The evolutionary history of the order Antipatharia (Cnidaria: Anthozoa: Hexacorallia) as inferred from mitochondrial and nuclear DNA: implications for black coral taxonomy and systematics

Although black corals inhabit all the world's oceans, they have been relatively understudied as ～185 of 247 species occur at depths > 50 m. Antipatharians have been included in several phylogenetic studies; however, sample sizes are small and taxonomic coverage minimal. Low levels of mitochondrial (mt) sequence divergence within Scleractinia and Octocorallia are assumed to apply to all anthozoans, although no formal study has been conducted on the order Antipatharia. To quantify genetic variation in the black coral mitogenome, we analysed DNA sequences of the two longest intergenic regions (IGRs) and cox3‐cox1 for 26 of 41 genera, representing all families and subfamilies. We also quantified divergence at the intraspecific level using six mtIGRs and their flanking protein‐coding genes and rRNA for 100+ colonies of Antipathes griggi. Utilizing sequence data from the two mtIGRs, cox3‐cox1, as well as nuclear 18S and 28S, we constructed the first multi‐locus phylogenies of the Antipatharia. Reconstructions revealed that species in the genus Stichopathes are split across two families, Sibopathes macrospina groups among North Atlantic Parantipathes (suggesting the actinopharynx and mesenteries were secondarily lost), and three families are polyphyletic. These and other results provide novel, independent insights into the evolutionary history of antipatharians and support placement of species into higher‐level groupings based on microscopic skeletal features rather than gross colony morphology. An illustrated key to the seven currently recognized families is also provided. © 2013 The Linnean Society of London     

Genetic assessment of population structure and connectivity in the threatened Mediterranean coral Astroides calycularis (Scleractinia, Dendrophylliidae) at different spatial scales

Understanding dispersal patterns, population structure and connectivity among populations is helpful in the management and conservation of threatened species. Molecular markers are useful tools as indirect estimators of these characteristics. In this study, we assess the population genetic structure of the orange coral Astroides calycularis in the Alboran Sea at local and regional scale, and at three localities outside of this basin. Bayesian clustering methods, traditional F-statistics and D(est) statistics were used to determine the patterns of genetic structure. Likelihood and coalescence approaches were used to infer migration patterns and effective population sizes. The results obtained reveal a high level of connectivity among localities separated by as much as 1 km and moderate levels of genetic differentiation among more distant localities, somewhat corresponding with a stepping-stone model of gene flow and connectivity. These data suggest that connectivity among populations of this coral is mainly driven by the biology of the species, with low dispersal abilities; in addition, hydrodynamic processes, oceanographic fronts and the distribution of rocky substrate along the coastline may influence larval dispersal.     

Phenotypic variation among local populations of phlebotomine sand flies (Diptera: Psychodidae) in southern Turkey.

The wing-shape morphology of local populations of the medically important phlebotomine sand flies, Phlebotomus sergenti, P. papatasi, P. tobbi, and P. similis, were examined in both sexes by using geometric morphometrics. There are three major mountain ranges that may serve as geographical barriers for species distribution in the study area and four main gaps were recognized among these barriers. We found no statistically important differences in wing morphology in all examined species in both sexes for all local populations. These results show that the barriers are not sufficient to stop gene flow among local populations of sand flies. The graphical depiction of PCA, CVA, and F-test confirmed our morphometric study suggesting that the difference in wing morphology between P. similis and P. sergenti indicates that these are clearly different species. These two show sympatric distribution in the Konya Plain of Anatolia.     

Structures of benthic insect communities in two southeastern Wyoming (USA) streams: similarities and differences among spatial units at different local scales

Four sites on each of two southeastern Wyoming streams, Medicine Bow River (MBR) and Rock Creek (RC), were investigated during the summer and autumn of 2001 and 2002. This investigation resulted in inventories of benthic insect communities being obtained from these two streams. It also resulted in twelve metrics being calculated from benthic insect communities, and these metrics were compared between two spatial units at different local scales. Of the metrics used, five indicated taxa richness, four indicated relative abundance, two indicated diversity, and one involved a biotic index for organic pollution. More specifically, we used each metric to compare the montane with the plains sub-basin, as well as to compare two distinctly different types of substrates within each of the sub-basins. Also, metrics were compared between the two streams. Results indicated that few differences were observed between naturally-occurring substrates within sub-basins. In addition, few differences were observed between the two streams. In contrast, however, several differences were observed between the montane and plains sub-basins. Such differences were caused from naturally-occurring variations in hydraulic and ecological conditions. These findings suggest that the spatial scale should be carefully considered when selecting metrics for use in monitoring programs that are designed to detect anthropogenic disturbances in lotic systems. Handling editor: K. Martens     

High levels of morphological variation despite close genetic relatedness between Zoanthus aff. vietnamensis and Zoanthus kuroshio (Anthozoa: Hexacorallia)

Recent investigations into the encrusting anemone genus Zoanthus using molecular and morphological techniques have begun to bring order to this taxonomically neglected group. Previous studies have confirmed the existence of three distinct species present in southern Japan: Z. sansibaricus, Z. kuroshio, and Z. gigantus. Results from such studies show species of Zoanthus to be highly morphologically plastic, often incorporating morphotypes with varying oral disk color and oral disk diameter. Literature lists the species Z. aff. vietnamensis as occurring in southern Japan and throughout the western Pacific Ocean, but due to the morphological plasticity of Zoanthus species, a re-examination of Z. aff. vietnamensis using molecular techniques was needed. Here, using mitochondrial 16S rDNA and the nuclear internal transcribed spacer of ribosomal DNA (ITS-rDNA) sequences, as well as morphological data, we have examined several nominal Z. aff. vietnamensis samples collected from Kagoshima Bay and Yakushima Island, Japan. Based on polyp length and diameter, oral disk diameter, mesentery and tentacle numbers, and colony form, Z. aff. vietnamensis is easily distinguishable from Z. sansibaricus, Z. kuroshio, and Z. gigantus. However, despite these clear morphological differences, our mitochondrial and nuclear sequence-based phylogenies indicate that Z. aff. vietnamensis and Z. kuroshio are very closely related (perhaps conspecific), highlighting the morphological plasticity of this genus and the difficulty of species identification based on morphological data alone.     

Comparative analysis of population structure across environments and geographical scales at major histocompatibility complex and microsatellite loci in Atlantic salmon (Salmo salar)

Evidence of selection acting on major histocompatibility complex (MHC) genes has been illustrated with the analysis of their nucleotide sequences and allele frequency distribution. Comparing the patterns of population differentiation at neutral markers and MHC genes in the wild may provide further insights about the relative role of selection and neutrality in shaping their diversity. In this study, we combine both methods to assess the role of selection on a MHC gene in Atlantic salmon. We compare variation at a MHC class II B locus and microsatellites among 14 samples from seven different rivers and seven subpopulations within a single river system covering a variety of habitats and different geographical scales. We show that diversifying selection is acting on the sites involved in antigen presentation and that balancing selection maintains a high level of polymorphism within populations. Despite important differences in habitat type, the comparison of the population structure at MHC and microsatellites on large geographical scales reveals a correlation between patterns of differentiation, indicating that drift and migration have been more important than selection in shaping population differentiation at the MHC locus. In contrast, strong discrepancies between patterns of population differentiation at the two types of markers provides support for the role of selection in shaping population structure within rivers. Together, these results confirm that natural selection is influencing MHC gene diversity in wild Atlantic salmon although neutral forces may also be important in their evolution.     

Relationships among biological elements (macrophytes, macroinvertebrates and ichthyofauna) for different core river types across Europe at two different spatial scales

The objective of this study was to evaluate differences in correlations among Biological Elements and environmental parameters for different river types, analysed at two different spatial scales. A total of 82 sites, with at least good ecological status, were sampled across Europe, representing three core river types: Mountain rivers (26 sites); Lowland rivers (29 sites) and Mediterranean rivers (17 sites). At each site samples of macrophytes, macroinvertebrates and fishes were taken during spring, following the methodological procedures established by the European STAR project. Environmental parameters were also recorded, based on a site protocol developed by the European projects AQEM and STAR. Environmental parameters were divided into three categories: aquatic habitats (mesohabitat scale), global features (reach scale) and obligatory typology parameters of Water Framework Directive (WFD) (geographical scale). Data were analysed to evaluate at the two scales, first, relationships among biological elements, and second, relationships between biological elements and environmental parameters. Within each river type, correlation matrices (Bray–Curtis distance) were calculated separately for each biological element and for each category of environmental parameters. All biological elements were correlated (p<0.01) to the larger spatial scale: macrophytes and macroinvertebrates are more correlated in lowland and mountain rivers, while in Mediterranean rivers, fish and macrophytes presented higher correlations. These links tend to be consistent for different spatial scales, except if they are weak on a larger regional scale, obligatory parameters of WFD were, in most cases, significantly correlated with the three biological communities (p<0.05). Results at different spatial scales supported the hierarchical theory of river formation. Reach and mesohabitat environmental parameters tend to explain aquatic communities at a lower spatial scale, while geographical parameters tend to explain the communities at a major spatial scale.     

Climate history,human impacts and global body size of Carnivora (Mammalia: Eutheria) at multiple evolutionary scales

Aim One of the longest recognized patterns in macroecology, Bergmann’s rule, describes the tendency for homeothermic animals to have larger body sizes in cooler climates than their phylogenetic relatives in warmer climates. Here we provide an integrative process‐based explanation for Bergmann’s rule at the global scale for the mammal order Carnivora. Location Global. Methods Our database comprises the body sizes of 209 species of extant terrestrial Carnivora, which were analysed using phylogenetic autocorrelation and phylogenetic eigenvector regression. The interspecific variation in body size was partitioned into phylogenetic (P) and specific (S) components, and mean P‐ and S‐components across species were correlated with environmental variables and human occupation both globally and for regions glaciated or not during the last Ice Age. Results Three‐quarters of the variation in body size can be explained by phylogenetic relationships among species, and the geographical pattern of mean values of the P‐component is the opposite of the pattern predicted by Bergmann’s rule. Partial regression revealed that at least 43% of global variation in the mean phylogenetic component is explained by current environmental factors. In contrast, the mean S‐component of body size shows large positive deviations from ancestors across the Holarctic, and negative deviations in southern South America, the Sahara Desert, and tropical Asia. There is a moderately strong relationship between the human footprint and body size in glaciated regions, explaining 19% of the variance of the mean P‐component. The relationship with the human footprint and the P‐component is much weaker in the rest of the world, and there is no relationship between human footprint and S‐component in any region. Main conclusions Bergmannian clines are stronger at higher latitudes in the Northern Hemisphere because of the continuous alternation of glacial–interglacial cycles throughout the late Pliocene and Pleistocene, which generated increased species turnover, differential colonization and more intense adaptive processes soon after glaciated areas became exposed. Our analyses provide a unified explanation for an adaptive Bergmann’s rule within species and for an interspecific trend towards larger body sizes in assemblages resulting from historical changes in climate and contemporary human impacts.     

Allozyme variation among Rana balcanica,R. levantina,and R. ridibunda (Amphibia: Anura)1

The allozyme variation among water frogs of the species R. balcanica, R. levantina and R. ridibunda, all formerly considered as one species (R. ridibunda Pallas, 1771), was studied using horizontal starch gel electrophoresis. Blood samples (N # 63) of frogs were collected from five populations in Greece and Israel. Samples (N = 9) of the hybrid frog R. esculenta collected from a locality in Germany were used as an outgroup for phylogenetic analyses. Fifteen enzymes controlled by twenty presumptive loci were identified. Thirteen loci were polymorphic within or among the studied populations. Genetic differentiation among the species was considerably greater than among populations of the same species. Even at Nestos River where R. ridibunda and R. balcanica occur in the same habitats, individuals could be assigned to either species due to characteristic differences of the genotypes (GPI1). This indicates reproductive isolation among these species. The reconstruction of phylogenetic relationships among the three species based on the allozyme data corroborated the model presented on the basis of bioacoustic data: R. ridibunda and R. balcanica (Nei's genetic distance D = 0.0820) are sibling species pertaining to an Eurasian lineage, whereas R. levantina (distance to the European species D = 0.1780 - 0.1955) together with R. perezi represent an independent afroasian lineage.     

Intragenomic variation within ITS1 and ITS2 of freshwater crayfishes (Decapoda: Cambaridae): implications for phylogenetic and microsatellite studies

Intragenomic variation in ITS1 and ITS2 is known to exit but is widely ignored in phylogenetic studies using these gene regions. The amount of variation in seven crayfish species, including three populations of Orconectes luteus and two of Procambarus clarkii, was assessed by sequencing 3, 5, or 10 clones from the same individuals, for a total of 77 sequences. The ITS1 and ITS2 sequences reported here are some of the longest known, with aligned lengths of 760 and 1,300 bp, respectively. They contain multiple microsatellite insertions, all of which show considerable intragenomic variation in the number of repeat elements. This variation is enough to obscure phylogenetic relationships at the population level, although relationships between species can be estimated. Given the hybridization techniques used to locate microsatellites, multiple-copy regions like ITS1 and ITS2 will be preferentially found if they contain microsatellites, and in these cases the microsatellites will not behave as typical Mendelian markers and could give spurious results.     

How to allow SAR collapse across local and continental scales: a resolution of the controversy between Storch et al. (2012) and Lazarina et al. (2013)

Up‐scaling species richness from local to continental scales is an unsolved problem of macroecology. Macroecologists hope that proper up‐scaling can uncover the hidden rules that underlie spatial patterns in species richness, but a machinery to up‐scale species richness also has a purely practical side at the scales and for the habitats where direct observations cannot be performed. The species–area relationship (SAR) could provide a tool for up‐scaling, but no valid method has yet been put forward. Such a method would have resulted from Storch et al.'s (2012) suggestion that there is a universal curve to which each rescaled SAR collapses, if Lazarina et al. (2013) had not shown that it does not: both arguments were supported by data analyses. Here we present an analytical model for mainland SAR and argue in favour of the latter authors. We identify 1) the variation in mean species‐range size, 2) the variation in forces that drive SAR at various scales, and 3) the finite‐area effect, as the reasons for the absence of collapse. Finally, we suggest a rescaling that might fix the problem. We conclude, however, that ecologists are still far from finding a practical, robust and easy‐to‐use solution for up‐scaling species richness from SARs.     

Life tables of the processionary caterpillar Ochrogaster lunifer Herrich-Schäffer (Lepidoptera: Thaumetopoeidae) at local and regional scales

A major ongoing debate in population ecology has surrounded the causative factors underlying the abundance of phytophagous insects and whether or not these factors limit or regulate herbivore populations. However, it is often difficult to identify mortality agents in census data, and their distribution and relative importance across large spatial scales are rarely understood. Here, we present life tables for egg batches and larval cohorts of the processionary caterpillar Ochrogaster lunifer Herrich-Schäffer, using intensive local sampling combined with extensive regional monitoring to ascertain the relative importance of different mortality factors at different localities. Extinction of entire cohorts (representing the entire reproductive output of one female) at natural localities was high, with 82% of the initial 492 cohorts going extinct. Mortality was highest in the egg and early instar stages due to predation from dermestid beetles, and while different mortality factors (e.g. hatching failure, egg parasitism and failure to establish on the host) were present at many localities, dermestid predation, either directly observed or inferred from indirect evidence, was the dominant mortality factor at 89% of localities surveyed. Predation was significantly higher in plantations than in natural habitats. The second most important mortality factor was resource depletion, with 14 cohorts defoliating their hosts. Egg and larval parasitism were not major mortality agents. A combination of predation and resource depletion consistently accounted for the majority of mortality across localities, suggesting that both factors are important in limiting population abundance. This evidence shows that O. lunifer is not regulated by natural enemies alone, but that resource patches ( Acacia trees) ultimately, and frequently, act together to limit population growth.     

Genetic variation and population structure in Korean endemic species: III.Hosta minor (Liliaceae)

Hosta minor, an insect-pollinated and rhizomatous herbaceous perennial, occurs in eastern and southern Korean Peninsula. AlthoughH. minor is a Korean endemic species and most populations of the species are scattered, the species maintains considerably high levels of genetic variation within the species, with a moderate level of variation (14%) found among populations. Nineteen of the 29 putative loci resolved (66%) were polymorphic within the species, the mean number of alleles per locus was 2.10 across all populations and averaged 1.68 within populations. In addition, genetic diversity was a considerably higher (for species and population level, mean estimates of genetic diversity were 0.275 and 0.230, respectively) than the average for other long-lived herbaceous perennials. Indirect estimate of the number of migrants per generation (Nm=1.03, calculated from mean G_ST) was moderate. Factors contributing to the high levels of genetic diversity found within populations ofH. minor include population maintenance via sexual and asexual modes of reproduction, primarily outcrossing breeding system, long generation time, probable ancient polyploid origin of the species, and moderate levels of seed dispersal by wind. Human disturbance in South Korea such as road and apartment constructions appears to be the major threat to this genetically diverse species.     

Mitochondrial DNA variation among populations of Oedura reticulata (Gekkonidae) in remnant vegetation: implications for metapopulation structure and population decline

Restriction fragment length polymorphism (RFLP) analysis of mitochondrial DNA was used to examine the regional population structure of a species of gecko (Oedura reticulata) in vegetation remnants within the Western Australian wheatbelt. The species exhibited considerable polymorphism within and between populations with 22 haplotypes recognized among 12 populations. Phylogenetic analysis of haplotypes and clustering of nucleotide divergence among populations demonstrated little regional structure within the species with several haplotypes present in all three regions surveyed. This contrasted markedly with variation in haplotype frequency among populations which showed a high degree of independence between populations indicating that current levels of maternal gene flow are low and that the populations are too small to prevent genetic drift. This conclusion is supported by generally lower numbers of haplotypes in remnant populations than in nearby nature reserves. These findings, combined with demographic data from a previous study, suggest that post-fragmentation populations of O. reticulata are unable to form a metapopulation structure in the habitat that remains and that stochastic extinction forces alone will be sufficient to severely reduce the regional distribution of this species. This study demonstrates that mtDNA is a useful tool for detecting contemporary population phenomena and can provide qualitative information of practical importance to wildlife managers.     

Extensive intraspecific chloroplast DNA (cpDNA) variation in the alpine Draba aizoides L. (Brassicaceae): haplotype relationships and population structure

Chloroplast DNA (cpDNA) sequence variation is currently the most widely used tool for the inference of phylogenetic relationships among plants at all taxonomic levels. Generally, noncoding regions tend to evolve faster than coding sequences and have recently been applied to the study of phylogenetic relationships among closely related taxa. An implicit assumption of many of these studies is that intraspecific cpDNA variation is either absent or low and therefore will not interfere with the reconstruction of interspecific relationships. A survey of cpDNA sequence variation in the common alpine plant species Draba aizoides L. was undertaken to assess levels of intraspecific cpDNA sequence variation. These levels were compared to levels of interspecific sequence divergence between D. aizoides and related alpine Draba species. Intraspecific cpDNA sequence divergence was extensive in D. aizoides, and intraspecific differences were often larger than interspecific differences. cpDNA haplotype relationships were explored using a maximum parsimony approach and minimum-spanning networks. Results from both methods were largely congruent but comparisons provided interesting insights into the presumed evolutionary history of cpDNA haplotypes. A combined effect of cpDNA introgression and complex lineage sorting was inferred to explain the pattern of cpDNA variation found in D. aizoides. Our results suggest that intraspecific cpDNA variation can be extensive and that intraspecific variation needs to be taken into account when inferring phylogenetic relationships among closely related taxa.     

Phylogeography of the temperate marine bivalve Cerastoderma edule (Linnaeus, 1758) (Bivalvia: Cardiidae) in the Subarctic: Unique diversity and strong population structuring at different spatial scales

Using mitochondrial COI sequencing, we explored the genetic diversity and population structuring of the common cockle Cerastoderma edule (Linnaeus, 1758) in the Norwegian and Barents Seas. Phylogeographic diversity and hence the evolutionary history of C. edule on the Scandinavian and Russian coastlines were found to be richer than expected for populations of temperate species in postglacially colonized seas. A major phylogeographic break at Lofoten Islands separated a group of subarctic populations dominated by a distinct star‐shaped clade of haplotypes from those to the south, extending to the North Sea and having highest gene diversities (h). At the northeastern edge of the range of C. edule, the Russian Murman coast, populations show a mosaic structure with considerable admixture of haplotypes from the south and high local‐scale variation in haplotype diversity (ranging between 0 and 0.8). To explain this mosaic we refer to the core‐satellite metapopulation model, with Norwegian populations as core, and Murman populations as satellites. Our results contradict the conventional biogeographic paradigm implying lack of metapopulation structuring in marine broadcast spawning invertebrates. Hypotheses considered to explain the origin of the unique variation in cockles from Northern Norway involve an early postglacial colonization and establishment of these populations (10–12 ka ago), a persistent oceanographic break at Lofoten, and a mitochondrial selective sweep associated with the postglacial recolonization of the subarctic seas by the boreal C. edule.     

ITS rDNA variation of the Coprinopsis phlyctidospora (syn.: Coprinus phlyctidosporus) complex in the Northern and Southern Hemispheres

 Coprinopsis phlyctidospora (syn: Coprinus phlyctidosporus) from the Netherlands, Japan, New Zealand, and Australia can be segregated into two groups, northern and southern, based on the nucleotide sequences of their ITS regions. The mating type of a C. phlyctidospora isolate was tetrapolar. Mating reactions were compatible between monokaryotic testers derived from basidiospores of a Japanese isolate and dikaryotic isolates obtained from a wide geographic area in Japan. In contrast, mating between the Japanese monokaryotic and dikaryotic isolates from Australia and New Zealand were incompatible. These results indicated that C. phlyctidospora was complex and individuals currently recognized as C. phlyctidospora in the Northern Hemisphere and those in the Southern Hemisphere are distinct taxa. The relationship between the clades and the biogeography of the C. phlyctidospora complex are also discussed. Received: January 22, 2002 / Accepted: March 15, 2002     

Isoelectric focusing of red cell phosphoglucomutase (E.C.:2.7.5.1) at the PGM1 locus in a French-Canadian population

Summary Phosphoglucomutase₁ (PGM₁) polymorphism was studied in a French-Canadian population of Québec city, Canada by means of a low voltage (max 500 V) isoelectric focusing (IEF) procedure on vertical polyacrylamide gel slabs. Frequencies of the four common PGM₁ genes estimated from the phenotype distribution in 308 unrelated individuals were PGM ₁ ¹⁺ , 0.61 (±0.02); PGM ₁ ^1- , 0.13 (±0.01); PGM ₁ ¹⁺ , 0.61 (±0.02); PGM ₁ ^1- , 0.18 (±0.02); and PGM ₁ ¹⁺ , 0.61 (±0.02); PGM ₁ ^1- , 0.08 (±0.01). The segregation patterns observed in 154 families, which included 31 different mating types and 353 children, confirmed a Mendelian inheritance of four autosomal genes. The distribution of the PGM₁ phenotypes observed or expected in a Hardy-Weinberg equilibrium was compared with that of other populations. A significant (P<0.001) difference was found between the Québec population and a Black population from Keneba, Gambia, West-Africa.     

Phylogenetic relationships among Strobilanthes s.l. (Acanthaceae): evidence from ITS nrDNA, trnL-F cpDNA, and morphology

Chloroplast trnL-F sequence data, nuclear ribosomal internal transcribed spacer (ITS) sequence data, and morphology were used to analyze phylogenetic relationships among members of the subtribe Strobilanthinae. Parsimony and maximum likelihood analyses of trnL-F indicate that the Strobilanthinae are a monophyletic group. While parsimony analysis of ITS recovers a nonmonophyletic subtribe, maximum likelihood analysis of ITS corroborates results from trnL-F and suggests that systematic error is impacting on ITS parsimony analysis. A combined ITS and trnL-F analysis strengthens the signal and also recovers a monophyletic subtribe. All analyses indicate that Hemigraphis, Sericocalyx, and Strobilanthes are nonmonophyletic. With one exception, all morphological characters included in a combined ITS and morphological analysis are homoplastic. The prospect for a new informative generic classification of the Strobilanthinae aiming to recognize and diagnose only monophyletic groups is considered. While some groups can be diagnosed, adequate diagnosis of the majority of groups remains problematic. Consequently, a single expanded genus Strobilanthes sensu lato is proposed at the level of the well-supported and monophyletic Strobilanthinae.