Parallel evolution of Myobiidae (Acari: Prostigmata) mites and jerboas (Rodentia: Dipodoidea)

The phenomenon of the parallel evolution is considered with the example of the myobiid mites (Acari: Prostigmata: Myobiidae) and the jerboas (Rodentia: Dipodoidea). According to recent phylogenetic studies of the superfamily Dipodoidea it is separated into 4 family: Allactagidae, Dipodidae, Zapodidae and Sminthidae (Shenbrot e. a., 1995). The myobiid mites of the subenus Dipodomyobia (11 species) of the genus Cryptomyobia are known as specific parasites associated with jerboas of the families Dipodidae and Allactagidae. One more species (Radfordia ewingi) considered as incertae sedis species within the genus Radfordia is found on the jerboas of the family Zapodidae. The myobiid mites are apparently absent on the members of the family Sminthidae. The reconstruction of phylogeny of the myobiid subgenus Dipodomyobia was carried out by the cladistic method (software PAUP 3.0 s). The analysis was based on 13 morphological characters. At the first step of analysis 42 parsimonious trees have been obtained. The strict consensus tree displays one distinct cluster, which incorporates mites of the allactaga species of group restricted to the jerboa family Allactagidae, and several plesions, species of which are usually refferred to as dipi species group and associated with the family Dipodidae (fig. 1). At the second step of analysis, two characters, which appeared as homoplasies at the first step of analysis were excluded, and one new characters (structure of male genital shield) was additionally included. Single cladogram obtained displays two general clusters and one plesion. The first cluster comprises the allactaga species group (parasites of Allactagidae). The second cluster incorporates the dipi species group, the parasites of subfamilies Dipodinae and Paradipodinae of Dipodidae). The plesion is represented by one species Cryptomyobia baranovae being a specific parasite of Salpingotus crassicauda (Cardiocraninae, Dipodidae). There is the high level congruence between the pattern of myobiid cladogram and jerboas phylogeny proposed by Shenbrot (1992) (fig. 2). The position of one species C. paradipi (the parasite of Paradipus ctenodactylus, single representative of subfam. Paradipodinae) does not fit to this phylogenetic system of the jerboas. This mite species belongs to the claster dipi. All others myobiid species of this group are the parasites of the subfamily Dipodinae. In the cladogram of jerboas, the subfam. Paradipodinae is a sister group of Cardiocraninae, but not of Dipodinae, as it is suggested by the parasitological data. If sinapomorphies in the node Paradipodinae--Cardiocraninae are not correct (as Shenbrot admitted), there would be a complete congruence between the phylogenetic pattern of myobiid and of jerboas. The general phylogeny of Dipodoidea based on citogenetical data was proposed by Vorontsov e. a. (1971). 3 families only were recognized within Dipodoidea: Zapodidae, Sminthidae and Dipodidae. The latter family included 3 subfamilies: Dipodinae, Cardiocraninae and Allactaginae. The version of the jerboa phylogeny proposed in the present paper based on parasitological data corresponds in general lines to the hypotesis of Vorontsov e. a. (1971). The myobiid mites are absent on Sminthidae, they are represented by one species incertae sedis on Zapodidae, and by the subgenus Dipodomyobia on others jerboas (Dipodidae sensu Vorontsov e. a.). According to the parasitological data, the subfamilies Dipodinae and Allactaginae are the sister groups, because the myobiid mites of the subgenus Dipodomyobia parazitise on the jerboas of these taxa only. The subfamily Paradipodinae (sensu Shenbrot) is a sister group for Dipodinae, as far as species C. paradipi is the sister species to other members of the dipi group. The subfamily Cardiocraninae is a sister group for the node Dipodinae-Paradipodinae and also should be included to Dipodidae, because the aberrant species C. baranovae is obviously related to the dipi species group.     

Phylogeny and Rates of Molecular Evolution of Planktonic Foraminifera: SSU rDNA Sequences Compared to the Fossil Record

Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 × 10⁻⁹ substitutions/site/year in the Globigerinidae to less than 1.0 × 10⁻⁹ substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions. Received: 21 January 1997 / Accepted: 17 April 1997     

Fossil Evidence and the Origin of Bats

The phylogenetic and geographic origins of bats (Chiroptera) remain unknown. The earliest confirmed records of bats date from the early Eocene (approximately 51 Ma) in North America with other early Eocene bat taxa also being represented from Europe, Africa, and Australia. Where known, skeletons of these early taxa indicate that many of the anatomical specializations characteristic of bats had already been achieved by the early Eocene, including forelimb and manus elongation in conjunction with structural changes in the pectoral skeleton, hind limb reorientation, and the presence of rudimentary echolocating abilities. By the middle Eocene, the diversification of bats was well underway with many modern families being represented among fossil forms. A new phylogenetic analysis indicates that several early fossil bats are consecutive sister taxa to the extant crown group (including megabats), and suggests a single origin for the order, at least by the late Paleocene. Although morphological studies have long placed bats in the Grandorder Archonta, (along with primates dermopterans, and tree shrews), recent molecular studies have refuted this hypothesis, instead strongly supporting placement of bats in Laurasiatheria. Primitively, proto-bats were likely insectivorous, under-branch hangers and elementary gliders that exploited terminal branch habitats. Recent work has indicated that a number of other mammalian groups began to exploit similar arboreal, terminal branch habitats in the Paleocene, including multituberculates, eulipotyphlans, dermopterans, and plesiadapiforms. This may offer an ecological explanation for morphological convergences that led to the erroneous inclusion of bats within Archonta: ancestral archontan groups as well as proto-bats apparently were exploiting similar arboreal habitats, which may have led to concurrent development of homoplasic morphological attributes.     

Phylogeny and evolutionary history of the Aplodontoidea (Mammalia: Rodentia)

Athough over a hundred species of fossil aplodontoids have been described since the extant species, Aplodontia rufa (the mountain beaver), was first described by Rafinesque in 1817, a thorough survey of the relationships among all the species in this clade has not been undertaken since McGrew's study in 1941. Here, a complete phylogenetic analysis of all published species of aplodontoids is used to reconstruct the evolutionary relationships within the clade, and to present an updated classification of the Aplodontoidea. Several of the traditionally recognized subfamilies are found to be paraphyletic, namely the Prosciurinae, the Allomyinae, and the Meniscomyinae. Others, however, including the Aplodontinae and the Mylagaulidae, appear to be monophyletic. These latter two taxa, which include all of the hypsodont members of the aplodontoid clade, seem to be sister taxa. The history of the aplodontoid clade shows several episodes of rapid diversification in the Early Oligocene, the Late Oligocene, and the Early to Middle Miocene. The Ansomyinae and Aplodontinae show comparatively low speciation rates. The patterns of change in morphology and evolutionary rates suggest a need for a more detailed study of the causes of diversification, extinction, and ecological change in this lineage.  © 2008 The Linnean Society of London, Zoological Journal of the Linnean Society, 2008, 153 , 769–838.     

Evolutionary and developmental dynamics of the dentition in Muroidea and Dipodoidea (Rodentia, Mammalia)

SUMMARY When it comes to mouse evo‐devo, the fourth premolar–first molar (P4–M1) dental complex becomes a source of longstanding controversies among paleontologists and biologists. Muroidea possess only molar teeth but with additional mesial cusps on their M1. Developmental studies tend to demonstrate that the formation of such mesial cusps could result from the integration of a P4 germ into M1 during odontogenesis. Conversely, most Dipodoidea conserve their fourth upper premolars and those that lost these teeth can also bear additional mesial cusps on their first upper molars. The aim of this study is to assess this developmental model in both Muroidea and Dipodoidea by documenting the morphological evolution of the P4–M1 complex across 50 Ma. Fourteen extinct and extant species, including abnormal and mutant specimens were investigated. We found that, even if their dental evolutionary pathways strongly differ, Dipodoidea and Muroidea retain common developmental characteristics because some of them can present similar dental morphological trends. It also appears that the acquisition of a mesial cusp on M1 is independent from the loss of P4 in both superfamilies. Actually, the progressive decrease of the inhibitory effect of P4, consequent to its regression, could allow the M1 to lengthen and mesial cusps to grow in Muroidea. Apart from these developmental explanations, patternings of the mesial part of first molars are also deeply constrained by morpho‐functional requirements. As there is no obvious evidence of such mechanisms in Dipodoidea given their more variable dental morphologies, further developmental investigations are needed.     

Phylogeny and Evolutionary History of the Ground Squirrels (Rodentia: Marmotinae)

Although ground squirrels (Spermophilus) and prairie dogs (Cynomys) are among the most intensively studied groups of mammals with respect to their ecology and behavior, a well-resolved phylogeny has not been available to provide a framework for comparative and historical analyses. We used complete mitochondrial cytochrome b sequences to construct a phylogeny that includes all 43 currently recognized species in the two genera, as well as representatives of two closely related genera (Marmota and Ammospermophilus). In addition, divergence times for ground squirrel lineages were estimated using Bayesian techniques that do not assume a molecular clock. All methods of phylogenetic analysis recovered the same major clades, and showed the genus Spermophilus to be paraphyletic with respect to both Marmota and Cynomys. Not only is the phylogeny at odds with previous hypotheses of ground squirrel relationships, but it suggests that convergence in morphology has been a common theme in ground squirrel evolution. A well-supported basal clade, including Ammospermophilus and two species in the subgenus Otospermophilus, diverged from all other ground squirrels an estimated 17.5 million years ago. Between 10 and 14 million years ago, a relatively rapid diversification gave rise to lineages leading to marmots and to several distinct groups of ground squirrels. The Eurasian ground squirrels diverged from their North American relatives during this period, far earlier than previously hypothesized. This period of diversification corresponded to warming climate and spread of grasslands in western North America and Eurasia. Close geographic proximity of related forms suggests that most species evolved in or near their current ranges.     

Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi)

The rodent superfamily Octodontoidea comprises 6 families, 38 genera, and 193 living species of spiny rats, tuco-tucos, degus, hutias, and their relatives. All are endemic to the Neotropical Region where they represent roughly three-quarters of extant caviomorphs. Although caviomorph monophyly is well established and phylogenetic hypotheses exist for several families, understanding of octodontoid relationships is clouded by sparse taxon sampling and single-gene analyses. We examined sequence variation in one mitochondrial (12S rRNA) and three nuclear genes (vWF, GHR, and RAG1) across all caviomorph families (including 47 octodontoid species), all phiomorph families, and the sole remaining hystricognath family, using the gundi (Ctenodactylus) and springhaas (Pedetes) as outgroups. Our analyses support the monophyly of Phiomorpha, Caviomorpha, and the caviomorph superfamilies Cavioidea (Dasyproctidae, Cuniculidae, and Caviidae, the latter including Hydrochoerus), Erethizontoidea, Chinchilloidea (including Dinomyidae), and Octodontoidea. Cavioids and erethizontoids are strongly supported as sisters, whereas chinchilloids appear to be sister to octodontoids. Among octodontoids, Abrocomidae is consistently recovered as the basal element, sister to a pair of strongly supported clades; one includes Octodontidae and Ctenomyidae as reciprocally monophyletic lineages, whereas the other includes taxa currently allocated to Echimyidae, Capromyidae and Myocastoridae. Capromys appears near the base of this clade, in keeping with current classification, but Myocastor is nested securely inside a clade of Echimyidae that also contains eumysopines, echimyines and dactylomyines. Another, more weakly supported clade of Echimyidae contains fossorial and scansorial taxa from the Chaco-Cerrado-Caatinga and the Atlantic Forest. Biogeographic analyses robustly recover the Patagonia-Southern Andes complex as ancestral for the Octodontoidea, with three component lineages emerging by the Oligocene-Miocene boundary (～23Ma): (1) stem abrocomids in the Central and Southern Andes; (2) a lineage leading to octodontids plus ctenomyids in Patagonia, later dispersing into the Chaco-Cerrado-Caatinga; and (3) a lineage leading to echimyids, capromyids, and myocastorids that subsequently radiated in more mesic biomes, including Amazonia, Atlantic Forest, and the Antilles. This reconstruction refutes earlier ideas that the diverse, generalized, mainly lowland family Echimyidae, which appears early in the fossil record, gave rise to the Andean lineages of octodontoids-instead, the reverse derivation appears to be true. We recommend formal synonymy of Myocastoridae with Echimyidae but defer a similar treatment of Capromyidae until additional hutia taxa and sequences can be analyzed.     

A Molecular Genetic Timescale for the Diversification of Autotrophic Stramenopiles (Ochrophyta): Substantive Underestimation of Putative Fossil Ages

Background

Stramenopiles constitute a large and diverse eukaryotic clade that is currently poorly characterized from both phylogenetic and temporal perspectives at deeper taxonomic levels. To better understand this group, and in particular the photosynthetic stramenopiles (Ochrophyta), we analyzed sequence data from 135 taxa representing most major lineages. Our analytical approach utilized several recently developed methods that more realistically model the temporal evolutionary process.

Methodology/Principal Findings

Phylogenetic reconstruction employed a Bayesian joint rate- and pattern-heterogeneity model to reconstruct the evolutionary history of these taxa. Inferred phylogenetic resolution was generally high at all taxonomic levels, sister-class relationships in particular receiving good statistical support. A signal for heterotachy was detected in clustered portions of the tree, although this does not seem to have had a major influence on topological inference. Divergence time estimates, assuming a lognormally-distributed relaxed molecular clock while accommodating topological uncertainty, were broadly congruent over alternative temporal prior distributions. These data suggest that Ochrophyta originated near the Proterozoic-Phanerozoic boundary, diverging from their sister-taxon Oomycota. The evolution of the major ochrophyte lineages appears to have proceeded gradually thereafter, with most lineages coming into existence by ∼200 million years ago.

Conclusions/Significance

The evolutionary timescale of the autotrophic stramenopiles reconstructed here is generally older than previously inferred from molecular clocks. However, this more ancient timescale nevertheless casts serious doubt on the taxonomic validity of putative xanthophyte/phaeophyte fossils from the Proterozoic, which predate by as much as a half billion years or more the age suggested by our molecular genetic data. If these fossils truly represent crown stramenopile lineages, then this would imply that molecular rate evolution in this group proceeds in a fashion that is fundamentally incompatible with the relaxed molecular clock model employed here. A more likely scenario is that there is considerable convergent morphological evolution within Heterokonta, and that these fossils have been taxonomically misdiagnosed.     

Molecular Phylogeny of Grey Mullets (Teleostei: Mugilidae) in Greece: Evidence from Sequence Analysis of mtDNA Segments

Mitochondrial DNA sequence analysis has been used to explore genetic differentiation and phylogenetic relationships among five species of the Mugilidae family, Mugil cephalus, Chelon labrosus, Liza aurata, Liza ramada, and Liza saliens. DNA was isolated from samples originating from the Messolongi Lagoon in Greece. Three mtDNA segments (12s rRNA, 16s rRNA, and CO I) were PCR amplified and sequenced. Sequencing analysis revealed that the greatest genetic differentiation was observed between M. cephalus and all the other species studied, while C. labrosus and L. aurata were the closest taxa. Dendrograms obtained by the neighbor-joining method and Bayesian inference analysis exhibited the same topology. According to this topology, M. cephalus is the most distinct species and the remaining taxa are clustered together, with C. labrosus and L. aurata forming a single group. The latter result brings into question the monophyletic origin of the genus Liza.     

Phylogeny of Oriental voles (Rodentia: Muridae: Arvicolinae): molecular and morphological evidence

The systematics of Oriental voles remains controversial despite numerous previous studies. In this study, we explore the systematics of all species of Oriental voles, except Eothenomys wardi, using a combination of DNA sequences and morphological data. Our molecular phylogeny, based on two mitochondrial genes (COI and cyt b), resolves the Oriental voles as a monophyletic group with strong support. Four distinct lineages are resolved: Eothenomys, Anteliomys, Caryomys, and the new subgenus Ermites. Based on morphology, we consider Caryomys and Eothenomys to be valid genera. Eothenomys, Anteliomys, and Ermites are subgenera of Eothenomys. The molecular phylogeny resolves subgenera Anteliomys and Ermites as sister taxa. Subgenus Eothenomys is sister to the clade Anteliomys + Ermites. Caryomys is the sister group to genus Eothenomys. Further, the subspecies E. custos hintoni and E. chinensis tarquinius do not cluster with E. custos custos and E. chinensis chinensis, respectively, and the former two taxa are elevated to species level and assigned to the new subgenus Ermites.     

Molecular Evidence for the Hybrid Origin of Ilex dabieshanensis (Aquifoliaceae)

Ilex, the largest genus of dioecious woody plants, is a good study system to assess the role of hybridization in speciation and evolution. Ilex dabieshanensis, a tree endemic to Dabieshan Mountains region, was initially described as a new species. Based on morphological intermediacy and sympatric distribution with its putative parental species, I. cornuta and I. latifolia, we proposed it as a natural hybrid between them. In this study, we sequenced one chloroplast intergenic spacer (trnH-psbA) and two nuclear genes (gapC and nepGS) in I. dabieshanensis and its putative parental species to test the hybrid origin hypothesis. Our results showed that there were one to two differentially fixed sequence differences between I. cornuta and I. latifolia at the two nuclear genes. Twelve of the 14 individuals of I. dabieshanensis exhibited additivity in chromatograms on these differentially fixed sites at both nuclear genes, and the remaining two exhibited additivity in chromatograms on the fixed site at only the nepGS gene. Except one haplotype of I. cornuta at the nepGS gene, all of the haplotypes of I. cornuta at the two nuclear genes were well separated from those of I. latifolia, and most haplotypes of I. dabieshanensis were shared with those of I. cornuta and I. latifolia. Phylogenetic analysis of these haplotypes was largely consistent with haplotype network analysis. I. cornuta and I. latifolia differed by two nucleotide substitutions in the chloroplast intergenic spacer, and 12 individuals of I. dabieshanensis had the same sequences as I. latifolia, while the remaining two were identical with I. cornuta. The molecular data provide convincing evidence for the hybrid origin of I. dabieshanensis and asymmetrical direction of hybridization. One haplotype of I. cornuta at the nepGS gene was nested with those of I. latifolia, indicating introgression to I. cornuta.     

基于孢子形态和分子证据探讨鳞盖蕨属(碗蕨科)系统分类

孢粉学是解决植物分类中疑难类群物种微形态分化的重要方法, 随着分子系统学的发展, 结合这两门学科的优势可以更加有效地解决疑难类群的分类学问题。鳞盖蕨属(Microlepia)是一个分类困难的疑难类群, 采用孢粉学与分子系统学一一对应的方法, 以及居群取样方式, 选取280份样本, 联合4个叶绿体片段(rbcL、trnL-F、psbA-trnH和rps4), 采用最大似然法和贝叶斯法构建该属的系统发生关系, 在此基础上对凭证标本中100份材料的孢子进行观察和分析。综合分子系统学和孢粉学的研究结果, 得出结论: (1) 在形态学研究中广泛被接受的15个物种得到了单系支持, 并厘清了分类困难的复合群; (2) 发现边缘鳞盖蕨(M. marginata)可能存在隐性种; (3) 建议恢复过去归并处理为异名的瑶山鳞盖蕨(M. yaoshanica)、罗浮鳞盖蕨(M. lofoushanensis)、四川鳞盖蕨(M. szechuanica)以及滇西鳞盖蕨(M. subspeluncae); (4) 提出鳞盖蕨属可能存在杂交现象; (5) 提出鳞盖蕨属完整的属下分类建议。     

A Molecular Phylogeny of the Octopoda (Mollusca: Cephalopoda) Evaluated in Light of Morphological Evidence

In this paper we examine the phylogenetic relationships of the Octopoda utilizing molecular sequence data from the cytochrome c oxidase subunit I (COI) gene and compare results from analyses of molecular data with classifications and phylogenies based on previous morphological studies. Partial COI sequences (657 bp, excluding primers) were obtained from 28 species representing most of the diversity in the Order Octopoda, along with a sequence from the established sister taxon to the Octopoda, Vampyroteuthis infernalis. Our results exhibit a number of basic differences from inferences based on standard morphological data. We attempt to resolve these differences based on our confidence in various morphological features. An important finding is the failure of the molecular data to support the monophyly of the Octopodidae. This family contains over 90% of the species in the Suborder Incirrata and has always been difficult to define. Statistical tests constraining Octopodidae monophyly by use of parsimony and maximum-likelihood techniques suggest that all incirrates may be derived from octopodids.     

Molecular Phylogeny of Tuco-Tucos, Genus Ctenomys (Rodentia: Octodontidae): Evaluation of the mendocinus Species Group and the Evolution of Asymmetric Sperm

The phylogenetic relationships among 23 individuals representing 14 species of underground hystricognath rodents of the genus Ctenomys were studied by analyzing variation of complete cytochrome b gene sequences. Maximum parsimony, neighbor joining, and maximum likelihood analyses were performed, using the octodontine genera Octodon and Tympanoctomys as outgroups. Our analyses support previous studies based on chromosomes and skull morphology that suggested a clade comprised of Argentinean and Uruguayan populations of C. rionegrensis. This clade is closely related to one comprised of C. flamarioni and the C. mendocinus species complex. Our analyses provide evidence that the symmetric sperm morph, which is common to other South American hystricognath rodents, is the plesiomorphic character state in Ctenomys and in Hystricognathi. Our analyses do not support the hypothesis that the sperm morphs define two major lineages of tuco-tuco species, because species with asymmetric sperm are diphyletic on the basis of cytochrome b sequences, and this morphology appears to have evolved twice in Ctenomys.     

Molecular Phylogeny of Eupatorieae (Asteraceae) Estimated from cpDNA RFLP and its Implication for the Polyploid Origin Hypothesis of the Tribe

Neomirandea (x=17 and 25), Ageratina (x=17) and Sclerolepis (x=15) with the higher chromosome base numbers, and the other includes Mikania (x=17) and the remaining genera with lower chromosome base numbers (x=10–11). However, the monophyly of the former clade is supported with a low bootstrap value. In the latter clade, Mikania (x=17) diverged first, then Stevia (x=11), and finally eight genera with x=10 diverged in succession. This result supports the hypothesis that the genera in the tribe Eupatorieae with x =10 evolved from an ancestor with a higher base number, and the tribe is of polyploid origin. Received 13 September 1999/ Accepted in revised form 20 January 2000