Detecting areas of endemism with a taxonomically diverse data set: plants,mammals, reptiles,amphibians, birds,and insects from Argentina

The idea of an area of endemism implies that different groups of plants and animals should have largely coincident distributions. This paper analyses an area of 1152 000 km², between parallels 21 and 32°S and meridians 70 and 53°W to examine whether a large and taxonomically diverse data set actually displays areas supported by different groups. The data set includes the distribution of 805 species of plants (45 families), mammals (25 families), reptiles (six families), amphibians (five families), birds (18 families), and insects (30 families), and is analysed with the optimality criterion (based on the notion of endemism) implemented in the program NDM/VNDM. Almost 50% of the areas obtained are supported by three or more major groups; areas supported by fewer major groups generally contain species from different genera, families, or orders. © The Willi Hennig Society 2011.     

Fold designability, distribution, and disease

Fold designability has been estimated by the number of families contained in that fold. Here, we show that among orthologous proteins, sequence divergence is higher for folds with greater numbers of families. Folds with greater numbers of families also tend to have families that appear more often in the proteome and greater promiscuity (the number of unique “partner” folds that the fold is found with within the same protein). We also find that many disease-related proteins have folds with relatively few families. In particular, a number of these proteins are associated with diseases occurring at high frequency. These results suggest that family counts reflect how certain structures are distributed in nature and is an important characteristic associated with many human diseases.     

西藏佩枯错种子植物区系研究

为了丰富西藏高原植物区系地理研究资料,深入开展该区域植被生态学研究、生物资源开发利用与保护,该研究通过野外调查、标本采集以及查阅相关的文献资料,对西藏佩枯错种子植物区系进行了统计分析。结果表明:(1)植物种类较贫乏。佩枯错共有种子植物31科77属115种,仅占西藏种子植物的18.90%、6.73%、2.17%。其中裸子植物2科2属2种,被子植物29科75属113种;被子植物中双子叶植物有23科58属91种,单子叶植物6科17属22种。(2)优势科明显,单种科占绝对优势。所有科中有5个科至少含有7种种子植物,占该研究区总种数的39.13%,是该区系的主要组分;同时科数中有11科仅含1种植物,该类科占一定优势。(3)种子植物的区系成分较复杂,划分为3个科分布区类型和10个属分布区类型,其中温带成分占绝对优势:温带分布科、属分别占总数的29.03%和77.92%,表明本区系具有明显温带性质。(4)科属特有现象不明显,没有中国特有科分布,仅有1个中国特有属分布,说明佩枯错植物区系的特有化程度极低,表现出寒旱化与高山、高原特化综合而成的高寒植物区系的年轻性。     

Morphology and phylogenetic interrelationships of the Asteraceae,Calyceraceae, Campanulaceae,Goodeniaceae, and related families (Asterales)

In search for the sister group of the Asteraceae, morphological evidence was assembled for investigating the relationship between the Asteraceae and those families most frequently considered to be their closest relatives, in particular the Calyceraceae, Campanulaceae (along with the frequently included Lobeliaceae, Cyphiaceae, Cyphocarpaceae, and Nemacladaceae), and Goodeniaceae (and the sometimes included Brunoniaceae). Several other families that have been associated with this group of families, the “Asterales-Campanulales-complex,” were also considered: Pentaphragmataceae, Sphenocleaceae, Stylidiaceae, Donatiaceae, Menyanthaceae, and Argophyllaceae. In order to delineate the complex more precisely, another eight putatively related families were also included in the analysis. Cladistic parsimony analysis of 46 morphological and chemical characters for the 23 families was undertaken. Stability of the branches was estimated by the number of extra steps necessary to lose the group, as well as by the number of reweighted extra steps (using rescaled consistency indices) necessary to lose the group (a new approach). The results indicate that there is a monophyletic group of 14 families comprising those of the Asterales-Campanulales-complex as well as Pentaphragmataceae, Sphenocleaceae, Stylidiaceae, Donatiaceae, and Menyanthaceae; this group is recognized as the order Asterales. Within the order, the Asteraceae, Calyceraceae, Brunoniaceae, and Goodeniaceae form one comparatively well-supported clade and the five families of the Campanulaceae sensu lato form another well-supported clade.     

The Medicinal Flora of Sambalpur District,Orissa,India

This paper describes an analysis of the plants of Sambalpur district of Orissa,India which have been used medicinally by local people. The families having medicinal values are analysed using Moerman's method of regression analysis. There were 136 plant families recorded from the study area. The analysis of families showed that the Euphorbiaceae family being used most ethnomedicinally by the local people in Sambalpur district of Orissa,whereas Poaceae is used least one. This type of study determines the degree of importance of plant families in the medicinal flora of the region.     

The Medicinal Flora of Sambalpur District, Orissa, India

This paper describes an analysis of the plants of Sambalpur district of Orissa, India which have been used medicinally by local people. The families having medicinal values are analysed using Moerman's method of regression analysis. There were 136 plant families recorded from the study area. The analysis of families showed that the Euphorbiaceae family being used most ethnomedicinally by the local people in Sambalpur district of Orissa, whereas Poaceae is used least one. This type of study determines the degree of importance of plant families in the medicinal flora of the region.     

Comparative genomics of prokaryotic GTP-binding proteins (the Era, Obg, EngA, ThdF (TrmE), YchF and YihA families) and their relationship to eukaryotic GTP-binding proteins (the DRG, ARF, RAB, RAN, RAS and RHO families)

Several GTP-binding proteins with poorly defined functions were previously identified in Escherichia coli (i.e. Era, ThdF (TrmE)), Bacillus subtilis (i.e. Obg) and Neisseria gonorrhoeae (i.e. EngA). In these species, every individual protein is encoded by an essential gene. BLAST searches were used to detect orthologs in genomes of various organisms. Alignments of orthologous sequences allowed the construction of phylogenetic trees and the definition of protein families. The BLAST searches also resulted in the identification of two additional families, the YchF and YihA families, named after the ychF and yihA genes of E. coli. Most families are not present in archaeal genomes, but representatives of each family were also detected in eukaryotic genomes. Only representatives of the YchF family are present in every genome sequenced to date, suggesting that YchF-like proteins might be involved in a fundamental life process. The GTP1/DRG family consisting of eukaryotic and archaeal proteins is related to the YchF family of GTP-binding proteins. The relationship of the six prokaryotic families of GTP-binding proteins and the GTP1/DRG family to eukaryotic GTPase families was also investigated: With the exception of the ARF family, a clear separation of the six prokaryotic families and the GTP1/DRG family with respect to eukaryotic (RAB, RAN, RAS and RHO) GTPases was observed.     

Taxon age,origination, and extinction through geologic time

Changes in the taxon ages of fossil marine families that are alive and those that become extinct in each stage of the Phanerozoic reflect changes in the origination rate, differences in the extinction rate of families with different taxon ages, and mass extinction events. Extinct families are generally much younger than the population from which they were drawn. Periods dominated by higher numbers of younger families are more susceptible to larger size extinctions and greater variation in extinction size. As a result the relative size of extinction peaks must be viewed with regard to the taxon age structure of the population. Mass extinctions cause little change in the taxon age of the fauna. However, adaptive radiations cause a large drop in the average age of the families that are alive at any given time. Families must be treated as dynamic entities in macroevolutionary studies because their probabilities of extinction change over time.     

Congenital malformations and developmental disabilities in ataxia-telangiectasia, Fanconi anemia, and xeroderma pigmentosum families.

Heterozygous carriers of an ataxia-telangiectasia (A-T), Fanconi anemia (FA), or xeroderma pigmentosum (XP) gene may be predisposed to some of the same congenital malformations or developmental disabilities that are common among homozygotes. To test this hypothesis, medical records, death certificates, and questionnaires from 27 A-T families, 25 FA families, and 31 XP families were reviewed. Eleven XP blood relatives (out of 1,100) were found with moderate or severe unexplained mental retardation, a significant excess compared to the FA and A-T families (3/1,439). There were four microcephalic XP blood relatives and none in the FA or A-T families. In the A-T families, idiopathic scoliosis and vertebral anomalies were in excess, while genitourinary and distal limb malformations were found in the FA families. A-T, FA, or XP heterozygotes may constitute an important proportion of individuals at risk for specific malformations or developmental abnormalities.     

广东中山市五桂山保健植物调查研究

据调查,广东中山市共有保健植物44科68属88种,其中裸子植物2科2属3种,双子叶植物37科59属76种,单子叶植物5科7属9种;文中还就五桂山保健植物的开发利用提出建议。     

深圳梧桐山蕨类植物区系

对深圳梧桐山蕨类区系进行了研究。结果表明,梧桐山蕨类植物区系由33科63属126种和2变种组成,含8种以上的科有水龙骨科、金星蕨科、鳞毛蕨科、卷柏科、蹄盖蕨科和风尾蕨科;依据植物的现代地理分布,梧桐山蕨类植物种的分布可以划归为9个分布区类型和6个亚型,其中热带亚洲分布成分和东亚分布成分构成了该区系的主体。区系分析表明,该植物区系带有较明显的热带性质,约67％的种类属于热带分布。     

Internal organization of large protein families: relationship between the sequence, structure, and function-based clustering

The protein universe can be organized in families that group proteins sharing common ancestry. Such families display variable levels of structural and functional divergence, from homogenous families, where all members have the same function and very similar structure, to very divergent families, where large variations in function and structure are observed. For practical purposes of structure and function prediction, it would be beneficial to identify sub-groups of proteins with highly similar structures (iso-structural) and/or functions (iso-functional) within divergent protein families. We compared three algorithms in their ability to cluster large protein families and discuss whether any of these methods could reliably identify such iso-structural or iso-functional groups. We show that clustering using profile-sequence and profile-profile comparison methods closely reproduces clusters based on similarities between 3D structures or clusters of proteins with similar biological functions. In contrast, the still commonly used sequence-based methods with fixed thresholds result in vast overestimates of structural and functional diversity in protein families. As a result, these methods also overestimate the number of protein structures that have to be determined to fully characterize structural space of such families. The fact that one can build reliable models based on apparently distantly related templates is crucial for extracting maximal amount of information from new sequencing projects.     

Ostracoda (Crustacea) from Lizard Island,northern Great Barrier Reef,Australia. I. Families: Cytherellidae,Loxoconchidae, Cytherideidae,Cytheruridae, Paracytherideidae,Pectocytheridae, Krithidae,Cytheromatiidae, Bythocytheridae,Cytheridae

This paper deals with the taxonomy of the ostracod families Cytherellidae, Cytheridae, Cytheromatidae, Cytherideidae, Krithidae, Loxoconchidae, Paracytherideidae, Cytheruridae, Pectocytheridae and Bythocytheridae from the coral reefs around Lizard Island, northern Great Barrier Reef, Australia. 22 species belonging to these families were found. 7 species had been described from Australian coasts, 1 from the Red Sea and 1 with Indopacific-Westatlantic distribution. 9 species are newly described and 4 species remain in open nomenclature.     

Comparative floral structure and systematics in Oxalidales (Oxalidaceae, Connaraceae, Brunelliaceae, Cephalotaceae, Cunoniaceae, Elaeocarpaceae, Tremandraceae)

Floral morphology, anatomy and histology were studied in representatives of all families of current Oxalidales, which were recently constituted as a result of molecular systematic studies by other authors, and are composed of families of different positions in traditional classifications (Oxalidaceae, Connaraceae, Brunelliaceae, Cephalotaceae, Cunoniaceae, Elaeocarpaceae, Tremandraceae). Two of the three pairs of sister (or nested) families that come out in molecular analyses are highly supported by floral structure: Oxalidaceae/Connaraceae and Elaeocarpaceae/Tremandraceae, whereas Cephalotaceae/Cunoniaceae are not especially similar at the level of Oxalidales. Oxalidaceae and Connaraceae share petals that are postgenitally united into a basal tube (although they are imbricate in both) but free at the insertion zone, stamens that are congenitally united at the base, uniseriate glandular hairs on the stamen filaments, and ovules that are hemianatropous to almost orthotropous. The sharing of a special type of sieve-tube plastids and of trimorphic heterostyly, studied by other authors, should also be mentioned. With Brunelliaceae, the two families share an androgynophore and nectaries at the base of the stamens in alternisepalous sectors. Elaeocarpaceae and Tremandraceae share buzz-pollinated flowers and a syndrome of features functionally connected with it. In addition, petals are larger than sepals in advanced bud, they are valvate, involute and enwrap part of the adjacent stamens, they have three vascular traces. Lignified hairs are common on the anthers and are found in the ovary locules and on the ovules (not lignified) of representatives of both families. Ovules have a chalazal appendage, and the inner integument is much thicker than the outer.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 140 , 321–381.     

家蚕LTR逆转录转座子的鉴定、分类及系统发育分析

转座子是真核生物基因组的重要组成成分。为了研究家蚕Bombyx mori长末端重复序列 (long terminal repeat, LTR)逆转录转座子的分类及进化, 本研究采用de novo预测和同源性搜索相结合的方法, 在家蚕基因组中共鉴定出了38个LTR逆转录转座子家族, 序列长度占整个基因组的0.64%, 远小于先前预测的11.8%, 其中有6个家族为本研究的新发现。38个家族中, 26个家族有表达序列标签 (expression sequence tag, EST)证据, 表明这些家族具有潜在的活性。对有EST证据的6个家族和没有EST证据的5个家族用RT-PCR进行了组织表达谱实验, 结果表明这11个家族在一些组织中有表达, 这进一步证实了这些家族具有转录活性, 基于此我们推测家蚕中大部分的LTR逆转录转座子家族很可能具有潜在活性。对转座子的插入时间进行估计, 结果表明绝大部分元件都是最近1百万年内插入到家蚕基因组中的。我们还比较了黑腹果蝇Drosophila melanogaster、 冈比亚按蚊Anopheles gambiae和家蚕B. mori中Ty3/Gypsy超家族分支的差异, 结果表明不同枝在不同昆虫中有着不同的扩张。家蚕中LTR逆转录转座子的鉴定和系统分析有助于我们理解逆转录转座子在昆虫进化中的作用。     

Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families

The representation of protein structures as small-world networks facilitates the search for topological determinants, which may relate to functionally important residues. Here, we aimed to investigate the performance of residue centrality, viewed as a family fold characteristic, in identifying functionally important residues in protein families. Our study is based on 46 families, including 29 enzyme and 17 non-enzyme families. A total of 80% of these central positions corresponded to active site residues or residues in direct contact with these sites. For enzyme families, this percentage increased to 91%, while for non-enzyme families the percentage decreased substantially to 48%. A total of 70% of these central positions are located in catalytic sites in the enzyme families, 64% are in hetero-atom binding sites in those families binding hetero-atoms, and only 16% belong to protein-protein interfaces in families with protein-protein interaction data. These differences reflect the active site shape: enzyme active sites locate in surface clefts, hetero-atom binding residues are in deep cavities, while protein-protein interactions involve a more planar configuration. On the other hand, not all surface cavities or clefts are comprised of central residues. Thus, closeness centrality identifies functionally important residues in enzymes. While here we focus on binding sites, we expect to identify key residues for the integration and transmission of the information to the rest of the protein, reflecting the relationship between fold and function. Residue centrality is more conserved than the protein sequence, emphasizing the robustness of protein structures.     

Dicotyledons of cretaceous, palaeogene, and neogene. Adaptogenesis of the terminal phloem

A database containing information on the trait complex for terminal phloem of dicots leaf having been created during the last thirty years was analyzed. The typology of terminal phloem was verified. The monotypy of plant taxa up to the family level was confirmed. For orders and subclasses, the wide distribution of structural parallelisms was demonstrated. The lists of plant families with similar structures of the phloem terminals was elaborated. As a result of comparative analysis of these lists and paleobotanic data on the age of plant families, the specificity of the types of terminal phloem and the associated morphological and functional characteristics of the groups of families of the same evolutionary, age were revealed. Ancestral type prevails among the families belonging to Prodicots, which were emerged during Cretaceous. Symplastic type is characteristic to the families of Eudicots and biomes appeared in Paleogene, while the apoplastic type is characteristic to the families and biomes of Neogene. For each group to taxa, plant stem and root parasitism is characteristic for the crown taxa completing the structural sequences of trees and herbs. All these data allow discussion of the questions of climatic adaptogenesis of the character complex studied here, the impossibility of structural iterations in morphological evolution, and the reasons of similarities and differences in the evolutionary and contemporary zonal series of the terminal phloem in Dicots.     

Family origin and the response of threespine stickleback, Gasterosteus aculeatus, to thermal acclimation

To establish whether family origin affects the response of the threespine stickleback (Gasterosteus aculeatus) to thermal acclimation, we examined the rates of feeding, growth, and food conversion, relative tissue and organ masses and activities of a mitochondrial and a glycolytic enzyme in pectoral and axial muscle of individually housed fish from six families during acclimation to 8 degrees C and 23 degrees C. Feeding rates differed among families but were consistently higher in warm-acclimated than cold-acclimated fish. Growth rates differed among families. In four families growth was greater at 8 degrees C; these families generally had higher conversion efficiencies at 8 degrees C than 23 degrees C. For two families, growth was greater at 23 degrees C than 8 degrees C and conversion efficiencies did not differ between 8 degrees C and 23 degrees C. Relative tissue and organ masses (percent axial muscle, hepatosomatic, gut and kidney indices) differed with gender and among families (hepatosomatic, gut and kidney indices) but little with acclimation status. In all families and in both muscles, activities of the mitochondrial enzyme, citrate synthase (CS), were increased by cold acclimation. Axial muscle levels of the glycolytic enzyme, lactate dehydrogenase (LDH), were not affected by thermal acclimation or family origin, but were strongly correlated with the hepatosomatic index and axial muscle protein content. Pectoral muscle levels of LDH were affected by family origin which also influenced the response to thermal acclimation. Similar patterns were observed for specific activities and total muscle contents of these enzymes. Stickleback family origin influenced rates of feeding and growth and the thermal sensitivity of growth rates but not the compensatory increase in muscle CS levels with cold acclimation. The differing thermal sensitivities of growth could reflect distinct strategies for the timing of juvenile growth.     

Domain combinations in archaeal, eubacterial and eukaryotic proteomes.

There is a limited repertoire of domain families that are duplicated and combined in different ways to form the set of proteins in a genome. Proteins are gene products, and at the level of genes, duplication, recombination, fusion and fission are the processes that produce new genes. We attempt to gain an overview of these processes by studying the evolutionary units in proteins, domains, in the protein sequences of 40 genomes. The domain and superfamily definitions in the Structural Classification of Proteins Database are used, so that we can view all pairs of adjacent domains in genome sequences in terms of their superfamily combinations. We find 783 out of the 859 superfamilies in SCOP in these genomes, and the 783 families occur in 1307 pairwise combinations. Most families are observed in combination with one or two other families, while a few families are very versatile in their combinatorial behaviour; 209 families do not make combinations with other families. This type of pattern can be described as a scale-free network. We also study the N to C-terminal orientation of domain pairs and domain repeats. The phylogenetic distribution of domain combinations is surveyed, to establish the extent of common and kingdom-specific combinations. Of the kingdom-specific combinations, significantly more combinations consist of families present in all three kingdoms than of families present in one or two kingdoms. Hence, we are led to conclude that recombination between common families, as compared to the invention of new families and recombination among these, has also been a major contribution to the evolution of kingdom-specific and species-specific functions in organisms in all three kingdoms. Finally, we compare the set of the domain combinations in the genomes to those in the RCSB Protein Data Bank, and discuss the implications for structural genomics.