Assumption 2: opaque to intuition?

Aim The aim of this paper was to revise the historical biogeographical method for resolving complicated distribution patterns through a technique that has come to be called assumption 2. Assumption 2 was used to resolve multiple areas on a single terminal branch (masts) as well as paralogous and missing areas in two or more areagrams. Recent examples, however, have shown that assumption 2 may be using rather than resolving paralogy. The paper attempts to resolve this problem by formulating a separate procedure to avoid using paralogous (redundant) area data in area cladistic analyses. Method The revision results in a new derivative method, the transparent method, to replace assumptions 1 and 2. It separates the procedures for resolving paralogy and for solving distribution patterns that occur in more than one area (masts). Results Several hypothetical examples show how the transparent method reduces paralogy and masts. The results show that paralogy can be reduced if the paralogy subtree method is applied after uncovering all possible relationships as single components on the terminals of areagrams. Conclusion The transparent method is a significant step forward in cladistic biogeography as it utilizes area relationships rather than generating general areagrams based on paralogous data.     

Circadian control of neurogenesis

The life-long addition of new neurons has been documented in many regions of the vertebrate and invertebrate brain, including the hippocampus of mammals (Altman and Das, 1965; Eriksson et al., 1998; Jacobs et al., 2000), song control nuclei of birds (Alvarez-Buylla et al., 1990), and olfactory pathway of rodents (Lois and Alvarez-Buylla, 1994), insects (Cayre et al., 1996) and crustaceans (Harzsch and Dawirs, 1996; Sandeman et al., 1998; Harzsch et al., 1999; Schmidt, 2001). The possibility of persistent neurogenesis in the neocortex of primates is also being widely discussed (Gould et al., 1999; Kornack and Rakic, 2001). In these systems, an effort is underway to understand the regulatory mechanisms that control the timing and rate of neurogenesis. Hormonal cycles (Rasika et al., 1994; Harrison et al., 2001), serotonin (Gould, 1999; Brezun and Daszuta, 2000; Beltz et al., 2001), physical activity (Van Praag et al., 1999) and living conditions (Kemperman and Gage, 1999; Sandeman and Sandeman, 2000) influence the rate of neuronal proliferation and survival in a variety of organisms, suggesting that mechanisms controlling life-long neurogenesis are conserved across a range of vertebrate and invertebrate species. The present article extends these findings by demonstrating circadian control of neurogenesis. Data show a diurnal rhythm of neurogenesis among the olfactory projection neurons in the crustacean brain, with peak proliferation during the hours surrounding dusk, the most active period for lobsters. These data raise the possibility that light-controlled rhythms are a primary regulator of neuronal proliferation, and that previously-demonstrated hormonal and activity-driven influences over neurogenesis may be secondary events in a complex circadian control pathway.     

饲养条件下川金丝猴群中主雄的移除和替换对社群行为的影响

在上海野生动物园对一群半散养的川金丝猴进行了为期一年的行为学研究。在此期间,猴群中发生了4起家庭主雄被移除和替代事件和一个雌性群因繁殖需要引入一个成年雄猴的事件,该过程在饲养条件下首次被完整记录。观察发现,繁殖群中,在家庭主雄猴的健康状况良好期间,群中各雄性成员间的社会等级关系相当稳定,很少变动。主雄猴有效地控制着群体的秩序,并严格地看护着其家庭中的雌猴免受其他雄猴的侵扰,而且它也很少对其他低序位雄猴主动攻击。全雄群中则再由一个高序位雄猴控制其他低序位雄猴。疾病、衰老、前主雄猴的存在以及被饲养人员从群中移除进行治疗等都可能引起猴群社会发生很大动荡,尤其是全雄群中各雄猴的社会等级序位发生剧烈改变,甚至发生家庭主雄的替代。在本报道中,人为因素在主雄替代过程中起着主要作用。主雄替代一旦成功,新主雄会把原主雄赶入全雄群,攻击追撵其他低序位雄猴,并彻底与全雄群完全脱离。对于每一个新主雄,家庭中的雌猴对其的接纳表现出明显的选择倾向。雌性性选择可能是野生猴群中新家庭群建立一种内在基础机制,同时提示偷配发生的可能性。     

Metal hyperaccumulation: a model system for coevolutionary studies

Recent years have seen a flurry of research activity concerning the hyperaccumulation of heavy metals by plants. Much of the interest in hyperaccumulation has been fueled by the commercial potential of phytoremediation, the use of plants to clean up contaminated soils (Baker et al ., 1994; Salt et al ., 1995; Chaney et al ., 1997, 2000). These applications have in turn spurred many studies of the genetics and physiology of metal uptake (e.g. Krämer et al ., 1996; Lasat et al ., 1996; Salt & Krämer, 1999; Baker et al ., 2000; see also Krämer, 2000; Lombi et al ., 2000). Although phytoremediation provides an intriguing and potentially profitable backdrop, the ecology and evolution of hyperaccumulation in natural populations are interesting subjects in their own right. Two papers in this issue (Ghaderian et al ., pp. 219–224; Davis & Boyd, pp. 211–217) are exciting contributions to the growing consensus that hyperaccumulation may act as a defense against herbivores and pathogens, and suggest that hyperaccumulation may become a model system for research in this area.     

A note on an interaction between Rhinopithecus bieti and a buzzard at Baima Snow Moutain

Predation avoidance relies primarily on behavioural mechanisms [van Schaik and van Hooff, 1983]. Primates alarm call at predators, including most birds and mammals [Cheney and Wrangham, 1987]. Alarm calls could be used to signal to the predator that it has been spotted [Zuberbühler et al., 1999], thereby probably decreasing the likelihood of an attack [Schultz, 2001], and they also inform prey of the presence of the predator, thereby increasing overall attention levels [Schülke, 2001]. Although eagles are reported to be one of the predators of Rhinopithecus bieti [Bai et al., 1987], few interactions between these monkeys and raptors have been documented to date. Here I document an interaction witnessed between R. bieti and a buzzard [Buteo sp., Yang X-J, pers. comm.].     

Cladistic biogeography and the art of discovery

Aims

Cladistic biogeography is about discovering geographical congruence. The agreement of several taxon‐area cladograms (TACs) rarely yields a perfect result. Areas may overlap, taxa may not be evenly distributed, and thus, ambiguity may be prevalent in the data. Ambiguity is incongruence and may be resolved by reducing paralogy and resolving potential information. Recently, several new approaches in cladistic biogeography [i.e. Brooks parsimony analysis (BPA), Assumption 0] interpret ambiguity as congruence. These methods are problematic, as they are generational. Methods constructed under the generation paradigm are flawed concepts that are immunized from falsifying evidence. A critique of modified BPA reveals that taking an evolutionary stance in biogeography leads to flaws in implementation.

Methods

Area cladistics is a new development in cladistic biogeography. Area cladistics adopts paralogy‐free subtree analysis using Assumption 2, to discover the relative positions of continents through time.

Results

Geographical congruence is the result of allopatric (geographical) speciation. Vicariance, dispersal and combinations of both, are recognized causes for allopatric speciation. Area cladistics highlights the concept that all these events occur in response to geological changes (e.g. continental drift) either directly, by geographical boundaries, or indirectly, at the level of ocean currents. Samples of chosen examples all respond to the geological process. The examples include Ordovician–Silurian and Lower Devonian trilobites to yield a general areagram which is a representational branching diagram that depicts the relationships of areas.

Main conclusion

Finding one common biogeographical pattern from several unrelated groups is a qualitative approach to interpret the positions of continental margins through time. Area cladistics is not a substitute for palaeomaps that are derived from palaeomagnetic data, but general areagrams adding to the body of knowledge that yields more precise interpretations of the earth's past.

     

贵州遵义松林黑沙坡早寒武世牛蹄塘生物群中镇巴虫的发现

贵州遵义松林中南村黑沙坡下寒武统牛蹄塘生物群下部层位产有大型三叶虫,计有2属3种,1未定种：Zhenbaspis subconica S. G Zhang in Lu et al. , 1974, Z. longa Zhou in Lee et al. , 1975 ; Zhenbaspis sp. , Runnania similis Lee in Yin et Lee, , 1978, 确认 Zhenbaspis (Zhenxiongaspis) Lin et Yin in Yin et Lee, 1978,为 Zhenbastn‘sChang et Chu in Lu et al. ,1974的同义名。探讨Zhenbaspis的古地理分布及演化趋势。论文还描述与Zhenbaspis,Runnania共生的Tsunyidiscus及Mianxiandiscus,其中Mianxiandiscus产于下生物群即牛蹄塘组近底部,再次证实牛蹄塘下生物群的时代早于澄江生物群。     

Congruent and synchronic patterns in biogeography and speciation among seabirds, pinnipeds, and cestodes.

Congruence in biogeographic patterns among diverse assemblages of taxa indicates uniformity in the historical determinants of biotic distributions. Comparisons of host and parasite phylogenies and the elucidation of distributional area relationships are requisite components of analyses in historical biogeography. Host-parasite associations with broad geographic ranges are often archaic and have been structured largely by coevolutionary processes. In contrast, the origins and radiation of the primary cestode faunas of some seabirds (Alcataenia spp./Alcidae) and pinnipeds (Anophryocephalus spp./Phocidae and Otariidae) are associated with colonization. These young colonizing faunas, in the Holarctic Region, were influenced by a common history during the late Pliocene and Pleistocene epochs. Periodic range contraction, with isolation in refugial centers, and subsequent expansion into postglacial habitats for hosts and parasites coincided with the cyclic pattern of stadials and interstadials. During the past 2-3 million years following colonization, these dramatic climatic fluctuations strongly influenced the continuity of ecological associations in marine habitats and appear to have been the determinants of congruent and synchronic patterns of speciation among these disparate taxa of marine homeotherms and eucestodes.     

Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea,Mammalia): new data and phylogenetic analyses of Elephantidae

The phylogenetic relationships between recent Elephantidae (Proboscidea, Mammalia), that is to say extant elephants (Asian and African) and extinct woolly mammoth, have remained unclear to date. The prevailing morphological scheme (mammoth grouped with Asian elephant) is either supported or questioned by the molecular results. Recently, the monophyly of woolly mammoths on mitochondrial grounds has been demonstrated (Thomas, et al., 2000), but it conflicts with previous studies (Barriel et al., 1999; Derenko et al., 1997). Here, we report the partial sequencing of two mitochondrial genes: 128 bp of 12S rDNA and 561 bp of cytochrome b for the Lyakhov mammoth, a 49,000-year-old Siberian individual. We use the most comprehensive sample of mammoth (11 sequences) to determine whether the sequences achieved by former studies were congruent or not. The monophyly of a major subset of mammoths sequences (including ours) is recovered. Such a result is assumed to be a good criterion for ascertaining the origin of ancient DNA. Our sequence is incongruent with that of Yang et al. (1996), though obtained for the same individual. As far as the latter sequence is concerned, a contamination by non-identified exogenous DNA is suspected. The robustness and reliability of the sister group relation between Mammuthus primigenius and Loxodonta africana are examined: down-weighting saturated substitutions has no impact on the topology; analyzing data partitions proves that the support of this clade can be assigned to the most conservative phylogenetic signal; insufficient taxonomic and/or characters sampling contributed to former discordant conclusions. We therefore assume the monophyly of "real mammoth sequences" and the (Mammuthus, Loxodonta) clade.     

Location of zinc and 65Zn in spinal ganglia of the rat

Following the works of Velazquez et al. (1999), Jo-Seung et al. (2000), Wang et al. (2001), Danscher et al. (2001) and the criteria of Zinc-containing neurons established by Frederickson et al.(2000), we have found the presence and localisation of Zinc in the neurons of the dorsal root ganglia of Wistar rat, by using Timm's thecnique and by studying the autoradiographic uptake of 65Zn. The agreement between the results of both techniques allows us to classify these spinal ganglion neurons as Zinc-containing neurons and also, to confirm some of the results of Velazquez et al. (1999).     

Plant-food and tool transfer among savanna chimpanzees at Fongoli, Senegal

Transferring food is considered a defining characteristic of humans, as such behavior is relatively uncommon in other animal species save for kin-based transfer. Chimpanzees (Pan troglodytes) are one exception, as they commonly transfer meat among nonrelatives but rarely transfer other resources. New observations at Fongoli, Senegal, show habitual transfer of wild-plant foods and other non-meat resources among community members beyond transfers from mother to offspring. We explore various explanations for these behaviors with a focus on age- and sex-class patterns in transfer events. In a total of 27 of 41 cases, male chimpanzees at Fongoli transferred wild-plant foods or tools to females. Most other cases involved transfer among males or males taking food from females. In light of male–female transfer patterns at Fongoli, we examine four hypotheses that have been applied to food transfer in apes: (1) testing for male-coercive tendency (van Noordwijk and van Schaik, Behav Ecol Sociobiol 63:883–890, 2009), (2) costly signaling (Hockings et al. PLoS ONE 2:e886, 2007), (3) food-for-sex (Gomes and Boesch, PLoS ONE 4:5116, 2009), and (4) sharing-under-pressure (Gilby, Anim Behav 71:953–963, 2006). We also consider hypotheses posed to explain transfer among callitrichids, where such behavior is more common (Ruiz-Miranda et al. Am J Primatol 48:305–320, 1999). Finally, we examine variables such as patch and food size and food transport. We discuss our findings relative to general patterns of non-meat transfer in Pan and examine them in the context of chimpanzee sociality in particular. We then contrast chimpanzee species and subspecies in terms of non-meat food and tool transfer and address the possibility that a savanna environment contributes to the unusual pattern observed at Fongoli.     

NOTHOFAGUS AND PACIFIC BIOGEOGRAPHY

Abstract — Gondwanan biogeography, particularly the relationships between southern South America, New Zealand, Australia, New Guinea and New Caledonia, has been much studied. Nothofagus is often used as the "test taxon", and many papers have been directed at using Nothofagus to explain Gondwanan biogeography. Cladistic biogeographers, working on plant material, have generally failed to find congruence among taxa expected from the southern Pacific disjunctions. New morphological and molecular data on the phytogeny of Nothofagus have re-opened the issue, and we analysed these data to construct a new hypothesis of the biogeography of the genus. We assembled all plant taxa for which we could find reasonably robust phylogenetic hypotheses, and sought a parsimonious biogeographical pattern common to all. Two analyses, based on different assumptions, produced the same general areacladogram. We use the general area-cladogram, in conjunction with the fossil record of Nothofagus to construct a historical scenario for the evolution of the genus. This scenario indicates extensive extinction, but also suggests that Australia has a more recent relationship to New Zealand than to southern South America. This is not congruent with the current geological theories, nor with the patterns evident from insect biogeography. We suggest that concordant dispersal is an unlikely explanation for this pattern, and propose that the solution might be found in alternative geological hypotheses.     

A measure of phase ambiguity in pairs of SNPs in the presence of linkage disequilibrium

The extent of haplotype ambiguity in a string of single-nucleotide polymorphisms (SNPs) was quantified by Hodge et al. [Nat Genet 1999;21:360]. In their measure, the level of ambiguity increases with increasing numbers of loci and as loci become more polymorphic. That work assumed linkage equilibrium (LE). However, linkage disequilibrium (LD) provides additional information about the haplotypes at a site, thereby diluting the level of ambiguity. The ambiguity vanishes altogether when LD reaches its maximum value. Here, we introduce the ambiguity measure, Phi, to allow for LD (between pairs of SNPs). We derive the formula Phi = 4x(2)x(3) for ambiguity in individuals, where x(1), x(2), x(3) and x(4) are the probabilities of the A(1)A(2), A(1)B(2), B(1)A(2) and B(1)B(2) haplotypes, respectively, and w.l.o.g. x(1)x(4) > or = x(2)x(3). Alternatively, Phi can be expressed in terms of the allele frequencies and the LD parameter delta. We also extend the formula to triads of two parents plus one child. We estimate our measure Phi for relevant SNPs in the published lipoprotein lipase (LPL) gene dataset [Clark et al., Am J Hum Genet 1998;63:595; Nickerson et al., Nat Genet 1998;19:233], obtaining values ranging from a low of 0 to a high of 0.11 among adjacent pairs of sites. In genome-wide LD studies to map common disease genes, a dense map of SNPs may be utilized to detect association between a marker and disease. Therefore, the measurement of ambiguity can potentially help investigators to determine a more efficient map, designed to minimize ambiguity and subsequent information loss.     

子树分析和TASS程序及其在锦鸡儿属植物中的应用

子树分析和三分法 (TASS)程序是历史生物地理学中分布区关系的一种分析途径。它以分类群分支图为基础 ,以剔除其中分布区关系相悖理的结点并确定具信息的子树为目标 ,以便更有效地利用分布区信息。对分布区关系可以用若干子树和一个分布区分支图来表示。对锦鸡儿属 (Caragana)植物 72种和 13个分布区的子树分析和TASS程序运算后 ,得到 7个具信息的子树 ,它们分别表达了锦鸡儿属属内组、系所具有的分布区关系。属的分布区分支图也表达了 13个分布区的关系。与以前我们对本属成分分析的结果相吻合。     

Horizontal gene transfer in microbial genome evolution

Horizontal gene transfer is the collective name for processes that permit the exchange of DNA among organisms of different species. Only recently has it been recognized as a significant contribution to inter-organismal gene exchange. Traditionally, it was thought that microorganisms evolved clonally, passing genes from mother to daughter cells with little or no exchange of DNA among diverse species. Studies of microbial genomes, however, have shown that genomes contain genes that are closely related to a number of different prokaryotes, sometimes to phylogenetically very distantly related ones. (Doolittle et al., 1990, J. Mol. Evol. 31, 383-388; Karlin et al., 1997, J. Bacteriol. 179, 3899-3913; Karlin et al., 1998, Annu. Rev. Genet. 32, 185-225; Lawrence and Ochman, 1998, Proc. Natl. Acad. Sci. USA 95, 9413-9417; Rivera et al., 1998, Proc. Natl. Acad. Sci. USA 95, 6239-6244; Campbell, 2000, Theor. Popul. Biol. 57 71-77; Doolittle, 2000, Sci. Am. 282, 90-95; Ochman and Jones, 2000, Embo. J. 19, 6637-6643; Boucher et al. 2001, Curr. Opin., Microbiol. 4, 285-289; Wang et al., 2001, Mol. Biol. Evol. 18, 792-800). Whereas prokaryotic and eukaryotic evolution was once reconstructed from a single 16S ribosomal RNA (rRNA) gene, the analysis of complete genomes is beginning to yield a different picture of microbial evolution, one that is wrought with the lateral movement of genes across vast phylogenetic distances. (Lane et al., 1988, Methods Enzymol. 167, 138-144; Lake and Rivera, 1996, Proc. Natl. Acad. Sci. USA 91, 2880-2881; Lake et al., 1999, Science 283, 2027-2028).     

基于线粒体控制区序列的猕猴属系统发育研究

通过线粒体部分控制区DNA序列数据探讨7种猕猴属物种的分子系统发育关系。结果表明熊猴的核苷酸多样度最高,而藏酋猴核苷酸多样度较低。基于控制区序列数据所构建的最大似然树,不考虑食蟹猴的位置,7种猕猴物种可粗略地分为3个种组,即狮尾猴组(包括北平顶猴)、头巾猴组(包括红面猴、熊猴和藏酋猴)和食蟹猴组(包括恒河猴和台湾猴)。与前人(Fooden＆Lanyon,1989;Tosi et al,2003a;Deinard＆Smith,2001;Evans et al,1999;Hayasaka et al,1996;Morales＆Melnick,1998)的结果不同,我们的结果支持食蟹猴比北平顶猴分化早的假设;东部恒河猴(相对于台湾猴)和东部熊猴(相对于藏酋猴)出现并系。与Y染色体、等位酶、核基因以及部分形态学数据推测的结果(Delson,1980;Fooden＆Lanyon。1989;Fooden,1990;Tosi et al,2000,2003a,b;Deinard＆Smith,2001)一致,红面猴应归于头巾猴组,但此结论与前人(Hayasaka et al,1996;Morales＆Melnick,1998;Tosi et al,2003a)依据线粒体得到的结果有较大分歧。     

Do deposed adult male Sichuan snub-nosed monkeys Rhinopithecus roxellana roam as solitary bachelors or continue to interact with former band members?

Dispersal patterns exhibited by group-living animals play an important role in individual reproductive success and survival,as well as population and social dynamics(Greenwood,1980;Isbell and van Vuren,1996;Kappeler and van Schaik,2002).Dispersing individuals may emigrate voluntarily,or they may be forcibly evicted by other individuals(Pusey and Packer,1987;Clobert et al.,2001).One cause of individual dispersal is when an extra-group male compels another male to leave a group of females.This phenomenon has ...     

An aquatic perspective on the concepts of Ingestad relating plant nutrition to plant growth

Oil bodies are lipid storage organelles which have been analyzed biochemically due to the economic importance of oil seeds. Although oil bodies are structurally simple, the mechanisms involved in their formation and degradation remain controversial. At present, only two proteins associated with oil bodies have been described, oleosin and caleosin. Oleosin is thought to be important for oil body stabilization in the cytosol, although neither the structure nor the function of oleosin has been fully elucidated. Even less is known about caleosin, which has only recently been described [Chen et al. (1999) Plant Cell Physiol 40: 1079–1086; Næsted et al. (2000) Plant Mol Biol 44: 463–476]. Caleosin and caleosin-like proteins are not unique to oil bodies and are associated with an endoplasmatic reticulum subdomain in some cell types. Here we review the synthesis and degradation of oil bodies as they relate to structural and functional aspects of oleosin and caleosin.     

Patterns of Amazonian area relationships based on raw distributions of papilionid butterflies (Lepidoptera: Papilioninae)

Diversifications within a biota are due to several factors. Although some of these are untestable with current analytical methods, hierarchical congruence obtained with different cladistic methods and based on independent taxa are undoubtedly important. In the recent past, most hypotheses of historical biogeography (e.g. refugial, riverine, disturbance, vicariance) were tested on the Amazonian biota, selecting a number of diverse organisms such as plants, anurans, lizards, butterflies, birds and monkeys. In this study we used parsimony analysis of endemicity to infer historical relationships among 16 interfluvial areas in the Amazonian lowlands based on raw distributions of 114 Papilioninae (Lepidoptera). The analysis yielded two most parsimonious trees of area relationships. One tree was characterized by two main clusters of areas which showed a separation of Guyanan + south-east Amazonian interfluvial areas from western Amazonian interfluvial areas. The second tree showed the Guyanan interfluvial areas basal to a cluster which included all the other interfluvial areas. This latter cluster was subdivided into two main groups of areas separating the south-east Amazonian and the western Amazonian interfluvial areas. This result is discussed in the light of previous hypotheses obtained with the same method using some vertebrate taxa in the Amazonian lowlands. Likewise, comparisons with other hypotheses on lineages of birds, mammals and butterflies obtained applying cladistic biogeographical methods are made. The two alternative vicariant patterns presented for papilionid butterflies are strictly congruent with those for birds.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 345–357.