The evolution and maintenance of delayed implantation in the mustelidae (mammalia: carnivora)

Diapause, the temporary cessation of development at an early life-history stage, is widespread among animals and plants. The range of taxa exhibiting various forms of diapause indicates its enormous ecological significance and highlights its value as a model for examining life-history trait evolution. However, despite the impact of diapause on species ecology, there is little understanding of its adaptive value in many groups. Furthermore, the relative roles of phylogeny and ecology in determining the contemporary expression of the trait remain unresolved. Delayed implantation (DI) is a type of diapause found in several orders of mammals. It is particularly prevalent in the Mustelidae, with mustelids making up more than half of all mammals known to exhibit DI. This taxon is thus ideal for examining life-history predictors of DI and investigating the mode of evolution. Both maximum likelihood and maximum parsimony methods of ancestral state reconstruction indicated DI to be plesiomorphic in the mustelids, although multiple state changes are required to explain its contemporary distribution. After controlling for phylogeny, species with and without DI could be discriminated using just three variables: longevity, maximum latitude of the geographical distribution, and a term describing maternal investment. Our analyses supported the hypothesis that DI is more prevalent in seasonal climates. We also showed that longer-lived species are more likely to exhibit DI, suggesting a time cost to the trait. We found no correlate for the highly variable duration of DI, which remains unexplained. Although ecological factors can predict the distribution of DI in modern mustelids, phylogenetic constraint is likely to play an important role.     

Three gene phylogeny of the Thoreales (Rhodophyta) reveals high species diversity

The freshwater red algal order Thoreales has triphasic life history composed of a diminutive diploid “Chantransia” stage, a distinctive macroscopic gametophyte with multi‐axial growth and carposporophytes that develop on the gametophyte thallus. This order is comprised of two genera, Thorea and Nemalionopsis. Thorea has been widely reported with numerous species, whereas Nemalionopsis has been more rarely observed with only a few species described. DNA sequences from three loci (rbcL, cox1, and LSU) were used to examine the phylogenetic affinity of specimens collected from geographically distant locations including North America, South America, Europe, Pacific Islands, Southeast Asia, China, and India. Sixteen species of Thorea and two species of Nemalionopsis were recognized. Morphological observations confirmed the distinctness of the two genera and also provided some characters to distinguish species. However, many of the collections were in “Chantransia” stage rather than gametophyte stage, meaning that key diagnostic morphological characters were unavailable. Three new species are proposed primarily based on the DNA sequence data generated in this study, Thorea kokosinga‐pueschelii, T. mauitukitukii, and T. quisqueyana. In addition to these newly described species, one DNA sequence from GenBank was not closely associated with other Thorea clades and may represent further diversity in the genus. Two species in Nemalionopsis are recognized, N. shawii and N. parkeri nom. et stat. nov. Thorea harbors more diversity than had been recognized by morphological data alone. Distribution data indicated that Nemalionopsis is common in the Pacific region, whereas Thorea is more globally distributed. Most species of Thorea have a regional distribution, but Thorea hispida appears to be cosmopolitan.     

Molecular phylogeny of avian genus Syrmaticus based on the mitochondrial cytochrome B gene and control region

Mitochondrial DNA cytochrome b (cyt b) and control region (CR) nucleotide sequences were used to study the molecular phylogeny of the genus Syrmaticus. We found that the substitution rates among the three codon positions of cyt b were heterogeneous and the transition-transversion ratio was highly biased. As to CR sequences of the genus, most variable sites were in the peripheral domains. All molecular phylogenetic trees based on the two genes showed that: 1) the Syrmaticus was monophyletic and included five species with the following cladistic relationship: (S. reevesii, (S. soemmerringii, (S. mikado, (S. humiae and S. ellioti)))). Using the TN genetic distance of cyt b, we inferred the divergence time of the five species according to putative molecular clock and found that values were largely in agreement with the geological scenarios. The origin and speciation processes of the studied group were inferred by combining molecular and biogeographical evidences.     

Molecular phylogeny of the genus Alticola (Cricetidae, Rodentia) as inferred from the sequence of the cytochrome b gene

Central Asian mountain voles Alticola is one of the least known groups of voles both in evolution and life history. This genus includes three subgenera Alticola s.str., Aschizomys and Platycranius, and belongs to the tribe Clethrionomyini comprising also red‐backed voles Clethrionomys and oriental voles Eothenomys. In order to elucidate the phylogenetic relationships within Alticola and to examine its position within the tribe, mitochondrial cytochrome b (cyt b) gene variation was estimated, and the results were compared with morphological and palaeontological data. Maximum likelihood (ML), neighbor‐joining (NJ), maximum parsimony (MP) and Bayesian phylogenetic analyses show that the genus Alticola does not appear to be a monophyletic group since the representatives of Aschizomys branch within Clethrionomys, whereas two other subgenera (Alticola and Platycranius) form a separate monophyletic clade. Flat‐headed vole Alticola (Platycranius) strelzowi is nested within the nominative subgenus showing close association with A. (Alticola) semicanus. Surprisingly, the two species of Aschizomys do not form a monophyletic group. The results of the relaxed‐clock analysis suggest that the Alticola clade splits from the Clethrionomys stem in early Middle Pliocene while basal cladogenetic events within Alticola s.str. dates back to the late Middle to early Late Pliocene. A scenario of evolution in Clethrionomyini is put forward implying rapid parallel morphological changes in different lineages leading to the formation of Alticola‐like biomorphs adapted to mountain and arid petrophilous habitats. Corresponding author: Vladimir S. Lebedev, Zoological Museum, Moscow State University, B. Nikitskaya 6, 125009 Moscow, Russia. E‐mail: wslebedev@hotmail.com Anna A. Bannikova, Lomonosov Moscow State University, Vorobievy Gory, 119992 Moscow, Russia. E‐mail: hylomys@mail.ru Alexey S. Tesakov, Geological Institute RAS, Pyzhevsky 7, 119017 Moscow, Russia. E‐mail: tesak@ginras.ru Natalia I. Abramson, Zoological Institute RAS, Universitetskaya nab. 1, 199034 St Petersburg, Russia. E‐mail: lemmus@zin.ru     

Phylogeny and zoogeography of six squirrel species of the genus sciurus (mammalia, rodentia), inferred from cytochrome B gene sequences

To investigate the phylogenetic relationships between the New World Sciurus and the Old World Sciurus and their biogeographic history, the partial mitochondrial cytochrome b gene sequences (1,040 base pairs) were analyzed on six Sciurus species: S. aberti, S. carolinensis, S. lis, S. niger, S. stramineus, and S. vulgaris. Phylogenetic trees (maximum parsimony, neighbor-joining, and maximum likelihood methods) commonly showed two groups with high bootstrap values (73-100%): one consisting of the New World Sciurus and the other consisting of the Old World Sciurus. Genetic distances among the New World Sciurus species were remarkably larger than that between two Sciurus species of the Old World, suggesting the earlier radiation of the New World Sciurus than the Old World Sciurus.     

New species, phylogeny, host-associations and geographic distribution of genus Cryptosporella (Gnomoniaceae, Diaporthales)

The phylogeny of Cryptosporella is revised to include recently discovered species. Eight species new to science are described and two new combinations are proposed, raising the total number of species accepted in Cryptosporella to 19. The species delimitation and phylogeny for Cryptosporella are determined based on analyses of DNA sequences from three genes (β-tubulin, ITS and tef1-α), comparative morphology of sexual structures on their host substrate, and host associations. The inferred phylogeny suggests that Cryptosporella has speciated primarily on Betulaceae with 16 species occurring on hosts in that plant family. The host range of most species seems to be narrow with nine species reported from a single host species or subspecies and seven species occurring on plants within a single host genus. A key to species is provided. The known distribution of Cryptosporella is expanded to mountain cloud forests of the provinces of Chiriquí in Panama and Tucumán in Argentina.     

Molecular phylogeny of the western Atlantic species of the genus Portunus (Crustacea, Brachyura, Portunidae)

The genus Portunus encompasses a comparatively large number of species distributed worldwide in temperate to tropical waters. Although much has been reported about the biology of selected species, taxonomic identification of several species is problematic on the basis of strictly adult morphology. Relationships among species of the genus are also poorly understood, and systematic review of the group is long overdue. Prior to the present study, there had been no comprehensive attempt to resolve taxonomic questions or determine evolutionary relationships within this genus on the basis of molecular genetics. Phylogenetic relationships among 14 putative species of Portunus from the Gulf of Mexico and other waters of the western Atlantic were examined using 16S sequences of the rRNA gene. The resultant molecularly based phylogeny disagrees in several respects with current morphologically based classification of Portunus from this geographical region. Of the 14 species generally recognized, only 12 appear to be valid. We recommend that P. vossi be hereafter regarded as a junior synonym of P. spinimanus and that P. bahamensis be regarded as a junior synonym of P. depressifrons . Our analysis suggests that western Atlantic members of the genus can be subdivided into at least three well-defined clades. Pending further molecular analyses with a large subset of species, it appears that the genus is not monophyletic and that it warrants further taxonomic revision.  © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society , 2007, 150 , 211–220.     

A molecular phylogeny of the lizard genus Phymaturus (Squamata,Liolaemini): Implications for species diversity and historical biogeography of southern South America

The lizard genus Phymaturus is widely distributed in Argentina and along the eastern edge of Chile between 25° and 45° south. We sampled 27 of the 38 currently recognized species plus 22 candidate species using two mitochondrial genes (cytb and 12S), four protein coding nuclear genes and seven anonymous nuclear loci, and present the first comprehensive molecular phylogenetic hypothesis for the clade. We recovered two large clades (the palluma or northern group and patagonicus or southern group) previously recognized on the basis of morphological and mitochondrial sequence evidence, and compared results obtained from concatenated-gene analyses with results of a coalescent-based species-tree approach (BEST). With both methods we identified four main clades within the palluma group (mallimaccii, roigorum, verdugo, and vociferator) and five main clades within the patagonicus group (calcogaster, indistinctus, payuniae, somuncurensis, and spurcus). We found several instances of non-monophyly with cytb and cases of incongruence between mitochondrial vs nuclear data for which we discuss alternative hypotheses. Although with lower support values, combined BEST results are more congruent with concatenated nuclear data than with combined concatenated analyses, suggesting that BEST is less influenced by demographic processes than combined concatenated analyses. We discuss the taxonomic, biogeographic and conservation implications of these results and how the future integration of phylogeographic and morphological approaches will allow the further testing of demographic and biogeographic hypotheses.     

Molecular phylogeny and larval morphological diversity of the lanternfish genus Hygophum (Teleostei: Myctophidae)

Larvae of the deep-sea lanternfish genus Hygophum (Myctophidae) exhibit a remarkable morphological diversity that is quite unexpected, considering their homogeneous adult morphology. In an attempt to elucidate the evolutionary patterns of such larval morphological diversity, nucleotide sequences of a portion of the mitochondrially encoded 16S ribosomal RNA gene were determined for seven Hygophum species and three outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 1172 bp of unambiguously aligned sequences, which were subjected to phylogenetic analyses using maximum-parsimony, maximum-likelihood, and neighbor-joining methods. The resultant tree topologies from the three methods were congruent, with most nodes, including that of the genus Hygophum, being strongly supported by various tree statistics. The most parsimonious reconstruction of the three previously recognized, distinct larval morphs onto the molecular phylogeny revealed that one of the morphs had originated as the common ancestor of the genus, the other two having diversified separately in two subsequent major clades. The patterns of such diversification are discussed in terms of the unusual larval eye morphology and geographic distribution.     

Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae)

Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora, and including either introgression (e.g., with the western American Spartina foliosa) or allopolyploid speciation (e.g., with the Euro-African Spartina maritima). Molecular phylogenetic analysis of the genus has been undertaken in order to understand phylogenetic relationships and genetic divergence among these hybridizing species. Twelve Spartina species have been sequenced for two nuclear DNA regions (ITS of ribosomal DNA, and part of the Waxy gene) and one chloroplast DNA spacer (trnT-trnL). Separate and conditional combined phylogenetic analyses using Cynodon dactylon as the outgroup have been conducted. Spartina is composed of two lineages. The first clade includes all hexaploid species: the Euro-African S. maritima (2n = 60), the East-American S. alterniflora (2n = 62) and the West-American S. foliosa (2n = 60). Spartina alterniflora appears as a closely related sister species to S. foliosa. Although belonging to the same lineage, Spartina maritima appears consistently more genetically differentiated from S. alterniflora than S. foliosa. The tetraploid species S. argentinensis (2n = 40) is placed at the base of this first clade according to the Waxy data, but its position is not well resolved by the other sequences. The second well-supported main lineage within genus Spartina includes the other tetraploid American species. Significant incongruence has been encountered between the waxy based tree and both the ITS and trnT-trnL trees concerning the position of S. densiflora, suggesting a possible reticulate evolution for this species. The results agree with hybridization patterns occurring in Spartina: introgression involving closely related species (S. alterniflora and S. foliosa) on one hand, and alloploid speciation involving more differentiated species (S. alterniflora and S. maritima) on the other hand.     

Phylogeny and species diversity of the genus Herichthys (Teleostei: Cichlidae)

We provide a review of the systematics of Herichthys by evaluating the usefulness of several mitochondrial and nuclear genetic markers together with morphological data. The nDNA next‐generation sequencing ddRAD analysis together with the mtDNA cytochrome b gene provided well‐resolved and well‐supported phylogenies of Herichthys. On the other hand, the nDNA S7 introns have limited resolution and support and the COI barcoding analysis completely failed to recover all but one species of Herichthys as monophyletic. The COI barcoding as currently implemented is thus insufficient to distinguish clearly distinct species in the genus Herichthys that are supported by other molecular markers and by morphological characters. Based on our results, Herichthys is composed of 11 species and includes two main clades (the H. labridens and H. cyanoguttatus species groups). Herichthys bartoni is in many respects the most plesiomorphic species in the genus and has a conflicting phylogenetic position between mtDNA and nDNA markers, where the robust nDNA ddRAD data place it as a rather distant basal member of the H. labridens species group. The mtDNA of H. bartoni is on the other hand only slightly divergent from the sympatric and syntopic H. labridens, and the species thus probably have hybridized in the relatively recent past. The sympatric and syntopic Herichthys steindachneri and H. pame are supported as sister species. The Herichthys cyanoguttatus species group shows two well‐separated basal species (the northernmost H. minckleyi and the southernmost H. deppii) followed by the closely related and centrally distributed species H. cyanoguttatus, H. tepehua, H. carpintis, and H. tamasopoensis whose relationships differ between analyses and show likely hybridizations between themselves and the two basal species as suggested by conflicts between DNA analyses. Several instances of introgressions/hybridizations have also been found between the two main clades of Herichthys.     

基于mtDNA CO I基因的十种长小蠹分子系统进化研究 (鞘翅目:长小蠹科)

全世界记录的长小蠹(鞘翅目:长小蠹科)有1 500余种,其分类地位一直存在争议.本研究通过分子基因信息探讨长小蠹科昆虫的分子系统进化关系,测定了中对长小蠹Euplatypus parallelus(Fabricius)、希氏长小蠹E. hintzi Schaufuss、散对长小蠹E. solutus Schedl、杯长小蠹Dinoplatypus cupulatus Chapuis、小杯长小蠹D.cupulatulus Schedl、芦苇黄截尾长小蠹D.calamus Blandford、五棘长小蠹Diapus quinquespinatus Chapuis、锥长小蠹Treptoplatypus solidus Walk、栎长小蠹Platypus quercivorus Murayama和东亚长小蠹P.lewosi Blandford等长小蠹科5属10种mtDNA CO I基因部分序列(549 bp);采用MEGA3.1分析了序列组成及遗传距离,应用PAUP4.0分别构建了长小蠹NJ,MP和ML等3种分子系统树,同时结合长小蠹的形态分类,探讨10种长小蠹及其所在属的系统进化.结果表明:长小蠹科昆虫在碱基使用频率上有很大的偏向性;长小蠹科与外群小蠹科松瘤小蠹Orthotomicus erosus Wollaston之间的遗传距离(0.288～0.338)远大于科内种间距离(0～0.226);Diapus属分化最早,Euplatypus属独成一支,Treptohlatypus,Dinoplatypus和Platypus 3属分化为一支.长小蠹科分子系统进化研究结果与Wood(1993)新修订的分类系统基本一致,说明长小蠹科的分类系统更趋于合理.     

Molecular phylogeny and taxonomy of wood mice (genus Apodemus Kaup, 1829) based on complete mtDNA cytochrome b sequences, with emphasis on Chinese species

Phylogenetic relationships among 15 species of wood mice (genus Apodemus) were reconstructed to explore some long-standing taxonomic problems. The results provided support for the monophyly of the genus Apodemus, but could not reject the hypothesis of paraphyly for this genus. Our data divided the 15 species into four major groups: (1) the Sylvaemus group (A. sylvaticus, A. flavicollis, A. alpicola, and A. uralensis), (2) the Apodemus group (A. peninsulae, A. chevreri, A. agrarius, A. speciosus, A. draco, A. ilex, A. semotus, A. latronum, and A. mystacinus), (3) A. argenteus, and (4) A. gurkha. Our results also suggested that orestes should be a valid subspecies of A. draco rather than an independent species; in contrast, A. ilex from Yunnan may be regarded as a separate species rather than a synonym of orestes or draco. The species level status of A. latronum, tscherga as synonyms of A. uralensis, and A. chevrieri as a valid species and the closest sibling species of A. agrarius were further corroborated by our data. Applying a molecular clock with the divergences of Mus and Rattus set at 12 million years ago (Mya) as a calibration point, it was estimated that five old lineages (A. mystacinus and four major groups above) diverged in the late Miocene (7.82-12.74 Mya). Then the Apodemus group (excluding A. mystacinus) split into two subgroups: agrarius and draco, at about 7.17-9.95 Mya. Four species of the Sylvaemus group were estimated to diverge at about 2.92-5.21 Mya. The Hengduan Mountains Region was hypothesized to have played important roles in Apodemus evolutionary histories since the Pleistocene.     

Genetic diversity and differentiation in six species of the genus Rhinanthus (Orobanchaceae)

The intricate genus Rhinanthus L. contains many taxonomically unresolved taxa. The assessment of genetic diversity may clarify the differentiation and taxonomic relationships between species and help to determine their mating system, which is important for understanding the future prospects of populations and species. Isozymes were used to assess the mating system, genetic diversity, and differentiation in R. rumelicus, R. osiliensis, R. wagneri, R. alectorolophus, and R. angustifolius from sect. Cleistolemus and R. minor from sect. Rhinanthus. Genetic diversity at species level was found to be higher in widespread R. angustifolius and R. rumelicus compared with insular endemic R. osiliensis. Positive inbreeding coefficient revealed dominant inbreeding in endemic R. osiliensis and R. wagneri. We also detected a significant departure from Hardy–Weinberg equilibrium in some populations of R. rumelicus and R. angustifolius. The common R. alectorolophus and R. minor and several populations of R. rumelicus and R. angustifolius displayed a mixed mating mode. Six studied species divided into three distinct clusters. Rhinanthus alectorolophus was the most differentiated taxon among the investigated species. The species of sect. Cleistolemus formed two distinct groups. The first cluster consisted only of R. alectorolophus while another comprised R. rumelicus, R. osiliensis, R. wagneri, and R. angustifolius, indicating their close affinity. Thus, our isozyme results call into question the monophyly of section Cleistolemus and the taxonomic position of R. alectorolophus.