Molecular systematics of the family Mormoopidae (Chiroptera) based on cytochrome b and recombination activating gene 2 sequences

We examined 1140 bp of the mitochondrial cytochrome b gene and 1398 bp of the nuclear RAG2 gene to investigate the systematics of the eight species of bats within the family Mormoopidae. It was concluded that within the genus Pteronotus there were four valid subgenera: Phyllodia, Chilonycteris, Pteronotus, and an undescribed subgenus. Within Pteronotus, P. parnellii either was part of an unresolved tetratomy with the other three subgenera (cytochrome b data) or was basal (RAG2 and combined data). For three species, P. gymnonotus, P. macleayii, and P. quadridens, our sample revealed little geographic variation. In P. davyi and P. parnellii, the magnitude of genetic distance suggests the possibility of two biological species existing within the currently recognized taxa. Within P. personatus, there was substantial geographic variation partitioned in a step-like fashion among our specimens. Neither of the species within the genus Mormoops showed the deep distance nodes present in P. davyi, P. parnellii, and P. personatus. Cytochrome b and RAG2 data indicated that M. megalophylla evolved recently from its common ancestor. Although there was considerable agreement among the branching patterns for the nuclear and mitochondrial genes, both genes failed to provide robust data concerning the evolutionary relationships among the subgenera.     

Molecular Phylogeny of the Chipmunks Inferred from Mitochondrial Cytochrome b and Cytochrome Oxidase II Gene Sequences

There are currently 25 recognized species of the chipmunk genus Tamias. In this study we sequenced the complete mitochondrial cytochrome b (cyt b) gene of 23 Tamias species. We analyzed the cyt b sequence and then analyzed a combined data set of cyt b along with a previous data set of cytochrome oxidase subunit II (COII) sequence. Maximum-likelihood was used to further test the fit of models of evolution to the cyt b data. Other sciurid cyt b sequence was added to examine the evolution of Tamias in the context of other sciurids. Relationships among Tamias species are discussed, particularly the possibility of a current sorting event among taxa of the southwestern United States and the extreme divergences among the three subgenera (Neotamias, Eutamias, and Tamias).     

Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest

Competing hypotheses explaining species’ use of resources have been advanced. Resource limitations in habitat and/or food are factors that affect assemblages of species. These limitations could drive the evolution of morphological and/or behavioural specialization, permitting the coexistence of closely related species through resource partitioning and niche differentiation. Alternatively, when resources are unlimited, fluctuations in resources availability will cause concomitant shifts in resource use regardless of species identity. Here, we used next‐generation sequencing to test these hypotheses and characterize the diversity, overlap and seasonal variation in the diet of three species of insectivorous bats of the genus Pteronotus. We identified 465 prey (MOTUs) in the guano of 192 individuals. Lepidoptera and Diptera represented the most consumed insect orders. Diet of bats exhibited a moderate level of overlap, with the highest value between Pteronotus parnellii and Pteronotus personatus in the wet season. We found higher dietary overlap between species during the same seasons than within any single species across seasons. This suggests that diets of the three species are driven more by prey availability than by any particular predator‐specific characteristic. P. davyi and P. personatus increased their dietary breadth during the dry season, whereas P. parnellii diet was broader and had the highest effective number of prey species in all seasons. This supports the existence of dietary flexibility in generalist bats and dietary niche overlapping among groups of closely related species in highly seasonal ecosystems. Moreover, the abundance and availability of insect prey may drive the diet of insectivores.     

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.     

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.     

Monophyly and phylogenetic relationships of the catfish genus Glyptothorax (Teleostei: Sisoridae) inferred from nuclear and mitochondrial gene sequences

GlyptothoraxBlyth (1860) is the most species-diverse and widely-distributed genus in the Sisoridae, but few studies have examined monophyly of the genus and phylogenetic relations within it. We used the nuclear RAG2 gene and mitochondrial COI and Cyt b genes from 50 of the approximately 70 species to examine monophyly of Glyptothorax and phylogenetic relationships within the genus. Molecular phylogenetic trees were constructed using maximum parsimony, maximum likelihood and Bayesian inference methods. All methods strongly supported monophyly of Glyptothorax, with Bagarius as its sister group. Both analyses of two- and three-gene datasets recovered nine major subclades of Glyptothorax, but some internal nodes remained poorly resolved. The phylogenetic relationships within the genus and existing taxonomic problems are discussed.     

Phylogeny of the East Asian botiine loaches (Cypriniformes,Botiidae) inferred from mitochondrial cytochrome <Emphasis Type="Italic">b</Emphasis> gene sequences

The Botiinae have traditionally represented a subfamily of the Cobitidae. At present, the classification and phylogenetic relationships of the Botiinae are controversial. To address systematic and phylogenetic questions concerning this group, we sequenced the complete cytochrome b gene from 34 samples, of which 24 represented 13 species of the East Asian botiine fishes, while the other 10 were non-botiine loach species. For the 1140 bp sequences determined, 494 sites were variable ones, of which 424 were parsimony informative. With Myxocyprinus asiaticus as an outgroup, molecular phylogenetic trees were constructed using the neighbor-joining, maximum parsimony, maximum likelihood and Bayesian methods. All molecular phylogenetic trees revealed that botiine fishes form a monophyletic group and are distantly related to other loaches, suggesting that the Botiinae should be placed in their own family. Within the Botiinae, there are three genera; Botia, Parabotia, andLeptobotia, each genus forming a monophyletic group, with the genus Botia as the most ancestral split. Our molecular results are in agreement with morphological analyses of botiines, suggesting that Botia is the ancestral genus, while Leptobotia and Parabotia were resolved as more derived sister groups.     

Evolutionary relationships of flying foxes (genus Pteropus) in the Philippines inferred from DNA sequences of cytochrome b gene

Six flying fox species, genus Pteropus (four from the Philippines) were investigated using complete cytochrome b gene sequences (1140 bp) to infer their evolutionary relationships. The DNA sequences generated via polymerase chain reaction were analyzed using the neighbor-joining, parsimony, and maximum likelihood methods. We estimated that the first evolutionary event among these Pteropus species occurred approximately 13.90 ± 1.49 MYA. Within this short period of evolutionary time we further hypothesized that the ancestors of the flying foxes found in the Philippines experienced a subsequent diversification forming two clusters in the topology. The first cluster is composed of P. pumilus (Philippine endemic), P. speciosus (restricted in western Mindanao) with P. scapulatus, while the second one comprised P. vampyrus and P. dasymallus species based on the analysis from first and second codon positions. Consistently, all phylogenetic analyses divulged close association of P. dasymallus with P. vampyrus contradicting the previous report categorizing P. dasymallus under subniger species group with P. pumilus, P. speciosus, and P. hypomelanus. The Philippine endemic species (P. pumilus) is closely linked with P. speciosus. The representative samples of P. vampyrus showed a large genetic distance of 1.87%. The large genetic distance between P. dasymallus and P. hypomelanus, P. pumilus and P. speciosus denotes a distinct species group.     

Molecular phylogeny of Phalaenopsis Blume (Orchidaceae) based on the internal transcribed spacer of the nuclear ribosomal DNA

The internal transcribed spacer (ITS1, 5.8S rDNA, and ITS2) region of nuclear ribosomal DNA (nrDNA) was sequenced from 53 species, which represent most of the living species diversity in the genus Phalaenopsis (Orchidaceae). A phylogeny was developed for the genus based on the neighbor-joining and maximum parsimony analyses of molecular data. Results of these analyses provided support for the monophyly of the genus Phalaenopsis and concurred in that the genera Doritis and Kingidium should be treated as being parts of the genus Phalaenopsis as suggested by Christenson (2001). Within the genus Phalaenopsis, neither subgenera Aphyllae nor Parishianae were monophyletic, and they were highly clustered with subgenus Proboscidioides plus sections Esmeralda and Deliciosae of subgenus Phalaenopsis based on ITS data. Those species also have the same characters of morphology of four pollinia and similar biogeographies. Furthermore, neither subgenus Phalaenopsis nor Polychilos was monophyletic. Within the subgenus Phalaenopsis, only section Phalaenopsis was highly supported as being monophyletic. As for the subgenus Polychilos, only section Polychilos was moderately supported as being monophyletic. In conclusion, the present molecular data obtained from the ITS sequence of nrDNA of the genus Phalaenopsis provide valuable information for elucidating the phylogeny of this genus.     

Molecular phylogeny of Allograpta (Diptera, Syrphidae) reveals diversity of lineages and non-monophyly of phytophagous taxa

Phylogenetic relationships of genera Allograpta, Sphaerophoria and Exallandra (Diptera, Syrphidae) were analyzed based on sequence data from the mitochondrial protein-coding gene cytochrome c oxidase subunit I (COI) and the nuclear 28S and 18S ribosomal RNA genes. The three genera are members of the subfamily Syrphinae, where nearly all members feed as larvae on soft-bodied Hemiptera and other arthropods. Phytophagous species have recently been discovered in two subgenera of Allograpta, sg Fazia and a new subgenus from Costa Rica. Phylogenetic analyses of the combined datasets were performed using parsimony, under static alignment and direct optimization, maximum likelihood and Bayesian inference. Congruent topologies obtained from all the analyses indicate paraphyly of the genus Allograpta with respect to Sphaerophoria and Exallandra. Exallandra appears embedded in the genus Sphaerophoria, and both genera are placed within Allograpta. The distribution of phytophagous taxa in Allograpta indicates that plant feeding evolved at least twice in this group.     

Phylogenetic relationships in <Emphasis Type="Italic">Betula</Emphasis> (Betulaceae) based on AFLP markers

The genus Betula comprises various species in boreal and temperate climate zones of the Northern Hemisphere. The taxonomy of Betula is controversial and complicated by parallel evolution of morphological traits, polyploidization events, and extensive hybridization and introgression among species. Multilocus molecular data from AFLPs were used to provide phylogenetic information. A large number of polymorphic markers (321 variable bands) were produced in 107 Betula accessions from 23 species and 11 hybrids. The AFLP results were largely congruent with the results from previously examined nuclear DNA markers. Four distinct subgenera were identified within the genus Betula. These subgenera were partly in disagreement with the traditional (but disputed) division of the genus. In addition, the results indicated several groups of conspecific taxa. The majority of the species fell within subgenus Betula and shared a high degree of similarity with B. pendula. All hybrids were associated with this group, and the AFLP data contained signals on putative parents for some of the interspecific hybrids. Subgenus Chamaebetula and part of the Neurobetula species should be merged with Betula. The subgenera Betulenta, Betulaster, and the remaining part of Neurobetula are distinct and well supported. Although our results indicate that four major taxonomic groups can be recognized within the genus Betula, the relationship between them remains unclear. This may be due to the occurrence of hybridization and introgression, which would have a homogenizing effect on the relationships between species. Naturally occurring Betula species of hybrid origin may explain the low bootstrap values within the Betula clade. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Evolutionary adaptations of cochlear function in Jamaican mormoopid bats

Mormoopid bat species have their echolocation system adapted to different hunting strategies. To study the corresponding mechanical properties of their inner ear, we measured distortion-product otoacoustic emissions to assess cochlear sensitivity and tuning. Mormoops blainvillii, Pteronotus macleayii and P. quadridens use frequency-modulated echolocation signals, sometimes preceded by a short narrowband signal component. Their distortion-product otoacoustic emission-threshold curves are most sensitive between 30 and 50 kHz and show no adaptation to the narrowband echolocation components. In contrast, the constant-frequency bat P. parnellii always uses long constant-frequency call components. Its inner ear is maximally sensitive at 62 kHz, the echo-frequency of the dominant constant-frequency component, and pronounced insensitivities at 61 and 93 kHz (CF2 and CF3 call frequency) are the major evolutionary change in comparison to its relatives. Furthermore, in P. parnellii, the optimum cochlear frequency separation is minimal at 62 and 93 kHz, associated with enhanced cochlear tuning, while for the other mormoopids there is no indication of enhanced tuning. The phylogeny of mormoopids, assessed by mitochondrial DNA analysis, shows a close relationship between the Pteronotus species. This suggests that major cochlear redesign, associated with the acquisition of echolocation-call specific cochlear processing in P. parnellii, has occurred within a relatively short evolutionary time scale. Accepted: 30 April 1999     

Molecular phylogeny of Mugilidae fishes revised

Systematics derived from morphological characters often does not correspond with the evolutionary processes underlying the divergence within a group of organisms. In the family Mugilidae (Teleostei) morphological similarities have resulted in inconsistencies between taxonomy and phylogeny among its species, and particularly for the genera Mugil, Liza and Chelon where both intrageneric and intergeneric phylogenetic clarifications are needed. To address these issues, the direct sequencing of the mitochondrial region that encodes Phenylalanine (69 bp), 12S rRNA (842 bp), cytochrome c oxidase subunit I (651 bp) and cytochrome b (702 bp) was carried out. The data reveal that Mugil platanus and Mugil liza represent a continuum of a single species, closely related to but distinct from Mugil cephalus which itself appears to comprise a grouping of multiple and closely related species. This species complex was genetically distinct from Mugil curema, which, based on three clearly diverged species identified in this study along the Atlantic coast of the Americas, requires extensive taxonomic revision throughout its world-wide distribution. Unlike the monophyly supported within Mugil, relationships within Liza are paraphyletic, and a taxonomic revision of the genera Liza, Chelon and Oedalechilus is needed.     

A Phylogenetic View on Species Radiation in Apodemus Inferred from Variation of Nuclear and Mitochondrial Genes

Species of field mice (genus Apodemus) are the most common rodents inhabiting woodlands and forests of the Palaearctic region. We examined the cytochrome b (cyt b) gene in mitochondrial DNA (1140 bp) and the interphotoreceptor retinoid binding protein (IRBP) gene in nuclear DNA (1152 bp) in nine species of Apodemus. Based on the genetic variation, the nine species were grouped into four lineages: (1) Agrarius group (A. agrarius, A. peninsulae, A. semotus, and A. speciosus), (2) Argenteus group (A. argenteus), (3) Gurkha group (A. gurkha), and (4) Sylvaticus group (A. alpicola, A. flavicollis, and A. sylvaticus). It was shown that these four lineages diverged within a short period of evolutionary time, suggestive of a radiation event. Soon after the radiation, the Agrarius group was likely to have differentiated again into the species lineages simultaneously. In contrast, the European clade, the Sylvaticus group, radiated rather recently. The relative ratio of the extent of sequence divergence among the four main lineages to that among the members of the subfamily Murinae (including Mus and Rattus) was calculated to be 72.4% in the cyt b gene with transversional substitutions, and 58.5% in the IRBP gene with all substitutions, using the Kimura two-parameter method. The value for the three European lineages was 27.6% in the cyt b gene and 12.3% in the IRBP gene. These results may have a correlation with the notion that deciduous broadleaf forests remained in Central East Asia through the late Tertiary to the present, while those in Europe to a large extent had disappeared by the Pliocene.     

Phylogenetic Relationships Within the Genus Potorous (Marsupialia: Potoroidae) Based on Allozyme Electrophoresis and Sequence Analysis of the Cytochrome b Gene

Controversy over the taxonomic designations within the genus Potorous has highlighted problems associated with using only morphological data. The recent rediscovery of Gilbert's Potoroo has allowed us to reexamine the relationship of this species to other extant potoroos. Phylogenetic relationships and estimated divergence times are presented, based on electrophoretic and cytochrome b sequence data. There was considerable concordance between the data sets. We conclude that Gilbert's Potoroo is a separate species and should be referred to by its original name, Potorous gilbertii (Gould 1841). Estimates for potoroid divergences are in line with those of Flannery (1989).     

Evidence of paraphyly in the neotropical Porcellanid genus Neopisosoma (Crustacea: Anomura: Porcellanidae) based on molecular characters

Molecular data were used to evaluate the validity of the genus Neopisosoma Haig, 1960. Comparisons of morphological features within Neopisosoma suggest the existence of two lineages, represented among others, by N. angustifrons (Benedict, 1901) and N. neglectum Werding (1986). Both lineages of Neopisosoma are more similar to two morphologically different species groups of the genus Pachycheles, than to congeners of the other group. Comparative morphology of larvae from N. angustifrons, N. neglectum and species of Pachycheles shows that N. angustifrons closely resembles Pachycheles species, whilst N. neglectum is set apart. Sequences of a 465 bp segment of the mitochondrial gene cytochrome oxidase I (COI) were obtained and used to infer phylogenetic relationships among N. angustifrons, N. neglectum, one species of Pachycheles and seven other species of porcellanids, representing three other genera. Results of the molecular analysis were congruent to results of comparative morphological studies of larvae: N. angustifrons grouped with the Pachycheles species, whereas N. neglectum is placed apart. This led us to the conclusion that the genus Neopisosoma is probably paraphyletic and that the criterion used by Haig (1960) is not reliable to define the genus. A revision on a world-wide basis of the genera included, and additional sequence information will be necessary to satisfactorily resolve relationships within the Porcellanidae.     

Evolution of the Gibbon Subgenera Inferred from CytochromebDNA Sequence Data

DNA sequences for the mitochondrial cytochromebgene from the four extant gibbon subgenera are described. The data confirm that the gibbon subgenera evolved from a common hylobatid ancestor and suggest that they diverged from each other after the divergence of the extant African great ape species. The cytochromebgene does not resolve the evolutionary relationships between the gibbon subgenera themselves.     

Morphological and molecular investigations of Paramecium schewiakoffi sp. nov. (Ciliophora, Oligohymenophorea) and current status of distribution and taxonomy of Paramecium spp.

Paramecium schewiakoffi sp. nov. is described from a pond in Shanghai, China. It is a freshwater species belonging to the “aurelia” subgroup of the genus. It is of similar size and shape to P. jenningsi, but has a single large micronucleus of the “chromosomal” morphological type, while P. jenningsi has two smaller micronuclei. The general morphology, morphometric characteristics and nuclear reorganization pattern, a random amplified polymorphic DNA (RAPD) fingerprint pattern, and the small subunit rRNA gene sequence are presented for the species. Comparison of P. schewiakoffi with the other species of Paramecium indicates that it is a valid new species of the genus. Geographical locations reported for many Paramecium species do not support the theory that all ciliates have a cosmopolitan distribution. It is proposed that, in an extension of Jankowski's earlier suggestion, the genus Paramecium should be subdivided into four subgenera: Chloroparamecium, Helianter, Cypriostomum and Paramecium, on the basis of morphometric, biological and molecular differences.     

Temporal, spatial, and ecological modes of evolution of Eurasian Mus based on mitochondrial and nuclear gene sequences

We sequenced mitochondrial (cytochrome b, 12S rRNA) and nuclear (IRBP, RAG1) genes for 17 species of the Old World murine genus Mus, drawn primarily from the Eurasian subgenus Mus. Phylogenetic analysis of the newly and previously available sequences support recognition of four subgenera within Mus (Mus, Coelomys, Nannomys, and Pyromys), with an unresolved basal polytomy. Our data further indicate that the subgenus Mus contains three distinct 'species groups': (1) a Mus booduga Species Group, also including Mus terricolor and Mus fragilicauda (probably also Mus famulus); (2) a Mus cervicolor Species Group, also including Mus caroli and Mus cookii; and (3) a Mus musculus Species Group, also including Mus macedonicus, Mus spicilegus, and Mus spretus. Species diversity in Eurasian Mus is probably explicable in terms of several phases of range expansion and vicariance, and by a propensity within the group to undergo biotope transitions. IRBP and RAG1 molecular clocks for Mus date the origin of subgenera to around 5-6 mya and the origin of Species Groups within subgenus Mus to around 2-3 mya. The temporal pattern of evolution among Eurasian Mus is more complex than that within the Eurasian temperate genus Apodemus.     

Phylogenetic Relationships of South China Sea Snappers (Genus <Emphasis Type="Italic">Lutjanus</Emphasis>; Family Lutjanidae) Based on Mitochondrial DNA Sequences

Phylogenetic relationships of intra- and interspecies were elucidated based on complete cytochrome b (cyt b) and cytochrome c oxidase subunit II (COII) gene sequences from 12 recognized species of genus Lutjanus Bloch in the South China Sea (SCS). Using the combined data set of consensus cyt b and COII gene sequences, interspecific relationships for all 12 recognized species in SCS were consistent with Allen’s morphology-based identifications, with strong correlation between the molecular and morphological characteristics. Monophyly of eight species (L. malabaricus, L. russellii, L. stellatus, L. bohar, L. johnii, L. sebae, L. fulvus, and L. fulviflamma) was strongly supported; however, the pairs L. vitta/L. ophuysenii and L. erythropterus/L. argentimaculatus were more similar than expected We inferred that L. malabaricus exists in SCS, and the introgression caused by hybridization is the reason for the unexpectedly high homogeneity. Guangdong Ocean University and Hunan Normal University contributed equally to this study.