Phylogenetic relationships among Bactrocera species (Diptera: Tephritidae) inferred from mitochondrial DNA sequences

Several members of the dipteran family Tephritdae are serious pests because females lay eggs in ripening fruit. The genus Bactrocera is one of the largest within the family with over 500 described species arranged in 28 subgenera. The phylogenetic relationships among the various species and subgenera, and the monophyly of specific groups have not been examined using a rigorous phylogenetic analysis. Therefore, phylogenetic relationships among 24 Bactrocera species belonging to 9 subgenera were inferred from DNA sequence of portions of the mitochondrial 16S rRNA, cytochrome oxidase II, tRNA(Lys), and tRNA(Asp) genes. Two morphological characters that traditionally have been used to define the four groups within the subgenus Bactrocera were evaluated in a phylogenetic context by mapping the character states onto the parsimony tree. In addition, the evolutionary trend in male-lure response was evaluated in a phylogenetic context. Maximum parsimony analyses suggested the following relationships: (1) the genus Bactrocera is monophyletic, (2) the subgenus B. (Zeugodacus) is paraphyletic, (3) the subgenus B. (Daculus) is a sister group to subgenus B. (Bactrocera), and (4) the subgenus B. (Bactrocera) is monophyletic. The mapping analyses suggested that the morphological characters exhibit a simple evolutionary transition from one character state to another. Male-lure response was identified as being a labile behavior that has been lost on multiple occasions. Cue-lure response was plesiomorphic to methyl-eugenol response, and the latter has evolved independently within the Bactrocera and Zeugodacus groups of subgenera. The implications of our results for devising a coherent, consolidated classification for Bactrocera is discussed.     

小叶、中间和柠条三种锦鸡儿的分布式样及其生态适应

确定了小叶锦鸡儿、中间锦鸡儿和柠条锦鸡儿3种植物的分布式样:小叶锦鸡儿为蒙古高原东部-F松辽平原西部-华北山地分布种,中间锦鸡儿为东戈壁-鄂尔多斯高原-黄土高原北部分布种,柠条锦鸡儿为南阿拉善-西鄂尔多斯分布种。小叶锦鸡儿适应分布于蒙古高原典型草原带和森林草原带以及华北山地落叶阔叶林带,在草原带高平原上可形成灌丛化草原的景观,在草原带的沙地上可形成以小叶锦鸡儿为建群种的沙地灌丛植被;中间锦鸡儿适应分布于蒙古高原的荒漠化草原及草原化荒漠带、鄂尔多斯高原的典型草原和荒漠化草原带的沙地及梁地上、黄土高原北部的黄土丘坡上,常形成以中间锦鸡儿为建群种的沙地灌丛植被;柠条锦鸡儿则适应分布于草原化荒漠和典型荒漠带的固定和半固定沙地上。近缘的3种锦鸡儿的地带性分布从东至西或从北向南形成明显的有规律的地理替代分布格局。     

Molecular systematics of bats of the genus Myotis (Vespertilionidae) suggests deterministic ecomorphological convergences.

Based on extensive phenetic analyses, bats of the genus Myotis have been classically subdivided into four major subgenera each of which comprise many species with similar morphological and ecological adaptations. Each subgenus thus corresponds to a distinct "ecomorph" encompassing bat species exploiting their environment in a similar fashion. As three of these subgenera are cosmopolitan, regional species assemblages of Myotis usually include sympatric representatives of each ecomorph. If species within these ecomorphs are monophyletic, such assemblages would suggest extensive secondary dispersal across geographic areas. Conversely, these ecomorphological adaptations may have evolved independently through deterministic processes, such as adaptive radiation. In this case, phylogenetic reconstructions are not expected to sort species of the same ecomorph into monophyletic clades. To test these predictions, we reconstructed the phylogenetic history of 13 American, 11 Palaearctic, and 6 other Myotis species, using sequence data obtained from nearly 2 kb of mitochondrial genes (cytochrome b and nd1). Separate or combined analyses of these sequences clearly demonstrate the existence of several pairs of morphologically very similar species (i.e., sibling species) which are phylogenetically not closely related. None of the three tested subgenera constitute monophyletic units. For instance, Nearctic and Neotropical species currently classified into the three subgenera were clustered in a single, well-supported monophyletic clade. These species thus evolved independently of their ecological equivalents from the Palaearctic region. Independent adaptive radiations among species of the genus Myotis therefore produced strikingly similar evolutionary solutions in different parts of the world. Furthermore, all phylogenetic reconstructions based on mtDNA strongly supported the existence of an unsuspected monophyletic clade which included all assayed New World species plus M. brandtii (from the Palaearctic Region). This "American" clade thus radiated into a morphologically diverse species assemblage which evolved after the first Myotis species colonized the Americas. Molecular reconstructions support paleontological evidence that species of the genus Myotis had a burst of diversification during the late Miocene-early Pliocene epoch.     

The classification of genus Anopheles (Diptera: Culicidae): a working hypothesis of phylogenetic relationships

The internal classification of genus Anopheles is updated to reflect taxonomic actions published since the classification was last reviewed in 1994. Both formal and informal taxa are included. The classification is intended to aid researchers and students who are interested in analysing species relationships, making group comparisons and testing phylogenetic hypotheses. The genus includes 444 formally named and 40 provisionally designated extant species divided between six subgenera: Anopheles, Cellia, Kerteszia, Lophopodomyia, Nyssorhynchus and Stethomyia. Subgenera Anopheles, Cellia and Nyssorhynchus are subdivided hierarchically into nested informal groups of morphologically similar species that are believed to represent monophyletic lineages based on morphological similarity. Changes to the classification include additional species, eliminated species and changes to the hierarchical organization and composition of supraspecific groups, some as a result of molecular studies.     

Phylogeny of the genus Peperomia (Piperaceae) inferred from the trnK/matK region (cpDNA)

The genus Peperomia is one of the largest genera of basal angiosperms, comprising about 1500-1700 pantropically distributed species. The currently accepted infrageneric classification divides Peperomia into nine subgenera and seven sections. This classification is based on some 200 species, primarily using fruit morphology. The monophyly of these infrageneric taxa has never been tested and molecular phylogenetic studies of a representative sampling within Peperomia do not exist. This paper provides the first molecular phylogeny for the genus Peperomia. Monophyletic clades within Peperomia are identified and previously used morphological characters are critically reviewed. We show that the importance of some morphological characters has been overestimated and that some of these characters presumably have evolved several times independently. Only one previously described subgenus has been confirmed to be monophyletic.     

Phylogeny of Drosophila and related genera: conflict between molecular and anatomical analyses

Drosophila species are extensively used in biological research; yet, important phylogenetic relationships within the genus and with related genera remain unresolved. The combined data for three genes (Adh, Sod, and Gpdh) statistically resolves outstanding issues. We define the genus Drosophila inclusively so as to include Scaptomyza and Zaprionus (considered distinct genera in the taxonomy of Wheeler, 1981) but excluding Scaptodrosophila. The genus Drosophila so defined is monophyletic. The subgenus Sophophora (including the melanogaster, obscura, and willistoni groups) is monophyletic and the sister clade to all other Drosophila subgenera. The Hawaiian Drosophila (including Scaptomyza) is a monophyletic group, but the subgenus Drosophila is not monophyletic, because the immigrans group is more closely related to the subgenus Hirtodrosophila than to other species of the subgenus Drosophila, such as the virilis and repleta groups.     

Phylogeny of the genus Aleochara inferred from mitochondrial cytochrome oxidase sequences (Coleoptera: Staphylinidae)

The phylogeny of the genus Aleochara was previously poorly understood due to difficulties with phylogenetic reconstruction by morphological characters. We present here a phylogeny based on the sequences of a 2022-bp fragment of the COI/II genes; 50 Aleochara and 10 outgroup species were included in the analysis. We used parsimony, minimum-evolution, and maximum-likelihood analyses to infer the phylogeny of the group. Our data do not support the commonly assumed sister group relationship between Aleocharini and Hoplandriini. Aleochara is resolved as a monophylum, although A. clavicornis might not belong to the genus. Within Aleochara, there are two large monophyletic clades. Many of the existing subgenera are shown to be para- or polyphyletic; others are likely to be monophyletic. Tinotus morion, previously assigned to the Hoplandriini, is strongly supported as belonging to Aleochara. According to our data, the mesosternal carina that has been used as an important character for classification has arisen and been reduced independently in several clades within Aleochara.     

Phylogenetics and evolution of the aphid genus Uroleucon based on mitochondrial and nuclear DNA sequences

The genus Uroleucon, and the related genus Macrosiphoniella, represent a large Tertiary radiation of aphids, with a total of about 300 species distributed throughout the world, primarily on host plant species in the family Asteraceae. A molecular phylogenetic study was conducted to identify major clades within Uroleucon and to address the cladistic validity of current subgeneric categories, the evolution of host plant associations, the age of origin, and intercontinental movements in this genus. The seventeen study species included members of the three major subgenera of Uroleucon, species from Europe and North America, one member of Macrosiphoniella, and two outgroups. Data consisted of DNA sequences for three mitochondrial regions and the nuclear gene EF1alpha, for a total of 4287 sites. Nodes supported strongly in both parsimony and maximum likelihood analyses suggest that: (1) Nearctic Uromelan are a monophyletic group branching near the base of the genus and not related to European Uromelan, (2) the New World subgenus Lambersius is possibly monophyletic but is not a tightly related group and is not closely related to other North American species, and (3) Nearctic members of subgenus Uroleucon are a closely related monophyletic group not allied with Nearctic Uromelan or Lambersius. Instead they represent a separate colonization by an Old World ancestor, as they are nested within a strongly supported clade containing European members of both subgenera Uroleucon and Uromelan. Neither of these subgenera is monophyletic. Molecular clock calculations, based on calibrations of mitochondrial divergences from other insects, suggest that Uroleucon + Macrosiphoniella is a relatively recent radiation, probably no more than 5–10 million years old. Although largely confined to Asteraceae, this clade did not radiate in parallel with its host plants. Rather, lateral movement between lineages of Asteraceae must have occurred repeatedly.     

基于12S,16S和28S rRNA基因序列的中国小毛瓢虫属系统发育分析

【目的】小毛瓢虫属Scymnus Kugelann昆虫主要捕食蚜虫、蚧虫等害虫,是一类经济上重要的天敌昆虫。目前针对小毛瓢虫属的系统发育研究尚属空白,亚属之间的系统演化关系尚不明确,为了建立合理的分类系统,亟需对小毛瓢虫属的亲缘关系进行研究和探讨。【方法】以华南农业大学馆藏的小毛瓢虫属5亚属共44种为研究对象,采用PCR技术对12S, 16S和28S rRNA基因的部分序列进行扩增;运用MEGA 7.0分析了小毛瓢虫属内12S, 16S和28S rRNA基因的碱基组成,基于K2P模型计算了小毛瓢虫属44种的种间遗传距离;采用最大似然法(maximum-likelihood, ML)和贝叶斯推断法(Bayesian-inference, BI)构建该属的系统发育树。【结果】扩增获得小毛瓢虫属44种的12S rRNA基因序列平均长度为356 bp, 16S rRNA基因序列平均长度为351 bp, 28S rRNA基因序列平均长度为315 bp;序列分析表明,12S rRNA基因的A, T, G和C平均含量分别为38.8%, 43.5%, 11.9%和5.8%, 16S rRNA基因的A, T, G和C平均含量分别为37.6%, 40.3%, 14.4%和7.7%, 28S rRNA基因的A, T, G和C平均含量分别为26.7%, 18.3%, 31.4%和23.5%;基于联合序列分析的种间遗传距离为0.004～0.276,平均遗传距离为0.115。系统发育分析结果表明,小毛瓢虫属为单系起源,而小毛瓢虫亚属Scymnus(Scymnus) Kugelann、毛瓢虫亚属Scymnus(Neopullus) Sasaji、小瓢虫亚属Scymnus(Pullus) Mulsant和拟小瓢虫亚属Scymnus(Parapullus) Yang均为并系起源。【结论】基于12S, 16S和28S rRNA基因序列的小毛瓢虫属系统发育分析显示传统的形态学分类体系与基于分子数据分析的结果部分不一致,这表明应该对该属内各亚属的鉴别特征进行全面检视,筛选并确立各亚属的形态指标,同时也表明该属内的亚属分类单元需重新厘定。     

Molecular phylogeny of the genus Philodendron (Araceae): delimitation and infrageneric classification

The genus Philodendron (Araceae) is a large neotropical group whose classification remains unclear. Previous classifications are based on morphological characters, mainly from the inflorescence, flower and leaf shape. The classification by Krause, with few modifications, is still the most commonly used system. To examine phylogenetic relationships in the genus, two ribosomal DNA nuclear markers, internal transcribed spacer (ITS) and external transcribed spacer (ETS), and the chloroplast intron rpl 16, were sequenced and analysed for more than 80 species of Philodendron and its close relative Homalomena . According to the resulting phylogeny, the genus Homalomena may be paraphyletic to the genus Philodendron . The inclusion of the American Homalomena species within the genus Philodendron might resolve this taxonomic problem. All three subgenera of Philodendron were revealed as monophyletic. Below the subgeneric level, the groups obtained in our phylogeny globally correspond to sections recognized in previous classifications. Among the morphological characters used by previous taxonomists to build their classifications, and which we optimized onto one of the most parsimonious trees, most characters were found to be homoplasious. However, leaf shape, characteristics of the sterile zone on the spadix and venation patterns are useful for delimiting subgenera and sections within the genus.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 13–27.     

Molecular phylogeny of the palm genus Chamaedorea, based on the low-copy nuclear genes PRK and RPB2

Sequence data from the low-copy nuclear genes encoding phosphoribulokinase (PRK) and the second largest subunit of RNA polymerase II (RPB2) are used to generate the first phylogenetic analysis of Chamaedorea (Arecaceae: Arecoideae: Chamaedoreeae), the largest neotropical genus of palms. The prevailing current taxonomy of Chamaedorea recognizes approximately 100 species in eight subgenera, all delimited using floral characters, which provide a useful starting point to explore species-level systematics. Sequence data from 63 species, including representatives of all eight subgenera, were analyzed using maximum parsimony and Bayesian inference optimality criteria. Genus Chamaedorea is resolved as monophyletic with strong support in all separate and combined analyses. The less species-rich subgenera are convincingly monophyletic and can be diagnosed using morphological synapomorphies. In contrast, the two largest subgenera, Chamaedorea and Chamaedoropsis, which are supposedly distinguishable from each other by the degree of connation in the staminate petals, are both resolved as highly polyphyletic. Several well supported monophyletic groups resolved by these gene regions have never before been proposed within Chamaedorea and are challenging to delimit using morphological criteria. Although PRK proved more informative than RPB2, both regions have strong utility for interpreting species-level relationships among the palms, which are notoriously recalcitrant subjects for molecular phylogenetic studies. In addition, a paralog of the target copy of PRK identified during the analysis represents a potentially valuable source of phylogenetic information for future studies.     

Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae)

Ainscough, B.J., Breinholt, J.W., Robison, H.W. & Crandall, K.A. (2013). Molecular phylogenetics of the burrowing crayfish genus Fallicambarus (Decapoda: Cambaridae). —Zoologica Scripta, 42, 306–316. The crayfish genus Fallicambarus contains 19 species of primary burrowing freshwater crayfish divided into two distinct subgenera. We test current hypotheses of the phylogenetic relationships among species within the genus as well as the monophyly of the genus. Our study samples all 19 species for five gene regions (both nuclear and mitochondrial) to estimate a robust phylogenetic hypothesis for the genus. We show that the genus is not a monophyletic group. The subgenus Creaserinus does fall out as a monophyletic group, but distinct from the subgenus Fallicambarus. The subgenus Fallicambarus appears to be monophyletic with the exception of the species Procambarus (Tenuicambarus) tenuis, which falls in the midst of this subgenus suggesting that it might be better classified as a Fallicambarus species. We also show that the species Fallicambarus fodiens is a species complex with distinct evolutionary lineages that are regionalized to different geographic areas.     

Molecular Systematics of Bats of the Genus Myotis (Vespertilionidae) Suggests Deterministic Ecomorphological Convergences

Based on extensive phenetic analyses, bats of the genus Myotis have been classically subdivided into four major subgenera each of which comprise many species with similar morphological and ecological adaptations. Each subgenus thus corresponds to a distinct “ecomorph” encompassing bat species exploiting their environment in a similar fashion. As three of these subgenera are cosmopolitan, regional species assemblages of Myotis usually include sympatric representatives of each ecomorph. If species within these ecomorphs are monophyletic, such assemblages would suggest extensive secondary dispersal across geographic areas. Conversely, these ecomorphological adaptations may have evolved independently through deterministic processes, such as adaptive radiation. In this case, phylogenetic reconstructions are not expected to sort species of the same ecomorph into monophyletic clades. To test these predictions, we reconstructed the phylogenetic history of 13 American, 11 Palaearctic, and 6 other Myotis species, using sequence data obtained from nearly 2 kb of mitochondrial genes (cytochrome b and nd1). Separate or combined analyses of these sequences clearly demonstrate the existence of several pairs of morphologically very similar species (i.e., sibling species) which are phylogenetically not closely related. None of the three tested subgenera constitute monophyletic units. For instance, Nearctic and Neotropical species currently classified into the three subgenera were clustered in a single, well-supported monophyletic clade. These species thus evolved independently of their ecological equivalents from the Palaearctic region. Independent adaptive radiations among species of the genus Myotis therefore produced strikingly similar evolutionary solutions in different parts of the world. Furthermore, all phylogenetic reconstructions based on mtDNA strongly supported the existence of an unsuspected monophyletic clade which included all assayed New World species plus M. brandtii (from the Palaearctic Region). This “American” clade thus radiated into a morphologically diverse species assemblage which evolved after the first Myotis species colonized the Americas. Molecular reconstructions support paleontological evidence that species of the genus Myotis had a burst of diversification during the late Miocene–early Pliocene epoch.     

A cladistic phylogeny of the genus Littorina (Gastropoda): implications for evolution of reproductive strategies and for classification

Gross anatomical characters of all 18 species of Littorina are used to construct a phylogenetic hypothesis for the genus, by the method of cladistic analysis. The resulting cladogram suggests that of the four subgenera of Littorina, one (Littorina) is paraphyletic. It is uncertain whether the genus Mainwaringia should be included in Littorina. It is shown that the non-planktotrophic Littorina species in the northern Atlantic comprise a monophyletic group, with the sister-species L. kurila and/or L. subrotundata in the northern Pacific. Invasion of the Atlantic by a minimum of two Pacific species, across the Arctic migration route established during the late Cenozoic, is sufficient to account for the modern distribution of the subgenera Littorina and Neritrema. The importance of the cladogram as a basis for hypotheses of adaptation is illustrated by a discussion of spawn and development in Littorina.     

Molecular phylogeny and systematic in the genus Brachycaudus (Homoptera: Aphididae): insights from a combined analysis of nuclear and mitochondrial genes

Phylogenetic relationships among members of the Aphid genus Brachycaudus (Homoptera: Aphididae) were inferred from partial sequences of mitochondrial cytochrome B oxidase (CytB), two partial fragments of mitochondrial cytochrome C oxidase subunit I (COI) and the internal transcribed spacer II (ITS2) of ribosomal DNA. Twenty-nine species, with several specimens per species, were included, representing all the historically recognized species-groups and subgenera used in the genus except the monospecific subgenus Mordvilkomemor. Results indicate that the genus Brachycaudus is a well-supported monophyletic group. While our results validate the monophyly of subgenera Thuleaphis , Appelia and Brachycaudus s. str. , they reveal two discrepancies in the classical taxonomy. First, the monotypic subgenus Nevskyaphis does not appear valid. Second, the traditionally defined Acaudus subgenus is not monophyletic. On the other hand, our phylogenetic trees corroborate Andreev's recent definition of Acaudus and Brachycaudina. However, they clearly show that the subgenera Prunaphis , Nevskyaphis and Scrophulaphis as defined by this author do not form monophyletic groups. Our results also highlight a highly supported clade that has not been discussed by previous authors; this clade could form a new subgenus, the subgenus Nevskyaphis . Finally, our study shows that molecular data and morphology meet the same limits in delimiting species groups and species themselves. Species groups in which taxonomic treatment is difficult are polytomous. Furthermore, except for one node clustering Brachycaudus s. str . and Appelia, intersubgeneric relationships remain poorly resolved even when several genes are added to the phylogenetic analysis. These results, together with previous studies in other aphid groups suggest that diversification might have been a rapid process in aphids.     

Systematics and phylogeny of fish of the genus <Emphasis Type="Italic">Liparis</Emphasis> (Liparidae,Scorpaeniformes)

Taxonomic revision of fish of the genus Liparis (Liparidae, Scorpaeniformes), whose species inhabit the shelves of the seas of the northern hemisphere, is performed on the basis of a a large collection of material. It is established that the genus, which includes 71 species, represents a monophyletic group. The classification of the genus is elaborated, providing justification of its separation into five subgenera: Neoliparis Steindachner, 1876; Lyoliparis Jordan et Evermann, 1896; Liparis Scopoli, 1777; Lycocara Gill, 1884; and Careliparis Garman, 1892. Keys to species and species groups are provided.     

A molecular phylogeny for the large African orchid genus Disa

Phylogenetic relationships were inferred for the African subtribe Disinae (Orchidoideae, Orchidaceae), which include the large genus Disa and the small genus Schizodium. One nuclear (ITS) gene region and two plastid (trnLF and matK) gene regions were sequenced for 136 ingroup, representing 70% of all known Disinae species, as well as for 7 outgroup taxa. The combined data matrix contained 4094 characters and was analysed using parsimony and Bayesian inference. Our results show that the generic status of Schizodium can no longer be supported, as it is deeply embedded within the genus Disa. Furthermore, the currently recognised subgenera do not reflect the phylogenetic relationships and should be rejected. Several of the currently recognised sections are monophyletic, others contain misplaced elements, while some are polyphyletic. Morphological divergence, rather than convergence, has hampered previous attempts at a phylogenetic classification of the Disinae. On the basis of our molecular phylogenetic hypothesis, we propose a monotypic subtribe Disinae and a subdivision of the genus Disa into 18 sections.     

雪雀属系统发育关系的研究（雀形目：文鸟科)

雷雀属Montifringilla7种36个形态特征作为分类单元,进行支序分析。以麻雀属Passer、石雀属Petronia部分种类作为比较外群,讨论雪雀属的分类地位及其与近缘属麻雀属、石雀属系统发育关系;分析了雪雀属内种间的系统发育。支序分析的结果表明雪雀属为单系群,建议将雪雀属划分成两个亚属,讨论了雪雀属种类在进货上的位置,在3个近缘属的系统发育关系中,麻雀属类群较原始,雪雀属类群较进化,石雀属在进货中介于二之间。