Reanalysis of oviposition and development rates in the Phytoseiidae using a phylogenetic autoregressive method

Life history patterns are usually identified by comparisons of extant species. Because of inferences regarding phylogenetic constraints, comparative data are often not statistically independent. In order to remove phylogenetic patterns embedded in life history data completely, we adopted a phylogenetic autoregressive method to reanalyse a data set of the ovipositional and developmental rates of 45 Phytoseiidae species. We first calculated the phylogenetic correlation in relation to different taxonomic levels using Moran's I statistics. Significant and positive phylogenetic correlations were found at the subgenus and subfamily levels. This indicates that some variation in both of these life-history traits could be accounted for by phylogeny. Phylogenetic associations, therefore, were removed by a phylogenetic autoregressive method. Using corrected data from this method, the specific components of the ovipositional rate are positively correlated with the specific components of th e developmental rate. The method that we have used obtains the same conclusion as others but differs from the phylogenetic effect in the way that it influences the relationship between comparative data. Because of no data reduction in the phylogenetic autoregressive method, the specific components are more useful than the mean values derived from the higher taxonomic nodes for testing ecological and evolutionary hypotheses about life history patterns. © Rapid Science Ltd. 1998     

Molecular phylogeny of Pamphagidae (Acridoidea,Orthoptera) from China based on mitochondrial cytochrome oxidase II sequences

Abstract Phylogenetic relationships of Pamphagidae were examined using cytochrome oxidase subunit II (COII) mtDNA sequences (684 bp). Twenty‐seven species of Acridoidea from 20 genera were sequenced to obtain mtDNA data, along with four species from the GenBank nucleotide database. The purpose of this study was analyzing the phylogenetic relationships among subfamilies within Pamphagidae and interpreting the phylogenetic position of this family within the Acridoidea superfamily. Phylogenetic trees were reconstructed using neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian inference (BI) methods. The 684 bp analyzed fragment included 126 parsimony informative sites. Sequences diverged 1.0%–11.1% between genera within subfamilies, and 8.8%–12.3% between subfamilies. Amino acid sequence diverged 0–6.1% between genera within subfamilies, and 0.4%–7.5% between subfamilies. Our phylogenetic trees revealed the monophyly of Pamphagidae and three distinct major groups within this family. Moreover, several well supported and stable clades were found in Pamphagidae. The global clustering results were similar to that obtained through classical morphological classification: Prionotropisinae, Thrinchinae and Pamphaginae were monophyletic groups. However, the current genus Filchnerella (Prionotropisinae) was not a monophyletic group and the genus Asiotmethis (Prionotropisinae) was a sister group of the genus Thrinchus (Thrinchinae). Further molecular and morphological studies are required to clarify the phylogenetic relationships of the genera Filchnerella and Asiotmethis.     

Phylogenetic classification of the Drosophilidae Rondani (Diptera): the role of morphology in the postgenomic era

Molecular sequences now overwhelm morphology in phylogenetic inference. Nonetheless, most molecular studies are conducted on a limited number of taxa, as DNA rarely can be analysed from old museum types or fossils. During the last 20 years, more than 150 molecular studies have challenged the current phylogenetic classification of the family Drosophilidae Rondani based on morphological characters. Most studies concerned a single genus, Drosophila Fallén, and included only few representative species from 17 out of the 78 genera of the family. Therefore, these molecular studies were unable to provide an alternative classification scheme. A supermatrix analysis of seven nuclear and one mitochondrial genes (8248 bp) for 33 genera was conducted using outgroups from one calyptrate and four ephydroid families. The Bayesian phylogeny was consistent with previous molecular studies including whole genome sequences and divided the Drosophilidae into four monophyletic clades. Morphological characters, mostly male genitalia, then were compared thoroughly between the four clades and homologous character states were identified. These states were then checked for 70 genera and a revised phylogenetic, family‐group classification for the Drosophilidae is proposed. Two genera –Cladochaeta Coquillett and Diathoneura Duda – of the tribe Cladochaetini Grimaldi are transferred to the family Ephydridae. The Drosophilidae is divided into two subfamilies: Steganinae Hendel (30 genera) and Drosophilinae Rondani (43 genera). A further two genera, Apacrochaeta Duda and Sphyrnoceps de Meijere, are incertae sedis, and Palmophila Grimaldi, is synonymized with Drosophila syn.n. The Drosophilinae is subdivided into two tribes: the re‐elevated Colocasiomyini Okada (nine genera) and Drosophilini Okada. The paraphyly of the genus Drosophila was not resolved to avoid affecting the binomina of important laboratory model species; however, its subgeneric classification was revised in light of molecular and morphological data. Three subgenera, namely Chusqueophila Brncic, Phloridosa Sturtevant and Psilodorha Okada, were synonymized with the subgenus Drosophila (Drosophila) Fallén syns.n. Among the 45 species groups and 5 species complexes of Drosophila (Drosophila), 22 groups and 1 complex were transferred to the subgenus Drosophila (Siphlodora) Patterson & Mainland and 6 groups, 2 species subgroups and 3 complexes are considered incertae sedis within the genus Drosophila. Different morphological characters provide different signals at different phylogenetic scales: thoracic characters (wing venation and presternal shape) discriminate families; grasping and erection‐related characters discriminate subfamilies to tribes; whereas phallic paraphyses, i.e. auxiliary intromittent organs, discriminate genera and Drosophila subgenera. The study shows the necessity of analysing morphological characters within a molecular phylogenetic framework to translate molecular phylogenies into taxonomically‐comprehensive classifications.     

Diversity of phytoseiid mites (Acari: Mesostigmata: Phytoseiidae) in the Atlantic Forest of São Paulo

The objective of this study was to evaluate the diversity of Phytoseiidae in the Atlantic Forest of São Paulo State, Brazil, and to estimate the possible role of this ecosystem as a reservoir for mites of this family. Samples were taken from 187 plant species belonging to 73 plant families in three vegetation types of the Atlantic Forest, from February 2001 to October 2002. In total, 1102 specimens of 54 species belonging to 20 genera of the three phytoseiid subfamilies were found. Most specimens (93%) and species (91%) belonged to the Amblyseiinae. The majority of species found belong to taxonomic groups largely composed of generalist predators (especially Amblyseius and Euseius). In general, the more abundant mites were found on a diversity of plant species, but a few of the abundant species were found on only a small number of plant species. Only nine of the mites encountered during this study are of known agricultural importance. The results obtained suggest the importance of the wide plant diversity in the region to sustain a wide diversity of phytoseiids. The extensive clearance of the Brazilian Atlantic Forest is a threat to the diversity of these mites, important predators of mite pests.     

The effect of phylogeny on interspecific body shape variation in darters (Pisces: Percidae)

We conducted a geometric morphometric analysis of interspecific body shape variation among representatives of 31 species of darters (Pisces: Percidae) to determine whether there is evidence of a phylogenetic effect in body shape variation. Cartesian transformation grids representing relative shape differences of individual species and subspecies revealed qualitative similarities within most traditionally recognized taxonomic groups (genera and subgenera). Canonical variates analysis and a UPGMA cluster analysis were conducted to explore further the relationships among body shapes of species; both analyses revealed patterns of variation consistent with the interpretation that shape is associated with taxonomic affinities. Normalized Mantel statistics revealed a significant positive association between body shape differences and phylogenetic interrelatedness for each of four recent phylogenetic hypotheses, providing evidence of a phylogenetic effect. This result is somewhat surprising, however, given the largely incompatible nature of these four phylogenies. We provide evidence that this result may be due to (1) the inclusion of multiple sets of closely related species to represent the traditionally recognized genera and subgenera within each phylogeny and/or (2) the inclusion of several species with relatively divergent shapes and their particular positions within the phylogenies relative to one another or to the other species of darters.     

Phylogenetic relationships, character evolution, and taxonomic implications within the slipper lobsters (Crustacea: Decapoda: Scyllaridae)

The slipper lobsters belong to the family Scyllaridae which contains a total of 20 genera and 89 species distributed across four subfamilies (Arctidinae, Ibacinae, Scyllarinae, and Theninae). We have collected nucleotide sequence data from regions of five different genes (16S, 18S, COI, 28S, H3) to estimate phylogenetic relationships among 54 species from the Scyllaridae with a focus on the species rich subfamily Scyllarinae. We have included in our analyses at least one representative from all 20 genera in the Scyllaridae and 35 of the 52 species within the Scyllarinae. Our resulting phylogenetic estimate shows the subfamilies are monophyletic, except for Ibacinae, which has paraphyletic relationships among genera. Many of the genera within the Scyllarinae form non-monophyletic groups, while the genera from all other subfamilies form well supported clades. We discuss the implications of this history on the evolution of morphological characters and ecological transitions (nearshore vs. offshore) within the slipper lobsters. Finally, we identify, through ancestral state character reconstructions, key morphological features diagnostic of the major clades of diversity within the Scyllaridae and relate this character evolution to current taxonomy and classification.     

Molecular phylogeny of European muroid rodents based on complete cytochrome b sequences

Phylogenetic relationships among 18 species of mainly European muroid rodents that belong to three subfamilies were estimated using complete sequences of the mitochondrial cytochrome b gene. The inferred monophyly of the subfamilies Murinae (mice and rats) and Arvicolinae (voles, lemmings, and muskrats) is in agreement with previous studies. Within the Murinae, the morphology-based division of the genus Apodemus into three subgenera is supported by these DNA sequence data. The relationships among the different genera of the Murinae were generally poorly resolved, and the relationships of Micromys and Acomys to the other murine genera remained unresolved. Within the subfamily Arvicolinae, the relations of the genera Arvicola, Clethrionomys, and Microtus remained tentative with our data. However, within the Microtus group, there is a good molecular support for the phylogenetic relationships. These findings suggest that the origin of the different murine and arvicoline lineages was rapid, indicating an adaptive radiation with fast speciation.     

Major clades and a revised classification of Magnolia and Magnoliaceae based on whole plastid genome sequences via genome skimming

With more than 300 species, the Magnoliaceae family represents a major Magnoliid lineage that is disjunctly distributed in Asia and the New World. The classification of Magnolia s.l. has been highly controversial among taxonomists, varying from one genus with several subgenera, sections, and subsections to several (up to 16) genera. We conducted a comprehensive phylogenetic study of Magnoliaceae on the basis of sequences of the complete chloroplast genomes with a broad taxon sampling of 86 species. The phylogenetic analyses strongly support 15 major clades within Magnolia s.l. due to the non‐monophyly of subgen. Magnolia, the previous subgeneric treatment that recognizes three subgenera, is not supported. Based on the phylogenetic, morphological, and geographic evidence, we recognize two subfamilies in Magnoliaceae: Liriodendroideae and Magnolioideae, each with one genus, Liriodendron and Magnolia, respectively. Magnolia is herein classified into 15 sections: sects. Magnolia, Manglietia, Michelia, Gwillimia, Gynopodium, Kmeria, Maingola, Oyama, Rytidospermum, Splendentes, Talauma, Tuliparia, Macrophylla, Tulipastrum, and Yulania.     

Phylogenetic relations in the family pholidae (Perciformes: Zoarcoidei) based on genetic and morphological data

Molecular-genetic study of Pholidae of the suborder Zoarcoidei was first performed. Analysis of variation of genes of COI, cytochrome b, and 16S rRNA of mitochondrial DNA indicates different phylogenetic isolation of the family taxa. The groundlessness of separating subgenera (or genera) Enedrias and Allopholis and the rightfulness of including them in the composition of the genus Pholis are shown. Genetic close relation of the genera Pholis and Rhodymenichthys and their differences from the genus Apodichthys are established. The obtained results agree with the data of Makushok (1958) who separated in the composition of the family two subfamilies—Pholinae (with genera Pholis and Rhodymenichthys) and Apodichthyinae (with the genera Apodichthys, Xererpes, and Ulvicola). A key to species, genera, and subfamilies of gunnels of the northern part of the Pacific Ocean is provided.     

Phylogeny of Molossidae Gervais (Mammalia: Chiroptera) inferred by morphological data

Molossidae is a large (roughly 100 species) pantropically distributed clade of swift aerially insectivorous bats for which the phylogeny remains relatively unknown and little studied compared with other speciose groups of bats. We investigated phylogenetic relationships among 62 species, representing all extant molossid genera and most of the subgenera, using 102 morphological characters from the skull, dentition, postcrania, external morphology, tongue, and penis, based on direct observation and literature reports. Both parsimony and Bayesian analyses were used in phylogenetic reconstruction. Our analysis supports two main clades of molossids, both of which mingle Old World and New World taxa. One clade is comprised of Mormopterus,Platymops, Sauromys, Neoplatymops, Molossops, Cynomops, Cheiromeles, Molossus, and Promops. The other clade includes Tadarida, Otomops, Nyctinomops, Eumops, Chaerephon, and Mops. The position of Myopterus with respect to these two groups is unclear. As in other recent analyses, we find that several genera do not appear to be monophyletic (e.g. Tadarida, Chaerephon, and Molossops sensu lato). We recommend that the subgenera of Molossops sensu lato and Austronomus be recognized at the generic level. We conclude that much more data are needed to investigate lower level problems (generic monophyly and relationships within genera) and to resolve the higher‐level branching pattern of the family.     

利用叶绿体基因组数据解析锦葵科梧桐亚科的系统位置和属间关系

分子系统学研究将传统梧桐科与锦葵科、木棉科和椴树科合并为广义锦葵科,并进一步分为9个亚科.然而,9个亚科之间的关系尚未完全明确,且梧桐亚科内的属间关系也未得到解决.为了明确梧桐亚科在锦葵科中的系统发育位置,厘清梧桐亚科内部属间系统发育关系,该研究对锦葵科8个亚科进行取样,共选取55个样本,基于叶绿体基因组数据,采用最大...     

Molecular evolution of tephritid fruit flies in the genus Bactrocera based on the cytochrome oxidase I gene

Fruit flies of the genus Bactrocera (Diptera: Tephritidae) are one of the major economically important insects in Asia and Australia. Little attention has been given to analyses of molecular phylogenetic relationships among Bactrocera subgenera. By using mitochondrial cytochrome oxidase I gene (COI) sequences, the phylogenetic relationships among four subgenera, Asiadacus, Bactrocera, Hemigymnodacus, and Zeugodacus, were investigated. Nucleotide diversity within subgenera ranged from 11.7 to 12.4%, and the net divergence among subgenera ranged from 11.2 to 15.7%. Phylogenetic trees calculated from both maximum parsimony and neighbor-joining phylogenetic analysis methods were highly congruent in terms of tree topologies. Phylogenetic analysis of mitochondrial COI sequences suggests that tephritid fruit fly species, which attack cucurbit plants, that is, Asiadacus, Hemigymnodacus and Zeugodacus, were more closely related to each other than to fruit fly species of the subgenus Bactrocera, which attack plants of numerous families. Our data supports previous classification of Bactrocera based on morphological characters. However, the phylogenetic tree showed the polyphyletic of fruit flies in subgenus Zeugodacus. Possible causes of speciation among fruit flies species in this genus were also discussed.     

Molecular phylogeny of the sawfly subfamily Nematinae (Hymenoptera: Tenthredinidae)

Abstract.  Nematinae is one of the largest subfamilies in the sawfly family Tenthredinidae, but internal relationships are unknown in the absence of any formal phylogenetic analysis. To understand the internal phylogeny of Nematinae, we sequenced a portion of the mitochondrial cytochrome oxidase I gene and the nuclear elongation factor-1α gene from thirteen outgroup taxa and sixty-eight nematine species, the ingroup taxa of which represent all major genera and subgenera within the subfamily. Maximum parsimony and Bayesian phylogenetic analyses of the DNA sequence data show that: (1) Nematinae are monophyletic in a broad sense which includes Hoplocampa , Susana and the tribe Cladiini, which have been classified often into separate subfamilies; together with Craterocercus , these taxa form a paraphyletic basal grade with respect to the remaining Nematinae, but among-group relationships within the grade remain weakly resolved; (2) the remainder of the ingroup, Nematinae s. str, is monophyletic in all combined-data analyses; (3) within Nematinae s. str, the 'Higher' Nematinae is divided into three groups, Mesoneura and the large tribes Nematini and Pristiphorini; (4) although the traditional classifications at the tribal level are largely upheld, some of the largest tribes and genera are obviously para- or polyphyletic; (5) according to rate-smoothed phylogenies dated with two fossil calibration points, Nematinae originated 50–120 million years ago. In addition, the results from all Bayesian analyses provide strong and consistent support for the monophyly of Tenthredinidae, which has been difficult to demonstrate in previous parsimony analyses of morphological and molecular data.     

MtDNA Evidence for Repeated Pulses of Speciation Within Arvicoline and Murid Rodents

We examined temporal aspects of phylogenetic relationships among 5 murid rodent subfamilies and 11 arvicoline genera based on DNA sequences of the cytochrome b gene (n = 92) and ND4 gene (n = 17). We found monophyly for Muridae but a polytomy among murid subfamilies. Arvicolinae was monophyletic, but most genera within this subfamily arose from a polytomy. Microtus was monophyletic, but within the genus, species arose rapidly. This pattern of nested pulses (polytomies) was recovered across parsimony, distance, and likelihood methods and indicates that accumulation of taxonomic diversity in murids was sporadic, rather than gradual. Arvicolines appeared in the Late Miocene and diversified later, between 3 and 5 million years ago. A relatively high rate of sequence evolution (i.e., 2.3% in third-position transversions per million years) helps reconcile the diversification of fossils and mtDNA lineages.     

Patterns and processes in shorebird survival rates: a global review

Changes in demographic rates underpin changes in population size, and understanding demographic rates can greatly aid the design and development of strategies to maintain populations in the face of environmental changes. However, acquiring estimates of demographic parameters at relevant spatial scales is difficult. Measures of annual survival rates can be particularly challenging to obtain because large‐scale, long‐term tracking of individuals is difficult and the resulting data contain many inherent biases. In recent years, advances in both tracking and analytical techniques have meant that, for some taxonomic groups, sufficient numbers of survival estimates are available to allow variation within and among species to be explored. Here we review published estimates of annual adult survival rates in shorebird species across the globe, and construct models to explore the phylogenetic, geographical, seasonal and sex‐based variation in survival rates. Models of 295 survival estimates from 56 species show that survival rates calculated from recoveries of dead individuals or from return rates of marked individuals are significantly lower than estimates from mark–recapture models. Survival rates also vary across flyways, largely as a consequence of differences in the genera that have been studied and the analytical methods used, with published estimates from the Americas and from smaller shorebirds (Actitis, Calidris and Charadrius spp.) tending to be underestimated. By incorporating the analytical method used to generate each estimate within a mixed model framework, we provide method‐corrected species‐specific and genus‐specific adult annual survival estimates for 52 species of 15 genera.     

A phylogenetic analysis of relationships among genera of Conopidae (Diptera) based on molecular and morphological data

Members of the family Conopidae (Diptera) have been the focus of little targeted phylogenetic research. The most comprehensive test of phylogenetic support for the present subfamily classification of Conopidae is presented here using 66 specimens, including 59 species of Conopidae and seven outgroup taxa. Relationships among subfamily clades are also explored. A total of 6824 bp of DNA sequence data from five gene regions (12S ribosomal DNA, cytochrome c oxidase subunit I, cytochrome b, 28S ribosomal DNA and alanyl‐tRNA synthetase) are combined with 111 morphological characters in a combined analysis using both parsimony and Bayesian methods. Parsimony analysis recovers three shortest trees. Bayesian analysis recovers a nearly identical tree. Five monophyletic subfamilies of Conopidae are recovered. The rarely acknowledged Zodioninae is restored, including the genera Zodion and Parazodion. The genus Sicus is removed from Myopinae. Morphological synapomorphies are discussed for each subfamily and inter‐subfamily clade, including a comprehensive review of the character interpretaions of previous authors. Included are detailed comparative illustrations of male and female genitalia of representatives of all five subfamilies with new morphological interpretation.     

Molecular phylogeny and taxonomic reconsideration of the subfamily Zapodinae (Rodentia: Dipodidae), with an emphasis on Chinese species

Although the subfamily Zapodinae (Rodentia, Dipodidae) contains only five species, the phylogeny and taxonomy of these species are still being disputed. First, whether Eozapus and Napaeozapus should be treated as independent genera or subgenera of Zapus has been argued for a long period. Second, the subspecific genetic differentiation of Chinese jumping mouse (Eozapus setchuanus) has not been studied in detail, neither from morphological nor molecular aspects. In this study, the phylogenetic relationship among all the five species of Zapodinae was reconstructed using DNA sequence data from the mitochondrial cytochrome b gene and the nuclear interphotoreceptor retinoid binding protein gene. Bayesian inference, maximum parsimony and maximum likelihood analyses were conducted. The results showed that two major clades could be recognized within Zapodinae. Eozapus setchuanus, is the species endemic to China, strongly formed a monophyletic clade. In the other clade, genus Zapus received significant support in all analyses to be the sister group of the genus Napaeozapus. By comparing genetic distances among these three genera, we conclude that both Eozapus and Napaeozapus should be considered as valid genera rather than subgenera of Zapus. Furthermore, we observed that the two subspecies of E. setchuanus did not form reciprocally monophyletic groups, thus the traditional taxonomy which divided E. setchuanus into two subspecies based on only one morphological character was questionable.     

Phylogenetic analysis of the New World Ptininae (Coleoptera: Bostrichoidea)

A phylogenetic analysis of the New World Ptininae (Anobiidae) was conducted with representatives of nine of ten New World genera, several Old World genera and seven more of the ten subfamilies of Anobiidae. One hundred and two characters (forty‐three multistate) from thirty‐four taxa were used. The single cladogram shows Ptininae as monophyletic and the sister group of the remaining Anobiidae, supporting their placement as subfamilies of a monophyletic Bostrichidae. Genus Niptus Boieldieu is polyphyletic supporting recognition of Pseudeurostus Heyden and the creation of a new genus to encompass the remaining New World species of Niptus. Flightlessness has evolved a minimum of three times within Ptininae and myrmecophily has probably evolved three times within just the New World taxa. The classifications of Ptininae and the remaining Anobiidae are examined and the evolution of feeding habits, myrmecophily and wing loss are discussed.     

Morphological classification of loaches (Nemacheilinae)

Comprehensive comparative morphological analysis of loaches from the subfamily Nemacheilinae is conducted. Forty significant phylogenetic characters are suggested, and phylogenetic relationships are reconstructed. The subfamily Nemacheilinae is subdivided into five tribes (Vaillantellini, Lefuini nov., Yunnanilini nov., Triplophysini nov., and Nemacheilini), and the relationships between these tribes can be expressed by the following formula: Vaillantellini (Lefuini (Yunnanilini (Triplophysini + Nemacheilini))). The classification of highland Asian loaches (Triplophysini) is specified, and the revised diagnoses of the genera from this tribe are given. Heterogeneity of the genus Triplophysa is demonstrated. This genus can be divided into several subgenera, and three new subgenera (Labiatophysa subgen. nov., Indotriplophysa subgen. nov., and Tarimichthys subgen. nov.) are described. A new species Hedinichthys grummorum sp. n is described from the Turpan Depression (northwest China).