BANFF NATIONAL PARK AND KANANASKIS COUNTRY,ALBERTA

Abstract: The area in and around Banff National Park (BNP) in southwestern Alberta, Canada, is 1 of the most heavily used and developed areas where grizzly bears (Ursus arctos) still exist. During 1994–2002, we radiomarked and monitored 37 female and 34 male bears in this area to estimate rates of survival, reproduction, and population growth. Annual survival rates of bears other than dependent young averaged 95% for females and 81–85% for males. Although this area was largely unhunted, humans caused 75% of female mortality and 86% of male mortality. Females produced their first surviving litter at 6–12 years of age (x̄ = 8.4 years). Litters averaged 1.84 cubs spaced at 4.4-year intervals. Adult (≥6-years-old) females produced 0.24 female cubs per year and were expected to produce an average of 1.7 female cubs in their lifetime, based on rates of reproduction and survival. Cub survival was 79%, yearling survival was 91%, and survival through independence at 2.5–5.5 years of age was 72%, as no dependent young older than yearlings died. Although this is the slowest-reproducing grizzly bear population yet studied, high rates of survival seem to have enabled positive population growth (Λ = 1.04, 95% CI = 0.99–1.09), based on analyses using Leslie matrices. Current management practices, instituted in the late 1980s, focus on alleviating human-caused bear mortality. If the 1970–1980s style of management had continued, we estimated that an average of 1 more radiomarked female would have been killed each year, reducing female survival to the point that the population would have declined.