A Molecular Phylogeny for the Frog Genus Limnodynastes (Anura: Myobatrachidae)

Members of the genus Limnodynastes are a prominent and widespread feature of the Australian frog fauna. Yet despite their potential to be informative about biogeographic history and mechanisms of speciation, the relationships among these taxa are not well known. We investigated phylogenetic relationships within the genus Limnodynastes via sequencing of mitochondrial (mt)DNA from current members of the genus Limnodynastes and the monotypic genus Megistolotis. a 450-bp fragment of the 16S rRNA gene and a 370-bp fragment of the protein-coding gene ND4 were used to infer a molecular phylogeny. We revise traditional species groupings and now recognize four species groups within Limnodynastes: the L. ornatus group (L. ornatus and L. spenceri), the L. peronii group (L. peronii, L. tasmaniensis, L. fletcheri, the L. depressus), the L. salmini group (L. salmini, L. convexiusculus, and L. lignarius), and the L. dorsalis group (L. dorsalis, L. terraereginae, L. dumerilii and L. interioris). The L. ornatus species group forms a highly distinctive clade that is a sister group to the other Limnodynastes groups. Pending broader phylogenetic studies it could be removed from the genus Limnodynastes. Our results concur with previous suggestions that Megistolotis lignarius is nested within Limnodynastes, and we therefore reclassify this species as Limnodynastes lignarius. Furthermore, specimens identified as L. depressus form a mtDNA lineage distinct from other species in the genus, confirming the validity of the species. Specimens of species from the L. dorsalis group (L. dorsalis, L. dumerilii, L. interioris, and L. terraereginae) are closely related such that L. dumerilii is paraphyletic with two other species. Finally, our study provides broad support for previous phylogenies based on microcomplement fixation.     

Comparative phylogeography of two open forest frogs from eastern Australia

We investigated the phylogeography of two closely related Australian frog species from open forest habitats, Limnodynastes tasmaniensis and L. peronii , using mitochondrial ND4 sequence data. Comparison of our results with previous work on Litoria fallax allowed us to test the generality of phylogeographic patterns among non-rainforest anurans along the east coast of Australia. In general, there was no strong evidence for congruence between overall patterns of genetic structure in the three species. However, phylogenetic breaks congruent with the position of the Burdekin Gap were detected at some level in all species. As previously noted for closed forest taxa, this area of dry habitat appears to have been an important influence on the evolution of several open forest taxa. There were broad geographic similarities in the phylogenetic structuring of southern populations of L. peronii and L. tasmaniensis. Contrarily, although the McPherson Range has previously been noted to coincide geographically with a major mtDNA phylogenetic break in Litoria fallax this pattern is not apparent in L. peronii or L. tasmaniensis. It appears that major phylogeographic splits within L. peronii and L. tasmaniensis may predate the Quaternary. We conclude that phylogeographies of open forest frogs are complex and more difficult to predict than for rainforest taxa, mainly due to an absence of palæomodels for historical distributions of non-rainforest habitats.     

Variation in body size and sexual dimorphism across geographical and environmental space in the frogs Limnodynastes tasmaniensis and L. peronii

This study aimed to identify potential factors responsible for geographically structured morphological variation within the widespread Australian frogs Limnodynastes tasmaniensis Günther and L. peronii Duméril & Bibron. There was support for James's rule, and both latitude and present climate explained large amounts of the variation in body size and shape (particularly in L. peronii ). There was also some support for the influence of several biogeographical barriers. Finally, both species were sexually dimorphic for body size and the degree of sexual size dimorphism (SSD) varied geographically. Climate was an important explanation for SSD variation in L. peronii , while latitude was most important for L. tasmaniensis . Geographical variations in sexual selection via male–male physical competition and climate-related resources are suggested as potential explanations for SSD variation in L. peronii .  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 82 , 39–56.     

Direct and indirect effects of the introduced toad Bufo marinus (Anura: Bufonidae) on populations of native anuran larvae in Australia

Introduced species are frequently believed to have adverse effects on native biota and ecosystems. However, much of our knowledge of the ecological impacts of introduced species is anecdotal, and the mechanisms controlling these effects are often poorly understood. I used replicated artificial pond experiments to investigate the impact of eggs and hatchlings of the introduced toad Bufo marinus on populations of native anuran larvae (Limnodynastes ornatus and Litoria rubella) in Australia. Bufo marinus eggs and hatchlings are highly toxic to predatory native tadpoles. Under naturalistic conditions, populations of predatory L. ornatus tadpoles experienced significantly reduced survival when exposed to Bufo eggs and hatchlings. The impact of Bufo on L. ornatus survival was positively correlated with Bufo density. However, the toxic effects of Bufo on L. ornatus indirectly facilitated the survival of later-breeding L. rubella by altering predator-prey interactions between L. ornatus and L. rubella. Limnodynastes ornatus tadpoles are voracious predators of L. rubella eggs and hatchlings. Consequently, the negative impact of Bufo on populations of L. ornatus tadpoles reduced the intensity of predation by L. ornatus tadpoles on L. rubella eggs and hatchlings, thereby increasing L. rubella survival. The results demonstrate that B. marinus plays an important role in structuring native larval anuran communities via direct and indirect mechanisms, and that Bufo may have both negative and positive effects on populations of native anuran larvae. As far as I am aware, these are the first quantitative data to demonstrate that introduced fauna may affect populations of native biota via toxic effects.     

Inability of adult Limnodynastes peronii (Amphibia: Anura) to thermally acclimate locomotor performance

Despite several studies on adult amphibians, only larvae of the striped marsh frog (Limnodynastes peronii) have been reported to possess the ability to compensate for the effects of cool temperature on locomotor performance by thermal acclimation. In this study, we investigated whether this thermal acclimatory ability is shared by adult L. peronii. We exposed adult L. peronii to either 18 or 30 degrees C for 8 weeks and tested their swimming and jumping performance at six temperatures between 8 and 35 degrees C. Acute changes in temperature affected both maximum swimming and jumping performance, however there was no difference between the two treatment groups in locomotor performance between 8 and 30 degrees C. Maximum swimming velocity of both groups increased from 0.62+/-0.02 at 8 degrees C to 1.02+/-0.03 m s(-1) at 30 degrees C, while maximum jump distance increased from approximately 20 to >60 cm over the same temperature range. Although adult L. peronii acclimated to 18 degrees C failed to produce a locomotor response at 35 degrees C, this most likely reflected a change in thermal tolerance limits with acclimation rather than modifications in the locomotor system. As all adult amphibians studied to date are incapable of thermally acclimating locomotor performance, including adults of L. peronii, this acclimatory capacity appears to be absent from the adult stage of development.     

Testing geographical pathways of speciation in a recent island radiation

Determining the mode, or geographical context, of speciation is a critical first step to understanding the evolutionary mechanisms that cause new species to arise. In this study, we estimated phylogenetic relationships in the cerasina species group of the Hawaiian cricket genus Laupala (Orthoptera: Gryllidae) to test competing phylogeographical hypotheses and thus infer the mode of speciation. A previous phylogenetic result based on nuclear sequence data suggested that populations of L. cerasina on the Big Island of Hawaii are the result of two independent colonizations from Maui, implying parallel speciation and convergent song evolution, and contradicting systematic hypotheses based on behavioural and morphological data. We used amplified fragment length polymorphisms to investigate further the relationships among species and populations in the cerasina species group. Results of these analyses provide a robust estimate of phylogenetic relationships and support the phylogeographical history indicated by behavioural and morphological data.     

Phylogenetic relationships of Oriental torrent frogs in the genus Amolops and its allies (Amphibia, Anura, Ranidae)

We investigated the phylogenetic relationships among 20 species of Oriental torrent frogs in the genus Amolops and its allies from China and Southeast Asia based on 1346-bp sequences of the mitochondrial 12S and 16S rRNA genes. Oriental species of the tribe Ranini form a monophyletic group containing 11 clades (Rana temporaria + Pseudoamolops, R. chalconota, four clades of Amolops, Meristogenys, three clades of Huia species, and Staurois) for which the phylogenetic relationships are unresolved. The genus Amolops consists of southern Chinese, southwestern Chinese, Thai, and Vietnamese-Malaysian lineages, but their relationships are also unresolved. The separation of southern and southwestern lineages within China conforms to previous morphological and karyological results. Species of Huia do not form a monophyletic group, whereas those of Meristogenys are monophyletic. Because P. sauteri is a sister species of R. temporaria, distinct generic status of Pseudoamolops is unwarranted.     

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.     

A molecular approach to the tangled intrageneric relationships underlying phylogeny in Euplotes (Ciliophora, Spirotrichea).

The cosmopolitan genus Euplotes is remarkable among ciliates for its species richness. To understand the still tangled taxonomy and phylogenetic relationships within the genus, small subunit rRNA sequences of 11 morphologically defined species colonizing different habitats were determined. Euplotes 18S rRNA is unique among ciliates for its anomalous length and high evolutionary rate. Phylogenetic reconstruction pointed to a high divergence between this genus and the other Spirotrichea, together with a high variability within the genus. Some of the relationships within the Euplotes group were also resolved. Data from the literature, based on morphological features, habitat, and symbiotic relationships, have been compared with our results and are critically discussed. In many cases, the molecular phylogenetic analysis disagreed with species relatedness established on morphological and ecological grounds. The occurrence of a radiation phenomenon in the evolution of the genus is postulated.     

Chromosomal evolution in Malagasy lemurs. IX. Chromosomal banding studies of Lepilemur mustelinus, L. dorsalis, and L. edwardsi

The karyotypes of three Lepilemuridae species, Lepilemur mustelinus, L. edwardsi, and L. dorsalis, are described and compared to those of three Lepilemur species previously reported. The phylogenetic relationships between the six species and their presumed last common ancestor are given. The results obtained, and the comparison with other groups, strongly suggest a monophyletic origin for all Malagasy lemurs.     

Phylogeny of the scathophagidae (Diptera, calyptratae) based on mitochondrial DNA sequences

The family Scathophagidae constitutes, together with members of the families Muscidae, Fannidae, and Anthomyiidae, the Muscoidea superfamily. The species Scathophaga stercoraria has been used extensively to investigate questions in animal ecology and evolution, particularly as a model system for studies of sperm competition and life history evolution. However, no phylogenetic studies have ever been performed on the Scathophagidae and the relationships within this family remain unclear. This study represents a molecular approach aimed at uncovering the phylogenetic relationships among 61 species representing 22 genera of Scathophagidae. A fragment of the terminal region of the mitochondrial gene COI (subunit I of the cytochrome oxidase gene) was sequenced in scathophagid species covering a wide geographic area, as well as a diverse spectrum of ecological habitats. Several clades grouping different genera and species have been identified, but the resolution power of the COI was insufficient to establish the exact relationships between these clades. The molecular data confirm the existence of a group consisting of the genera Delina, Chylizosoma, and Americina, which could represent the subfamily Delinae. Concerning the controversial position of the genus Phrosia, our data clearly suggest that it should be removed from the Delinae and placed within the genus Cordilura. Monophyly of most genera was confirmed, except for the genus Scathophaga, which should be divided into several different taxa.     

Phylogenetic relationships among Secale species revealed by amplified fragment length polymorphisms.

Amplified fragment length polymorphism (AFLP) data were utilized to analyze the phylogenetic relationships among 29 accessions representing 14 of the most commonly recognized ranked species or subspecies in the genus Secale. We observed 789 AFLP markers of 1130 fragments utilizing 18 P-/M- and E-/M- primer combinations. All polymorphic fragments were used to construct phenetic and phylogenetic trees. The resulting phenogram and cladogram had similar tree topologies. Cluster analysis showed that Secale sylvestre was the most distantly related to all other ryes. Annual forms were grouped together, and the perennial forms appeared more closely related to each other. This suggested that life cycle could have played an important role in determining the relationships among Secale species. Secale sylvestre was considered to be the most ancient species, whereas Secale cereale was the most recently evolved species. Amplified fragment length polymorphism analysis clearly separated all Secale species into only 3 major species groups, within the genus Secale: S. sylvestre, Secale montanum (syn. Secale strictum) for perennial forms, and S. cereale for annual forms. This study demonstrated that the AFLP approach is a useful tool for discriminating species differences, and also gave a much better resolution in discerning genetic relationships among Secale species as compared with previous studies using other approaches.     

燕雀亚科鸟类的贝叶斯系统发生:非洲鹂雀的分类地位及朱雀属的进化与异质起源

鹂雀(Linurgus olivaceus)是非洲热带森林中一种独特的鸣禽,为鹂雀属(Linurgus)的惟一物种。在已有的研究中,通过对鹂雀和雀形目现存鸟类中每个科及亚科至少一个物种的线粒体DNA序列测定,分析了鹂雀与其它现存雀形目鸟类的系统发生关系;在遗传上,对鹂雀与金丝雀、金翅雀及燕雀亚科其它鸟类亦有比较研究。本研究共使用了燕雀亚科83种鸟类,重点对该亚科的系统发生进行了修订。使用贝叶斯法构建了系统发生树,结果表明:鹂雀属于燕雀亚科,系统发生树中聚在金翅雀族(Carduelini),与金丝雀属(Serinus)、金翅雀属(Carduelis)及交嘴雀属(Loxia)的种类形成一组;在系统发生中,鹂雀可能是一个基部物种,它同金丝雀属和金翅雀属鸟类一同进化并分歧出来。在本研究中未能涉及的一些已灭绝种类,可能与鹂雀有着较近的遗传学关系。另一方面,研究也表明锡嘴雀(Coccotharustes coccothraustes)肯定包括在欧亚蜡嘴雀(蜡嘴雀属Eophona和拟蜡嘴雀属Mycerobas)中,美洲的朱雀(Carpodacus)可能是从亚洲种类分歧出来并经过进化辐射形成。     

Phylogenetic structure of the genera Flexibacter,Flexithrix, and Microscilla deduced from 16S rRNA sequence analysis

The 16S rDNA sequences of 40 strains of 17 species in the genus Flexibacter, 5 strains of 4 species in the genus Microscilla, and 1 strain of Flexithrix dorotheae, including all type strains of approved and validated species in these genera, were determined to reveal their phylogenetic relationships. The 16S rRNA sequence analysis demonstrated the extreme heterogeneity of the genera Flexibacter and Microscilla. The strains examined diverged into 24 distinct lines of descent (1 group included both flexibacteria and flexithrix, and 1 group included both flexibacteria and microscilla) that were remote from each other at the genus level or higher. Flexibacter strains were scattered across the cytophaga-flavobacteria-bacteroides phylum and divided into 20 phylogenetic groups, and the genus Microscilla was separated into 5 groups. Flexibacter flexilis, the type species of the genus Flexibacter, and Microscilla marina, the type species of the genus Microscilla, were isolated from other organisms in their respective genera. This means that each genus should be restricted to only the type species. Flexithrix dorotheae, the type species of the genus Flexithrix, clustered with Flexibacter aggregans. The heterogeneity was found not only within genera but also within species. Flexibacter aggregans, Flexibacter aurantiacus, Flexibacter flexilis, Flexibacter roseolus, Flexibacter tractuosus, and "Microscilla sericea" each contained phylogenetically distant strains. The taxonomic concept of the genera Flexibacter, Flexithrix, and Microscilla should be reorganized in accordance with the natural relationships revealed in this study.     

Systematics and phylogeography of pocket gophers in the genera Cratogeomys and Pappogeomys.

Mitochondrial-DNA sequence data were analyzed from individuals sampled from 38 localities across the complete geographic range of the closely related pocket gopher genera Pappogeomys and Cratogeomys. Results of phylogenetic analysis of 1133 base pairs from the cytochrome b gene are consistent with past hypotheses of relationships among members of the castanops species group within the genus Cratogeomys. However, phylogeographic variation within the gymnurus species group of the genus Cratogeomys differs significantly from relationships reflected by current taxonomy. The data indicate that there are five geographically distinct clades within the gymnurus species group. Members of the two nominal species C. gymnurus and C. tylorhinus are scattered among these clades. The three peripherally isolated species, C. fumosus, C. neglectus, and C. zinseri, do not appear to be genetically distinct from other gymnurus species group taxa. An historical biogeographic hypothesis is proposed that will be tested using nuclear DNA data.     

The polymorphism, mimicry, and host plant relationships of Hypolimnas butterflies

The 30 species of Hypolimnas butterflies recognized are divided amongst six pattern morphism classes: monomorphic, weakly dimorphic, simple dual, unimodal polymorphic, partial 9-limited polymorphic, and multiple ♀ dual polymorphic. Eighty per cent of Hypolimnas species belong to one or other of the first three categories. About 60% of the species show evidence of mimicry, some 40% being mimetic in both sexes. In the Oriental region the great majority of mimetic species within the genus are modelled on Euptoea , whilst those of the Afrotropical region are mostly modelled on Amauris. The host plants recorded for the genus strongly suggest that the Urticaceae are primitive for the group, but eleven other families of flowering plants are recorded as hosts. The apparent non-utilization of Urticaceae by H. misippus (L.), the most widespread species of the group, is discussed in terms of its possible ecological and phylogenetic relationships with H. bolina (L.). A check-list of butterflies feeding on Ipomoea (a host plant for both H. bolina and H. misippus) , and on other Convolvulaceae, is included.     

Phylogenetic relationships among the Canary Island Steganacaridae (Acari, Oribatida) inferred from mitochondrial DNA sequence data

The mite genus Steganacarus is represented in the Canary Islands by three endemic species, one recently discovered species, and several morphotypes of uncertain taxonomic position. We used a fragment of the mitochondrial cytochrome oxidase I gene to reconstruct the phylogenetic relationships among representatives of the different taxa from the three central islands of the archipelago, Tenerife, La Gomera and Gran Canaria. Sequence data were analysed by both maximum parsimony and maximum likelihood methods. The inferred phylogenetic relationships do not correlate well with current morphological taxonomy but reveal four deeply divergent and geographically coherent lineages, one each on Gran Canaria and La Gomera and two on Tenerife. No pattern of molecular differentiation was observed among different morphotypes. Possible explanations for this incongruence are suggested in relation to the ecology and biogeography of the group. A recently discovered Steganacarus species from La Gomera, morphologically quite distinct from the other Canarian Steganacarus, is clearly identified as a taxon distantly related to all the other Canarian samples.     

Using RAPD for estimating genetic polymorphism in and phylogenetic relationships among species of the genus Lycopersicon (Tourn.) Mill

RAPD genome analysis of 53 species and cultivars of the genus Lycopersicon (Tourn.) Mill. revealed their high genetic polymorphism (Tourn.) Mill., based on which their phylogenetic relationships were inferred. In total, 248 polymorphic DNA fragments were amplified. Intraspecific polymorphism was maximum (79%) in L. peruvianum and minimum (9%) in L. parviflorum. In general, genome divergence among cross-pollinating tomato species was substantially higher than in self-pollinating species. An UPGMA dendrogram constructed from the RAPD patterns was consisted with the Lycopersicon phylogeny inferred from the molecular data of RFLP, ISSR, and microsatellite analyses and with a classification based on morphological characters. The relationships of taxa within the genus Lycopersicon are discussed.