Genetic differentiation and phylogeographical structure of the Brachionus calyciflorus complex in eastern China

Spatio-temporal patterns and processes of genetic differentiation in passively dispersing zooplankton are drawing much attention from both ecologists and evolutionary biologists. Two opposite phylogeographical scenarios have already been demonstrated in rotifers, which consist of high levels of genetic differentiation among populations even on small geographical scales on the one hand and the traditionally known cosmopolitanism that is associated with high levels of gene flow and long-distance dispersal via diapausing stages on the other hand. Here, we analysed the population genetic structure and the phylogeography of the Brachionus calyciflorus species complex in eastern China. By screening a total of 318 individuals from ten locations along a 2320-km gradient and analysing samples from two growing seasons, we aimed at focusing on both small- and large-scale patterns. We identified eight cryptic species and verified species status of two of these by sexual reproduction tests. Samples in summer and winter yielded different cryptic species. The distribution patterns of these genetically distinct cryptic species were diverse across eastern China, from full cosmopolitanism to local endemism. The two most abundant cryptic species BcWIII and BcSW showed a pattern of strong genetic differentiation among populations and no significant isolation by distance. Long-distance colonization, secondary contact and recent range expansion are probably responsible for the indistinct pattern of isolation by distance. Our results suggest that geographical distance is more important than temporal segregation across seasons in explaining population differentiation and the occurrence of cryptic species. We explain the current phylogeographical structure in the B. calyciflorus species complex by a combination of recent population expansion, restricted gene flow, priority effects and long-distance colonization.     

Mitochondrial DNA variation and the evolutionary history of the Mediterranean species of Cicada L. (Hemiptera,Cicadoidea)

Cicadas are widely distributed in the Mediterranean area and are mainly distinguished by male acoustic signals, which act as specific mate recognition systems. Within the genus Cicada L. several species have diverged in their calling songs without showing external morphological differences, so acoustic recordings and genetic studies are particularly useful for systematic, biogeography and evolutionary studies. This study assesses sequence variation in closely related species of Cicada from the Mediterranean area, using domain III of the 12S rRNA mitochondrial gene in order to determine the phylogenetic relationships and the evolutionary history of this group, as well as the population structure of the two most common species, C. orni and C. barbara. Five distinct haplogroups were identified, C. orni, C. barbara, C. mordoganensis, C. cretensis and C. lodosi, each corresponding to a distinct evolutionary group. C. barbara was the most divergent species within this group, while C. orni and C. mordoganensis were the most similar. The population structure and demographic parameters of the species were not completely resolved. However, there is evidence for the separation of the C. orni Greek populations from the rest of Europe and also for demographic expansions probably related to Pleistocene climate changes. © 2009 The Linnean Society of London, Zoological Journal of the Linnean Society, 2009, 155 , 266–288.     

Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability

Species exhibiting morphological homogeneity and strong population structuring present challenging taxonomic problems: morphology-based approaches infer few species, whereas genetic approaches often indicate more. Morphologically cryptic, yet genetically divergent species groups require alternative approaches to delimiting species that assess adaptive divergence and ecological interchangeability of lineages. We apply such an approach to Promyrmekiaphila, a small genus (three nominal taxa) of trapdoor spiders endemic to northern California to define cohesion species (lineages that are genetically exchangeable and ecologically interchangeable). Genetic exchangeability is evaluated using standard phylogeographical techniques (e.g. nested clade analysis); ecological interchangeability is assessed using two GIS-based approaches. First, climatic values are extracted from layer data for each locality point and utilized in a principal components analysis followed by MANOVA. Second, niche-based distribution models of genetically divergent lineages are created using a maximum-entropy modelling approach; the amount of overlap among lineages is calculated and evaluated against a probability distribution of null overlap. Lineages that have significant amounts of predicted overlap are considered ecologically interchangeable. Based on a synthetic evaluation of ecological interchangeability, geographical concordance, and morphological differentiation, we conclude that Promyrmekiaphila comprises six cohesion species, five of which are cryptic (i.e. undetectable by conventional means).     

An integrative taxonomic review of the Natal mountain catfish,Amphilius natalensis Boulenger 1917 (Siluriformes,Amphiliidae), with description of four new species

Species delimitation is a permanent issue in systematics. The increasing recognition of geographically isolated populations as independent lineages allowed by new methods of analysis has inflated the species-populations dilemma, which involves deciding whether to consider separate lineages as different species or structured genetic populations. This is commonly observed between fishes of adjacent river basins, with some lineages being considered allopatric sister species and others considered isolated populations or variants of the same species. Pseudocorynopoma doriae is a characid diagnosed from its single congener by the number of anal-fin rays and sexually dimorphic characters of males, including distinct fin colouration. The authors found variation in the colour pattern between isolated populations previously identified as P. doriae but no variation in scale or fin-ray counts. They analysed molecular evidence at the population level and morphological differences related to life history (e.g., colour dimorphism related to inseminating behaviour). The results provide compelling evidence for the recognition of a new species of Pseudocorynopoma despite the lack of discrete differences in meristic data. The recognition of the new species is consistent with biogeographical evidence for the long-term isolation of the respective river drainages and with differences between the ichthyofaunal communities of these rivers.     

The species identity and biogeography of Blanus (Amphisbaenia: Blanidae) in Lebanon

The genus Blanus Wagler, 1830 represents limbless, burrowing reptiles of the family Blanidae with disjunct circum-Mediterranean distribution. The recently described species Blanus alexandri Sindaco, Kornilios, Sacchi & Lymberakis, 2014 is known from south-eastern Turkey with a presumed occurrence in the Levant and Iraq. We provide here records from Lebanon and confirm the affiliation of Lebanese populations to this species by mitochondrial and nuclear DNA. Blanus alexandri comprises at least seven deeply evolved phylogenetic clades with up to 11% of uncorrected p-distances in their mitochondrial DNA. This suggests a probably older than the Miocene origin of some of these clades. Populations from Lebanon form a different clade with a genetic diversity that is close to populations from southern Turkey.     

The significance of relatedness and gene flow on population genetic structure in the subsocial spider Eresus cinnaberinus (Araneae: Eresidae)

Interdemic selection, inbreeding and highly structured populations have been invoked to explain the evolution of cooperative social behaviour in the otherwise solitary and cannibalistic spiders. The family Eresidae consists of species ranging from solitary and intermediate subsocial to species exhibiting fully cooperative social behaviour. In this study we, in a hierarchical analysis, investigated relatedness of putative family clusters, inbreeding and population genetic structure of the subsocial spider Eresus cinnaberinus. Five hierarchical levels of investigation ranging from large scale genetic structure (distances of 250 and 50 km level 1 and 2) over microgeographic structure (20 km² and 4 km², level 3 and 4) to a single hill transect of 200 m (level 5) were performed. The purpose of level 5 was two-fold: (1) to investigate the relatedness of putative family groups, and (2) to evaluate the influence of both family living and sampling design on higher level estimates. Relatedness estimates of putative family groups showed an average relatedness of R=0.26. There was no indication of inbreeding. In contrast to social spiders, genetic variation was abundant, H_e?0.10. The population genetic structure was intermediate between social and asocial spiders. Genetic variance increased continually across hierarchical levels. Family structured neighbourhoods biased differentiation estimates among level 5 samples (F_ST? 0.04) and level 3 and 4 samples (0.07ST<0.18), and apparent inbreeding among level 3 and 4 samples, F_IS>0, was caused by disjunct sampling from separate neighbourhoods. Larger scale samples were highly differentiated 0.12ST<0.26, depending on level and sampling design. Due to a distance effect family living did not influence estimates of the higher level 1. Although the dispersing sex among social spiders and the subsocial E. cinnebarinus differ, females versus males, female behaviour of both sociality classes lead to high genetic variance.     

First record of the Brassy Chub Kyphosus vaigiensis (Quoy & Gaimard, 1825) in the Eastern Mediterranean (Osteichthyes: Perciformes: Kyphosidae)

The Brassy Chub, Kyphosus vaigiensis, first recorded in the Mediterranean in 1998, is reported herein from the coast of Israel. The identity of the specimen was confirmed by morphological and molecular analysis. This is the first record of K. vaigiensis from the Eastern Mediterranean. The possible origins of the Israeli record is discussed.     

Evolutionary systematics of the Australian Cyzicidae (Crustacea,Branchiopoda, Spinicaudata) with the description of a new genus

In Australia's arid and semi‐arid zone, most aquatic habitats are nonpermanent. Although approximately 70% of its land surface belongs to these zones, very little is known of the iconic ‘large branchiopods’ that inhabit these important and widespread habitats. In the present study, we investigated 737 Australian specimens of the spinicaudatan taxa Caenestheria and Caenestheriella with a combination of one mitochondrial (cytochrome oxidase subunit I; COI) and three nuclear (elongation factor 1α, internal transcribed spacer 2, and 28S) markers to assess the diversity of species, their phylogenetic relationships, and phylogeographical history. The initial species delimitation was based on COI employing a combination of phylogenetic analyses and two automated approaches to species delimitation (general mixed Yule coalescent model and Automated Barcode Gap Discovery). The outcome was tested by the nuclear markers and considered under differing species concepts. The number of delineated species ranged from 14–27, in no case being in full agreement with any of the two automated approaches. The lower numbers resulted if inferred reproductive isolation, as required for the biological or Hennigian species concept, was employed. Although nuclear markers did not indicate ongoing reproduction, the lack of sympatric co‐occurrences inhibited inferences of definitive reproductive isolation in several instances. If monophyly or an ‘independent evolutionary fate’ was employed, as required for the phylogenetic or evolutionary species concepts, the species' distribution was of no importance and up to 27 species could be delimitated. Because the Australian representatives of both studied genera could not be clearly separated from each other but constitute a single monophyletic clade separated from all available non‐Australian representatives of these genera, we describe a new spinicaudatan genus Ozestheria gen. nov. to accommodate these species. Populations revealed relatively small levels of genetic differentiation over large areas of central and eastern Australia. By far the most pronounced levels of genetic differentiation were observed towards the north‐eastern regions, a pattern possibly explainable by ecological conditions and the movement of nomadic water birds that disperse resting eggs. © 2015 The Linnean Society of London     

Evidence for ecological speciation in the sister species Candidula unifasciata (Poiret, 1801) and C. rugosiuscula (Michaud, 1831) (Helicellinae, Gastropoda)

This paper studies the speciation of two land snail species in south-east France. By using two mitochondrial and one nuclear gene, the species are shown to be sister species within the larger clade of western European Candidula species. The species never occurred syntopically, but a narrow contact zone population was identified. Recent range expansions inferred from phylogeographical methods indicated that the present day distributions are not limited by the colonization capacity of the species. Analysis of environmental variables suggested distribution along an ecotone. The gastropod community is also correlated to this gradient. Morphometric shell analysis showed that the divergence between the sister species is a result of desiccation-resistant shell characters. We therefore conclude that the cause for the ecological speciation is most probably the establishment of the Mediterranean climate ≈ 3.2 mya. A model of ecological speciation with a moving ecotone is put forward.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 79, 611–628.     

基于线粒体ND1和16S rRNA基因序列探讨中国蝴蝶12科的系统发育关系(鳞翅目: 双孔次亚目: 蝶类)

对中国12科共32种代表蝶类的ND1基因和16S rRNA 基因进行了序列测定（包括新测30种ND1基因和9种16S rRNA基因）和比较分析, 同时采用邻接法、最大似然法和贝叶斯法构建了12科蝶类的系统发育树, 探讨了其高级分类群的系统发育关系。序列分析的结果显示: 经比对处理后的两个基因总长度为869 bp, 其中保守位点373个, 可变位点496个, 简约信息位点375个; A+T的平均含量为80.2％, 明显高于C+G的平均含量19.8％。分子系统树表明: 蛱蝶科不是单系群; 珍蝶类、斑蝶类和喙蝶类位于蛱蝶科内; 粉蝶科和凤蝶科具有共同祖先。据此建议: 绢蝶科应归入凤蝶科; 蚬蝶科归入灰蝶科; 珍蝶类、斑蝶类和喙蝶类作为蛱蝶科中的亚科, 眼蝶类从蛱蝶科中分离出来独立成科。另外, 环蝶类的系统分类地位还有待于进一步研究。     

Phylogenetic analyses of mtDNA sequences reveal three cryptic lineages in the widespread neotropical frog Leptodactylus fuscus (Schneider, 1799) (Anura, Leptodactylidae)

Leptodactylus fuscus is a neotropical frog ranging from Panamá to Argentina, to the east of the Andes mountains, and also inhabiting Margarita, Trinidad, and the Tobago islands. We performed phylogenetic analyses of 12S rRNA, 16S rRNA, tRNA-Leu, and ND1 mitochondrial (mt) DNA sequences from specimens collected across the geographic distribution of L. fuscus to examine two alternative hypotheses: (i) L. fuscus is a single, widely distributed species, or (ii) L. fuscus is a species complex. We tested statistically for geographic association and partitioning of genetic variation among mtDNA clades. The mtDNA data supported the hypothesis of several cryptic species within L. fuscus. Unlinked mtDNA and nuclear markers supported independently the distinctness of a 'northern' phylogenetic unit. In addition, the mtDNA data divided the southern populations into two clades that showed no sister relationship to each other, consistent with high differentiation and lack of gene flow among southern populations as suggested by allozyme data. Concordance between mtDNA and allozyme patterns suggests that cryptic speciation has occurred in L. fuscus without morphological or call differentiation. This study illustrates a case in which lineage splitting during the speciation process took place without divergence in reproductive isolation mechanisms (e.g. advertisement call in frogs), contrary to expectations predicted using a biological species framework.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society, 2006, 87 , 325–341. No claim to original US government works.     

Genetic structure of the protist Physarum albescens (Amoebozoa) revealed by multiple markers and genotyping by sequencing

Myxomycetes are terrestrial protists with many presumably cosmopolitan species dispersing via airborne spores. A truly cosmopolitan species would suffer from outbreeding depression hampering local adaptation, while locally adapted species with limited distribution would be at a higher risk of extinction in changing environments. Here, we investigate intraspecific genetic diversity and phylogeography of Physarum albescens over the entire Northern Hemisphere. We sequenced 324 field collections of fruit bodies for 1–3 genetic markers (SSU, EF1A, COI) and analysed 98 specimens with genotyping by sequencing. The structure of the three-gene phylogeny, SNP-based phylogeny, phylogenetic networks, and the observed recombination pattern of three independently inherited gene markers can be best explained by the presence of at least 18 reproductively isolated groups, which can be seen as cryptic species. In all intensively sampled regions and in many localities, members of several phylogroups coexisted. Some phylogroups were found to be abundant in only one region and completely absent in other well-studied regions, and thus may represent regional endemics. Our results demonstrate that the widely distributed myxomycete species Ph. albescens represents a complex of at least 18 cryptic species, and some of these seem to have a limited geographical distribution. In addition, the presence of groups of presumably clonal specimens suggests that sexual and asexual reproduction coexist in natural populations of myxomycetes.     

Habitat Utilization and Depth Distribution of Small Cryptobenthic Fishes (Blenniidae, Gobiesocidae, Gobiidae, Tripterygiidae) in Ibiza (Western Mediterranean Sea)

The paper describes the habitat utilization of small cryptobenthic fishes of the families Blenniidae (Lipophrys nigriceps, and Parablennius zvonimiri), Gobiesocidae (Apletodon incognitus, Gouania wildenowi, Lepadogaster candollei, and L. lepadogaster), Gobiidae (Chromogobius zebratus, Corcyrogobius liechtensteini, Didogobius splechtnai, Gammogobius steinitzi, Millerigobius macrocephalus, Thorogobius ephippiatus, T. macrolepis, and Zebrus zebrus), and Tripterygiidae (Tripterygion melanurus). Nine different habitats from the waterline to a depth of about 40m were examined. The depth distributions of the single species and co-occurrences with other cryptobenthic fish species are given.     

The evolutionary history of the Mediterranean centipede Scolopendra cingulata (Latreille, 1829) (Chilopoda: Scolopendridae) across the Aegean archipelago

In this study we investigate the evolutionary relationships of Scolopendra cingulata (Latreille, 1829) within insular Greece. Our main goal is to infer the time frame of the differentiation of the species in the study area. In this regard, sequence data originating from three mitochondrial genes are used to reconstruct the evolutionary history of 47 insular populations of S. cingulata from the Aegean archipelago. Within the phylogenetic framework and by implementing a relaxed molecular clock methodology, we infer the time estimates of separations of the S. cingulata lineages. The results of the phylogenetic analysis support the presence of three distinct S. cingulata groups in the region. The first group accommodates populations from the eastern Aegean islands, and is closely related to the second group that hosts mainly populations of northern and central Cyclades. The third group is composed of insular populations originating from southern Cyclades. Different temporal splitting scenarios have been evaluated. Based on the scenario strongly supported by the data, we propose a biogeographical scenario that could account for the contemporary distribution of the species' lineages. The splitting events of S. cingulata are estimated to have occurred within the late Miocene. The historical events of the last 13.77 Myr have shaped, through a series of mostly vicariant and dispersal incidents, the present‐day biogeographical pattern of the species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 507–521.     

Coastal fish otoliths from the early Pleistocene of Rhodes (eastern Mediterranean)

Coastal fish assemblages are especially vulnerable to environmental changes, but little is known about their evolution through time, mainly due to the scarcity of fossil material from such settings. The aim of this study is to characterize the early Pleistocene coastal fish assemblages of the eastern Mediterranean and to reconstruct the related paleobathymetric and paleoecologic conditions. Based on otolith findings, we identified thirty-seven teleost fish species from three sedimentary outcrops on the northeastern part of Rhodes Island (southeastern Aegean, Greece, Eastern Mediterranean), which have been placed within the Gelasian (early Pleistocene). The stratigraphic distribution of fifteen taxa is expanded for this interval, while five species are reported for the first time as fossils. The otolith assemblages provided paleodepth estimates indicative of shallow coastal environments. The ecosystem consisted mostly of substrates of sand and mud, with significant rocky micro-habitats and underwater vegetation; the climate was subtropical. These data complement existing knowledge on the study area, while providing new information on the composition of the ichthyofauna of the eastern Mediterranean during the Gelasian.     

A multigene molecular assessment of cryptic biodiversity in the iconic freshwater blackfishes (Teleostei: Percichthyidae: Gadopsis) of south‐eastern Australia

Freshwater biodiversity is under ever increasing threat from human activities, and its conservation and management require a sound knowledge of species‐level taxonomy. Cryptic biodiversity is a common feature for aquatic systems, particularly in Australia, where recent genetic assessments suggest that the actual number of freshwater fish species may be considerably higher than currently listed. The freshwater blackfishes (genus Gadopsis) are an iconic group in south‐eastern Australia and, in combination with their broad, naturally divided distribution and biological attributes that might limit dispersal, as well as ongoing taxonomic uncertainty, they comprise an ideal study group for assessing cryptic biodiversity. We used a multigene molecular assessment including both nuclear (51 allozyme loci; two S7 introns) and matrilineal markers (cytb) to assess species boundaries and broad genetic substructure within freshwater blackfishes. Range‐wide examination demonstrates the presence of at least six candidate species across two nominal taxa, Gadopsis marmoratus and Gadopsis bispinosus. Phylogeographical patterns often aligned to purported biogeographical provinces but occasionally reflected more restricted and unexpected relationships. We highlight key issues with taxonomy, conservation, and management for a species group in a highly modified region. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 521–540.