Phylogeography of the red-tailed chipmunk (Tamias ruficaudus), a northern Rocky Mountain endemic

The northern Rocky Mountains have experienced a complex history of geological events and environmental fluctuation, including Pleistocene glaciation. To provide an initial assessment of the genetic impact of this history on the regional biota we estimated phylogenetic relationships within Tamias ruficaudus, a regional endemic, from cytochrome b sequence variation using parsimony, maximum likelihood, and nested clade analysis. Analyses of sequence variation in 187 individuals from 43 localities across the distribution of T. ruficaudus indicate a history of vicariance events and range fluctuation consistent with successive periods of extensive Pleistocene glaciation in the northern Rocky Mountains. Intraspecific divergence levels (c. 4.7% uncorrected) and phylogenetic structure are consistent with a genealogical vicariance initiated prior to the Late Pleistocene, whereas nested clade analyses indicate more recent population history structured by both fragmentation and range expansion. A comparison of sequence variation with bacular morphology indicates that the two genetically and morphologically differentiated entities exhibit a zone of differential character introgression. Sequence data support a multiple refugia hypothesis and provide a phylogeographical case study for the ongoing synthesis of regional biogeography for northern Rocky Mountain endemics.     

Genetic consequences of ecological reserve design guidelines: An empirical investigation

We assessed the geneticdiversity consequences of applying ecologicalreserve design guidelines to four federally-listedglobally-rare plant species. Consequences weremeasured using two metrics: proportion of allalleles and of common alleles included inreserves. Common alleles were defined as those alleleshaving a frequency of 0.05 in at least onepopulation. Four conservation professionalsapplied ecological reserve guidelines to choosespecific populations of each species forinclusion in reserves of size 1 to N – 1, whereN is the total number of populations of each species.Information regarding genetic diversity was notused in selecting populations. The resulting reservedesigns were compared to random designs, andthe agreement among experts was assessed usingKendall's coefficient of concordance.Application of ecological reserve design guidelines provedmostly ineffective in capturing more geneticdiversity than is captured selectingpopulations randomly. Meeting establishedtargets for genetic diversity, such as one advocated by theCenter for Plant Conservation, required largernumbers of populations than are suggested to besufficient. Relative performance of expertdesigns differed among species and wasdependent on whether the proportion of allalleles or of common alleles was used as a measure ofdiversity. Furthermore there was no significantconcordance among experts in order in whichpopulations were incorporated into reserves asexperts differed in priority they placed onindividual guidelines.     

Five-year study on the autumn food habits of the Asiatic black bear in relation to nut production

We studied the autumn food habits of the Asiatic black bear (Ursus thibetanus) from 1993 to 1997, based on 202 fecal samples in the Chichibu Mountains, central Japan. Nuts occupied the highest proportions of autumn foods (59.9–85.8% important values). Although the proportion of nuts of Quercus crispula, Fagus crenata and Fagus japonica varied greatly between the years, acorns of Q.crispula were most prevalent in four of the five years. We also determined the relative nut production of these three species by counting the number of nuts or cupules on the ground. Black bears consumed the nuts according to their relative availabilities. Nuts of Q.crispula appeared to be the most important food because: (i) these nuts were eaten in the highest proportion in four of the five study years; and (ii) even in poor years the bears consumed acorns of Q.crispula, whereas nuts of Fagus spp. were not consumed. We discuss the significance of alternative foods for black bears in relation to food tree diversity in the forest and the necessity for long-term studies examining the food habits of Asiatic black bears.     

Three-dimensional structure determined for a subunit of human tRNA splicing endonuclease (Sen15) reveals a novel dimeric fold

Splicing of eukaryal intron-containing tRNAs requires the action of the heterotetrameric splicing endonuclease, which is composed of two catalytic subunits, Sen34 and Sen2, and two structural subunits, Sen15 and Sen54. Here we report the solution structure of the human tRNA splicing endonuclease subunit HsSen15. To facilitate the structure determination, we removed the disordered 35 N-terminal and 14 C-terminal residues of the full-length protein to produce HsSen15(36-157). The structure of HsSen15(36-157), the first for a subunit of a eukaryal splicing endonuclease, revealed that the protein possesses a novel homodimeric fold. Each monomer consists of three alpha-helices and a mixed antiparallel/parallel beta-sheet, arranged in a topology similar to that of the C-terminal domain of Methanocaldococcus jannaschii endonuclease. The dimeric interface is dominated by a beta-barrel structure, formed by face-to-face packing of two, three-stranded beta-sheets. Each of the beta-sheets results from reciprocal parallel pairing of one beta-strand from one subunit with two other beta-strands from the symmetric subunit. The structural model provides insights into the functional assembly of the human tRNA splicing endonuclease.     

Spatial Population Structure of Yellowstone Bison

Abstract: Increases in Yellowstone National Park, USA, bison (Bison bison) numbers and shifts in seasonal distribution have resulted in more frequent movements of bison beyond park boundaries and development of an interagency management plan for the Yellowstone bison population. Implementation of the plan under the adaptive management paradigm requires an understanding of the spatial and temporal structure of the population. We used polythetic agglomerative hierarchical cluster analysis of radiolocations obtained from free-ranging bison to investigate seasonal movements and aggregations. We classified radiolocations into 4 periods: annual, peak rut (15 Jul-15 Sep), extended rut (1 Jun-31 Oct), and winter (1 Nov-31 May). We documented spatial separation of Yellowstone bison into 2 segments, the northern and central herds, during all periods. The estimated year-round exchange rate (4.85-5.83%) of instrumented bison varied with the fusion strategy employed. We did not observe exchange between the 2 segments during the peak rut and it varied during the extended rut (2.15-3.23%). We estimated a winter exchange of 4.85-7.77%. The outcome and effectiveness of management actions directed at Yellowstone bison may be affected by spatial segregation and herd affinity within the population. Reductions based on total population size, but not applied to the entire population, may adversely affect one herd while having little effect on the other. Similarly, management actions targeting a segment of the population may benefit from the spatial segregation exhibited.     

Variable fluorescence in green sulfur bacteria

Green sulfur bacteria possess a complex photosynthetic machinery. The dominant light harvesting systems are chlorosomes, which consist of bacteriochlorophyll c, d or e oligomers with small amounts of protein. The chlorosomes are energetically coupled to the membrane-embedded iron sulfur-type reaction center via a bacteriochlorophyll a-containing baseplate protein and the Fenna-Matthews-Olson (FMO) antenna protein. The fluorescence yield and spectral properties of these photosynthetic complexes were investigated in intact cells of several species of green sulfur bacteria under physiological, anaerobic conditions. Surprisingly, green sulfur bacteria show a complex modulation of fluorescence yield upon illumination that is very similar to that observed in oxygenic phototrophs. Within a few seconds of illumination, the fluorescence reaches a maximum, which decreases within a minute of illumination to a lower steady state. Fluorescence spectroscopy reveals that the fluorescence yield during both processes is primarily modulated on the FMO-protein level, while the emission from chlorosomes remains mostly unchanged. The two most likely candidates that modulate bacteriochlorophyll fluorescence are (1) direct excitation quenching at the FMO-protein level and (2) indirect modulation of FMO-protein fluorescence by the reduction state of electron carriers that are part of the reaction center.     

Stomatal behavior of ozone-sensitive and -insensitive coneflowers (Rudbeckia laciniata var. digitata) in Great Smoky Mountains National Park

* Morphological and physiological attributes were assessed to elucidate the underlying mechanisms of ozone (O(3)) sensitivity in a highly sensitive species, cutleaf coneflower (Rudbeckia laciniata var. digitata). * Foliage at the same height in the canopy on paired O(3)-sensitive and -insensitive cutleaf coneflowers was assessed for level of foliar symptoms, stomatal density, stomatal responsiveness to dynamic changes in light and leaf-to-air vapor pressure deficit (VPD), steady-state responses to light and CO(2), intrinsic transpirational efficiency, and plant water balance. * There were no morphological differences between the sensitivity types that might have contributed to greater O(3) uptake in sensitive individuals. Stomata of sensitive plants were less responsive than those of insensitive plants to experimentally increased and decreased light intensities, and to increased VPD. O(3)-insensitive plants had greater intrinsic transpirational efficiencies, greater maximum assimilation rates under saturating CO(2) and light, and greater carboxylation rates. * Different physiological attributes vary independently within an individual plant, which collectively confer sensitivity or insensitivity to O(3) injury.     

Foraminifers and algae of the late Tournaisian–early Viséan boundary interval (MFZ8–9) in the Gachal Formation (Central Iran)

Three sections of the Gachal Formation, Tang-e Vaveila, Rahdar, and Bakhshi, located in the Kalmard area near the Tabas town (Central Iran) are revised. Tang-e Vaveila is dated as latest Tournaisian (upper MFZ8) to early Viséan (upper MFZ9); Rahdar is latest Tournaisian (latest MFZ8); and Bakhshi exposes the whole early Viséan (lower and upper MFZ9) succession. The upper MFZ8 subzone is indicated by the presence of Eoparastaffellina ex gr. rotunda; the lower MFZ9 subzone by the appearance of Eoparastaffella ex gr. simplex, and the upper MFZ9 subzone by the more or less concomitant appearances of Eostaffella and Lapparentidiscus. Among the foraminiferal assemblages, the endothyroids and loeblichioids are diversified, whereas the eoparastaffellins, tournayelloids and lituotubelloids remain rare. Regionally, the tetrataxins are interesting, because five species of Tetrataxis succeed one another across the MFZ9 biozone. Rich populations of Eotextularia were also observed. Incertae sedis algae are relatively diversified with the classical moravamminales and aoujgaliales. An interesting true alga is mentioned, but left in open nomenclature, as Epimastoporeae indet. Among the other microfossils, Cryptophyllus, Hamulusella?, Draffania, and hexaphyllids are noteworthy. The new taxa are: Eoparastaffellinae n. subfam., Endolaxina paralaxa n. sp., and Vissarionovella? iranica n. sp.     

Of plants and pikas: evidence for a climate-mediated decline in forage and cache quality

Background: Animals that hoard food to mediate seasonal deficits in resource availability might be particularly vulnerable to climate-mediated reductions in the quality and accessibility of food during the caching season. Central-place foragers might be additionally impacted by climatic constraints on their already restricted foraging range.

Aims: We sought evidence for these patterns in a study of the American pika (Ochotona princeps), a territorial, central-place forager sensitive to climate.

Methods: Pika food caches and available forage were re-sampled using historical methods at two long-term study sites, to quantify changes over two decades. Taxa that changed in availability or use were analysed for primary and secondary metabolites.

Results: Both sites trended towards warmer summers, and snowmelt trended earlier at the lower latitude site. Graminoid cover increased at each site, and caching trends appeared to reflect available forage rather than primary metabolites. Pikas at the lower latitude site preferred species higher in secondary metabolites, known to provide higher-nutrient winter forage. However, caching of lower-nutrient graminoids increased in proportion with graminoid availability at that site.

Conclusions: If our results represent trends in climate, cache quality and available forage, we predict that pikas at the lower latitude site will soon face nutritional deficiencies.     

大兴安岭呼中区紫貂生境格局变化及采伐的影响

本文根据紫貂（Martes zibellina）行为生态学特征,利用景观生态学的原理和技术,将大兴安岭呼中区紫貂生境划分成最适、一般适宜和非适宜三种类型。以其紧邻的呼中自然保护区核心区1989年的生境格局代表呼中区1970年开发前的原始生境,揭示原始生境、1989年、2000年3个时期紫貂生境格局及变化。结果表明,1970-2000年紫貂生境格局持续恶化,已极不利于紫貂的生存。适宜生境向非适宜生境呈单一方向转变,且适宜生境由沟谷两侧向远离河谷的森林腹地大幅度萎缩。生境格局变化与经营时问长短关系密切,原始状态是以适宜生境为基质的均质状态,开发至一定时期,生境格局的异质化程度增大,继续开发则异质化程度又减小,形成以非适宜生境为基质的相对均质状态。大于巢区最小面积f4km0）的生境斑块的面积百分比、斑块密度明显下降,斑块间距离显著增大。进而对导致生境格局变化的要素进行分析后发现,持续采伐是紫貂生境格局变化的主要驱动因子,采伐改变了植被条件,而植被条件的非适宜性造成了紫貂非适宜生境。1989-2000年的采伐格局也并不合理,各年伐区在研究区内均匀分布,采伐设计时没有考虑动物生境保护。但可以推断,1999年后开始逐步实施的“天然林保护工程”有利于紫貂生境的恢复,本研究强调森林采伐经营的空间格局与动物生境保护之间的关系,旨在促进决策部门将生物保护作为采伐经营政策制定的重要决策因子。