Lactate dehydrogenase (LDH) gene duplication during chordate evolution: the cDNA sequence of the LDH of the tunicate Styela plicata

L-Lactate dehydrogenase (L-LDH, E.C. 1.1.1.27) is encoded by two or three loci in all vertebrates examined, with the exception of lampreys, which have a single LDH locus. Biochemical characterizations of LDH proteins have suggested that a gene duplication early in vertebrate evolution gave rise to Ldh-A and Ldh-B and that an additional locus, Ldh-C arose in a number of lineages more recently. Although some phylogenetic studies of LDH protein sequences have supported this pattern of gene duplication, others have contradicted it. In particular, a number of studies have suggested that Ldh-C represents the earliest divergence among vertebrate LDHs and that it may have diverged from the other loci well before the origin of vertebrates. Such hypotheses make explicit statements about the relationship of vertebrate and invertebrate LDHs, but to date, no closely related invertebrate LDH sequences have been available for comparison. We have attempted to provide further data on the timing of gene duplications leading to multiple vertebrate LDHs by determining the cDNA sequence of the LDH of the tunicate Styela plicata. Phylogenetic analyses of this and other LDH sequences provide strong support for the duplications giving rise to multiple vertebrate LDHs having occurred after vertebrates diverged from tunicates. The timing of these LDH duplications is consistent with data from a number of other gene families suggesting widespread gene duplication near the origin of vertebrates. With respect to the relationships among vertebrate LDHs, our data are not consistent with previous claims that Ldh-C represented the earliest divergence. However, the precise relationships among some of the main lineages of vertebrate LDHs were not resolved in our analyses.      

Phylogenetic Analysis of Heterothallic Neurospora Species

We examined the phylogenetic relationships among five heterothallic species of Neurospora using restriction fragment polymorphisms derived from cosmid probes and sequence data from the upstream regions of two genes, al-1 and frq. Distance, maximum likelihood, and parsimony trees derived from the data support the hypothesis that strains assigned to N. sitophila, N. discreta, and N. tetrasperma form respective monophyletic groups. Strains assigned to N. intermedia and N. crassa, however, did not form two respective monophyletic groups, consistent with a previous suggestion based on analysis of mitochondrial DNAs that N. crassa and N. intermedia may be incompletely resolved sister taxa. Trees derived from restriction fragments and the al-1 sequence position N. tetrasperma as the sister species of N. sitophila. None of the trees produced by our data supported a previous analysis of sequences in the region of the mating type idiomorph that grouped N. crassa and N. sitophila as sister taxa, as well as N. intermedia and N. tetrasperma as sister taxa. Moreover, sequences from al-1, frq, and the mating-type region produced different trees when analyzed separately. The lack of consensus obtained with different sequences could result from the sorting of ancestral polymorphism during speciation or gene flow across species boundaries, or both.     

Inductive Capacities for the Dorsal Mesoderm of the Dorsal Marginal Zone and Pharyngeal Endoderm in the Very Early Gastrula of the Newt,and Presumptive Pharyngeal Endoderm as an Initiator of the Organization Center*

The organization center of Cynops pyrrhogaster was divided into Parts 1, 2 and 3 of equal size (0.3×0.4 mm²) with presumptive fates as pharyngeal, pharyngeal+prechordal+trunk notochord, and trunk-tail notochord, respectively. Movements and changes in size and shape of each part were followed through gastrulation. Differentiation tendencies of each part were examined under three conditions: I, isolated; II, sandwiched with presumptive ectoderm; 111, sandwiched with presumptive ectoderm after preculture in isolation for various times. In I, Parts 2 and 3 differentiated into dorsal mesoderm. In II, each part induced dorsal mesoderm and neural tissues, the frequency being highest in Part 2 and lowest in Part 3. In III, Parts 1 and 2 realized their presumptive fates, through changes in inductive capacities from trunk-tail to head. This change progressed rapidly in Part 1, and slowly in Part 2. Part 3 required induction by neighbouring Part 2 to realize its presumptive fate. Changes of inductive capacity of Parts 1 and 2 respectively, were chronologically similar in normal development and in preculture experiments. Lastly, the primary presumptive pharyngeal zone at blastula was proposed to act as an initiator of the organization center, its programmed information being transmitted to Part 2, and then to Part 3.     

Mitochondrial DNA structure and colony expansion dynamics of New Zealand fur seals (Arctocephalus forsteri) around Banks Peninsula

New Zealand fur seals are one of many pinniped species that survived the commercial sealing of the eighteenth and nineteenth centuries in dangerously low numbers. After the enforcement of a series of protection measures in the early twentieth century, New Zealand fur seals began to recover from the brink of extinction. We examined the New Zealand fur seal populations of Banks Peninsula, South Island, New Zealand using the mitochondrial DNA control region. We identified a panmictic population structure around Banks Peninsula. The most abundant haplotype in the area showed a slight significant aggregated structure. The Horseshoe Bay colony showed the least number of shared haplotypes with other colonies, suggesting a different origin of re-colonisation of this specific colony. The effective population size of the New Zealand fur seal population at Banks Peninsula was estimated at approximately 2500 individuals. The exponential population growth rate parameter for the area was 35, which corresponds to an expanding population. In general, samples from adjacent colonies shared 4.4 haplotypes while samples collected from colonies separated by between five and eight bays shared 1.9 haplotypes. The genetic data support the spill-over dynamics of colony expansion already suggested for this species. Approximate Bayesian computations analysis suggests re-colonisation of the area from two main clades identified across New Zealand with a most likely admixture coefficient of 0.41 to form the Banks Peninsula population. Approximate Bayesian computations analysis estimated a founder population size of approximately 372 breeding individuals for the area, which then rapidly increased in size with successive waves of external recruitment. The population of fur seals in the area is probably in the late phase of maturity in the colony expansion dynamic.     

甘肃省被子植物分布新记录

报道了甘肃省分布的玄参科(Scrophulariaceae)水茫草属(Limosella Linn.)1个新记录属,以及玄参科(Scrophulariaceae)、木兰科(Magnoliaceae)、蓼科(Polygonaceae)、胡颓子科(Elaeagnaceae)、百合科(Liliaceae)5个新记录种——水茫草(Limosella aquatica Linn.)、峨眉含笑(Michelia wilsonii Finet et Gagnep.)、叉分蓼(Polygonum divaricatum L.)、棱果沙棘(Hippophae goniocarpa Y.S.Lian et al.ex SwensonBartish)、青海黄精(Polygontum qinghaiense Z.L.Wu et Y.C.Yang)。其中,峨眉含笑是国家二级重点保护野生植物。     

应用Illumina MiSeq高通量测序技术分析河西走廊地区盐碱土壤微生物多样性

【目的】以甘肃省河西走廊地区的9个盐碱土壤样品(原生盐碱土、次生盐碱土、农田土)为材料,研究该地区盐碱土壤中微生物群落的多样性。【方法】提取土壤微生物总DNA,应用Illumina Mi Seq高通量测序技术进行分析。【结果】从分布在河西走廊3个流域的9个盐碱土样品中共获得325 089条微生物的16S r RNA基因序列。冗余分析和热图分析表明,原生盐碱土与次生盐碱土、原生盐碱土与农田土微生物群落构成差异较大,次生盐碱土与农田土微生物群落差异较小。土壤p H对微生物群落组成的影响最显著。多样性指数和稀释性曲线分析得出,在9个土壤样品中,S6号Shannon指数最大,S1号Shannon指数最小,S1号Simpson指数最大,S6号Simpson指数最小,说明原生盐碱土的微生物群落多样性最低,次生盐碱土的微生物群落多样性最高。盐碱土壤中主要的微生物群落包括9个门,其中变形菌门占主导地位,其余依次是放线菌门、拟杆菌门、酸杆菌门、浮霉菌门、绿弯菌门、芽单胞菌门、厚壁菌门和疣微菌门。原生盐碱土和农田土中占优势的微生物群落是变形菌门,次生盐碱土中占优势的微生物群落是放线菌门。【结论】河西走廊地区盐碱土壤中微生物多样性非常丰富,存在大量的微生物类群,尤其是在次生盐碱土壤中。     

Responses of tropical cladocerans to a gradient of resource quality

1. The response of three tropical cladocerans to a gradient of resource quality was compared in a series of growth bioassays using seston collected from five lakes of different depth and trophic structure in Michigan, U.S.A. To assess the food quality in terms of digestibility, assimilation experiments were performed with ³²P‐labelled seston from the same lakes. Animals were also analysed for P‐content in their tissues at the end of these assays. 2. In general, assimilation efficiency was higher when animals fed on seston from shallow compared to deep lakes, and was significantly correlated with growth rates, suggesting that shallow lakes have the best food resources in terms of digestibility and P availability. 3. Results also showed that all cladoceran species responded similarly to the resource gradient, with lower growth rates in deep lakes and higher growth rates in shallow lakes, although the strength of response (sensitivity) was different among the species tested. 4. The cladoceran Moina micrura was the most sensitive species, and also displayed the highest P‐content and maximal growth rate, a pattern consistent with the growth rate hypothesis. 5. However, seston C : P ratio and growth rates in the different resources did not correlate with the animals’ P‐contents, showing an uncoupling between RNA‐phosphorus demands for growth and seston food quality. 6. In conclusion, our results support the idea that digestion resistance in algae is a major constraint to cladocerans in natural plankton communities.