Phylogeny and evolution of Burmanniaceae (Dioscoreales) based on nuclear and mitochondrial data

The mycoheterotrophic Burmanniaceae are one of the three families currently recognized in the order Dioscoreales. Phylogenetic inference using nucleotide sequences of the nuclear 18S rDNA region and the mitochondrial nad1 b-c intron revealed two well-supported, major lineages within the family, corresponding to the two tribes recognized in the family: Burmannieae and Thismieae. All data supported a strong relationship between Thismieae and Tacca (Dioscoreaceae) making both Burmanniaceae and Dioscoreaceae polyphyletic. The three largest Burmanniaceae genera, Burmannia, Gymnosiphon, and Thismia, are paraphyletic. The splitting of Burmanniaceae into Burmannieae and Thismieae indicates two independent origins of mycoheterotrophy and correlated loss of chlorophyll in Dioscoreales. In the genus Burmannia, in which many species still contain chlorophyll, the achlorophyllous species are nested in between the autotrophic species, suggesting many independent changes from autotrophy to heterotrophy or vice versa. A Bayesian relative rates test on the 18S rDNA data showed considerable variation in substitution rates among Burmanniaceae. The substitution rates in all Thismieae and many Burmannieae are significantly faster than in Dioscoreaceae, but there seems to be no correlation between rate increases and the loss of photosynthesis.     

油茶地蜂营巢生物学观察

对中国南部一种独栖性蜂类—油茶地蜂Andrena camellia Wu的巢穴及其行为进行了初步研究。在对巢穴的研究中,对2省4个样地23个巢穴进行了挖掘和观察,结果显示： 巢穴为无分岔的单支洞,主道在土质较好的地方倾斜角小,洞穴长度为90～150 cm; 在杂质多的土中,倾斜角较大,曲折,洞穴长度为30～60 cm。在一定深度之下开始在主道周边出现由小径连接主道的近椭圆形虫室。虫室通常在远主道端略向下倾斜。一个巢穴中的所有虫室多在一个近似的平面上。在洞口到第一个虫室之间主道通常是近竖直的,虽然时有小的弯折;从第一个虫室向下主道往往发生一或多次偏折,但角度通常不超过45°。在对成蜂行为的观察研究中,对4头油茶地蜂连续7天的全天行为进行记录,结果显示： 成蜂除雨天外均出巢采集油茶花粉; 每天出巢在1～5次不等,多数为2～3次;携粉量大。     

Nesting behaviour and foraging characteristics of Andrena cineraria (Hymenoptera: Andrenidae)

The current studies were carried out in the three experimental locations of Kashmir valley during 2013 to 2016. The species Andrena cineraria formed the dense nest aggregations in plan grounds, barren lands and hilly areas near the fruit orchards and other landscapes with clay loam soil type. The species start flying and foraging in the orchards from April till July. The nests were allodalous, 29–36 cm in depth, with cells located obliquely around the main barrow. The nests were dense with a maximum density of 11.09 nests/m² observed in landscapes of Budgam. The barrow diameters were found varying with depth from main entrance. The maximum barrow diameter recorded was 2.05 mm. At certain depth, the female constructs the first cell and the upper nest burrow is vertical and lower is oblique. The nest entrance is generally hidden under the tumulus. In the depth of average 30.48 cm, each cell directly opens to main burrow either alternately or unilaterally. The cell number, diameter, and length varied with depth. Foraging behaviour of A. cineraria on various fruit crops and other shrubs and social forestry trees were determined and the abundance, visitation rate, total visits and time spend per flower were found significant, especially on fruit crops. The significance of the studies is important for the melittologists, as it will help in the conservation of bee fauna. The study is also important in using this species for pollination purpose and would also help to detect and understand the possible pre-adaptation of species in temperate region of Kashmir valley.     

Analysis of Nesting Behavior Based on Daily Observation of Andrena vaga (Hymenoptera: Andrenidae)

We present a study on nesting behavior of the gregarious solitary bee, Andrena vaga Panzer. Based on the daily observation of individually marked females, we constructed an ethogram, determined a sequence of behavioral elements within the provisioning cycle, estimated their length and computed the transition probability between the elements. We confirmed the existence of distinctive pollen and nectar days in A. vaga and showed apparent differences in the overall daily provisioning pattern in pollen and nectar days as well as in the probability of transition between some behavioral elements. Bees typically performed one provisioning trip and carried no pollen on nectar days, but they performed up to four pollen-provisioning trips on pollen days. The duration of one pollen trip depended on the number and sequence of the trip in a given day, with the shortest trip usually occurring last in the day.     

油茶地蜂生活史及相关生物学习性

油茶地蜂Andrena camellia Wu 是江西、湖南等地油茶花期主要传粉昆虫之一。2006–2007年在江西宜春对油茶地蜂除成虫外各虫态的形态特征、生活史及幼虫和成虫的行为等生物学特性进行了观察研究。结果表明： 该蜂在江西宜春1年发生1代。成虫10月中旬开始出巢活动, 雄蜂早于雌蜂3 d左右出现,完成交尾后数日死亡,雄蜂出巢后寿命18 d左右,雌蜂约38 d。卵期约8 d。幼虫期24 d左右,幼虫取食完花粉球后长成老熟幼虫进入滞育期,滞育期约241 d。翌年9月中旬开始化蛹,蛹期约30 d。出土后的雌蜂当天就可以交配,交配后的雌蜂在羽化地点附近选址筑巢,采集油茶的花粉和花蜜于虫室中制成球形蜂粮并在上面产卵,每粒花粉球上产卵一枚。     

Phylogeny of the subgenus sophophora (Diptera: drosophilidae) based on combined analysis of nuclear and mitochondrial sequences

Sequences from the nuclear (nu) alcohol dehydrogenase gene, the nu 28S ribosomal RNA locus, and the mitochondrial cytochrome oxidase II gene were used both individually and in combined analyses to infer the phylogeny of the subgenus Sophophora (Diptera: Drosophilidae). We used several optimality criteria, including maximum likelihood, maximum parsimony, and minimum evolution, to analyze these partitions to test the monophyly of the subgenus Sophophora and its four largest species groups, melanogaster, obscura, saltans, and willistoni. Our results suggest that the melanogaster and obscura species groups are each monophyletic and form a closely related clade. The Neotropical clade, containing the saltans and willistoni species groups, is also recovered, as previous studies have suggested. While the saltans species group is strongly supported as monophyletic, the results of several analyses indicate that the willistoni species group may be paraphyletic with respect to the saltans species group.     

Phylogeny of Passerida (Aves: Passeriformes) based on nuclear and mitochondrial sequence data

Passerida is a monophyletic group of oscine passerines that includes almost 3500 species (about 36%) of all bird species in the world. The current understanding of higher-level relationships within Passerida is based on DNA-DNA hybridizations [C.G. Sibley, J.E. Ahlquist, Phylogeny and Classification of Birds, 1990, Yale University Press, New Haven, CT]. Our results are based on analyses of 3130 aligned nucleotide sequence data obtained from 48 ingroup and 13 outgroup genera. Three nuclear genes were sequenced: c-myc (498-510 bp), RAG-1 (930 bp), and myoglobin (693-722 bp), as well one mitochondrial gene; cytochrome b (879 bp). The data were analysed by parsimony, maximum-likelihood, and Bayesian inference. The African rockfowl and rockjumper are found to constitute the deepest branch within Passerida, but relationships among the other taxa are poorly resolved--only four major clades receive statistical support. One clade corresponds to Passeroidea of [C.G. Sibley, B.L. Monroe, Distribution and Taxonomy of Birds of the World, 1990, Yale University Press, New Haven, CT] and includes, e.g., flowerpeckers, sunbirds, accentors, weavers, estrilds, wagtails, finches, and sparrows. Starlings, mockingbirds, thrushes, Old World flycatchers, and dippers also group together in a clade corresponding to Muscicapoidea of Sibley and Monroe [op. cit.]. Monophyly of their Sylvioidea could not be corroborated--these taxa falls either into a clade with wrens, gnatcatchers, and nuthatches, or one with, e.g., warblers, bulbuls, babblers, and white-eyes. The tits, penduline tits, and waxwings belong to Passerida but have no close relatives among the taxa studied herein.     

Phylogeny of the bee genus Lasioglossum (Hymenoptera: Halictidae) based on mitochondrial COI sequence data

The bee genus Lasioglossum Curtis is a model taxon for studying the evolutionary origins of and reversals in eusociality. This paper presents a phylogenetic analysis of Lasioglossum species and subgenera based on a data set consisting of 1240 bp of the mitochondrial cytochrome oxidase I (COI) gene for seventy-seven taxa (sixty-six ingroup and eleven outgroup taxa). Maximum parsimony was used to analyse the data set (using paup *4.0) by a variety of weighting methods, including equal weights, a priori weighting and a posteriori weighting. All methods yielded roughly congruent results. Michener’s Hemihalictus series was found to be monophyletic in all analyses but one, while his Lasioglossum series formed a basal, paraphyletic assemblage in all analyses but one. Chilalictus was consistently found to be a basal taxon of Lasioglossum sensu lato and Lasioglossum sensu stricto was found to be monophyletic. Within the Hemihalictus series, major lineages included Dialictus + Paralictus, the acarinate Evylaeus + Hemihalictus + Sudila and the carinate Evylaeus + Sphecodogastra. Relationships within the Hemihalictus series were highly stable to altered weighting schemes, while relationships among the basal subgenera in the Lasioglossum series (Lasioglossum s.s., Chilalictus, Parasphecodes and Ctenonomia) were unclear. The social parasite of Dialictus, Paralictus, is consistently and unambiguously placed well within Dialictus, thus rendering Dialictus paraphyletic. The implications of this for understanding the origins of social parasitism are discussed.     

Evidence of Entrance Sharing and Subterranean Connections in Andrena agilissima (Hymenoptera; Andrenidae)

Andrena agilissima is a bee that nests on sloped or vertical earth walls. Data from 3 years of fieldwork presented here show that this species is communal and uses the same nesting site for many years. On an earth wall on Isola d'Elba (Tuscany, Italy), covered with many bee nest entrances, we studied an aggregation of Andrena agilissima to determine if bees share entrances, if the sharing provides evidence for subterranean connections, and if bees involved in sharing show a division of labor. We marked several females coming out of the same entrance, as well as recapturing the same females using different entrances. No division of labor was observed in our observations.     

油茶地蜂不同龄期幼虫肠道细菌多样性及其差异分析

蜜蜂肠道微生物在其宿主健康与调控宿主生长发育中起着重要作用。油茶地蜂Andrena camellia Wu是油茶的优势传粉昆虫。本研究从野外挖掘该蜂典型样地的巢穴得到油茶地蜂1~5龄及滞育阶段的幼虫,通过PCR扩增得到幼虫肠道微生物16S rRNA基因文库,利用Illumina Miseq二代高通量测序技术首次研究了油茶地蜂不同龄期幼虫肠道细菌的群落结构和多样性。结果显示,油茶地蜂幼虫肠道细菌菌群共检测到27个门,72个纲,155个目,278个科,570个属。其中,最主要的门为变形菌门Proteobacteria（占40.05%）,最主要的目为乳杆菌目Lactobacillales（占12.16%）,最主要的科为乳杆菌科Lactobacillaceae(占11.27%）,最主要的属是乳杆菌属Lactobacillus（占11.27%）。核心细菌群落组间差异、Alpha多样性以及Beta多样性分析显示：不同龄期油茶地蜂幼虫肠道细菌群落在组成、多样性以及结构上均存在显著差异。线性判别分析结果显示,不动杆菌属Acinetobacter和红球菌属Rhodococcus主要存在于5龄幼虫阶段,巴尔通氏体属Bartonella和肠杆菌属Enterobacter主要存在于1龄幼虫阶段。本研究明确了油茶地蜂不同龄期幼虫肠道微生物组成、优势菌群及其群落变化规律,为油茶地蜂等土壤筑巢独栖野生蜜蜂肠道微生物学及其保护生物学的相关研究提供理论依据及研究角度。     

An interesting case of gynandromorphism in Andrena helvola (Linnaeus, 1758) (Hymenoptera: Apoidea: Andrenidae)

A gynandromorphic specimen of Andrena helvola (Linnaeus, 1758) having secondary sexual characters on the head is described.     

Andinopanurgus, a new Andean subgenus of Protandrena (Hymenoptera, Andrenidae)

A new subgenus of Protandrena Cockerell (Panurginae: Protandrenini) from South America, Andinopanurgus Gonzalez & Engel, subgen. n., is described and figured for distinctive species of the genus occurring at mid- and high elevations in the Andes from Venezuela to Peru (1100-3400 m). In addition to the distribution, the subgenus is easily distinguished from other subgenera by a unique combination of morphological characters in both sexes, especially in the hidden sterna and genitalia of the male. Protandrena amyaesp. n., and Protandrena femoralissp. n., are also described and figured from the Ecuadorian and Peruvian Andes. New geographical records and a key to the species are also provided.     

Phylogeny of Anophelinae (Diptera: Culicidae) based on nuclear ribosomal and mitochondrial DNA sequences

Abstract Phylogenetic relationships among thirty-two species of mosquitoes in subfamily Anophelinae are inferred from portions of the mitochondrial genes COI and COII, the nuclear 18S small subunit rRNA gene and the expansion D2 region of the nuclear large subunit 28S rRNA gene. Sequences were obtained from the genera Anopheles , Bironella and Chagasia . Representatives of all six subgenera of Anopheles were included: Anopheles , Cellia , Kerteszia , Lophopodomyia , Nyssorhynchus and Stethomyia. Using parsimony and maximum likelihood methods, various combinations of these DNA sequence data were analysed separately: 18S, 28S, combined 18S and 28S, combined COI and COII, and combined 18S, 28S, COI and COII ('total evidence'). The combined rDNA data contain strong phylogenetic signal, moderately to strongly supporting most clades in MP and ML analyses; however, the mtDNA data (analysed as either nucleotide or amino acid sequences) contain little phylogenetic signal, except for relationships of very recently derived groups of species and, at the deepest level, for the monophyly of Anophelinae. The paraphyly of Anopheles relative to Bironella is confirmed by most analyses and statistical tests. Support for the monophyly of subgenera Anopheles , Cellia , Kerteszia and Nyssorhynchus is indicated by most analyses. Subgenus Lophopodomyia is reconstructed as the sister to Bironella , nested within a clade also containing Nyssorhynchus and Kerteszia . The most basal relationships within genus Anopheles are not well resolved by any of the data partitions, although the results of statistical analyses of the rDNA data (S-H-tests, likelihood ratio tests for monophyly and Bayesian MCMC analyses) suggest that the clade consisting of Bironella , Lophopodomyia , Nyssorhynchus and Kerteszia is the sister to the clade containing Cellia and Anopheles .     

Phylogeny of Lasius ants based on mitochondrial DNA and morphology, and the evolution of social parasitism in the Lasiini (Hymenoptera: Formicidae)

Phylogeny of ants of the tribe Lasiini (Lasius, Acanthomyops, Prenolepis, Euprenolepis, Paratrechina, Pseudolasius, and Myrmecocystus) was analysed using 81 morphological, ecological, and behavioural characters (for 41 species) and mitochondrial DNA sequences (COI, COII, tRNA-Leu; for 19 species). The free-living subgenus Lasius s. str. is paraphyletic with respect to the rest of genus; the traditional "genus" Acanthomyops should be considered a part of Lasius s. lat.; free-living subgenus Cautolasius is a member of the clade of socially parasitic Lasius ants (=Chtonolasius+Acanthomyops+Austrolasius+Dendrolasius). The tree topology is congruent with two alternative scenarios of origin of the temporary social parasitism: (i) a single origin of the parasitic strategy in a derived subclade of Lasius and a secondary loss of this trait in Cautolasius, (ii) a parallel origin of the social parasitism within the clade of hypogeic Lasius ants (in Chtonolasius, and in Acanthomyops+Dendrolasius+Austrolasius). Emery's rule in the strict sense does not apply to this group because most parasites exploit any ecologically available, even phylogenetically distant host species. The parasitic strategy in Lasius could have originated from the aggressive interactions between cofounding queens during pleometric colony founding and/or from the secondary queen adoption.     

Phylogeny of mysticete whales based on mitochondrial and nuclear data

Mysticetes or baleen whales are comprised of four groups: Eschrichtiidae, Neobalaenidae, Balaenidae, and Balaenopteridae. Various phylogenetic hypotheses among these four groups have been proposed. Previous studies have not satisfactorily determined relationships among the four groups with a high degree of confidence. The objective of this study is to determine the relationships among the mysticete whales. Mitochondrial and nuclear DNA were sequenced for phylogenetic analysis. Most species relationships determined using these data were well resolved and congruent. Balaenidae is the most basal group and Neobalaenidae is the second most basal and sister group to the balaenopterid-eschrichtiid clade. In this phylogenetic study, the resolution of Eschrichtiidae with two main lineages of Balaenopteridae was problematic. Some data partitions placed this group within the balaenopterids, and other partitions placed it as a sister taxon to the balaenopterids. An additive likelihood approach was used to determine the most optimal trees. Although it was not found in the combined phylogenetic analyses, the "best" tree found under the additive likelihood approach was one with a monophyletic Balaenopteridae.     

Phylogeny of Tubificidae (Annelida, Clitellata) based on mitochondrial and nuclear sequence data

The tubificid clitellates are a common component in the freshwater bottom fauna and are also the most abundant oligochaete group in marine habitats. There are over 800 described species classified in six subfamilies; Tubificinae, Limnodriloidinae, Rhyacodrilinae, Telmatodrilinae, Phallodrilinae, and Naidinae. In this study we examine the phylogenetic relationships in Tubificidae using a combination of mitochondrial 16S rDNA and nuclear 18S rDNA sequence data. Sequences were obtained from five outgroup and 56 ingroup taxa, including five of the six subfamilies of Tubificidae. The data were analysed by maximum parsimony and Bayesian inference. The resulting tree topologies are virtually without conflict. Several associations traditionally recognized within the family Tubificidae are supported, in the Bayesian analysis including a sister group relationship between Tubificinae and Limnodriloidinae. The results also indicate that Rhyacodrilinae is polyphyletic--some of its members (Heterodrilus spp.) fall into a clade with Phallodrilinae, all other groups with Naidinae. Naidinae is also polyphyletic with two rhyacodriline genera, Monopylephorus and Ainudrilus, nested within. Most of the tubificid genera included in the study are supported as monophyletic; however, Tubifex and Limnodriloides are refuted, and Tubificoides is unresolved from other tubificine taxa.     

Phylogeny and biogeography of the freshwater crayfish Euastacus (Decapoda: Parastacidae) based on nuclear and mitochondrial DNA

Euastacus crayfish are endemic to freshwater ecosystems of the eastern coast of Australia. While recent evolutionary studies have focused on a few of these species, here we provide a comprehensive phylogenetic estimate of relationships among the species within the genus. We sequenced three mitochondrial gene regions (COI, 16S, and 12S) and one nuclear region (28S) from 40 species of the genus Euastacus, as well as one undescribed species. Using these data, we estimated the phylogenetic relationships within the genus using maximum-likelihood, parsimony, and Bayesian Markov Chain Monte Carlo analyses. Using Bayes factors to test different model hypotheses, we found that the best phylogeny supports monophyletic groupings of all but two recognized species and suggests a widespread ancestor that diverged by vicariance. We also show that Euastacus and Astacopsis are most likely monophyletic sister genera. We use the resulting phylogeny as a framework to test biogeographic hypotheses relating to the diversification of the genus.     

Molecular systematics and evolution of the subgenus Mesocarabus Thomson, 1875 (Coleoptera: Carabidae: Carabus), based on mitochondrial and nuclear DNA

The subgenus Mesocarabus Thomson, 1875 is a western Palaearctic group that currently includes five species: four of them inhabiting western Europe (Carabus lusitanicus Fabricius, 1801, Carabus problematicus Herbst, 1786, Carabus dufourii Dejean & Boisduval, 1829, and Carabus macrocephalus Dejean, 1826) and one found in the Rif Mountains in northern Morocco (Carabus riffensis Fairmaire, 1872). Representatives of Mesocarabus have been included in previous molecular phylogenetic studies, but taxon‐ or gene‐sampling limitations yielded inconclusive results regarding its monophyly and sister relationship. Here we perform molecular phylogenetic analyses based on five mitochondrial (3625 nt) and eight nuclear (5970 nt) genes sequenced in many Mesocarabus populations, and in related western Palaearctic Carabus Linnaeus, 1758. We conducted parsimony, maximum‐likelihood, and Bayesian analyses and found a well‐supported sister relationship between a monophyletic Mesocarabus with Iberian species of the subgenus Oreocarabus Géhin, 1876. Within Mesocarabus, the European species form a monophyletic lineage sister to Moroccan C. riffensis. A time‐calibrated phylogeny suggests the split between Mesocarabus and Oreocarabus occurred at 11.8 Mya (95% highest posterior density, HPD, 8.7–15.3 Mya), and the divergence between C. riffensis and European Mesocarabus at 9.5 Mya (95% HPD 7.0–12.5 Mya). The early diversification of Mesocarabus and related subgenera during the Miocene, and alternative hypotheses concerning the origin of Mesocarabus in the Iberian Peninsula and the Betic‐Riffian plate are discussed using calibration data and dispersal–vicariance biogeographic analyses. Finally, we found instances of incongruence between mitochondrial DNA and nuclear‐based phylogenies of Mesocarabus, which are hypothesized to be the result of introgressive hybridization. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 166 , 787–804.     

Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes

The taxomic classification and phylogenetic relationships within the bear family remain argumentative subjects in recent years. Prior investigation has been concentrated on the application of different mitochondrial (mt) sequence data, herein we employ two nuclear single-copy gene segments, the partial exon 1 from gene encoding interphotoreceptor retinoid binding protein (IRBP) and the complete intron 1 from transthyretin (TTR) gene, in conjunction with previously published mt data, to clarify these enigmatic problems. The combined analyses of nuclear IRBP and TTR datasets not only corroborated prior hypotheses, positioning the spectacled bear most basally and grouping the brown and polar bear together but also provided new insights into the bear phylogeny, suggesting the sister-taxa association of sloth bear and sun bear with strong support. Analyses based on combination of nuclear and mt genes differed from nuclear analysis in recognizing the sloth bears as the earliest diverging species among the subfamily ursine representatives while the exact placement of the sun bear did not resolved. Asiatic and American black bears clustered as sister group in all analyses with moderate levels of bootstrap support and high posterior probabilities. Comparisons between the nuclear and mtDNA findings suggested that our combined nuclear dataset have the resolving power comparable to mtDNA dataset for the phylogenetic interpretation of the bear family. As can be seen from present study, the unanimous phylogeny for this recently derived family was still not produced and additional independent genetic markers were in need.     

Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

Trogidae constitute a monophyletic and biologically unique family within Scarabaeoidea, being the only keratinophagous group in the superfamily. Traditionally, the family has been divided into three distinctive genera, Polynoncus Burmeister, Omorgus Erichson and Trox Fabricius. Although the taxonomy of the group is relatively well studied, changes to the existing classification have recently been proposed and the family as currently constituted has not been subjected to phylogenetic analyses. Here we present a molecular phylogeny for this cosmopolitan family based on three partially sequenced gene regions: 16S rRNA, 18S rRNA and 28S rRNA (domain 2). Included in the analyses are representatives belonging to four of the five extant genera (and three of the four subgenera) from all major zoogeographic regions, representing about 20% of the known trogid species diversity in the family. Phylogenetic analyses performed included parsimony and Bayesian inference. We deduce their historical biogeography by using trogid fossils as calibration points for divergence estimates. Our analyses resolved relationships between and within genera and subgenera that are largely congruent with existing phylogeny hypotheses based on morphological data. We recovered four well‐supported radiations: Polynoncus, Omorgus, Holarctic Trox and African Phoberus MacLeay. On the basis of this study, it is proposed that taxonomic changes to the generic classification of the family be made. The subgenera Trox and Phoberus should be elevated to genera to include the Holarctic and all the Afrotropical species, respectively, and Afromorgus returned to subgeneric rank. Estimates of divergence time are consistent with a Pangaean origin of the family in the Early Jurassic. The subsequent diversification of the major lineages is largely attributed to the break‐up of Pangaea and Gondwana in the Middle Jurassic and early Late Cretaceous, respectively.