The biology and functional morphology of Arca noae (Bivalvia: Arcidae) from the Adriatic Sea, Croatia, with a discussion on the evolution of the bivalve mantle margin

In the Croatian Adriatic, Arca noae occurs from the low intertidal to a depth of 60 m; it can live for > 15 years and is either solitary or forms byssally attached clumps with Modiolus barbatus. The shell is anteriorly foreshortened and posteriorly elongate. The major inhalant flow is from the posterior although a remnant anterior stream is retained. There are no anterior but huge posterior byssal retractor muscles and both anterior and posterior pedal retractors. The ctenidia are of Type B(1a) and the ctenidial–labial palp junction is Category 3. The ctenidia collect, filter and undertake the primary sorting of potential food in the inhalant water. The labial palps are small with simple re‐sorting tracks on the ridges of their inner surfaces. The ciliary currents of the mantle cavity appear largely concerned with the rejection of particulate material. The mantle margin comprises an outer and an (either) inner or middle fold. The outer fold is divided into outer and inner components that secrete the shell and are photo‐sensory, respectively. The latter bears a large number of pallial eyes, especially posteriorly. The inner/middle mantle fold of A. noae, possibly representative of simpler, more primitive conditions, may have differentiated into distinct folds in other recent representatives of the Bivalvia.     

Cranial morphology and taxonomic resolution of some dolphin taxa (Delphinidae) in Australian waters,with a focus on the genus Tursiops

Phylogenetic relationships in the family Delphinidae have been widely debated. We examined 347 skulls of Tursiops, Stenella, Delphinus, Steno, Lagenodelphis, and Sousa in order to resolve the phylogenetic position of Australian species of Tursiops. Five Tursiops type specimens were included. Cranial morphology was described using 2‐dimensional (2‐D) and 3‐dimensional geometric morphometrics (3‐GM), counts and categorical data. Analyses showed a clear morphological separation of Tursiops, including type specimens, from other genera. The three Stenella species did not cluster together. Stenella attenuata clustered with Delphinus delphis, and Stenella coeruleoalba with Lagenodelphis hosei. Length and width of the skull and rostrum were important discriminators in both methods. For 3‐D data, round vs. angular posterior skull shape distinguished some genera. Taxa that overlapped in the multivariate analyses had different mean tooth counts. Our study challenges genetic studies that identified Tursiops as polyphyletic, with T. aduncus closer to S. attenuata.     

Molecular phylogeny of the diatom genera Amphora and Halamphora (Bacillariophyta) with a focus on morphological and ecological evolution

The taxonomic history of the diatom genus Amphora is one of a broad early morphological concept resulting in the inclusion of a diversity of taxa, followed by an extended period of revision and refinement. The introduction of molecular systematics has increased the pace of revision and has largely resolved the relationships between the major lineages, indicating homoplasy in the evolution of amphoroid symmetry. Within the two largest monophyletic lineages, the genus Halamphora and the now taxonomically refined genus Amphora, the intrageneric morphological and ecological relationships have yet to be explored within a phylogenetic framework. Critical among this is whether the range of morphological features exhibited within these diverse genera are reflective of evolutionary groupings or, as with many previously studied amphoroid features, are nonhomologous when examined phylogenetically. Presented here is a four‐marker molecular phylogeny that includes 31 taxa from the genus Amphora and 77 taxa from the genus Halamphora collected from fresh, brackish, and salt waters from coastal and inland habitats of the United States and Japan. These phylogenies illustrate complex patterns in the evolution of frustule morphology and ecology within the genera and the implications of this on the taxonomy, classification, and organization of the genera are discussed.     

The evolution of microendemism in a reef fish (Hypoplectrus maya)

Marine species tend to have extensive distributions, which are commonly attributed to the dispersal potential provided by planktonic larvae and the rarity of absolute barriers to dispersal in the ocean. Under this paradigm, the occurrence of marine microendemism without geographic isolation in species with planktonic larvae poses a dilemma. The recently described Maya hamlet (Hypoplectrus maya, Serranidae) is exactly such a case, being endemic to a 50‐km segment of the Mesoamerican Barrier Reef System (MBRS). We use whole‐genome analysis to infer the demographic history of the Maya hamlet and contrast it with the sympatric and pan‐Caribbean black (H. nigricans), barred (H. puella) and butter (H. unicolor) hamlets, as well as the allopatric but phenotypically similar blue hamlet (H. gemma). We show that H. maya is indeed a distinct evolutionary lineage, with genomic signatures of inbreeding and a unique demographic history of continuous decrease in effective population size since it diverged from congeners just ~3,000 generations ago. We suggest that this case of microendemism may be driven by the combination of a narrow ecological niche and restrictive oceanographic conditions in the southern MBRS, which is consistent with the occurrence of an unusually high number of marine microendemics in this region. The restricted distribution of the Maya hamlet, its decline in both census and effective population sizes, and the degradation of its habitat place it at risk of extinction. We conclude that the evolution of marine microendemism can be a fast and dynamic process, with extinction possibly occurring before speciation is complete.     

Reappraisal of early Miocene rails (Aves,Rallidae) from central France: diversity and character evolution

In Europe, Miocene rails (Aves, Rallidae) are quite abundant, but their phylogenetic placement in the context of recent forms has remained elusive. Rails from the early Miocene of the Saint‐Gérand‐le‐Puy area in central France were first described in the 19th century, and currently, only two species are recognized, namely Palaeoaramides christyi and Paraortygometra porzanoides. Our examination of the material however suggests the presence of four, likely coeval, species of rail from these deposits. Palaeoaramides eximius, previously synonymized with Palaeoaramides christyi, is here shown to probably be a distinct species, and a previously unrecognized rail, Baselrallus intermedius gen. et sp. nov., is described. To find out how these fossil rails are related to modern Rallidae, we compared them with an extensive sample of extant rails and identified plesiomorphic and derived features for crown group Rallidae. Our assessment does not support a particularly close relationship of either Palaeoaramides to Aramides or Paraortygometra to Crex (Ortygometra), and overall, these fossil rails are more primitive than previously assumed. Based on our observations of the morphology of the previously undescribed humerus of Palaeoaramides, we show this taxon to be outside crown group Rallidae, and perhaps closely related to the early Oligocene taxon Belgirallus. On the other hand, Paraortygometra porzanoides bears a resemblance to recent flufftails (Sarothrura spp.) in some elements, but whether it can be included in a clade together with flufftails is uncertain.     

Comparative morphology of sensilla on antenna,maxillary palp and labial palp of larvae of Eucryptorrhynchus scrobiculatus (Olivier) and E. brandti (Harold) (Coleoptera: Curculionidae)

Eucryptorrhynchus scrobiculatus (Olivier) and E. brandti (Harold) are two wood boring pests of Ailanthus altissima (Mill.) Swingle (tree of heaven) and the variety Ailanthus altissima var. Qiantouchun. These beetles attack healthy trees and bore into roots and trunks during the larval stage. We studied the typology, distribution and morphostructure of the sensilla on the antennae, maxillary palps and labial palps of E. scrobiculatus and E. brandti larvae using scanning and transmission electron microscopy. The results showed the following: (i) the antennae of the two weevil larvae had two types of sensilla, sensilla basiconica (S.b.1 and S.b.2) and sensilla twig basiconica (S.tb.1‐S.tb.3), with S.tb.4 observed only on the antennae of E. brandti larvae; (ii) the maxillary palps had three types of sensilla, S.b.2, S.tb. (S.tb.2, S.tb.3 and S.tb.5) and digitiform sensilla; (iii) the labial palps had two types of sensilla, S.b.2 and S.tb. (S.tb.2, S.tb.3 and S.tb.5); (iv) the quantity and distribution of sensilla on the antennae, maxillary palps and labial palps remained constant between E. scrobiculatus and E. brandti larvae; and (v) sensilla basiconica had distinct sidewall pores, an apical pore was observed on sensilla twig basiconica, and digitiform sensilla were oval in shape, with a distinct apical pore. Based on the microstructure of the cuticle wall and dendrite, we hypothesized that these sensilla functioned as olfactory, gustatory and hygro‐/thermo‐receptors, respectively. We discuss the relationships among types of sensilla and the types of damage caused by the larvae inside the host tree to understand olfactory and gustatory receptor mechanisms. The results of this study will provide a firm basis for future electrophysiological studies.     

The structure of anoline (Reptilia: Dactyloidae: Anolis) toe pads in relation to substratum conformity

Adhesive toe pads of geckos house modified components of vascular and/or connective tissues that promote conformity of the setal fields with the locomotor substratum. Similar modifications have been claimed for the digits of Anolis, but evidence for them is not compelling. Angiographic and histological investigations of Anolis failed to identify any evidence of either an intralamellar vascular reticular network or a central sinus. Instead, their vascularity more closely resembles that of lizards in general than that of pad‐bearing geckos. The loose connective tissue of the toe pads likely contributes to their general pliability and flexibility, promoting localized compliance with the substratum. Through the shedding cycle, the lamellae change shape as the replacing setae elongate. The outer epidermal generation lacunar cells on the inner lamellar faces simultaneously hypertrophy, providing for compatibility between overlapping lamellae, enabling reciprocity between them. This contributes to continuing compliance of the setal fields with the substratum. Overall, digital structure and attachment and release kinematics of the toe pads of Anolis are very similar to those of geckos exhibiting an incipient adhesive mechanism. Both lack major anatomical specializations for promoting conformity of the setae with the locomotor substratum beyond those of the seta‐bearing portions of the epidermis.     

The first instar larva of two species of Miltogramminae (Diptera: Sarcophagidae) from the Middle East – examples of peculiar morphology

The first instar larva is described for two species of Miltogramminae flesh flies representing the genera Miltogramma Meigen and Phrosinella Robineau‐Desvoidy. Using a combination of light microscopy and scanning electron microscopy, the habitus is documented along with all important exoskeletal and cephaloskeletal structures. The described first instar larvae show substantial modifications of their morphology in comparison with the saprophagous ground plan defined for calyptrate flies. Miltogramma (Miltogrammidium) efflatouni Rohdendorf possesses the general set of derived character states shared with other species of Miltogramma and shares larval synapomorphies with species representing the subgenera Anacanthothecum Rohdendorf, Cylindrothecum Rohdendorf and Miltogrammidium Rohdendorf. Unique character states of the first instar larva of this species are the spine‐like shape of antennal complex, laterally compressed apical part of mouthhooks and an extreme elongation of the sensilla of the maxillary palpus. Phrosinella (Asiometopa) ujgura (Rohdendorf) possesses a pair of retractable, robust processes on the ventral margin of the first thoracic segment and a very strong, elongated labrum. Both character states are present in other known first instar larvae of genus Phrosinella. A reduction of cuticular ridges on dorsal and lateral surfaces of abdominal segments supports a monophylum consisting of the subgenera Asiometopa Rohdendorf and Caspiomyia Rohdendorf within genus Phrosinella.     

Phylogeny and species delineation in the marine diatom Pseudo‐nitzschia (Bacillariophyta) using cox1, LSU,and ITS2 rRNA genes: A perspective in character evolution

Analyses of the mitochondrial cox1, the nuclear‐encoded large subunit (LSU), and the internal transcribed spacer 2 (ITS2) RNA coding region of Pseudo‐nitzschia revealed that the P. pseudodelicatissima complex can be phylogenetically grouped into three distinct clades (Groups I–III), while the P. delicatissima complex forms another distinct clade (Group IV) in both the LSU and ITS2 phylogenetic trees. It was elucidated that comprehensive taxon sampling (sampling of sequences), selection of appropriate target genes and outgroup, and alignment strategies influenced the phylogenetic accuracy. Based on the genetic divergence, ITS2 resulted in the most resolved trees, followed by cox1 and LSU. The morphological characters available for Pseudo‐nitzschia, although limited in number, were overall in agreement with the phylogenies when mapped onto the ITS2 tree. Information on the presence/absence of a central nodule, number of rows of poroids in each stria, and of sectors dividing the poroids mapped onto the ITS2 tree revealed the evolution of the recently diverged species. The morphologically based species complexes showed evolutionary relevance in agreement with molecular phylogeny inferred from ITS2 sequence–structure data. The data set of the hypervariable region of ITS2 improved the phylogenetic inference compared to the cox1 and LSU data sets. The taxonomic status of P. cuspidata and P. pseudodelicatissima requires further elucidation.     

The complete chloroplast genome of Gracilariopsis lemaneiformis (Rhodophyta) gives new insight into the evolution of family Gracilariaceae

The complete chloroplast genome of Gracilariopsis lemaneiformis was recovered from a Next Generation Sequencing data set. Without quadripartite structure, this chloroplast genome (183,013 bp, 27.40% GC content) contains 202 protein‐coding genes, 34 tRNA genes, 3 rRNA genes, and 1 tmRNA gene. Synteny analysis showed plasmid incorporation regions in chloroplast genomes of three species of family Gracilariaceae and in Grateloupia taiwanensis of family Halymeniaceae. Combined with reported red algal plasmid sequences in nuclear and mitochondrial genomes, we postulated that red algal plasmids may have played an important role in ancient horizontal gene transfer among nuclear, chloroplast, and mitochondrial genomes. Substitution rate analysis showed that purifying selective forces maintaining stability of protein‐coding genes of nine red algal chloroplast genomes over long periods must be strong and that the forces acting on gene groups and single genes of nine red algal chloroplast genomes were similar and consistent. The divergence of Gp. lemaneiformis occurred ~447.98 million years ago (Mya), close to the divergence time of genus Pyropia and Porphyra (443.62 Mya).     

Improved genome assembly of Chinese shrimp (Fenneropenaeus chinensis) suggests adaptation to the environment during evolution and domestication

A high-quality reference genome is necessary to determine the molecular mechanisms underlying important biological phenomena; therefore, in the present study, a chromosome-level genome assembly of the Chinese shrimp Fenneropenaeus chinensis was performed. Muscle of a male shrimp was sequenced using PacBio platform, and assembled by Hi-C technology. The assembled F. chinensis genome was 1.47 Gb with contig N50 of 472.84 Kb, including 57.73% repetitive sequences, and was anchored to 43 pseudochromosomes, with scaffold N50 of 36.87 Mb. In total, 25,026 protein-coding genes were predicted. The genome size of F. chinensis showed significant contraction in comparison with that of other penaeid species, which is likely related to migration observed in this species. However, the F. chinensis genome included several expanded gene families related to cellular processes and metabolic processes, and the contracted gene families were associated with virus infection process. The findings signify the adaptation of F. chinensis to the selection pressure of migration and cold environment. Furthermore, the selection signature analysis identified genes associated with metabolism, phototransduction, and nervous system in cultured shrimps when compared with wild population, indicating targeted, artificial selection of growth, vision, and behavior during domestication. The construction of the genome of F. chinensis provided valuable information for the further genetic mechanism analysis of important biological processes, and will facilitate the research of genetic changes during evolution.     

The relationship between cranial morphology,bite performance,diet and habitat in a radiation of dwarf chameleon (Bradypodion)

Many animals show unique morphological and behavioural adaptations to specific habitats. In particular, variation in cranial morphology is known to influence feeding performance, which in turn influences dietary habits and, ultimately, fitness. Dietary separation is an important means of partitioning ecological niches and avoiding inter‐ and intraspecific competition. Consequently, differences in dietary resources may help explain phenotypic divergence in closely‐related species occupying different habitats, as well as sexual dimorphism. We test this hypothesis on five phenotypic forms of a recent radiation of dwarf chameleons (Bradypodion) that vary extensively in habitat use and cranial morphology. By examining stomach contents, the dietary composition of each phenotypic form is compared to investigate potential differences in feeding strategies. Overall, chameleons in the present study exhibit considerable dietary overlap (at both inter‐ and intraspecific levels), indicating that diet is not a major driver of variation in cranial morphology within this radiation. However, the stomachs of closed‐canopy females were found to contain more prey items than male stomachs, possibly indicating that females require a greater caloric intake than their male counterparts.     

The evolution of a complex trait: cuticular hydrocarbons in ants evolve independent from phylogenetic constraints

Cuticular hydrocarbons (CHCs) are ubiquitous and highly diverse in insects, serving as communication signal and waterproofing agent. Despite their vital function, the causes, mechanisms and constraints on CHC diversification are still poorly understood. Here, we investigated phylogenetic constraints on the evolution of CHC profiles, using a global data set of the species‐rich and chemically diverse ant genus Crematogaster. We decomposed CHC profiles into quantitative (relative abundances, chain length) and qualitative traits (presence/absence of CHC classes). A species‐level phylogeny was estimated using newly generated and previously published sequences from five nuclear markers. Moreover, we reconstructed a phylogeny for the chemically diverse Crematogaster levior species group using cytochrome oxidase I. Phylogenetic signal was measured for these traits on genus and clade level and within the chemically diverse C. levior group. For most quantitative CHC traits, phylogenetic signal was low and did not differ from random expectation. This was true on the level of genus, clade and species group, indicating that CHC traits are evolutionary labile. In contrast, the presence or absence of alkenes and alkadienes was highly conserved within the C. levior group. Hence, the presence or absence of biosynthetic pathways may be phylogenetically constrained, especially at lower taxonomic levels. Our study shows that CHC composition can evolve rapidly, allowing insects to quickly adapt their chemical profiles to external selection pressures, whereas the presence of biosynthetic pathways appears more constrained. However, our results stress the importance to consider the taxonomic level when investigating phylogenetic constraints.     

Athletic anurans: the impact of morphology,ecology and evolution on climbing ability in invasive cane toads

Although primarily terrestrial, cane toads (Rhinella marina) sometimes climb near‐vertical surfaces (tree‐trunks, cliffs, fences) during foraging or dispersal activities. We scored climbing ability (in laboratory trials) of 288 cane toads from four regions in Australia, plus two sites on the island of Hawai'i. We found strong divergence in climbing ability associated not only with sex and relative limb length, but also population of origin. Within each population, longer‐limbed individuals (and hence, males rather than females) were better climbers, although the geographical divergence in climbing ability remained significant even when sex and limb length were included in multivariate regression models. The geographical difference in climbing ability (but not morphology) disappeared when the progeny were raised in captivity under identical conditions, without climbing opportunities. Although influenced by morphology, climbing ability in wild‐caught cane toads appears to be driven primarily by local environmental conditions that facilitate and/or reward arboreal activity.     

Genetic factors for short life span associated with evolution of the loss of flight ability

Acquisition or loss of flying ability is evolutionarily linked with maximum life span (MLS) in mammals and birds. Although ecological factors, such as extrinsic mortality, may lead to either shortened or extended life spans through natural selection, MLS is influenced by complex molecular and metabolic processes, and the genetic changes associated with flying ability that have led to either a longer or shorter MLS are unknown. Here, we examine the parallel evolution of flight in mammals and birds and investigate positively selected genes at branches where either the acquisition (in little brown bats and large flying foxes) or loss (in Adélie penguins, emperor penguins, common ostriches, emus, great spotted kiwis, little spotted kiwis, okarito brown kiwis, greater rheas, lesser rheas, and cassowaries) of flight abilities occurred. Although we found no shared genes under selection among all the branches of interest, 7 genes were found to be positively selected in 2 of the branches. Among the 7 genes, only IGF2BP2 is known to affect both life span and energy expenditure. The positively selected mutations detected in IGF2BP2 likely affected the functionality of the encoded protein. IGF2BP2, which has been reported to simultaneously prolong life span and increase energy expenditure, could be responsible for the evolution of shortened MLS associated with the loss of flying ability.     

Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular‐based research in ecology and evolution

Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next‐generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search.