Chemotaxonomic Considerations of the n‐Alkane Composition in Pinus heldreichii,P. nigra,and P. peuce

The n‐alkane composition in the leaf cuticular waxes of natural populations of Bosnian pine (Pinus heldreichii), Austrian pine (P. nigra), and Macedonian pine (P. peuce) was compared for the first time. The range of n‐alkanes was wider in P. nigra (C₁₆ – C₃₃) than in P. heldreichii and P. peuce (C₁₈ – C₃₃). Species also diverged in abundance and range of dominant n‐alkanes (P. heldreichii: C₂₃, C₂₇, and C₂₅; P. nigra: C₂₅, C₂₇, C₂₉, and C₂₃; P. peuce: C₂₉, C₂₅, C₂₇, and C₂₃). Multivariate statistical analyses (PCA, DA, and CA) generally pointed out separation of populations of P. nigra from populations of P. heldreichii and P. peuce (which were, to a greater or lesser extent, separated too). However, position of these species on the basis of n‐alkane composition was in accordance neither with infrageneric classification nor with recent molecular and terpene investigations.     

Phylogeography and diversification of an Amazonian understorey hummingbird: paraphyly and evidence for widespread cryptic speciation in the Plio‐Pleistocene

Straight‐billed Hermit Phaethornis bourcieri inhabits the understorey of upland terra firme forest throughout most of the Amazon basin. Currently, two allopatric taxa regarded as subspecies are recognized: P. b. bourcieri and P. b. major. However, the validity, interspecific limits and evolutionary history of these taxa are not yet fully elucidated. We use molecular characters to propose a phylogenetic hypothesis for populations and taxa grouped under Phaethornis bourcieri. Our results showed that P. bourcieri is part of the ‘Ametrornis’ clade, along with Phaethornis philippii and Phaethornis koepckeae, and that the subspecies major is more closely related to the latter two species than to populations grouped under nominate bourcieri. Our phylogenetic hypotheses recovered three main reciprocally monophyletic clades under nominate bourcieri separated by the lower Negro River and the Branco River or the Branco–Negro interfluve (clades B and C) and the upper Amazon (Solimões) or lower Marañon/Ucayali Rivers (clades C and D). Based on multi‐locus phylogeographic and population genetics approaches, we show that P. b. major is best treated as a separate species, and that P. b. bourcieri probably includes more than one evolutionary species, whose limits remain uncertain. The diversification of the ‘Ametrornis’ clade (P. bourcieri, P. philippii and P. koepckeae) is centred in the Amazon and appears to be closely linked to the formation of the modern Amazon drainage during the Plio‐Pleistocene.     

Red- and yellow-footed tortoises, <Emphasis Type="Italic">Chelonoidis carbonaria</Emphasis> and <Emphasis Type="Italic">C. denticulata</Emphasis> (Reptilia: Testudines: Testudinidae), in South American savannahs and forests: do their phylogeographies reflect distinct habitats?

Using sequence data of the mitochondrial cytochrome b gene, we investigated phylogeographic differentiation of the Amazonian tortoise species Chelonoidis carbonaria and C. denticulata. While C. carbonaria is generally restricted to savannah habitats and adjacent forests, C. denticulata is associated with wet tropical and subtropical forests. Our study suggests a correlation between distinct habitat preferences and phylogeography of the two species. In Maximum Parsimony, Maximum Likelihood and Bayesian analyses, haplotypes of C. carbonaria cluster in several distinct clades reflecting the species’ patchy distribution in savannah habitats. By contrast, haplotypes of C. denticulata are only weakly differentiated; a finding also confirmed by parsimony network analysis. This suggests that the contiguous Amazonian rainforest allows gene flow between populations of the forest-dwelling C. denticulata throughout the range, but significantly impedes gene flow in C. carbonaria. The phylogeographic structure and extant distribution pattern of C. carbonaria is supportive of former Amazonian rainforest fragmentation, enabling the dispersal of savannah species. Based on fossil calibration, we dated divergence times for the C. carbonaria clades using a relaxed molecular clock, resulting in average estimates ranging from 4.0–2.2 mya. This implies that the onset of rainforest fragmentation could predate the Pleistocene considerably. Furthermore, our findings call for further research on geographic and taxonomic variation in C. carbonaria and for a reassessment of the conservation status of the distinct genetic units.     

Genetic diversity and haplotype distribution of Pachymeniopsis gargiuli sp. nov. and P. lanceolata (Halymeniales,Rhodophyta) in Korea,with notes on their non‐native distributions

The red alga Pachymeniopsis lanceolata, formerly known as Grateloupia lanceolata, is a component of the native algal flora of northeast Asia and has been introduced to European and North American waters. It has been confused with a cryptic species collected from Korea and Italy. Our analyses of rbcL, cox3 and ITS from P. lanceolata and this cryptic species has revealed two distinct entities, forming a clade, which were clearly separated from its congeners and positioned with other Asian species. Here, we describe the cryptic species as P. gargiuli sp. nov., a species that differs from others by molecular sequence and subtle anatomical characters. We hypothesize that P. gargiuli may have been recently dispersed by anthropogenic vectors, possibly at or near the same time as was P. lanceolata. Our cox3 data set revealed that one haplotype of P. gargiuli, shared between Korea and Italy, and two haplotypes of P. lanceolata, commonly occurring in Korea and USA, are invasive haplotypes. This is the first report of the utility of the mitochondrial coding cox3 sequences in red algae.     

Evaluation of attractants and traps for monitoring small banded pine weevil Pissodes castaneus

This study aimed to develop a semiochemical‐baited trapping system to monitor the populations of small banded pine weevil, Pissodes castaneus, a serious pest in Pinus sylvestris young stands that are weakened by biotic and abiotic factors. The scope of the work included the development of a dispenser for compounds (ethanol and α‐pinene) emitted by P. sylvestris and the pheromones of P. castaneus: grandisol and grandisal. Additionally, the effectiveness of beetle catches in different types of traps (unitrap, cross‐unitrap and long and short pipe traps) baited with a dispenser was assessed. The olfactometric studies showed that most of the newly hatched beetles that had not fed were attracted by a mixture of grandisol and grandisal. However, in the group of feeding beetles, half were attracted by a mixture of ethanol and α‐pinene. These results indicated that both pheromones and α‐pinene plus ethanol should be useful for capturing P. castaneus beetles. In the field trials, the highest efficiency was found in baited unitraps that caught up to several hundred P. castaneus beetles, while the baited cross‐unitraps caught up to a few dozen beetles. No insects were found in either type of baited pipe trap or in any of the unbaited control traps. The baited unitraps and cross‐unitraps also collected, with varied intensity, Hylobius abietis beetles, a serious pest of reforestations. These results indicate the possibility of using a unitrap baited with a 4‐component attractant for monitoring P. castaneus in integrated pest management for the protection of young forests.     

Diversity of bladed Bangiales (Rhodophyta) in western Mediterranean: recognition of the genus Themis and descriptions of T. ballesterosii sp. nov., T. iberica sp. nov., and Pyropia parva sp. nov.

The diversity of the bladed species of the red algal order Bangiales from the Iberian Mediterranean shores has been reassessed after a detailed study of this region. Prior to this study, 11 bladed species of Bangiales had been reported from Mediterranean waters: Porphyra atropurpurea, P. cordata, P. coriacea, P. dioica, P. linearis, P. purpurea, P. umbilicalis, Pyropia leucosticta, Pyropia koreana (as P. olivii), Py. elongata (as P. rosengurttii) and Py. suborbiculata. A combined analysis of the nuclear nSSU and the plastid rbcL genes together with detailed morphological studies has confirmed the presence of species within the genera Porphyra and Pyropia and also revealed a third, undescribed genus, Themis gen. nov. Porphyra linearis, Pyropia elongata and the introduced Pyropia koreana had been previously listed for the Mediterranean and were recorded in this study. An additional four species, including the introduced Pyropia suborbiculata and three new species: Pyropia parva sp. nov., Themis ballesterosii sp. nov., and Themis iberica sp. nov. were also observed. Hence, most of the Porphyra species traditionally reported along these shores were not reported in this survey. This new floristic Bangiales composition confirms the importance of the Mediterranean basin as a hotspot for biodiversity, possible endemics of ancient origin and high proportion of introductions. Our data also continue to confirm the extent of Bangiales diversity at regional and worldwide levels.     

Phylogeographic patterns of a lower intertidal isopod in the Gulf of California and the Caribbean and comparison with other intertidal isopods

A growing body of knowledge on the diversity and evolution of intertidal isopods across different regions worldwide has enhanced our understanding on biological diversification at the poorly studied, yet vast, sea–land interface. High genetic divergences among numerous allopatric lineages have been identified within presumed single broadly distributed species. Excirolana mayana is an intertidal isopod that is commonly found in sandy beaches throughout the Gulf of California. Its distribution in the Pacific extends from this basin to Colombia and in the Atlantic from Florida to Venezuela. Despite its broad distribution and ecological importance, its evolutionary history has been largely neglected. Herein, we examined phylogeographic patterns of E. mayana in the Gulf of California and the Caribbean, based on maximum‐likelihood and Bayesian phylogenetic analyses of DNA sequences from four mitochondrial genes (16S rDNA, 12S rDNA, cytochrome oxidase I gene, and cytochrome b gene). We compared the phylogeographic patterns of E. mayana with those of the coastal isopods Ligia and Excirolana braziliensis (Gulf of California and Caribbean) and Tylos (Gulf of California). We found highly divergent lineages in both, the Gulf of California and Caribbean, suggesting the presence of multiple species. We identified two instances of Atlantic–Pacific divergences. Some geographical structuring among the major clades found in the Caribbean is observed. Haplotypes from the Gulf of California form a monophyletic group sister to a lineage found in Venezuela. Phylogeographic patterns of E. mayana in the Gulf of California differ from those observed in Ligia and Tylos in this region. Nonetheless, several clades of E. mayana have similar distributions to clades of these two other isopod taxa. The high levels of cryptic diversity detected in E. mayana also pose challenges for the conservation of this isopod and its fragile environment, the sandy shores.     

Terpenes as Useful Markers in Differentiation of Natural Populations of Relict Pines Pinus heldreichii,P. nigra,and P. peuce

Comparative analysis of terpene diversity and differentiation of relict pines Pinus heldreichii, P. nigra, and P. peuce from the central Balkans was performed at the population level. Multivariate statistical analyses showed that the composition of needle terpenes reflects clear divergence among the pine species from different subgenera: P. peuce (subgenus Strobus) vs. P. nigra and P. heldreichii (subgenus Pinus). In addition, despite the described morphological similarities and the fact that P. nigra and P. heldreichii may spontaneously hybridize, our results indicated differentiation of their populations naturally growing in the same area. In accordance with recently proposed concept of ‘flavonic evolution’ in the genus Pinus, we assumed that the terpene profile of soft pine P. peuce, defined by high amounts of six monoterpenes, is more basal than those of hard pines P. nigra and P. heldreichii, which were characterized by high content levels of mainly sesquiterpenes. In order to establish precise positions of P. heldreichii, P. nigra and P. peuce within the taxonomic and phylogenetic tree, as well as develop suitable conservation strategies and future breeding efforts, it is necessary to perform additional morphological, biochemical, and genetic studies.     

Differential Accumulation of Volatile Organic Compounds by Leaves and Roots of Two Guianese Philodendron Species,P. fragrantissimum Kunth and P. melinonii Brongn.

Leaf and root essential oils of two closely related but ecologically distant Philodendron species were extracted in natural conditions in French Guiana and analysed by GC/MS to i) describe the blends of volatile organic compounds (VOCs) produced by those species and ii) analyse species and environment‐based variations in extracts composition. A total of 135 VOCs were detected with a majority of aliphatic sesquiterpenes. P. fragrantissimum produced mainly β‐bisabolene (on average 29.12% of the extract) as well as α‐ and β‐selinene (14.52% and 17.50%, respectively) while in P. melinonii, four aliphatic sesquiterpenes could alternatively be the main component: (E)‐β‐farnesene (up to 91.42% of the extract), germacrene‐D (73.74%), β‐caryophyllene (51.63%) and trans‐α‐bergamotene (41.26%). A significant effect of species and organs on extracts composition was observed while the environment (sun exposure) only affected the relative proportions of monoterpenes and sesquiterpenes in roots of P. melinonii. These results are discussed in the light of the potential role of leaf and root terpenes in Philodendron species.     

Biogeography and host‐related factors trump parasite life history: limited congruence among the genetic structures of specific ectoparasitic lice and their rodent hosts

Parasites and hosts interact across both micro‐ and macroevolutionary scales where congruence among their phylogeographic and phylogenetic structures may be observed. Within southern Africa, the four‐striped mouse genus, Rhabdomys, is parasitized by the ectoparasitic sucking louse, Polyplax arvicanthis. Molecular data recently suggested the presence of two cryptic species within P. arvicanthis that are sympatrically distributed across the distributions of four putative Rhabdomys species. We tested the hypotheses of phylogeographic congruence and cophylogeny among the two parasite lineages and the four host taxa, utilizing mitochondrial and nuclear sequence data. Despite the documented host‐specificity of P. arvicanthis, limited phylogeographic correspondence and nonsignificant cophylogeny was observed. Instead, the parasite–host evolutionary history is characterized by limited codivergence and several duplication, sorting and host‐switching events. Despite the elevated mutational rates found for P. arvicanthis, the spatial genetic structure was not more pronounced in the parasite lineages compared with the hosts. These findings may be partly attributed to larger effective population sizes of the parasite lineages, the vagility and social behaviour of Rhabdomys, and the lack of host‐specificity observed in areas of host sympatry. Further, the patterns of genetic divergence within parasite and host lineages may also be largely attributed to historical biogeographic changes (expansion‐contraction cycles). It is thus evident that the association between P. arvicanthis and Rhabdomys has been shaped by the synergistic effects of parasite traits, host‐related factors and biogeography over evolutionary time.     

A quantitative real‐time PCR assay for identification and enumeration of the occasionally co‐occurring ichthyotoxic Pseudochattonella farcimen and P. verruculosa (Dictyochophyceae) and analysis of variation in gene copy numbers during the growth phase of single and mixed cultures

The ichthyotoxic genus Pseudochattonella forms recurrent extensive blooms in coastal waters in Japan, New Zealand and Northern Europe. It comprises of two morphologically similar species, P. verruculosa and P. farcimen, which complicates visual species identification and enumeration of live and fixed material. Primers designed previously could not quantitatively distinguish species in mixed assemblages. To address this issue we developed two primer sets: one revealed itself to be genus specific for Pseudochattonella and the other species‐specific for P. verruculosa. By subtracting cell estimates for P. verruculosa from combined results we could calculate cell numbers for P. farcimen. This approach has overcome the challenges posed by the very limited sequence availability and low gene variability between the two species. The qPCR assay was extensively tested for specificity, efficiency and sensitivity over an entire growth cycle in both single and mixed assemblages. Comparison of cell abundance estimates obtained by qPCR assay and microscopy showed no statistically significant difference until stationary and death phases. The assay was also tested on environmental samples collected during a small Pseudochattonella bloom in Denmark in March–April 2015. It was impossible to distinguish P. farcimen and P. verruculosa by light microscopy but qPCR showed both species were present. The two methods provided nearly identical cell numbers but the assay provided discrimination and enumeration of both species.     

Effects of habitat alteration caused by petrochemical activities and oil spills on the habitat use and interspecific relationships among four species of Afrotropical freshwater turtles

The large-scale effects of habitat alteration produced by oil-industry related pollution on the habitat use of four species of freshwater turtles (Pelusios castaneus, Pelusios niger, Pelomedusa subrufa, Trionyx triunguis) were studied in the River Niger Delta, southern Nigeria (West Africa) between 1996 and 2004. The numbers of turtle specimens observed during our study declined drastically in polluted sites, despite a nearly identical field effort. The number of specimens of all turtle species declined considerably at all habitat types, but complete disappearance in polluted areas was found only with regard to one habitat type for Trionyx triunguis and two habitat types for Pelomedusa subrufa. The mean values of species dominance and diversity indexes were not statistically significant between pristine and altered areas. Based on the interspecific similarity in proportional frequencies of turtle specimens found in each habitat type, a multivariate set of analyses (UPGMA) showed that the turtles were arranged in three ‘ecological’ clusters: a group formed by Pelomedusa subrufa at both polluted and unpolluted areas and Trionyx triunguis at polluted areas; (ii) a group formed by Pelusios castaneus in polluted areas and Pelusios niger in polluted areas; (iii) a group formed by Pelusios castaneus in unpolluted areas and Pelusios niger in unpolluted areas; however, this latter cluster was not very close, as the linkage distance was close to 80% of Euclidean distance. Habitat use similarity among turtles in both polluted and unpolluted study areas was evaluated by the use of two types of overlap formulas (Pianka and Czechanowski) and the use of Monte Carlo randomisations in order to control for the eventual role of chance in the actual data matrix. These data indicated that, for a pair of species (Pelusios niger vs. Pelusios castaneus), there was a statistically significant increase in the similarity of habitat use in the polluted areas vs. the unpolluted areas, and that this pattern was not dependent on the chance. Considering that these two species are ecologically and morphologically similar, we conclude that the most likely consequence at the community level is an increase in the intensity of interspecific competition for space between Pelusios niger and Pelusios castaneus in the polluted areas. Although the direction of the intensification of this competition process could not be easily predicted, it is likely that the species which is least adapted to life in main rivers and creeks may be disadvantaged over the other competitor. The general implications for habitat preservation are also discussed.     

Contrasting responses to Pleistocene climate changes: a case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai–Tibet Plateau

It has been hypothesized that species occurring in the eastern and the western Qinghai–Tibet Plateau (QTP) responded differently to climate changes during the Pleistocene. Here, we test this hypothesis by phylogeographic analysis of two sister species, Allium cyathophorum and A. spicata. We sequenced two chloroplast DNA (cpDNA) fragments (accD‐psaI and the rpl16 intron) of 150 individuals, and the nuclear (ITS) region of 114 individuals, from 19 populations throughout the distributional ranges of these species. The divergence between the two species was dated at 779 ‐ 714 thousand years before the present and was likely initiated by the most major glaciation in the QTP. Analysis of chlorotype diversity showed that A. spicata, the species occurring in the western QTP, contains much lower genetic diversity (0.25) than A. cyathophorum (0.93), which is distributed in the eastern QTP. Moreover, multiple independent tests suggested that the A. spicata population had expanded recently, while no such expansion was detected in A. cyathophorum, indicating a contrasting pattern of responses to Pleistocene climate changes. These findings highlight the importance of geographical topography in determining how species responded to the climate changes that took place in the QTP during the Pleistocene.     

Phylogenetic distribution of a male pheromone that may exploit a nonsexual preference in lampreys

Pheromones are among the most important sexual signals used by organisms throughout the animal kingdom. However, few are identified in vertebrates, leaving the evolutionary mechanisms underlying vertebrate pheromones poorly understood. Pre‐existing biases in receivers' perceptual systems shape visual and auditory signalling systems, but studies on how receiver biases influence the evolution of pheromone communication remain sparse. The lamprey Petromyzon marinus uses a relatively well‐understood suite of pheromones and offers a unique opportunity to study the evolution of vertebrate pheromone communication. Previous studies indicate that male signalling with the mating pheromone 3‐keto petromyzonol sulphate (3kPZS) may exploit a nonsexual attraction to juvenile‐released 3kPZS that guides migration into productive rearing habitat. Here, we infer the distribution of male signalling with 3kPZS using a phylogenetic comparison comprising six of 10 genera and two of three families. Our results indicate that only P. marinus and Ichthyomyzon castaneus release 3kPZS at high rates. Olfactory and behavioural assays with P. marinus, I. castaneus and a subset of three other species that do not use 3kPZS as a sexual signal indicate that male signalling might have driven the evolution of female adaptations to detect 3kPZS with specific olfactory mechanisms and respond to 3kPZS with targeted attraction relevant during mate search. We postulate that 3kPZS communication evolved independently in I. castaneus and P. marinus, but cannot eliminate the alternative that other species lost 3kPZS communication. Regardless, our results represent a rare macroevolutionary investigation of a vertebrate pheromone and provide insight into the evolutionary mechanisms underlying pheromone communication.     

Genetic differentiation of the pine processionary moth at the southern edge of its range: contrasting patterns between mitochondrial and nuclear markers

The pine processionary moth (Thaumetopoea pityocampa) is an important pest of coniferous forests at the southern edge of its range in Maghreb. Based on mitochondrial markers, a strong genetic differentiation was previously found in this species between western (pityocampa clade) and eastern Maghreb populations (ENA clade), with the contact zone between the clades located in Algeria. We focused on the moth range in Algeria, using both mitochondrial (a 648 bp fragment of the tRNA‐cox2) and nuclear (11 microsatellite loci) markers. A further analysis using a shorter mtDNA fragment and the same microsatellite loci was carried out on a transect in the contact zone between the mitochondrial clades. Mitochondrial diversity showed a strong geographical structure and a well‐defined contact zone between the two clades. In particular, in the pityocampa clade, two inner subclades were found whereas ENA did not show any further structure. Microsatellite analysis outlined a different pattern of differentiation, with two main groups not overlapping with the mitochondrial clades. The inconsistency between mitochondrial and nuclear markers is probably explained by sex‐biased dispersal and recent afforestation efforts that have bridged isolated populations.     

Late Pleistocene climate change promoted divergence between Picea asperata and P. crassifolia on the Qinghai–Tibet Plateau through recent bottlenecks

Divergence during the early stage of speciation can be driven by a population bottleneck via reduced gene flow and enhanced lineage sorting. In this study, we aimed to examine whether such bottlenecks occurred during the initial speciation of two closely related spruce species Picea asperata and P. crassifolia occurring on the Qinghai–Tibet Plateau (QTP). We analyzed sequences of three chloroplast, two mitochondrial DNA fragments and a further 13 nuclear loci from 216 individuals of the two species. Both species showed a low level of genetic diversity in contrast to other congeners occurring in the QTP and adjacent regions. The estimated population sizes of P. asperata and P. crassifolia are less than the ancestral population size before splitting. These results together with multiple statistical tests (Tajima's D, Fu and Li's D* and F*) suggest that these two species underwent recent bottlenecks. Based on approximate Bayesian computation (ABC), we also determined that the period of the population shrinkage was consistent with the interspecific divergence during the late Pleistocene. The reduced population sizes and the divergent selection may together have triggered the initial divergence under high gene flow between these two species. Our results therefore highlight the importance of climatic oscillations during the late Pleistocene in promoting speciation through changing demographic sizes of the ancestral species on the QTP and in adjacent regions.