Global versus Chinese perspectives on the phylogeny of the N-fixing clade

There has been increasing interest in integrating a regional tree of life with community assembly rules in the ecological research. This raises questions regarding the impacts of taxon sampling strategies at the regional versus global scales on the topology. To address this concern, we constructed two trees for the nitrogen-fixing clade: (i) a genus-level global tree including 1023 genera; and (ii) a regional tree comprising 303 genera, with taxon sampling limited to China. We used the supermatrix approach and performed maximum likelihood analyses on combined matK, rbcL, and trnL-F plastid sequences. We found that the topology of the global and the regional tree of the N-fixing clade were generally congruent. However, whereas relationships among the four orders obtained with the global tree agreed with the accepted topology obtained in focused analyses with more genes, the regional topology obtained different relationships, albeit weakly supported. At a finer scale, the phylogenetic position of the family Myricaceae was found to be sensitive to sampling density. We expect that internal support throughout the phylogeny could be improved with denser taxon sampling. The taxon sampling approach (global vs. regional) did not have a major impact on fine-level branching patterns of the N-fixing clade. Thus, a well-resolved phylogeny with relatively dense taxon sampling strategy at the regional scale appears, in this case, to be a good representation of the overall phylogenetic pattern and could be used in ecological research. Otherwise, the regional tree should be adjusted according to the correspondingly reliable global tree.     

真核生物系统发育和多样性概观

Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.     

Systematic revision and molecular phylogeny of the land snail genus Fruticocampylaea (Gastropoda: Hygromiidae) from the Caucasus region

This paper presents a systematic revision and a molecular phylogenetic analysis of the Caucasian land snail genus Fruticocampylaea. The genus is newly delimited based on the reduction of the cavities adjoining the seminal duct in the penial papilla. Shell and genitalia of all five species (F. narzanensis, F. kobensis, F. tushetica sp. nov., F. christophori, F. daghestana) are described and figures provided. All synonyms and all locality records are listed. Maximum likelihood and Bayesian analyses of mitochondrial and nuclear DNA sequences (fragments of cox1, 16S rDNA, ITS2 and 28S rDNA) confirm the monophyly of Fruticocampylaea. The reduction of the dart apparatus and the conical plug, via which the dart apparatus inserts into the vagina, as well as the molecular phylogenetic analyses, suggests a sister group relationship between Fruticocampylaea and Circassina (without Abchasohela). Furthermore, the molecular phylogenetic analyses indicate that the Fruticocampylaea species originated in a rapid radiation. The uplift of the Greater Caucasus in the Late Miocene or Pliocene or climatic changes at the end of the Pliocene or in the early Pleistocene may have caused the radiation of Fruticocampylaea. Low intraspecific variability can be explained by population bottlenecks during Pleistocene glacial periods followed by postglacial population increase.

http://zoobank.org/urn:lsid:zoobank.org:pub:AB15158D-21A3-4945-8D49-F7DE8E406E2B     

New insights into and limitations of the molecular phylogeny in the taxon-rich land snail genus Montenegrina (Mollusca: Gastropoda: Clausiliidae)

Rock-dwelling gastropods are usually patchily distributed in limestone habitats, presumably have low active and passive dispersal ability and often represent narrow-ranged endemic taxa. Their current taxonomy is predominantly shell morphology based, and it remains unknown whether the morphologically differentiated and geographically separated populations represent phylogenetic clades. In this study, we analysed the hyperdiverse, terrestrial door snail genus Montenegrina. Based on the current taxonomy defined by shell morphology, it contains 29 species and 106 subspecies distributed in the Balkan region. The constructed phylogenetic tree using three mitochondrial markers was used to test whether it agrees with the current taxonomy. In this comprehensive tree, about half of the species and subspecies are monophyletic. Some of the paraphylies could be reasonably resolved by taxonomic changes; that is, some subspecies should be reassigned or raised to species level. Other incongruencies probably arose due to introgression even between distant clades. The histone genes turned out to be unsuitable for elucidating the phylogeny of Montenegrina. In the species-delimitation tests, considerably more molecular operational taxonomic units were delimited than the number of presently described species. The present data indicate that (a) shell morphology-based taxonomy and taxon recognition can be problematic in such a large and morphologically highly variable genus; (b) the potential error due to incomplete sampling presents a problem in a genus as variable as Montenegrina; (c) multi-locus analyses should be conducted to arrive at a better basis for species delimitation; and (d) integrative approaches including genetic as well as morphological/anatomical data from a comprehensive geographic sample are necessary.     

A comprehensive generic-level phylogeny of the sunflower family: Implications for the systematics of Chinese Asteraceae

The sunflower family (Asteraceae) is the largest and the most diverse flowering plant family, comprising 24 000–30 000 species and 1600–1700 genera. In China, Asteraceae are also the largest family, with approximately 2336 indigenous species in 248 genera. In the past two decades, molecular phylogenetic analyses has contributed greatly to our understanding of the systematics of Asteraceae. Nevertheless, the large-scale analyses and knowledge about the relationships of Chinese Asteraceae at the generic level as a whole are far from complete due to difficulties in sampling. In this study, we presented a three-marker (rbcL, ndhF, and matK) phylogeny of Asteraceae, including 506 genera (i.e., approximately one-third of Asteraceae genera). The study sampled 200 Chinese genera (i.e., approximately 80% of Chinese Asteraceae genera). The backbones of the new phylogeny were largely congruent with earlier studies, with 13 subfamilies and 45 tribes recognized. Chinese Asteraceae were distributed in 7 subfamilies (Mutisioideae, Wunderlichioideae, Carduoideae, Pertyoideae, Gymnarrhenoideae, Cichorioideae, and Asteroideae) and 22 tribes (Mutiseae, Hyalideae, Cardueae, Pertyeae, Gymnarrheneae, Vernonieae, Cichorieae, Doroniceae, Senecioneae, Astereae, Anthemideae, Gnaphalieae, Calenduleae, Inuleae, Athroismeae, Helenieae, Coreopsideae, Neurolaeneae, Tageteae, Millieae, Eupatorieae, and Heliantheae). Chinese Asteraceae lacked 6 basal subfamilies and 23 tribes. Several previously ambiguous relationships were clarified. Our analyses also resolved some unplaced genera within Chinese Asteraceae. Finally, our phylogenetic tree was used to revise the classification for all genera of Chinese Asteraceae. In total, 255 genera, 22 tribes, and 7 subfamilies in China are recognized.     

The phylogeny of the world's bulbuls (Pycnonotidae) inferred using a supermatrix approach

The bulbuls comprise an ecologically important group of frugivorous, seed‐dispersing birds found in Asia and Africa. Although several studies have examined the phylogenetic relationships of subsets of bulbul species, a comprehensive phylogeny of the family Pycnonotidae has hitherto been lacking. We used publicly available sequences generated from previous phylogenetic studies, augmented by new sequences from several unstudied taxa, to create a supermatrix from which to infer the phylogeny of the family. In all, we compared 121 of the 130 bulbul species. Our tree supports the monophyly of the family and comprises an exclusively African and a predominantly Asian clade. Several genera were found not to be monophyletic and we suggest taxonomic changes to provide a more accurate classification based on phylogeny.     

A mitochondrial phylogeny uncovers taxonomic ambiguity and complex phylogeographic patterns in the eastern Australian land snail Austrochloritis (Stylommatophora,Camaenidae)

We analyzed the mitochondrial differentiation of the southeast Australian land snail genus Austrochloritis Pilsbry, 1890, family Camaenidae, which encompasses 34 currently accepted species. These species were exclusively described and delimited based on comparative shell morphology, while their reproductive anatomy has remained undocumented. Phylogenetic analyses of partial fragments of the cytochrome c oxidase subunit 1 gene (COI) and 16S rRNA (16S) genes revealed widespread incongruence between the shell-based species taxonomy and the branching patterns of phylogenetic trees indicating the urgent need of more comprehensive systematic review. The phylogeographic patterns in Austrochloritis are consistent with well-documented biogeographic barriers in southeastern Australia, namely the Hunter River Valley and the McPherson Range, which demarcate concomitant biogeographic breaks in the biota of the region. These breaks are thought to result from past expansions and contractions of mesic forests caused by the climatic oscillations during the mid to late Neogene. Our study also provides evidence for potentially widespread sympatry of Austrochloritis species in the northern part of their distribution, which is in conflict with contemporary paradigms that presume predominantly allopatric distributions in congeneric land snails in eastern Australia.     

Hidden in the Arabian Mountains: Multilocus phylogeny reveals cryptic diversity in the endemic Omanosaura lizards

An increase in studies in the Hajar Mountains from the southeastern Arabian Peninsula has revealed a high richness of endemic evolutionary lineages with many cryptic taxa. Omanosaura is the only lacertid lizard genus endemic to the Hajar Mountains, with two species O. cyanura and O. jayakari distributed throughout this mountain range. The phylogenetic relationships and genetic diversity between and within these species have been poorly studied. In this study, we collected mitochondrial (12S, cytb, and nd4) and nuclear (cmos and mc1r) sequences for 25 specimens of Omanosaura, including 15 individuals of O. jayakari and 10 of O. cyanura. We performed phylogenetic analyses based on network reconstruction, maximum likelihood and Bayesian inference to estimate the relationships and intraspecific genetic diversity of these species. We estimated the time of divergence between the two species in the Miocene, around 8.5 million years ago. Omanosaura jayakari shows little genetic diversity, while O. cyanura presents two differentiated lineages. These are reciprocally monophyletic at mitochondrial and nuclear genes and present a high genetic distance between them. These two lineages are associated with the geographic features of the Hajar Mountains, with one lineage distributed in the northernmost part of the Hajar Mountains and the other in the rest of the western Hajars, the Jebel Akhdar, and the eastern Hajars. This geographic relationship has been recovered previously in other reptile taxa and is generally associated with high levels of local genetic diversity. Our results suggest the existence of cryptic diversity within O. cyanura and support a general biogeographic pattern of high diversity and endemism in the northern Hajar Mountains that certainly deserves additional research in the future.     

Molecular phylogeny, taxonomy and evolution of the land snail genus Iberus (Pulmonata: Helicidae)

Partial DNA sequences of two mitochondrial genes [cytochrome oxidase subunit I (COI) and 16S rRNA] from 59 specimens of Iberus were used to test the validity of the described morphospecies of this genus, and examine genetic divergences within and between main phylogenetic groups. Both gene fragments showed phylogenetic concordance. The COI gene was found to be faster evolving than the 16S gene and was fully protein-coding with no insertions or deletions. 16S rRNA was more informative than COI for resolving basal nodes. Both individual and combined analyses of the two gene fragments revealed five main phylogroups. These five groups are genetically unique lineages that are allopatrically distributed and considered to have full species status. Further subdivisions were also considered. Shell morphology was suitable for delimiting species boundaries, but several incongruences between morphology and mtDNA phylogeny were observed. These incongruences were considered consequence of hybridization between Iberus cobosi and Iberus marmoratus , and the result of shell shape polymorphism in Iberus rositai . According to spatial patterns of sequence divergence, life habits and shell morphology may be concluded that the keeled-flat shelled snails independently originated several times within Iberus and they could represent cases of similar shell adaptation to a karstic arid environment.     

The evolution of extreme shell shape variation in the land snail Ainohelix editha: a phylogeny and hybrid zone analysis

Ainohelix editha from Hokkaido, Japan, exhibit great geographical variation in their shell morphology. In particular, A. editha in two quite separate locations, Shimamaki and Samani, are striking because they are extremely flat and have a sharp keel, whereas at adjacent sites the shells are globular or depressed-globular. We used mitochondrial 16S rRNA and nuclear ITS-2 sequences to infer a phylogeny among 47 snails from 29 locations. Snails from the two keeled-flat populations clustered separately in the phylogeny, suggesting that this unusual shell form could have evolved independently. A morphological analysis of shells collected along a transect between keeled-flat and globular snail sites showed a cline for shell shape and the angle of the keel. Two different mtDNA lineages were found across the transect, with a cline for an ITS-2 single nucleotide polymorphism. Together, the results may suggest a lack of reproductive isolation between keeled-flat and globular snails, with possible introgression by hybridization.     

Molecular phylogeny of the land snail genus Alopia (Gastropoda: Clausiliidae) reveals multiple inversions of chirality

Whereas the vast majority of gastropods possess dextral shell and body organization, members of the Clausiliidae family are almost exclusively sinistral. Within this group a unique feature of the alpine genus Alopia is the comparable representation of sinistral and dextral taxa, and the existence of enantiomorph taxon pairs that appear to differ only in their chirality. We carried out a molecular phylogenetic study, using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences, in order to find out whether chiral inversions are more frequent in this genus than in other genera of land snails. Our results revealed multiple independent inversions in the evolutionary history of Alopia and a close genetic relationship between members of the enantiomorph pairs. The inferred COI phylogeny also provided valuable clues for the taxonomic division and zoogeographical evaluation of Alopia species. The high number of inverse forms indicates unstable fixation of the coiling direction. This deficiency and the availability of enantiomorph pairs may make Alopia species attractive experimental models for genetic studies aimed at elucidating the molecular basis of chiral stability. © 2013 The Linnean Society of London     

Patterns of morphological and molecular polymorphism in the land snail Cepaea nemoralis

In the land snail Cepaea nemoralis , allele frequencies at loci controlling shell polymorphisms often show large areas of remarkable constancy which are separated by steep clines from neighbouring areas with strikingly different allele frequencies. It has recently been claimed that these 'area effects' exemplify a general tendency for population differentiation without geographic isolation in a variety of organisms of relatively low mobility. As such they could represent an early phase in the process of speciation. If this is true, population differentiation of shell polymorphisms in Cepaea would be expected to be accompanied by parallel differentiation at other gene loci, such as those detected by gel electrophoresis.
We have studied populations of C. nemoralis in North Wales and in the Valle de Aran of the Pyrenees. Levels of molecular heterogeneity are comparable to those found in related animals which show much less visible polymorphism. In spite of some statistical problems inherent in the analysis ol overlapping geographic patterns, there is no clear association between the patterns of geographic variation at the visible and molecular levels. Claims that genetic differentiation in the visible polymorphisms between C. nemoralis populations are a special case of the formation of geographic races are therefore probably not justified.     

分子生物学技术在双翅目实蝇科昆虫系统发育研究中的应用

分子生物学技术如同工酶电泳、RFLP、RAPD、核酸序列分析、微卫星DNA和探针杂交等,在实蝇科昆虫系统发育研究中具有重要作用。利用这些技术对实蝇种群进行系统发育研究,揭示其亲缘及进化关系,从生命本质上寻找实蝇种群间的内在联系。文章综述上述几种分子生物学技术在实蝇科昆虫核酸结构、种内和种间的亲缘及进化关系等方面的研究进展,分析在应用中存在的问题,展望这些分子生物学技术在实蝇科昆虫系统发育中的应用前景。     

Limitations of Phylogenomic Data Can Drive Inferred Speciation Rate Shifts

Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic data sets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.     

The evolution of reproductive strategies in dasyurid marsupials: implications of molecular phylogeny

Dasyurid marsupials show a remarkable diversity of reproductive patterns ranging from aseasonal polyoestry to restricted annual breeding in which males synchronously die after a brief mating season. Previous studies have categorized dasyurid reproduction into six strategies, defined on the basis of five life-history characters. We provide an up-to-date summary of reproductive traits in dasyurid species and examine the evolution of these characters on a phylogeny for the family recently obtained from DNA sequence data. Our results suggest that reproductive evolution in modern dasyurids is characterized by a basal separation of subfamily lineages employing Strategy II (monoestrous females, restricted breeding season, 11 months to maturity; Dasyurinae) and Strategy V (polyoestrous females, extended breeding season, 8–11 months to maturity; Sminthopsinae). Strategies I (male die-off) and III (facultative polyoestry) appear to have arisen several times from Strategy II or V ancestors, and Strategy IV appears to have arisen within Sminthopsis from a Strategy V ancestor. Strategy VI (aseasonal breeding) has arisen independently in each of the four major dasyurid lineages (tribes), and is highly (but not perfectly) correlated with New Guinean endemism. This scenario is not strongly affected if reproductive characters are optimized on an alternative phylogeny more consistent with morphology-based opinions on species relationships. When evaluated in light of current habitat associations and geographic distributions, the reproductive data suggest that the Miocene diversification of modern dasyurids may have been correlated with the invasion of dry forest or woodland habitats.     

A comparison of DNA‐based methods for delimiting species in a Cretan land snail radiation reveals shortcomings of exclusively molecular taxonomy

We compared the results of different approaches for delimiting species based on single‐locus DNA sequences with those of methods using binary multilocus data. As case study, we examined the radiation of the land snail genus Xerocrassa on Crete. Many of the methods based on mitochondrial sequences resulted in heavy under‐ or overestimations of the species number. The methods using AFLP data produced classifications with an on average higher concordance with the morphological classification than the methods based on mitochondrial sequences. However, the percentage of correct species classifications is low even with binary multilocus data. Gaussian clustering produced the classifications with the highest concordance with the morphological classification of all approaches applied in this study, both with single‐locus sequences and with binary multilocus data. There are two general problems that hamper species delimitation, namely rarity and the hierarchical structure of biodiversity. Methods for species delimitation using genetic data search for clusters of individuals, but do not implement criteria that are sufficient to distinguish clusters representing species from other clusters. The success of morphological species delimitation results from the potential to focus on characters that are directly involved in the speciation process, whereas molecular studies usually rely on markers that are not directly involved in speciation. © The Willi Hennig Society 2011.