What Cytogenetic Studies May Tell Us about Species Diversity and Speciation of Lemurs

I discuss the contribution of cytogenetic data to studies of systematics, phylogeny and speciation of several nocturnal lemurs. I examine specific distribution in Avahi and Lepilemur and propose a chromosomal mechanism involved in speciation of these two genera. I compare the contribution of cytogenetics to that of other techniques such as mitochondrial DNA sequencing. In rare situations wherein the respective systematic conclusions are contradictory, cytogenetic evidence clearly appears to be better supported.     

Phylogeographic history of the genus Tropheus,a lineage of rock-dwelling cichlid fishes endemic to Lake Tanganyika

Lake Tanganyika contains the oldest and most complex flock of cichlid fishes counting about 200 endemic species. It is comprised of 16 ecologically, morphologically and genetically highly distinct tribes. Many species are further subdivided into arrays of geographic morphs, each colonizing particular sections of the shore line. The genus Tropheus represents the most spectacular and best studied example for this phenomenon, counting more than 100 distinctly colored populations and sister species, some living in sympatry. Their present distribution and genetic structure was shaped by a series of lake level fluctuations which caused cycles of isolation and secondary admixis. The present study extends previous work on the phylogeography of Tropheus and aims at the fine-scale reconstruction of the origin and spread of lineages in the central and southern basin of the lake. The previously defined mtDNA lineages were evaluated on the basis of statistical parsimony networks. Haplotype networks were created for each lineage and related to their centers of diversity in terms of present distribution. A linearized tree analysis and a mismatch distribution analysis corroborate two of the three radiation waves suggested in earlier works, but the new data suggest a different primary colonization scenario for the southern basin.     

Phylogenetic Relationships between Asplenium bourgaei (Boiss.) Milde and A. jahandiezii (Litard.) Rouy Inferred from Morphological Characters and rbcL Sequences

Abstract: Micromorphological analysis reveals that A. jahandiezii, which occurs as a local endemic taxon in the Grand Canyon du Verdon in southern France, shows substantial differences to A. bourgaei, from the eastern Mediterranean region, in the surface structure of perispores, sporangial indehiscence and the size of stomatal subsidiary cells. Nucleotide sequences and genetic distances (0.9 % nucleotide substitutions) of the rbc L gene support the view that both taxa are related but distinct sibling species. Both species form a monophyletic group together with Asplenium fontanum and A. majoricum.     

Taxonomic Revision of Mouse Lemurs (Microcebus) in the Western Portions of Madagascar

The genus Microcebus (mouse lemurs) are the smallest extant primates. Until recently, they were considered to comprise two different species: Microcebus murinus, confined largely to dry forests on the western portion of Madagascar, and M. rufus, occurring in humid forest formations of eastern Madagascar. Specimens and recent field observations document rufous individuals in the west. However, the current taxonomy is entangled due to a lack of comparative material to quantify intrapopulation and intraspecific morphological variation. On the basis of recently collected specimens of Microcebus from 12 localities in portions of western Madagascar, from Ankarana in the north to Beza Mahafaly in the south, we present a revision using external, cranial, and dental characters. We recognize seven species of Microcebus from western Madagascar. We name and describe 3 spp., resurrect a previously synonymized species, and amend diagnoses for Microcebus murinus (J. F. Miller, 1777), M. myoxinus Peters, 1852, and M. ravelobensis Zimmermann et al., 1998.     

Molecular Markers and Concepts of Plant Evolutionary Relationships: Progress,Promise, and Future Prospects

In just the past 20 years systematics has progressed from the sequencing of individual genes for a few taxa to routine sequencing of complete plastid and even nuclear genomes. Recent technological advances have made it possible to compile very large data sets, the analyses of which have in turn provided unprecedented insights into phylogeny and evolution. Indeed, this narrow window of a few decades will likely be viewed as a golden era in systematics. Relationships have been resolved at all taxonomic levels across all groups of photosynthetic life. In the angiosperms, problematic deep-level relationships have either been largely resolved, or will be resolved within the next several years. The same large data sets have also provided new insights into the many rapid radiations that have characterized angiosperm evolution. For example, all of the major lineages of angiosperms likely arose within a narrow window of just a few million years. At the population level, the ease of DNA sequencing has given new life to phylogeographic studies, and microsatellite analyses have become more commonplace, with a concomitant impact on conservation and population biology. With the wealth of sequence data soon to be available, we are on the cusp of assembling the first semi-comprehensive tree of life for many of the 15,000 genera of flowering plants and indeed for much of green life. Accompanying these opportunities are also enormous new computational/informatic challenges including the management and phylogenetic analysis of such large, sometimes fragmentary data sets, and visualization of trees with thousands of terminals.     

基于部分线粒体DNA序列的疣螈属亚属(有尾目,蝾螈科,疣螈属)系统发育关系

对疣螈属Yaotriton亚属5个已知物种23个个体的mtDNA序列数据(ND2、tRNATrp、tRNAAla、tRNAAsn、tRNACys和tRNA Tyr,1421bp),使用贝叶斯(BI)和最大似然(M P)方法重建了疣螈属Yaotriton的系统发育关系。结果表明:1)Yaotriton亚属的所有物种形成1个单元群;2)海南疣螈T.hainanensis是Yaotriton亚属的1有效物种,不是细痣疣螈T.asperrimus的同物异名;3)文县疣螈T.wenxianensis雷山种群应是细痣疣螈的地理种群,细痣疣螈绥阳种群应是文县疣螈的地理种群;4)6个文县疣螈地理种群和3个细痣疣螈地理种群分别形成单系群,文县疣螈是Yaotriton亚属的1有效物种。     

Molecular Views of Human Origins

Over the last half century, comparative genomics has increasingly contributed to the definition, resolution and interpretation of human evolution. Early comparisons demonstrated that African apes and humans were more closely related and diverged later than commonly thought. However, it was difficult to determine the branching between humans, chimpanzees and gorillas. By the 1990s, sufficient biomolecular data had accumulated to demonstrate that chimpanzees and humans shared a common ancestor after the divergence of the gorilla. Current reconstructions place the divergence of humans and chimpanzees at 6–8 million years. Comparative genomics from complete genome sequencing to chromosome painting provide a scenario for the origin of the human genome. Starting form the ancestral mammalian karyotype, we can determine the major steps over the last 90 million years leading to the formation of each human chromosome. Despite considerable technical problems, studies of ancient DNA now provide a direct genetic witness of human evolution and add a temporal dimension to reconstructions of our evolutionary history and phylogeny. Ancient DNA has shown that Neanderthals probably did not interbreed with anatomically modern humans and did not make a significant contribution to the gene pool of our species. Ancient DNA has also contributed to the studies of the colonization of the Americas and the Pacific Island, and the domestication of plants and animals. Understanding the genetic basis of the physical and behavioral traits that distinguish humans from other primates presents one of the great future challenges of science.     

New gammaroid family, genera and species from subterranean waters of Japan, and their phylogenetic relationships (Crustacea: Amphipoda)

Luciobliviidae, a new family in the superfamily Gammaroidea (Amphipoda: Crustacea), is described on the basis of species in the genus Lucioblivio gen. nov. from subterranean waters of Japan. Mesogammaridae Bousfield, 1977 is rediagnosed; Octopupilla gen. nov. from subterranean waters of Japan is described and Eoniphargus (Uéno, 1955) from subterranean waters of Japan and Korea is included. The members of Lucioblivio , Octopupilla and Eoniphargus share several characters, including reduced eyes, a setose body, reduced coxae, feeble appendages and pedunculate coxal gills. To elucidate the phylogeny of the three genera among others, a sequence analysis of the 28S rRNA gene was conducted for 14 species in six families, including the three genera, from the superfamilies, Gammaroidea, Crangonyctoidea and Hadzioidea. The tree from a neighbour-joining analysis and the strict consensus tree from a maximum-parsimony analysis indicate monophyly of Mesogammaridae. Luciobliviidae is embedded within a clade of taxa belonging to the superfamily Gammaroidea. These results and the occurrence of gammarid-type calceoli in species of the new family indicate that Luciobliviidae should be placed within the superfamily Gammaroidea. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 149 , 643–670.     

A new genus and species of octocoral with aragonite calcium-carbonate skeleton (Octocorallia,Helioporacea) from Okinawa,Japan

A new genus and species of octocoral with a calcium-carbonate skeleton, Nanipora kamurai sp. n., is described from a shallow coral reef in Okinawa, Japan. Contrary to most octocorals, the skeleton is composed of crystalline aragonite as in blue coral Heliopora. The results of molecular phylogenetic analyses of sequences of mtMutS, COI, and ITS1-5.8s-ITS2-28S region suggest Nanipora gen. n. specimens should be included in order Helioporacea. Based on morphological results compared with other Helioporacea including the genus Epiphaxum (family Lithotelestidae), we establish the new genus Nanipora within Lithotelestidae. This is the first time that a close molecular phylogenetic relationship between Heliopora and a related genus within Helioporacea has been revealed.     

Phylogeny of Ptychostomum （Bryaceae,Musci） inferred from sequences of nuclear ribosomal DNA internal transcribed spacer （ITS） and chloroplast rps4

The phylogeny of Ptychostomum was first spacer （ITS） region of the nuclear ribosomal （nr） DNA DNA rps4 sequences. Maximum parsimony, maximum undertaken based on analysis of the internal transcribed and by combining data from nrDNA ITS and chloroplast likelihood, and Bayesian analyses all support the conclusion that the reinstated genus Ptychostomum is not monophyletic. Ptychostomum funkii （Schwagr.） J. R. Spence （≡ Bryum funkii Schwaigr.） is placed within a clade containing the type species of Bryum, B. argenteum Hedw. The remaining members of Ptychostomum investigated in the present study constitute another well-supported clade. The results are congruent with previous molecular analyses. On the basis of phylogenetic evidence, we agree with transferring B. amblyodon Mull. Hal. （≡ B. inclinatum （Brid.） Turton≡ Bryum archangelicum Bruch ＆ Schimp.）, Bryum lonchocaulon Mull. Hal., Bryum pallescens Schleich. ex Schwaigr., and Bryum pallens Sw. to Ptychostomum.     

Phylogenetic Relationships between some Members of the Subfamily Lamioideae (Family Labiatae) Inferred from Nucleotide Sequences of the rbcL Gene*

Total DNA was extracted from 25 species (8 genera) of the subfamily Lamioideae sensu Erdtman (family Labiatae). Using rbcL-specific primers, the rbcL gene was amplified by polymerase chain reaction (PCR) and 1420 bp were sequenced directly, or after cloning. RbcL sequences were evaluated with character-state (maximum parsimony; PAUP) and distance methods (neighbour-joining; MEGA). In agreement with classical systematics all taxa studied cluster outside the Nepetoideae. The following clades are apparent: I - Westringia/Prostanthera, II - Ajuga/Teucrium and III - Scutellaria, Stachys, Lamium and Marrubium. Lamium album, L. amplexicaule and L. garganicum appear as a sister clade to Marrubium. Both share a common ancestor with a second Lamium clade (including L. purpureum, L. maculatum and L. galeobdolon). The phylogenetic relationships are discussed with regard to the systematic classification of the subfamilies Lamioideae and Nepetoideae (sensu Erdtman).     

Polymorphism hides cryptic species in Oerstedia dorsalis (Nemertea, Hoplonemertea)

The marine hoplonemertean Oerstedia dorsalis is considered to be a highly polymorphic species with extensive geographic distribution. We show, based on mitochondrial cytochrome c oxidase subunit I, 16S and nuclear internal transcribed spacer sequences, that there are genetic subsets withing this species. Seventy-one specimens of various colours from different geographic localities (in Europe) were sequenced and analysed using statistical parsimony and Bayesian analysis. Both analyses supported nine major clades. We conclude that O. dorsalis hides different species with geographic resolution. These species, however, appear to be polymorphic as well, and we find no diagnostic features in pigmentation or external characters to separate species within this complex.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 556–567.     

基因组学时代的真菌分类学:机遇与挑战

真菌物种的形态特征有限,加之形态滞后和形态可塑性,仅靠外部形态、内部结构及生理生化指标,很难把握真菌的系统亲缘。应用DNA测序、基因组测序、比较基因组学及生物信息学等技术,研究人员可以快速识别真菌演化中出现的数量众多的单系支系,为建立各分类等级的新分类单元提供有力证据,为真菌分类学研究带来了新的希望和活力。自2000年以来,在真菌界至少发表了1新亚界、4新门、7新亚门、19新纲、9新亚纲、40余新目等高级分类单元。近3年来,我国发表了20余个真菌新属,其中绝大多数属的建立都有分子证据支持。可以预见,大量的新种、新属、新科乃至更高级分类单元将会在今后10年内持续发现和建立。这必将大大促进真菌分类学的发展,完善现有的真菌分类系统。我们应该顺势而上,利用我国丰富的真菌资源,为真菌分类学的发展做出应有贡献。与此同时,真菌分类学也面临着十分严峻的挑战。挑战主要来自3个方面,一是研究变得越来越综合,不但需要有相应的研究经费支持,而且要求从事该领域的研究人员技术更全面、知识更广博及知识更新速度更快捷;二是新物种描述进度偏慢,远远不能满足人们对物种认识和利用的日益增长的需要;三是研究人员亟需创新研究模式,以新技术、新思路、新机制来构建新的真菌分类学,加速新物种的发现和描述进度,最终为社会进步和科学发展服务。     

Systematics and biodiversity of Ophryotrocha (Annelida,Dorvilleidae) with descriptions of six new species from deep-sea whale-fall and wood-fall habitats in the north-east Pacific

Six new Ophryotrocha species are described from five whale-falls and two wood-falls off the southern Californian coast. Phylogenetic analyses based on the nuclear gene H3 and the mitochondrial genes COI and 16S using MrBayes and maximum likelihood analyses were performed on 40 dorvilleid taxa and one outgroup. Ophryotrocha batillus sp. nov. is morphologically identical to Ophryotrocha scutellus described from a shallow water whale-fall in the North Atlantic, although the two cryptic species differ genetically. Ophryotrocha langstrumpae sp. nov. is closely related in the molecular phylogenetic analyses to these two sibling species. Ophryotrocha flabella sp. nov. is similar to Ophryotrocha globopalpata, and although there are a few morphological differences, the genetic divergence is low between the two species. Ophryotrocha nauarchus sp. nov. is sexually dimorphic, with males having appendages on the first chaetiger. Ophryotrocha magnadentata sp. nov. and Ophryotrocha longicollaris sp. nov. are sister species in our molecular analyses, and together with O. nauarchus sp. nov. and O. flabella sp. nov. they fall within a clade that includes O. globopalpata and Exallopus jumarsi described from hydrothermal vents in the Pacific Ocean and Ophryotrocha longidentata from the shallow North Atlantic. Our results highlight the remarkable unknown diversity of deep-water habitats and the role of chemosynthetic ecosystems in the evolution of deep-sea life.     

18S ribosomal RNA gene sequences of Cochliopodium (Himatismenida) and the phylogeny of Amoebozoa

Cochliopodium is a very distinctive genus of discoid amoebae covered by a dorsal tectum of carbohydrate microscales. Its phylogenetic position is unclear, since although sharing many features with naked "gymnamoebae", the tectum sets it apart. We sequenced 18S ribosomal RNA genes from three Cochliopodium species (minus, spiniferum and Cochliopodium sp., a new species resembling C. minutum). Phylogenetic analysis shows Cochliopodium as robustly holophyletic and within Amoebozoa, in full accord with morphological data. Cochliopodium is always one of the basal branches within Amoebozoa but its precise position is unstable. In Bayesian analysis it is sister to holophyletic Glycostylida, but distance trees mostly place it between Dermamoeba and a possibly artifactual long-branch cluster including Thecamoeba. These positions are poorly supported and basal amoebozoan branching ill-resolved, making it unclear whether Discosea (Glycostylida, Himatismenida, Dermamoebida) is holophyletic; however, Thecamoeba seems not specifically related to Dermamoeba. We also sequenced the small-subunit rRNA gene of Vannella persistens, which constantly grouped with other Vannella species, and two Hartmannella strains. Our trees suggest that Vexilliferidae, Variosea and Hartmannella are polyphyletic, confirming the existence of two very distinct Hartmannella clades: that comprising H. cantabrigiensis and another divergent species is sister to Glaeseria, whilst Hartmannella vermiformis branches more deeply.     

Phylogeny and taxonomy of Afrocayratia,a new genus of Vitaceae from continental Africa and Madagascar

The genus Cayratia Juss. in the traditional sense (i.e., Cayratia s.l.) of the grape family has been shown to be non‐monophyletic. Previous studies supported the splitting of Cayratia s.l. into three genera, that is, Cayratia s.s., Causonis Raf., and a new genus representing the African Cayratia clade. However, the morphology of the African Cayratia clade has not been studied carefully and its phylogenetic position within Vitaceae remains unclear. Our study integrates molecular, distributional, and morphological data and supports the recognition of the new genus Afrocayratia from continental Africa and Madagascar. Phylogenetic analyses strongly support the monophyly of Afrocayratia and resolve it as a sister of Cayratia s.s. based on the chloroplast data, but it is placed sister to Cyphostemma based on the internal transcribed spacer dataset. Molecular dating suggests that Afrocayratia split with Cayratia s.s. during the Paleocene, but that the extant species of Afrocayratia did not diversify until the early Miocene. Afrocayratia differs from its allied genera in having short stigmas and seeds with subcircular ventral infold cavities in cross‐section. Three clades are detected within Afrocayratia, with A. debilis (Baker) J.Wen & L.M.Lu as the first diverged lineage. The second diverged lineage includes A. delicatula (Willems) J.Wen & Z.D.Chen and A. gracilis (Guill. & Perr.) J.Wen & Z.D.Chen. The third diverged lineage includes A. imerinensis (Baker) J.Wen & L.M.Lu, A. longiflora (Desc.) J.Wen & Rabarijaona, and A. triternata (Baker) J.Wen & Rabarijaona from Madagascar, which form a monophyletic group that diverged from the second lineage in the middle Miocene. Combining the morphological and molecular evidence, we formally describe the new genus Afrocayratia, make seven new combinations, and provide a key to species of the genus.     

A review of Gammaridae (Crustacea: Amphipoda): the family extent,its evolutionary history,and taxonomic redefinition of genera

By molecular analysis of a high number of gammarids, including 29 out‐group genera, we could assure the monophyly of Gammaridae. To avoid the paraphyly of the family, we propose the omission of Pontogammaridae, Typhlogammaridae, and all Baikalian families. Similarly, the genera Fontogammarus, Sinogammarus, Lagunogammarus, Pephredo, Neogammarus, and Laurogammarus may be cancelled. But, tens of Baikal genera, nested within Gammarus, are so diverse that they must be retained, although rendering Gammarus paraphyletic. Besides we propose the polyphyletic Echinogammarus–Chaetogammarus group to be divided into monophyletic genera Echinogammarus s. str., Homoeogammarus, Parhomoeogammarus, Marinogammarus, R elictogammarus gen. nov. , Chaetogammarus, and T richogammarus gen. nov. These solutions made it possible to complete the first analysis of the family evolution in light of its phylogeny. Perimarine clades are mainly basally split clades, whereas in some ancient lakes extremely rich endemic faunas had developed polyphyletically. The troglobiotic Typhlogammarus group from Dinarides and Caucasus formed a monophylum, whereas the troglobiotic assemblage of Gammarus species is highly polyphyletic. Reduction of the uropod III endopodite, which classically distinguishes between the genera Gammarus and Echinogammarus, appeared to be highly polyphyletic. Protective dorsal pleonal projections occur scattered across the family and beyond, whereas lateral projections were limited to species of ancient lakes, so both structures were polyphyletic. The evolutionary history of Gammaridae was investigated with ten different calibration schemes, which produced incompatible results; however, the most probable scenario is a late rise of the family, which can only explain the absence of Gammaridae species around the Indo‐Pacific. © 2015 The Linnean Society of London     

Karyological and molecular characterisation of subgenus Vicia (Fabaceae)

In the present report, we have analysed the subgenus Vicia by karyological and molecular approaches with the aim to clarify the relationships among Vicia species included in this subgenus by previously evidenced morphological investigations. Multivariate analysis using several karyomorphological parameters in addition to symmetry indices has allowed the construction of a dendrogram of linkage distances very useful to compare and to include in a phylogenetic tree obtained by internal transcribed spacer (ITS) rDNA sequences. Moreover, a separate analysis was performed combining our molecular data on ITS sequences with those reported in the literature for the section Vicilla. Our analyses partly confirm the monophyletic status of the various sections in which the subgenus Vicia has been divided, however questioning, in some cases, the real need to maintain all the nine sections so far accepted and the placement of some individual species in the two subgenera Vicia and Vicilla.     

Phylogeny and life-history evolution in Carabus (subtribe Carabina: Coleoptera, Carabidae) based on sequences of two nuclear genes

We reconstructed the phylogeny of the holarctic carabid subtribe Carabina (= Carabus s . l. ; Coleoptera, family Carabidae, supertribe Carabitae, tribe Carabini) using sequence data from two nuclear DNA loci: wingless ( Wg ) and phosphoenolpyruvate carboxykinase ( PepCK ). The analysis of the combined data resulted in a well-resolved tree, although Wg and PepCK had partially conflicting phylogenetic signals. The tree topology did not support the reciprocal monophyly of some previously proposed major divisions, whereas all but one of eight other previously proposed subdivisions were recovered as monophyletic clades; the exception was paraphyletic. When two key life-history traits, seasonal life cycle and larval diet, were mapped onto the combined tree, spring breeding (with no larval overwintering) and insectivorous were ancestral traits. Malacophagy has apparently evolved at least twice: once in a small basal group (ten species) and again in a large derived group ( c . 340 species) that accounts for 42% of the species of Carabina. A third type of larva, earthworm feeders, appeared in two related, derived clades and represented moderate species diversity (12%). From the ancestral spring-breeder type with no larval overwintering, autumn-breeder types with larval overwintering apparently evolved repeatedly in insectivorous and malacophagous species, but not in earthworm feeders. Therefore, the extant diversity of the Carabina depends on the high rate of differentiation in the most derived group of malacophagous species.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 81 , 135–149.