Molecular Phylogeny and Biogeography of the Genus Ilex L. (Aquifoliaceae)

The chloroplast atpB-rbcL spacer was sequenced for 115 speciesof Ilex and forNemopanthus mucronatus (Aquifoliaceae). In addition,rbcL sequences were obtained for 47 selected species. Takentogether with fossil records in the literature, the data indicatethat: (1) the lineage Ilex was already cosmopolitan long beforethe end of the Cretaceous. A relative test of the rate of nucleotidesubstitution indicates that extant species do not representthe entire lineage because of the extinction of its basal branches.The common ancestor of the extant species probably appearedat the upper Tertiary. (2) Several Asian/North American disjunctionsare observed, as well as North American/South American relationships.The directions of these relationships are yet to be determined.The African species Ilex mitis is closely related to Asian species.Ilex anomala (Hawaii and Tahiti) is related to American species.Ilex perado and Ilex canariensis (both in Macaronesia) havetotally different relationships, the former being related toEurasian species, while relationships of the latter remain obscure.(3) Gene trees substantially contradict the systematics of Loesener.Nemopanthus,closely related to Ilex amelanchier, is nested in the genusIlex. The family Aquifoliaceae is organized in four groups,each of them having a geographic or ecological peculiarity.Copyright 2000 Annals of Botany Company Aquifoliaceae, chloroplast DNA, fossil record, historical biogeography, Ilex (holly tree), molecular phylogeny.     

Experimental climate effect on seasonal variability of polyphenol/phenoloxidase interplay along a narrow fen–bog ecological gradient in Sphagnum fallax

Extracellular phenoloxidase enzymes play an important role in the stability of soil carbon storage by contributing to the cycling of complex recalcitrant phenolic compounds. Climate warming could affect peatland functioning through an alteration of polyphenol/phenoloxidase interplay, which could lead them to becoming weaker sinks of carbon. Here, we assessed the seasonal variability of total phenolics and phenoloxidases subjected to 2–3 °C increase in air temperature using open‐top chambers. The measurements were performed along a narrow fen–bog ecological gradient over one growing season. Climate warming had a weak effect on phenoloxidases, but reduced phenolics in both fen and bog areas. Multivariate analyses revealed a split between the areas and also showed that climate warming exacerbated the seasonal variability of polyphenols, culminating in a destabilization of the carbon cycle. A negative relationship between polyphenols and phenoloxidases was recorded in controls and climate treatments suggesting an inhibitory effect of phenolics on phenoloxidases. Any significant decrease of phenolics through repeatedly elevated temperature would greatly impact the ecosystem functioning and carbon cycle through an alteration of the interaction of polyphenols with microbial communities and the production of extracellular enzymes. Our climate treatments did not have the same impact along the fen–bog gradient and suggested that not all the peatland habitats would respond similarly to climate forcing.     

Patterns of genetic isolation in a widely distributed pelagic fish,the narrow‐barred Spanish mackerel (Scomberomorus commerson)

Although migratory pelagic fishes generally exhibit little geographic differentiation across oceans, as expected from their life history (broadcast spawning, pelagic larval life, swimming ability of adults) and the assumed homogeneity of the pelagic habitat, exceptions to the rule deserve scrutiny. One such exception is the narrow‐barred Spanish mackerel (Scomberomorus commerson Lacepède, 1800), where strong genetic heterogeneity at the regional scale has been previously reported. We investigated the genetic composition of S. commerson across the Indo‐West Pacific range using control‐region sequences (including previously published data sets), cytochrome b gene partial sequences, and eight microsatellite loci, to further explore its phylogeographic structure. All haplotypes sampled from the Indo‐Malay‐Papua archipelago (IMPA) and the south‐western Pacific coalesced into a clade (clade II) that was deeply separated (14.5% nucleotide divergence) from a clade grouping all haplotypes from the Persian Gulf and Oman Sea (clade I). Such a high level of genetic divergence suggested the occurrence of two sister species. Further phylogeographic partition was evident between the western IMPA and the regions sampled east and south of it, i.e. northern Australia, West Papua, and the Coral Sea. Strong allele‐frequency differences were found between local populations in the south‐western Pacific, both at the mitochondrial locus (Φ_st = 0.282–0.609) and at microsatellite loci ( = 0.202–0.313). Clade II consisted of four deeply divergent subclades (9.0–11.8% nucleotide divergence for the control region; 0.3–2.5% divergence at the cytochrome b locus). Mitochondrial subclades within clade II generally had narrow geographic distribution, demonstrating further genetic isolation. However, one particular haplogroup within clade II was present throughout the central Indo‐West Pacific: this haplogroup was found to be the sister group to a haplogroup restricted to West Papua and the Coral Sea, yielding evidence of recent secondary westward colonization. Such a complex structure is in sharp contrast with the generally weak phylogeographic patterns uncovered to date in other widely distributed, large pelagic fishes with pelagic eggs and larvae. We hypothesize that in S. commerson and possibly other Scomberomorus species, philopatric migration may play a role in maintaining the geographic isolation of populations by annihilating the potential consequences of passive dispersal. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 104 , 886–902.     

动物系统发育和大规模测序:进展和问题

Phylogenomics, the inference of phylogenetic trees using genome-scale data, is becoming the rule for resolving difficult parts of the tree of life. Its promise resides in the large amount of information available, which should eliminate stochastic error. However, systematic error, which is due to limitations of reconstruction methods, is becoming more apparent. We will illustrate, using animal phylogeny as a case study, the three most efficient approaches to avoid the pitfalls of phylogenomics (1) using a dense taxon sampling, (2) using probabilistic methods with complex models of sequence evolution that more accurately detect multiple substitutions, and (3) removing the fastest evolving part of the data (e.g., species and positions). The analysis of a dataset of 55 animal species and 102 proteins (25712 amino acid positions) shows that standard site-homogeneous model inference is sensitive to long-branch attraction artifact, whereas the site-heterogeneous CAT model is less so. The latter model correctly locates three very fast evolving species, the appendicularian tunicate Oikopleura, the acoel Convoluta and the myxozoan Buddenbrockia. Overall, the resulting tree is in excellent agreement with the new animal phylogeny, confirming that "simple" organisms like platyhelminths and nematodes are not necessarily of basal emergence. This further emphasizes the importance of secondary simplification in animals, and for organismal evolution in general.     

Etude exploratoire de la spermatogenèse induite par la chaleur chez l'escargot Helix aspersa en hibernation: Rôle du cerveau / An exploratory study on temperature-induced spermatogenesis in the hibernating snail Helix aspersa: the role of the brain

Summary

The male cells in the ovotestis of hibernating snails undergo multiplication when the temperature of the environment is raised from 5°C to 25°C. If the temperature is maintained at 25°C for 4 weeks the process of spermatogenesis is completed but the rate of spermatogenesis (DNA synthesis) starts decreasing from the 3rd week (Table 1; Fig. 1).

Brain ablation in hibernating snails maintained at 25°C causes a significant increase in DNA synthesis exclusively in male cells of the ovotestis. This suggests that the brain exerts an inhibitory influence on spermatogenic multiplication. This influence is effective only during the first and the fourth week of exposure of hibernating snails to 25°C (Fig. 1; Table 1) indicating the existence of an endogenous cyclical control. Spermiogenesis is, however, not affected by brain extirpation (Fig. 4 A,B,C).

When reimplanted in the head haemocoel the brain appears normal histologically (Fig. 5 A,B) and it reestablishes the inhibitory influence on DNA synthesis in the ovotestis only during the first day of temperature-induction. During the 1st, 3rd and 4th week the reimplanted brain, deprived of its neural connections, fails to exert its inhibitory influence suggesting that for this influence to function neural connections to the brain are essential. Surprisingly, the implanted brain seems to inhibit DNA synthesis during the 2nd week of temperature-induction (Table 1).

These experiments show that the brain control temperature-induced spermatogenic multiplication in the ovotestis in snails at the onset of hibernation and this control is exerted by one or more inhibitory factors originating from the brain which may function in concert or independently to produce the neuroendocrine effect. It seems therefore justified to consider spermatogenesis in hibernating snails as being neuroendocrinologically controlled.     

MATING SYSTEM ANALYSIS USING PROTEIN ELECTROPHORESIS IN THE SELF-FERTILE HERMAPHRODITE SPECIES BULINUS TRUNCATUS (GASTROPODA: PLANORBIDAE)

Uniparental reproduction in the tetraploid hermaphrodite speciesBulinus truncatus has been suggested to occur via self-fertilization,on the basis of cytological and genetic studies. However, recentanalyses of population genetic structure by protein electrophoresisindicated the occurrence of multi-banded phenotypes referredto as ‘fixed hetero-zygosity’. Although intrapopulationand geographical variation of multibanded phenotypes occur,many populations bear only one type of such patterns. This ledto the suggestion that parthenogenesis may well be the matingsyste in B. truncatus. However, such fixed heterozygosity patternsare expected in some tetraploid species in which double disomicinheritance of alleles occurs. It is therefore not possibleto determine from population genetic structure analysis alonewhether segregation occurs or not. Here, we investigate thestability of such patterns over one generation of uniparentalreproduction among four populations. We also present resultsof crossing experiments between individuals from two populations,using two diagnostic loci to analyse their offspring. Our resultsclearly indicate Mendelian segregation of alleles, and confirmsexual reproduction by self-fertilization and cross-fertilization.We interpret the multibanded patterns observed in populationsas the product of both diploid loci of the tetraploid genomewhen they are monomorphic for different alleles. Our study alsoallows us to suggest that partial selfing may be the regularmating system in B. truncatus. (Received 12 February 1992; accepted 7 September 1992)     

Allozyme, mitochondrial-DNA, and morphometrie variability indicate cryptic species of anchovy (Engraulis encrasicolus)

Previous surveys of population structure in the Atlantic-Mediterranean anchovy Engraulis encrasicolus L. have reported heterogeneity in morphology, allozyme frequencies, and mitochondrial DNA haplotype frequencies at a regional scale. In particular, two stocks of anchovy have been detected in the Adriatic Sea. In this paper, the available data is reviewed with the aim to relate genetic variation to geography at the widest possible geographical scale, for investigating the evolutionary mechanisms underlying stock structure in anchovy. Correspondence analysis of allozyme frequencies (24 samples, three polymorphic loci) compiled from the literature indicates three distinct entities in the Mediterranean Sea. Open-sea or oceanic anchovy populations are genetically different from inshore-water populations within a region (Nei's ^ G _ST = 0.035–0.067), while broadscale geographical variation is weak for each of these two habitat-specific forms (^ G _ST = 0.005–0.006). Mitochondrial-DNA haplotype frequencies support the distinction between an inshore form and an oceanic form (^ G _ST = 0.067–0.107), with virtually no genetic differences among oceanic populations across the Gulf of Biscay, the western Mediterranean and the Ionian Sea (^ G _ST = −0.001). If natural selection on marker loci is unimportant, these results indicate the occurrence of two parapatric, genetically distinct, habitat-specific forms that are widely distributed throughout the Mediterranean Sea. Persistent allele and haplotype-frequency differences between these forms indicate reproductive isolation and the presence of an E. encrasicolus species complex in the Mediterranean. © 2002 The Linnean Society of London, Biological Journal of the Linnean Society 75 : 261–269.     

Combined impacts of longline fisheries and climate on the persistence of the Amsterdam Albatross Diomedia amsterdamensis

Incidental capture of seabirds in longline fishing gear is a central issue in the conservation of many long-lived marine species. Despite growing evidence of climate-induced effects on population trends of long-lived species, climate change remains generally overlooked in most risk assessments of seabirds. Because variation in climate may interact with the detrimental effects of bycatch, considering climate is of great importance, especially in the context of ongoing global warming. This paper examines the combined effects of bycatch and climate change on the persistence of one of the world's rarest birds, the Amsterdam Albatross Diomedea amsterdamensis , which has a single population in the upland plateau of Amsterdam Island (Southeast Indian Ocean). Using continuous monitoring from 1983 onwards, we first estimated the relationship between climate and the species' demographic parameters. We then built a stochastic matrix population model to estimate the population growth rate and the probability that the population declines below the level recorded in 1983 of nine breeding pairs under different scenarios involving the joint effects of additional mortality caused by longline fisheries and climate change. The results suggest that the demography of the Amsterdam Albatross is influenced by climate in both breeding and wintering grounds and that these relationships may to some extent compensate for the impact of additive bycatch mortality. However, these compensatory effects would be negligible if the annual additional mortality exceeds around six individuals per year, suggesting that the resumption of longline fishery in the foraging range of the Amsterdam Albatross would rapidly put this species at risk of extinction.     

Curvilinear Three-Dimensional Modeling of Spinal Curves with Dual Kriging

In spinal deformation studies, three-dimensional reconstruction of the spine is frequently represented as a curve in space fitted to the vertebral centroids. Conventional interpolation techniques such as splines. Bezier and the least squares method are limited since they cannot describe precisely the great variety of spinal morphologies. This article presents a more general technique called dual kriging, which includes two mathematical constituents (drift and covariance) to adjust the interpolated functions to spinal deformity better. The cross-validation technique was used to compare the parametric representations of spinal curves with different combinations of drift and covariance functions. Model validation was performed from a series of analytic curves reflecting typical scoliotic spines. Calculation of geometric torsion, a sensitive parameter, was done to evaluate the accuracy of the kriging models. The best model showed an absolute mean difference of 1.2 x 10～5 (±7·1 × l()～ ⁵) mm^?1 between the analytical and estimated geometric torsions compared to 5·25 × 10～ (±3.7 × ³10～²) mm* ¹ for the commonly used least-squares Fourier series method, a significant improvement in spinal torsion evaluation.