Hybridization in freshwater fishes: a review of case studies and cytonuclear methods of biological inference

Interspecific hybridization occurs widelyacross a taxonomically diverse array of fishspecies. Multiple factors typically interactto effect the outcome of hybridization events. Human influences have been frequently cited ascontributing factors (nearly 50% of reviewedcase studies). Aquacultural activities,species introductions, and loss or alterationof habitats were frequently implicated. Wehighlight the utility of genetic markers andnovel methods of statistical analysis forinferring the extent, rate, direction, andlikely causes of hybridization. Emphasis isplaced on cytonuclear genetic systems. Wedemonstrate the utility of cytonuclear modelsfor hypothesis testing using empirical data.     

Phylogenetic relationships within the Laridae (Charadriiformes: Aves) inferred from mitochondrial markers

Gulls (Aves: Laridae) constitute a recent and cosmopolite family of well-studied seabirds for which a robust phylogeny is needed to perform comparative and biogeographical analyses. The present study, the first molecular phylogeny of all Larids species (N=53), is based on a combined segment of mtDNA (partial cytochrome b and control region). We discuss our phylogenetic tree in the light of previous suggestions based on morphological, behavioral, and plumage characters. Although the phylogeny is not fully resolved, it highlights several robust species groups and confirms or identifies for the first time some sister relationships that had never been suggested before. The Dolphin Gull (Leucophaeus scoresbii) for instance, is identified as the sister species of the Grey Gull (Larus modestus) and the Ross's Gull (Rhodostethia rosea) forms a monophyletic group with the Little Gull (Larus minutus). Our results clearly demonstrate that the genus Larus as currently defined is not monophyletic, since current taxonomy of gulls is based on the use of convergent phenotypic characters. We propose a new systematic arrangement that better reflects their evolutionary history.     

Biogeography and evolution of flower color in Veratrum (Melanthiaceae) through inference of a phylogeny based on multiple DNA markers

Veratrum (Melanthiaceae) comprises ca. 27 species with highly variable morphology. This study aims to construct the molecular phylogeny of this genus to infer its floral evolution and historical biogeography, which have not been examined in detail before. Maximum parsimony, maximum likelihood, and Bayesian analyses were performed on the separate and combined ITS, trnL-F, and atpB-rbcL sequences to reconstruct the phylogenetic tree of the genus. All Veratrum taxa formed a monophyletic group, within which two distinct clades were distinguished: species with white-to-green perianth formed one highly supported clade, and the species with black-purple perianth constituted another highly supported clade. Phylogenetic inference on flower color evolution suggested that white-to-green perianth was a plesiomorphic state and black-purple perianth was apomorphic for Veratrum. When species distribution areas were traced as a multi-state character, parsimonious optimization inferred that Veratrum possibly originated in East Asia. Our study confirmed previous phylogenetic and taxonomic suggestions on this genus and provided a typical example of plant radiation across the Northern Hemisphere.     

Species diversity within the Morchella esculenta group (Ascomycota: Morchellaceae) in Germany and France

The distribution of the Morchella esculenta group in Germany and France is examined based on 22 samples, a sample from Montenegro is studied as well. In the recent literature the group was often treated as a single species, M. esculenta sensu lato. Our study, based on the polymorphism of the internal transcribed spacer (ITS) region within the nuclear ribosomal DNA (nrDNA), indicates the presence of three distinct species: M. esculenta (L.) Pers., M. crassipes (Vent.) Pers. : Fr., and M. spongiola Boud. They can be identified easily by restriction fragment length polymorphisms (RFLP) of the ITS region.     

Rapid radiation and cryptic speciation in mediterranean triplefin blennies (Pisces: Tripterygiidae) combining multiple genes

The genus Tripterygion is the unique genus of the family Tripterygiidae in the Mediterranean Sea and in the northeastern Atlantic coast. Three species and four subspecies had been described: Tripterygion tripteronotus and Tripterygion melanurus (T. m. melanurus and T. m. minor) are endemic of the Mediterranean, and T. delaisi (T. d. delaisi and T. d. xanthosoma) is found in both areas. We used five different genes (12S, 16S, tRNA-val, COI, and 18S) to elucidate their taxonomy status and their phylogenetic relationships. We employed different phylogenetic reconstructions that yielded different tree topologies. This discrepancy may be caused by the speciation process making difficult the reconstruction of a highly supported tree. All pair comparisons between these three species showed the same genetic divergence indicating that the speciation process could have been resolved by a rapid radiation event after the Messinian Salinity Crisis (5.2Mya) leading to a trichotomy. Our molecular data revealed two clearly supported clades within T. tripteronotus, whose divergence largely exceeded that found between other fish species, consequently these two groups should be considered two cryptic species diverging 2.75-3.32Mya along the Pliocene glaciations. On the contrary, none of the genes studied supported the existence of two subspecies of T. melanurus. Finally, the two subspecies of T. delaisi were validated and probably originated during the Quaternary climatic fluctuations (1.10-1.23Mya), however their distribution ranges should be redefined.     

Microsatellite markers reveal spatial genetic structure of Tetranychus urticae (Acari: Tetranychidae) populations along a latitudinal gradient in Europe

The genetic structure of populations of the two-spotted spider mite Tetranychus urticae was investigated along a south–north European transect spanning from southern France to The Netherlands. Mites were collected on Urtica dioica in 6 sampling zones. Microsatellite variation at 5 loci revealed considerable genetic variation with an average heterozygozity of 0.49. Significant heterozygote deficiency was found in 7 populations out of the 18 samples analyzed and one of them was completely monomorphic. Tetranychus urticae populations show some level of genetic structuring. First, genetic differentiation between localities (F _ST estimates) was significant for all comparisons. Second, the analysis of molecular variance, AMOVA, indicates that there is an effect, albeit low (9%), of the locality in accounting for allele frequency variance. Geographic distance emerges as a factor responsible for this genetic structure. The results are discussed in relation to the biological features of the species and the known patterns of migration. Related agronomical issues are addressed.     

Molecular phylogeny and biogeography of the bipolar Euphrasia (Orobanchaceae): recent radiations in an old genus

Euphrasia includes perennial or annual green parasitic plants, and has a disjunct bipolar distribution except for one transtropical connection across the high mountains of Oceania. The disjunction is coupled with strikingly contrasting patterns of morphological diversity between the southern and northern hemispheres, making it an exciting model to study processes of evolutionary diversification which shaped present floras. We inferred the relationships among 51 species representing 14 of the 15 sections of the genus based on nrDNA ITS and cpDNA trnL intron, trnL-trnF and atpB-rbcL intergenic spacers. Maximum parsimony and Bayesian inference support monophyly of the genus and of several intrageneric groups characterized by morphology, ploidy level, and geographic range. Molecular phylogenetic dating using Bayesian “relaxed” clock methods suggests that the earliest Euphrasia radiations occurred minimum 11–8 Mya with bipolarity being achieved 7–5 Mya. Biogeographic analyses using explicit model-based approach inferred Eurasia as an ancestral area for the genus. The most parsimonious reconstruction found by a dispersal-vicariance analysis requires 17 dispersals to account for the current biogeographic pattern and supports Eurasian origin for Euphrasia. Both long-distance dispersal and across land vicariance can be invoked to explain the diversification in the genus, which experienced rapid radiations driven by new ecological opportunities of the late Pliocene and Pleistocene but also retained a set of local endemic or relict species of an earlier origin.     

Genetic differentiation,polyploidization and hybridization in northern EuropeanDactylorhiza (Orchidaceae): Evidence from allozyme markers

Taxa endemic to North-western Europe are rare, but the orchid genusDactylorhiza contains several species restricted to this area. Evidence from morphological and cytological studies have indicated that some species may have arisen recently and may be of hybrid origin. In the present report, I use allozymes to characterize the genomes in various species ofDactylorhiza and evaluate the possibilities for rapid evolutionary change in the genus. Allotetraploid species have evolved repeatedly from two principal diploid ancestral lineages. These lineages include extant diploid and autotetraploid species, from which allotetraploid derivatives may still arise. It is suggested that allotetraploidization dominates over introgression as speciation mechanism in the genus. The more common and widespread allotetraploid species could be characterized by their allozyme characters over considerable distances, indicating that each of them may have a unique origin and that they have spread from their ancestral populations to the present distribution areas. However, it is also possible that some allotetraploid species contain local populations that have been independently derived from the ancestral lineages.     

国产毛茛科驴蹄草属两种植物的细胞学研究

为探讨国产毛茛科(Ranunculaceae)驴蹄草属(Caltha L.)植物的细胞学特征,对驴蹄草(C.palustris L.)3个居群和花葶驴蹄草(C.scaposa Hook.f.&Thoms.)5个居群进行了细胞学研究。驴蹄草贵州纳雍居群的染色体数目为2n=32(四倍体),两个云南中甸居群的染色体数目均为2n=64(八倍体)。花葶驴蹄草四川红原、康定、石渠居群的染色体数目均为2n=32(四倍体),该数目为首次报道;西藏林芝和云南德钦居群的染色体数目均为2n=64(八倍体)。驴蹄草的染色体比花葶驴蹄草大。这两种植物的32或64条染色体分别以4条或8条为单位大致能够排列为8组同源染色体,但同一组内的染色体经常具有明显的异形性(heteromorphy),不同居群的核型组成多少具有差异。同时,还分析了驴蹄草和花葶驴蹄草的不同倍性细胞型在我国的地理分布式样。     

Scaphohippus, A New Genus of Horse (Mammalia: Equidae) from the Barstow Formation of California

A new genus of hypsodont equid, Scaphohippus, is recognized from the Green Hills Division (Ba1), Second Division (Ba1), and Barstow Faunas (Ba2) of the medial Miocene Barstow Formation, as well as from Ba1 and Ba2 faunas in the Punchbowl Formation of California, the Tesuque Formation of New Mexico, the Pawnee Creek Formation of Colorado, and the Olcott Formation of Nebraska. The genus includes two species, Scaphohippus sumani n. sp. and Scaphohippus intermontanus n. sp. Scaphohippus is a member of the “protohippine” clade, but is differentiated from its more derived sister taxon, Protohippus, by an arc-shaped incisor battery, a shorter I3-P1 diastema, and a more rounded protocone. The upper cheek teeth of S. sumani n. sp. have an unworn crown height of 40 mm. The protocone remains isolated until as much as 60% of wear, and the enamel fossettes are more complex than those of S. intermontanus n. sp. S. intermontanus n. sp. has an unworn crown height of 48–50 mm, the protocone opens by 30% of wear, and the enamel fossettes are simpler than those of S. sumani n. sp. Phyletic analysis shows S. sumani n. sp. to be the more primitive species. Similar facial and dental characteristics reveal a likely common ancestor with Merychippus insignis. The wider geographic and temporal range of S. sumani n. sp. reported here allows for useful phyletic and biogeographic interpretations. S. sumani n. sp. and M. insignis diverged during the late Hemingfordian (He2) of the Great Plains and both taxa dispersed throughout the western United States. S. intermontanus n. sp. is only recognized from the Barstow Formation, where it was likely directly descended from S. sumani n. sp.     

Modeling nucleotide evolution at the mesoscale: the phylogeny of the neotropical pitvipers of the Porthidium group (viperidae: crotalinae)

We analyzed the phylogeny of the Neotropical pitvipers within the Porthidium group (including intra-specific through inter-generic relationships) using 1.4 kb of DNA sequences from two mitochondrial protein-coding genes (ND4 and cyt-b). We investigated how Bayesian Markov chain Monte-Carlo (MCMC) phylogenetic hypotheses based on this 'mesoscale' dataset were affected by analysis under various complex models of nucleotide evolution that partition models across the dataset. We develop an approach, employing three statistics (Akaike weights, Bayes factors, and relative Bayes factors), for examining the performance of complex models in order to identify the best-fit model for data analysis. Our results suggest that: (1) model choice may have important practical effects on phylogenetic conclusions even for mesoscale datasets, (2) the use of a complex partitioned model did not produce widespread increases or decreases in nodal posterior probability support, and (3) most differences in resolution resulting from model choice were concentrated at deeper nodes. Our phylogenetic estimates of relationships among members of the Porthidium group (genera: Atropoides, Cerrophidion, and Porthidium) resolve the monophyly of the three genera. Bayesian MCMC results suggest that Cerrophidion and Porthidium form a clade that is the sister taxon to Atropoides. In addition to resolving the intra-specific relationships among a majority of Porthidium group taxa, our results highlight phylogeographic patterns across Middle and South America and suggest that each of the three genera may harbor undescribed species diversity.     

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.     

中国东、南部的3个腔蚓属蚯蚓新物种

本文报道了寡毛纲(Oligochaeta)巨蚓科(Megascolecidae)腔蚓属(Metaphire)3个新发现物种,分别是象头山腔蚓(M. xiangtoumontis Dong & Jiang sp. nov.),韩摆渡腔蚓(M. hanbaiduensis Dong & Sun sp. nov.)和长白山腔蚓(M. changbaimontis Dong & Shen sp. nov.)。象头山腔蚓受精囊孔2对,位于7/8 ~ 8/9节间,属于M. insulana物种群。韩摆渡腔蚓受精囊孔3对,位于6/7 ~ 8/9节间,属于M. houlleti物种群。长白山腔蚓受精囊孔2对,位于6/7 ~ 7/8节间,属于M. glandularis物种群。所有新物种均附有形态学描述、图片、与相似物种的形态学比较及与GenBank上亲缘关系相近物种的遗传距离计算分析。以上结果丰富了我国腔蚓属蚯蚓的物种多样性,并首次记录了采集于长白山国家级自然保护区的巨蚓科蚯蚓新物种。     

A new Indo-Malayan member of the Stenostiridae (Aves: Passeriformes) revealed by multilocus sequence data: Biogeographical implications for a morphologically diverse clade of flycatchers

Recent molecular studies on passerine birds have highlighted numerous discrepancies between traditional classification and the phylogenetic relationships recovered from sequence data. Among the traditional families that were shown to be highly polyphyletic are the Muscicapidae Old World flycatcher. This family formerly included all Old World passerines that forage on small insects by performing short sallies from a perch. Genera previously allocated to the Muscicapidae are now thought to belong to at least seven unrelated lineages. While the peculiarity of most of these lineages has been previously recognized by Linnean classification, usually at the rank of families, one, the so-called Stenostiridae, a clade comprising three Afrotropical and Indo-Malayan genera, has only recently been discovered. Here, we address in greater detail the phylogenetic relationships and biogeographic history of the Stenostiridae using a combination of mitochondrial and nuclear data. Our analyses revealed that one species, Rhipidura hypoxantha, previously attributed to the Rhipiduridae (fantails), is in fact a member of the Stenostiridae radiation and sister to the South African endemic genus Stenostira (Fairy Flycatcher). Our dating analyses, performed in a relative-time framework, suggest that the splits between Stenostira/R. hypoxantha and Culicicapa/Elminia occurred synchronously. Given that the Stenostiridae assemblage has been consistently recovered by independent studies, we clarify its taxonomic validity under the rules of the International Code of Zoological Nomenclature.     

Molecular phylogeny of Cypripedium (Orchidaceae: Cypripedioideae) inferred from multiple nuclear and chloroplast regions

A molecular analysis was performed on 56 taxa in the orchid genus Cypripedium using nrDNA ITS and five chloroplast regions (trnH-psbA, atpI-atpH, trnS-trnfM, trnL-F spacer, and the trnL intron). The genus Cypripedium was confirmed as monophyletic. Our data provided strong support for monophyletic grouping of eight infrageneric sections (Subtropica, Obtusipetala, Trigonopedia, Sinopedilum, Bifolia, Flabelinervia, Arietinum, and Cypripedium) defined in earlier taxonomic treatments, and paraphyletic grouping of two sections (Irapeana and Retinervi). Within the genus Cypripedium, the first divergent lineage consisted of two Mesomaerican species, and subsequently the Cypripedium debile lineage from eastern Asia was split. Our study did not support the notion that two Asian species (Cypripedium subtropicum and Cypripedium singchii) were closely related to either Mesoamerican Cypripedium irapeanum or North American Cypripedium californicum, as indicated by previous interpretations based on morphological evidences. In addition, one pair of vicariant species, Cypripedium plectrochilum (eastern Asia) and Cypripedium arietinum (North America), unique to section Arietinum, was confirmed. Furthermore, within the monophyletic section Cypripedium two previously recognized subsections, Cypripedium and Macrantha, were shown to be paraphyletic. Our results suggested that this section split into two groups based on distribution (North America vs. Eurasia) instead of such previously used, morphological traits as flower color, and the shape of the lips (labellum) and lateral petals.     

硅藻中国新记录属种——未知等片星杆藻

该文利用光学和扫描电子显微镜对采自青海省门源县水域的未知等片星杆藻形态特征进行了详细观察研究,并对其特征与其相似种类——拟星状等片星杆藻比较,以确定其分类属种。结果表明：(1)青海省门源县水域的未知等片星杆藻具有以下8个鉴定特征：①狭披针形的壳瓣外形和头状末端;② 3种类型的增厚横肋,即初生横肋、次生横肋和三生横肋;③ 星状细胞群体;④ 壳面上不均匀分布的线纹;⑤ 不凸起的胸骨;⑥每个壳瓣只着生一个唇形突;⑦ 非嵌入式顶孔区;⑧ 每条环带上只有一列孔纹;故确定该硅藻为未知等片星杆藻。(2)对未知等片星杆藻与其相似种类——拟星状等片星杆藻比较发现,二者最大区别是群体着生形态不同,前者可形成Z字形或星状群体,而后者是单生,不形成群体,表明二者为不同的种类,故支持其作为独立种类。(3)该研究结果扩大了未知等片星杆藻的地理分布区域;未知等片星杆藻为中国新记录属种,永久装片保存在吉首大学植物标本馆(JIU)。     

Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group)

We sequenced 998 base pairs (bp) of mitochondrial DNA cytochrome b and 799 bp of nuclear gene BRCA1 in the Lesser white-toothed shrew (Crocidura suaveolens group) over its geographic range from Portugal to Japan. The aims of the study were to identify the main clades within the group and respective refugia resulting from Pleistocene glaciations. Analyses revealed the Asian lesser white-toothed shrew (C. shantungensis) as the basal clade, followed by a major branch of C. suaveolens, subdivided sensu stricto into six clades, which split-up in the Upper Pliocene and Lower Pleistocene (1.9-0.9 Myr). The largest clade, occurring over a huge range from east Europe to Mongolia, shows evidence of population expansion after a bottleneck. West European clades originated from Iberian and Italo-Balkanic refugia. In the Near East, three clades evolved in an apparent hotspot of refugia (west Turkey, south-west and south-east of the Caucasus). Most clades include specimens of different morphotypes and the validity of many taxa in the C. suaveolens group has to be re-evaluated.     

Phylogeny of the cycads based on multiple single-copy nuclear genes: congruence of concatenated parsimony,likelihood and species tree inference methods

Background and aims

Despite a recent new classification, a stable phylogeny for the cycads has been elusive, particularly regarding resolution of Bowenia, Stangeria and Dioon. In this study, five single-copy nuclear genes (SCNGs) are applied to the phylogeny of the order Cycadales. The specific aim is to evaluate several gene tree–species tree reconciliation approaches for developing an accurate phylogeny of the order, to contrast them with concatenated parsimony analysis and to resolve the erstwhile problematic phylogenetic position of these three genera.

Methods

DNA sequences of five SCNGs were obtained for 20 cycad species representing all ten genera of Cycadales. These were analysed with parsimony, maximum likelihood (ML) and three Bayesian methods of gene tree–species tree reconciliation, using Cycas as the outgroup. A calibrated date estimation was developed with Bayesian methods, and biogeographic analysis was also conducted.

Key Results

Concatenated parsimony, ML and three species tree inference methods resolve exactly the same tree topology with high support at most nodes. Dioon and Bowenia are the first and second branches of Cycadales after Cycas, respectively, followed by an encephalartoid clade (Macrozamia–Lepidozamia–Encephalartos), which is sister to a zamioid clade, of which Ceratozamia is the first branch, and in which Stangeria is sister to Microcycas and Zamia.

Conclusions

A single, well-supported phylogenetic hypothesis of the generic relationships of the Cycadales is presented. However, massive extinction events inferred from the fossil record that eliminated broader ancestral distributions within Zamiaceae compromise accurate optimization of ancestral biogeographical areas for that hypothesis. While major lineages of Cycadales are ancient, crown ages of all modern genera are no older than 12 million years, supporting a recent hypothesis of mostly Miocene radiations. This phylogeny can contribute to an accurate infrafamilial classification of Zamiaceae.